Multiple sequence alignment - TraesCS3A01G278100

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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 TraesCS3A01G278100 chr3A 100.000 5547 0 0 1 5547 507641471 507635925 0.000000e+00 10244.0
1 TraesCS3A01G278100 chr3B 92.479 3590 133 56 1 3485 501502532 501498975 0.000000e+00 5007.0
2 TraesCS3A01G278100 chr3B 90.400 1802 89 31 3485 5279 501498909 501497185 0.000000e+00 2292.0
3 TraesCS3A01G278100 chr3D 96.978 1886 50 5 1411 3294 385474919 385473039 0.000000e+00 3160.0
4 TraesCS3A01G278100 chr3D 92.013 1853 81 29 3434 5279 385473001 385471209 0.000000e+00 2540.0
5 TraesCS3A01G278100 chr3D 87.033 1473 55 49 1 1378 385476697 385475266 0.000000e+00 1537.0
6 TraesCS3A01G278100 chr3D 97.308 260 7 0 5288 5547 500597144 500596885 5.100000e-120 442.0
7 TraesCS3A01G278100 chr2A 100.000 260 0 0 5288 5547 351425615 351425874 1.080000e-131 481.0
8 TraesCS3A01G278100 chr4B 99.231 260 2 0 5288 5547 286125740 286125999 2.340000e-128 470.0
9 TraesCS3A01G278100 chr6D 97.692 260 6 0 5288 5547 318401344 318401603 1.100000e-121 448.0
10 TraesCS3A01G278100 chr2B 90.769 260 24 0 5288 5547 161923681 161923422 1.140000e-91 348.0
11 TraesCS3A01G278100 chr2B 90.385 260 25 0 5288 5547 46683164 46682905 5.320000e-90 342.0
12 TraesCS3A01G278100 chrUn 90.385 260 25 0 5288 5547 247063232 247062973 5.320000e-90 342.0
13 TraesCS3A01G278100 chr2D 90.385 260 25 0 5288 5547 412619123 412618864 5.320000e-90 342.0
14 TraesCS3A01G278100 chr7D 89.615 260 27 0 5288 5547 603881378 603881119 1.150000e-86 331.0
15 TraesCS3A01G278100 chr7D 91.429 70 3 3 3351 3419 192076711 192076778 5.920000e-15 93.5
16 TraesCS3A01G278100 chr5B 100.000 52 0 0 3368 3419 128350949 128351000 4.570000e-16 97.1
17 TraesCS3A01G278100 chr5B 88.462 78 6 3 3364 3439 369259098 369259022 2.130000e-14 91.6
18 TraesCS3A01G278100 chr1D 96.552 58 1 1 3363 3419 256553265 256553322 1.650000e-15 95.3
19 TraesCS3A01G278100 chr1D 98.182 55 0 1 3366 3419 260956101 260956047 1.650000e-15 95.3
20 TraesCS3A01G278100 chr1B 98.148 54 1 0 3366 3419 560222249 560222196 1.650000e-15 95.3
21 TraesCS3A01G278100 chr1B 85.882 85 7 5 3358 3440 35449677 35449758 9.900000e-13 86.1
22 TraesCS3A01G278100 chr4D 89.474 76 5 3 3367 3440 73982626 73982552 5.920000e-15 93.5


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 TraesCS3A01G278100 chr3A 507635925 507641471 5546 True 10244.000000 10244 100.0000 1 5547 1 chr3A.!!$R1 5546
1 TraesCS3A01G278100 chr3B 501497185 501502532 5347 True 3649.500000 5007 91.4395 1 5279 2 chr3B.!!$R1 5278
2 TraesCS3A01G278100 chr3D 385471209 385476697 5488 True 2412.333333 3160 92.0080 1 5279 3 chr3D.!!$R2 5278


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
252 293 0.798776 GACAGTCTGCACGGGAAATG 59.201 55.000 0.0 0.0 0.00 2.32 F
599 677 1.153862 CTCAGCTGAGGCGAGACAC 60.154 63.158 32.3 0.0 44.37 3.67 F
1860 2310 0.738389 CGCCACCACCCAATTACATC 59.262 55.000 0.0 0.0 0.00 3.06 F
2925 3378 1.221466 ACTCCAACACGCATGTCACG 61.221 55.000 0.0 0.0 38.45 4.35 F
3099 3556 0.593128 CCGGGAAGTTGACAGCAAAG 59.407 55.000 0.0 0.0 35.42 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 2310 0.767446 AGGATCCTGCAGATGAGGGG 60.767 60.0 15.29 0.0 34.42 4.79 R
2538 2988 0.968901 TGACCCTCGTACGCCAATCT 60.969 55.0 11.24 0.0 0.00 2.40 R
2958 3411 0.244721 GCAATGGCTGTCTTTGGACC 59.755 55.0 9.51 0.0 41.47 4.46 R
4357 4892 0.036010 CCAGTGCTCTTACCACCTGG 60.036 60.0 0.00 0.0 42.17 4.45 R
4658 5193 0.107165 CCGGGGAGGACAAGGATTTC 60.107 60.0 0.00 0.0 45.00 2.17 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
26 27 6.321945 TCAGCATCGTACCCAGTAAACTATAA 59.678 38.462 0.00 0.00 0.00 0.98
27 28 6.420008 CAGCATCGTACCCAGTAAACTATAAC 59.580 42.308 0.00 0.00 0.00 1.89
28 29 5.400485 GCATCGTACCCAGTAAACTATAACG 59.600 44.000 0.00 0.00 0.00 3.18
29 30 6.728200 CATCGTACCCAGTAAACTATAACGA 58.272 40.000 9.88 9.88 0.00 3.85
30 31 6.363577 TCGTACCCAGTAAACTATAACGAG 57.636 41.667 0.00 0.00 0.00 4.18
32 33 7.045416 TCGTACCCAGTAAACTATAACGAGTA 58.955 38.462 0.00 0.00 0.00 2.59
35 36 6.856895 ACCCAGTAAACTATAACGAGTACAC 58.143 40.000 0.00 0.00 0.00 2.90
36 37 6.127619 ACCCAGTAAACTATAACGAGTACACC 60.128 42.308 0.00 0.00 0.00 4.16
37 38 6.268566 CCAGTAAACTATAACGAGTACACCC 58.731 44.000 0.00 0.00 0.00 4.61
38 39 6.096001 CCAGTAAACTATAACGAGTACACCCT 59.904 42.308 0.00 0.00 0.00 4.34
41 42 4.240881 ACTATAACGAGTACACCCTCCA 57.759 45.455 0.00 0.00 0.00 3.86
46 51 1.888736 GAGTACACCCTCCACCGTC 59.111 63.158 0.00 0.00 0.00 4.79
175 189 3.721706 CCAGCCGCCCTTCCTTCT 61.722 66.667 0.00 0.00 0.00 2.85
252 293 0.798776 GACAGTCTGCACGGGAAATG 59.201 55.000 0.00 0.00 0.00 2.32
295 336 2.442272 GCCCGACTCAGCTCCCTA 60.442 66.667 0.00 0.00 0.00 3.53
296 337 1.834822 GCCCGACTCAGCTCCCTAT 60.835 63.158 0.00 0.00 0.00 2.57
297 338 2.045280 CCCGACTCAGCTCCCTATG 58.955 63.158 0.00 0.00 0.00 2.23
335 376 2.820037 GCCAGTACCGCTTGCTCC 60.820 66.667 0.00 0.00 33.51 4.70
378 419 3.580319 GACCTGGCACCAACCCCT 61.580 66.667 0.00 0.00 0.00 4.79
379 420 3.569200 GACCTGGCACCAACCCCTC 62.569 68.421 0.00 0.00 0.00 4.30
427 501 9.694520 GAAGAAAATTGTTTTGAGAAAAGAAGC 57.305 29.630 0.00 0.00 37.12 3.86
430 504 9.992910 GAAAATTGTTTTGAGAAAAGAAGCAAT 57.007 25.926 0.00 0.00 37.12 3.56
596 674 2.362247 AGCTCAGCTGAGGCGAGA 60.362 61.111 37.86 7.34 44.37 4.04
597 675 2.202730 GCTCAGCTGAGGCGAGAC 60.203 66.667 37.86 20.64 44.37 3.36
598 676 2.999485 GCTCAGCTGAGGCGAGACA 61.999 63.158 37.86 5.84 44.37 3.41
599 677 1.153862 CTCAGCTGAGGCGAGACAC 60.154 63.158 32.30 0.00 44.37 3.67
600 678 1.871126 CTCAGCTGAGGCGAGACACA 61.871 60.000 32.30 0.00 44.37 3.72
601 679 1.735920 CAGCTGAGGCGAGACACAC 60.736 63.158 8.42 0.00 44.37 3.82
650 736 2.102749 CATTGCATTGGCCGACGG 59.897 61.111 10.29 10.29 40.13 4.79
797 927 2.039418 TCGGGAGAGAGAGAGAGAGAG 58.961 57.143 0.00 0.00 0.00 3.20
800 930 3.309296 GGGAGAGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
801 931 3.323403 GGGAGAGAGAGAGAGAGAGAGAG 59.677 56.522 0.00 0.00 0.00 3.20
802 932 3.323403 GGAGAGAGAGAGAGAGAGAGAGG 59.677 56.522 0.00 0.00 0.00 3.69
803 933 2.703007 AGAGAGAGAGAGAGAGAGAGGC 59.297 54.545 0.00 0.00 0.00 4.70
804 934 2.703007 GAGAGAGAGAGAGAGAGAGGCT 59.297 54.545 0.00 0.00 0.00 4.58
805 935 2.703007 AGAGAGAGAGAGAGAGAGGCTC 59.297 54.545 6.34 6.34 44.29 4.70
878 1008 2.753043 AGCTGCTTGATTGGGGCG 60.753 61.111 0.00 0.00 0.00 6.13
879 1009 2.751436 GCTGCTTGATTGGGGCGA 60.751 61.111 0.00 0.00 0.00 5.54
1257 1393 2.515523 CCTCCTCCAGCATTGCCG 60.516 66.667 4.70 0.00 0.00 5.69
1626 2076 3.208383 CCACATTATGCGCCGCCA 61.208 61.111 6.63 0.00 0.00 5.69
1860 2310 0.738389 CGCCACCACCCAATTACATC 59.262 55.000 0.00 0.00 0.00 3.06
1866 2316 1.568597 CCACCCAATTACATCCCCTCA 59.431 52.381 0.00 0.00 0.00 3.86
1872 2322 3.435457 CCAATTACATCCCCTCATCTGCA 60.435 47.826 0.00 0.00 0.00 4.41
1898 2348 4.720046 TCCTCACTAGCATCAGGTACTAG 58.280 47.826 0.00 0.00 36.02 2.57
1908 2358 9.469807 CTAGCATCAGGTACTAGAAAACATAAG 57.530 37.037 0.00 0.00 36.02 1.73
1959 2409 6.500684 TCTGCAGTTTCTAAATTTAGCCAG 57.499 37.500 18.68 15.44 0.00 4.85
2236 2686 2.559440 CCTGTGGCTATCAAGAAGCTC 58.441 52.381 0.00 0.00 39.97 4.09
2329 2779 6.435292 AGACATTTGGTTTCACTAGTAGGT 57.565 37.500 1.45 0.00 0.00 3.08
2422 2872 1.625315 CATGGTGAGAACTCCCTGTCA 59.375 52.381 0.00 0.00 0.00 3.58
2484 2934 2.967887 TGAGGCAGCTAGATTGCTCATA 59.032 45.455 16.23 2.61 41.98 2.15
2800 3250 3.939592 GGTGTATTAGTTCCAGCTTCCAC 59.060 47.826 0.00 0.00 0.00 4.02
2925 3378 1.221466 ACTCCAACACGCATGTCACG 61.221 55.000 0.00 0.00 38.45 4.35
2958 3411 4.085733 TGGGAACATTTGGGTGAGTAATG 58.914 43.478 0.00 0.00 35.82 1.90
2968 3421 3.244770 TGGGTGAGTAATGGTCCAAAGAC 60.245 47.826 0.00 0.00 42.73 3.01
3099 3556 0.593128 CCGGGAAGTTGACAGCAAAG 59.407 55.000 0.00 0.00 35.42 2.77
3419 3878 9.372189 CCTCATTCATTAATTAAGAGGGGAAAT 57.628 33.333 17.07 2.75 37.97 2.17
3436 3895 6.385759 AGGGGAAATTTTAGTTGAAGTTTGGT 59.614 34.615 0.00 0.00 0.00 3.67
3677 4204 3.206412 TGTATTATGTTGGCCCCTTCCAT 59.794 43.478 0.00 0.00 35.77 3.41
3729 4256 6.458206 CGAGAAAGTGATCTGGAGAGAACTAG 60.458 46.154 0.00 0.00 0.00 2.57
3871 4398 4.040339 TGTGGTGAGTCATGAAAGAAGCTA 59.960 41.667 0.00 0.00 0.00 3.32
3872 4399 4.997395 GTGGTGAGTCATGAAAGAAGCTAA 59.003 41.667 0.00 0.00 0.00 3.09
3909 4441 5.906772 AAACAGGGACCGATTATCCTAAT 57.093 39.130 0.00 0.00 36.40 1.73
3910 4442 7.291651 AGAAAACAGGGACCGATTATCCTAATA 59.708 37.037 0.00 0.00 36.40 0.98
3911 4443 7.569599 AAACAGGGACCGATTATCCTAATAT 57.430 36.000 0.00 0.00 36.40 1.28
3912 4444 8.674925 AAACAGGGACCGATTATCCTAATATA 57.325 34.615 0.00 0.00 36.40 0.86
3913 4445 8.855804 AACAGGGACCGATTATCCTAATATAT 57.144 34.615 0.00 0.00 36.40 0.86
3918 4450 8.027771 GGGACCGATTATCCTAATATATTAGCG 58.972 40.741 22.25 18.41 38.69 4.26
3985 4517 5.163581 ACACCTCATTGCTCTAAATGCATTC 60.164 40.000 13.38 0.00 40.34 2.67
3994 4526 4.685575 GCTCTAAATGCATTCCTCTCTGGT 60.686 45.833 13.38 0.00 37.07 4.00
4078 4611 4.139786 TCAAACTCTGCTCTTGCTGAAAT 58.860 39.130 0.00 0.00 44.45 2.17
4134 4667 0.757188 AGCATCGAGACTTCGGGGAT 60.757 55.000 0.00 0.00 46.67 3.85
4143 4676 1.328430 ACTTCGGGGATCTTCCGGAC 61.328 60.000 21.48 0.00 46.78 4.79
4161 4694 2.510613 GACCCGAGGATGGAAAACAAA 58.489 47.619 0.00 0.00 0.00 2.83
4164 4697 3.509967 ACCCGAGGATGGAAAACAAATTC 59.490 43.478 0.00 0.00 0.00 2.17
4295 4828 6.414732 TCATTCATTTTACCTCGTTCCTGAT 58.585 36.000 0.00 0.00 0.00 2.90
4327 4862 3.599730 TGACAGCACAGGACTAAGATG 57.400 47.619 0.00 0.00 0.00 2.90
4352 4887 4.348486 TGCCCATGTATTTTCCTTTGCTA 58.652 39.130 0.00 0.00 0.00 3.49
4353 4888 4.961730 TGCCCATGTATTTTCCTTTGCTAT 59.038 37.500 0.00 0.00 0.00 2.97
4357 4892 7.577616 GCCCATGTATTTTCCTTTGCTATATCC 60.578 40.741 0.00 0.00 0.00 2.59
4414 4949 1.892209 ACCTAAACAACGGCCTTCAG 58.108 50.000 0.00 0.00 0.00 3.02
4447 4982 3.423154 GTGTTCTTGGAGCCGCGG 61.423 66.667 24.05 24.05 0.00 6.46
4519 5054 4.828925 GACGAGCTGAGCCAGGCC 62.829 72.222 8.22 0.00 31.21 5.19
4547 5082 1.000993 AGCCGGAGAGACCTGTGAT 59.999 57.895 5.05 0.00 36.31 3.06
4548 5083 1.142748 GCCGGAGAGACCTGTGATG 59.857 63.158 5.05 0.00 36.31 3.07
4549 5084 1.608717 GCCGGAGAGACCTGTGATGT 61.609 60.000 5.05 0.00 36.31 3.06
4550 5085 0.174389 CCGGAGAGACCTGTGATGTG 59.826 60.000 0.00 0.00 36.31 3.21
4551 5086 1.177401 CGGAGAGACCTGTGATGTGA 58.823 55.000 0.00 0.00 36.31 3.58
4658 5193 1.785353 TTTTCCCCCTTCCCTGACGG 61.785 60.000 0.00 0.00 0.00 4.79
4678 5213 0.549169 AAATCCTTGTCCTCCCCGGA 60.549 55.000 0.73 0.00 40.30 5.14
4679 5214 0.983378 AATCCTTGTCCTCCCCGGAG 60.983 60.000 0.73 3.56 44.20 4.63
4680 5215 2.182858 ATCCTTGTCCTCCCCGGAGT 62.183 60.000 0.73 0.00 44.20 3.85
4681 5216 1.001248 CCTTGTCCTCCCCGGAGTA 59.999 63.158 0.73 0.00 44.20 2.59
4682 5217 0.616679 CCTTGTCCTCCCCGGAGTAA 60.617 60.000 0.73 1.98 44.20 2.24
4711 5246 7.900782 AATTTTGCAATTCTTTCAGGAGATG 57.099 32.000 0.00 0.00 0.00 2.90
4737 5272 9.885934 GAGTAAATTCCTTCTTTCTTTTCTGTC 57.114 33.333 0.00 0.00 0.00 3.51
4740 5275 7.517614 AATTCCTTCTTTCTTTTCTGTCCTC 57.482 36.000 0.00 0.00 0.00 3.71
4752 5287 3.762407 TCTGTCCTCGGTCAAATGAAA 57.238 42.857 0.00 0.00 0.00 2.69
4785 5320 1.684049 AGAGACTTCGGCTCCAGGG 60.684 63.158 0.00 0.00 32.82 4.45
4786 5321 2.685380 AGACTTCGGCTCCAGGGG 60.685 66.667 0.00 0.00 0.00 4.79
4790 5325 2.203938 TTCGGCTCCAGGGGTTCT 60.204 61.111 0.00 0.00 0.00 3.01
4797 5332 1.691434 GCTCCAGGGGTTCTCAGATAG 59.309 57.143 0.00 0.00 0.00 2.08
4807 5342 6.068971 AGGGGTTCTCAGATAGAGTAACTGTA 60.069 42.308 0.00 0.00 44.98 2.74
4814 5349 9.521841 TCTCAGATAGAGTAACTGTATTATGGG 57.478 37.037 0.00 0.00 44.98 4.00
4815 5350 9.303116 CTCAGATAGAGTAACTGTATTATGGGT 57.697 37.037 0.00 0.00 39.62 4.51
4871 5406 2.987547 TGCAAGCTTCAGCAGGGC 60.988 61.111 7.34 1.74 45.16 5.19
4877 5412 2.914289 CTTCAGCAGGGCCTAGGG 59.086 66.667 5.28 0.00 0.00 3.53
4901 5436 2.496817 GCAGTAGAGCTCGGTGGG 59.503 66.667 8.37 0.00 0.00 4.61
4924 5459 0.104304 ACTCGGGCCTTGTATTAGCG 59.896 55.000 0.84 0.00 0.00 4.26
4969 5505 5.757099 ACCCTAATGTTTATATCTCCGGG 57.243 43.478 0.00 0.00 0.00 5.73
5019 5555 2.190841 CCGCACCCTCCGTTTTGTT 61.191 57.895 0.00 0.00 0.00 2.83
5020 5556 1.730451 CCGCACCCTCCGTTTTGTTT 61.730 55.000 0.00 0.00 0.00 2.83
5021 5557 0.593773 CGCACCCTCCGTTTTGTTTG 60.594 55.000 0.00 0.00 0.00 2.93
5022 5558 0.458260 GCACCCTCCGTTTTGTTTGT 59.542 50.000 0.00 0.00 0.00 2.83
5108 5644 2.352915 CGCGTCCGATGCTCTCTC 60.353 66.667 10.81 0.00 36.29 3.20
5109 5645 2.829206 CGCGTCCGATGCTCTCTCT 61.829 63.158 10.81 0.00 36.29 3.10
5192 5728 5.005394 CGGTCGATAATTAAATGGGCGATAG 59.995 44.000 0.00 0.00 0.00 2.08
5279 5815 6.255020 CGCACCAAGAACGAAATAATACTACT 59.745 38.462 0.00 0.00 0.00 2.57
5280 5816 7.433131 CGCACCAAGAACGAAATAATACTACTA 59.567 37.037 0.00 0.00 0.00 1.82
5281 5817 8.538039 GCACCAAGAACGAAATAATACTACTAC 58.462 37.037 0.00 0.00 0.00 2.73
5282 5818 9.798994 CACCAAGAACGAAATAATACTACTACT 57.201 33.333 0.00 0.00 0.00 2.57
5320 5856 2.787473 TGTTCCTCAAGTGCCTATGG 57.213 50.000 0.00 0.00 0.00 2.74
5321 5857 2.265367 TGTTCCTCAAGTGCCTATGGA 58.735 47.619 0.00 0.00 0.00 3.41
5322 5858 2.846206 TGTTCCTCAAGTGCCTATGGAT 59.154 45.455 0.00 0.00 0.00 3.41
5323 5859 3.266772 TGTTCCTCAAGTGCCTATGGATT 59.733 43.478 0.00 0.00 0.00 3.01
5324 5860 4.473196 TGTTCCTCAAGTGCCTATGGATTA 59.527 41.667 0.00 0.00 0.00 1.75
5325 5861 4.689612 TCCTCAAGTGCCTATGGATTAC 57.310 45.455 0.00 0.00 0.00 1.89
5326 5862 4.037222 TCCTCAAGTGCCTATGGATTACA 58.963 43.478 0.00 0.00 0.00 2.41
5327 5863 4.101585 TCCTCAAGTGCCTATGGATTACAG 59.898 45.833 0.00 0.00 0.00 2.74
5328 5864 4.384056 CTCAAGTGCCTATGGATTACAGG 58.616 47.826 0.00 0.00 0.00 4.00
5337 5873 6.875972 CCTATGGATTACAGGCCTATTAGT 57.124 41.667 3.98 0.68 0.00 2.24
5338 5874 6.879400 CCTATGGATTACAGGCCTATTAGTC 58.121 44.000 3.98 6.23 0.00 2.59
5339 5875 6.670027 CCTATGGATTACAGGCCTATTAGTCT 59.330 42.308 3.98 0.00 0.00 3.24
5340 5876 7.181125 CCTATGGATTACAGGCCTATTAGTCTT 59.819 40.741 3.98 1.87 0.00 3.01
5341 5877 6.824958 TGGATTACAGGCCTATTAGTCTTT 57.175 37.500 3.98 0.00 0.00 2.52
5342 5878 6.591935 TGGATTACAGGCCTATTAGTCTTTG 58.408 40.000 3.98 0.00 0.00 2.77
5343 5879 6.157994 TGGATTACAGGCCTATTAGTCTTTGT 59.842 38.462 3.98 0.00 0.00 2.83
5344 5880 7.346175 TGGATTACAGGCCTATTAGTCTTTGTA 59.654 37.037 3.98 0.00 0.00 2.41
5345 5881 8.208903 GGATTACAGGCCTATTAGTCTTTGTAA 58.791 37.037 3.98 7.17 35.17 2.41
5346 5882 9.780186 GATTACAGGCCTATTAGTCTTTGTAAT 57.220 33.333 3.98 12.00 40.91 1.89
5347 5883 8.958119 TTACAGGCCTATTAGTCTTTGTAATG 57.042 34.615 3.98 0.00 0.00 1.90
5348 5884 6.958767 ACAGGCCTATTAGTCTTTGTAATGT 58.041 36.000 3.98 0.00 0.00 2.71
5349 5885 7.402862 ACAGGCCTATTAGTCTTTGTAATGTT 58.597 34.615 3.98 0.00 0.00 2.71
5350 5886 7.336931 ACAGGCCTATTAGTCTTTGTAATGTTG 59.663 37.037 3.98 0.00 0.00 3.33
5351 5887 7.336931 CAGGCCTATTAGTCTTTGTAATGTTGT 59.663 37.037 3.98 0.00 0.00 3.32
5352 5888 7.888546 AGGCCTATTAGTCTTTGTAATGTTGTT 59.111 33.333 1.29 0.00 0.00 2.83
5353 5889 8.520351 GGCCTATTAGTCTTTGTAATGTTGTTT 58.480 33.333 0.00 0.00 0.00 2.83
5379 5915 8.921353 ATAAGATCATTGCTAAATCTCTTGCT 57.079 30.769 0.00 0.00 31.72 3.91
5381 5917 8.743085 AAGATCATTGCTAAATCTCTTGCTAA 57.257 30.769 0.00 0.00 29.65 3.09
5382 5918 8.152309 AGATCATTGCTAAATCTCTTGCTAAC 57.848 34.615 0.00 0.00 0.00 2.34
5383 5919 7.772292 AGATCATTGCTAAATCTCTTGCTAACA 59.228 33.333 0.00 0.00 0.00 2.41
5384 5920 7.312657 TCATTGCTAAATCTCTTGCTAACAG 57.687 36.000 0.00 0.00 0.00 3.16
5385 5921 6.317140 TCATTGCTAAATCTCTTGCTAACAGG 59.683 38.462 0.00 0.00 0.00 4.00
5386 5922 5.420725 TGCTAAATCTCTTGCTAACAGGA 57.579 39.130 0.00 0.00 0.00 3.86
5387 5923 5.994250 TGCTAAATCTCTTGCTAACAGGAT 58.006 37.500 0.00 0.00 30.57 3.24
5388 5924 6.418101 TGCTAAATCTCTTGCTAACAGGATT 58.582 36.000 0.00 0.00 30.57 3.01
5389 5925 7.564793 TGCTAAATCTCTTGCTAACAGGATTA 58.435 34.615 0.00 0.00 30.57 1.75
5390 5926 8.046708 TGCTAAATCTCTTGCTAACAGGATTAA 58.953 33.333 0.00 0.00 30.57 1.40
5391 5927 8.893727 GCTAAATCTCTTGCTAACAGGATTAAA 58.106 33.333 0.00 0.00 30.57 1.52
5393 5929 7.631717 AATCTCTTGCTAACAGGATTAAACC 57.368 36.000 0.00 0.00 30.57 3.27
5394 5930 6.374417 TCTCTTGCTAACAGGATTAAACCT 57.626 37.500 0.00 0.00 41.43 3.50
5395 5931 6.407202 TCTCTTGCTAACAGGATTAAACCTC 58.593 40.000 0.37 0.00 38.32 3.85
5396 5932 6.013725 TCTCTTGCTAACAGGATTAAACCTCA 60.014 38.462 0.37 0.00 38.32 3.86
5397 5933 5.938125 TCTTGCTAACAGGATTAAACCTCAC 59.062 40.000 0.37 0.00 38.32 3.51
5398 5934 4.585879 TGCTAACAGGATTAAACCTCACC 58.414 43.478 0.37 0.00 38.32 4.02
5399 5935 4.288626 TGCTAACAGGATTAAACCTCACCT 59.711 41.667 0.37 0.00 38.32 4.00
5400 5936 5.222048 TGCTAACAGGATTAAACCTCACCTT 60.222 40.000 0.37 0.00 38.32 3.50
5401 5937 5.354513 GCTAACAGGATTAAACCTCACCTTC 59.645 44.000 0.37 0.00 38.32 3.46
5402 5938 4.302559 ACAGGATTAAACCTCACCTTCC 57.697 45.455 0.37 0.00 38.32 3.46
5403 5939 3.916989 ACAGGATTAAACCTCACCTTCCT 59.083 43.478 0.37 0.00 38.32 3.36
5404 5940 4.265073 CAGGATTAAACCTCACCTTCCTG 58.735 47.826 0.37 1.60 41.84 3.86
5405 5941 4.175962 AGGATTAAACCTCACCTTCCTGA 58.824 43.478 0.00 0.00 34.98 3.86
5406 5942 4.790790 AGGATTAAACCTCACCTTCCTGAT 59.209 41.667 0.00 0.00 34.98 2.90
5407 5943 5.254032 AGGATTAAACCTCACCTTCCTGATT 59.746 40.000 0.00 0.00 34.98 2.57
5408 5944 6.447084 AGGATTAAACCTCACCTTCCTGATTA 59.553 38.462 0.00 0.00 34.98 1.75
5409 5945 7.129504 AGGATTAAACCTCACCTTCCTGATTAT 59.870 37.037 0.00 0.00 34.98 1.28
5410 5946 8.437575 GGATTAAACCTCACCTTCCTGATTATA 58.562 37.037 0.00 0.00 0.00 0.98
5414 5950 8.798975 AAACCTCACCTTCCTGATTATATAGA 57.201 34.615 0.00 0.00 0.00 1.98
5415 5951 8.980832 AACCTCACCTTCCTGATTATATAGAT 57.019 34.615 0.00 0.00 0.00 1.98
5416 5952 8.602472 ACCTCACCTTCCTGATTATATAGATC 57.398 38.462 0.00 0.00 0.00 2.75
5417 5953 7.621683 ACCTCACCTTCCTGATTATATAGATCC 59.378 40.741 0.00 0.00 0.00 3.36
5418 5954 7.843760 CCTCACCTTCCTGATTATATAGATCCT 59.156 40.741 0.00 0.00 0.00 3.24
5419 5955 8.601047 TCACCTTCCTGATTATATAGATCCTG 57.399 38.462 0.00 0.00 0.00 3.86
5420 5956 7.124901 TCACCTTCCTGATTATATAGATCCTGC 59.875 40.741 0.00 0.00 0.00 4.85
5421 5957 6.385467 ACCTTCCTGATTATATAGATCCTGCC 59.615 42.308 0.00 0.00 0.00 4.85
5422 5958 6.183361 CCTTCCTGATTATATAGATCCTGCCC 60.183 46.154 0.00 0.00 0.00 5.36
5423 5959 5.853700 TCCTGATTATATAGATCCTGCCCA 58.146 41.667 0.00 0.00 0.00 5.36
5424 5960 6.271537 TCCTGATTATATAGATCCTGCCCAA 58.728 40.000 0.00 0.00 0.00 4.12
5425 5961 6.156949 TCCTGATTATATAGATCCTGCCCAAC 59.843 42.308 0.00 0.00 0.00 3.77
5426 5962 6.070021 CCTGATTATATAGATCCTGCCCAACA 60.070 42.308 0.00 0.00 0.00 3.33
5427 5963 6.950842 TGATTATATAGATCCTGCCCAACAG 58.049 40.000 0.00 0.00 46.77 3.16
5440 5976 1.547372 CCCAACAGGCTTTCATTGAGG 59.453 52.381 0.00 0.00 0.00 3.86
5441 5977 1.547372 CCAACAGGCTTTCATTGAGGG 59.453 52.381 0.00 0.00 0.00 4.30
5442 5978 2.242043 CAACAGGCTTTCATTGAGGGT 58.758 47.619 0.00 0.00 0.00 4.34
5443 5979 3.420893 CAACAGGCTTTCATTGAGGGTA 58.579 45.455 0.00 0.00 0.00 3.69
5444 5980 3.356529 ACAGGCTTTCATTGAGGGTAG 57.643 47.619 0.00 0.00 0.00 3.18
5445 5981 2.912956 ACAGGCTTTCATTGAGGGTAGA 59.087 45.455 0.00 0.00 0.00 2.59
5446 5982 3.330701 ACAGGCTTTCATTGAGGGTAGAA 59.669 43.478 0.00 0.00 0.00 2.10
5447 5983 3.944015 CAGGCTTTCATTGAGGGTAGAAG 59.056 47.826 0.00 0.00 0.00 2.85
5448 5984 3.846588 AGGCTTTCATTGAGGGTAGAAGA 59.153 43.478 0.00 0.00 0.00 2.87
5449 5985 4.289672 AGGCTTTCATTGAGGGTAGAAGAA 59.710 41.667 0.00 0.00 0.00 2.52
5450 5986 5.044550 AGGCTTTCATTGAGGGTAGAAGAAT 60.045 40.000 0.00 0.00 0.00 2.40
5451 5987 5.654209 GGCTTTCATTGAGGGTAGAAGAATT 59.346 40.000 0.00 0.00 0.00 2.17
5452 5988 6.828785 GGCTTTCATTGAGGGTAGAAGAATTA 59.171 38.462 0.00 0.00 0.00 1.40
5453 5989 7.012799 GGCTTTCATTGAGGGTAGAAGAATTAG 59.987 40.741 0.00 0.00 0.00 1.73
5454 5990 7.554476 GCTTTCATTGAGGGTAGAAGAATTAGT 59.446 37.037 0.00 0.00 0.00 2.24
5455 5991 8.792830 TTTCATTGAGGGTAGAAGAATTAGTG 57.207 34.615 0.00 0.00 0.00 2.74
5456 5992 7.733773 TCATTGAGGGTAGAAGAATTAGTGA 57.266 36.000 0.00 0.00 0.00 3.41
5457 5993 8.324191 TCATTGAGGGTAGAAGAATTAGTGAT 57.676 34.615 0.00 0.00 0.00 3.06
5458 5994 9.434275 TCATTGAGGGTAGAAGAATTAGTGATA 57.566 33.333 0.00 0.00 0.00 2.15
5487 6023 8.824159 TTATAATTGCTCAAGAGATAGCTCAC 57.176 34.615 11.20 0.00 43.81 3.51
5488 6024 5.356291 AATTGCTCAAGAGATAGCTCACT 57.644 39.130 11.20 0.00 43.81 3.41
5489 6025 4.383850 TTGCTCAAGAGATAGCTCACTC 57.616 45.455 11.20 10.81 43.81 3.51
5490 6026 3.630168 TGCTCAAGAGATAGCTCACTCT 58.370 45.455 11.20 14.32 43.81 3.24
5492 6028 4.465660 TGCTCAAGAGATAGCTCACTCTTT 59.534 41.667 23.69 12.44 46.86 2.52
5493 6029 5.043248 GCTCAAGAGATAGCTCACTCTTTC 58.957 45.833 23.69 15.64 46.86 2.62
5494 6030 5.163519 GCTCAAGAGATAGCTCACTCTTTCT 60.164 44.000 23.69 8.86 46.86 2.52
5495 6031 6.449635 TCAAGAGATAGCTCACTCTTTCTC 57.550 41.667 23.69 11.43 46.86 2.87
5496 6032 6.186957 TCAAGAGATAGCTCACTCTTTCTCT 58.813 40.000 23.69 12.98 46.86 3.10
5497 6033 6.318648 TCAAGAGATAGCTCACTCTTTCTCTC 59.681 42.308 23.69 9.47 46.86 3.20
5498 6034 6.006275 AGAGATAGCTCACTCTTTCTCTCT 57.994 41.667 11.20 0.00 43.34 3.10
5499 6035 6.058183 AGAGATAGCTCACTCTTTCTCTCTC 58.942 44.000 11.20 0.00 43.34 3.20
5500 6036 5.754782 AGATAGCTCACTCTTTCTCTCTCA 58.245 41.667 0.00 0.00 0.00 3.27
5501 6037 6.186957 AGATAGCTCACTCTTTCTCTCTCAA 58.813 40.000 0.00 0.00 0.00 3.02
5502 6038 6.663093 AGATAGCTCACTCTTTCTCTCTCAAA 59.337 38.462 0.00 0.00 0.00 2.69
5503 6039 5.743636 AGCTCACTCTTTCTCTCTCAAAT 57.256 39.130 0.00 0.00 0.00 2.32
5504 6040 5.723295 AGCTCACTCTTTCTCTCTCAAATC 58.277 41.667 0.00 0.00 0.00 2.17
5505 6041 5.481473 AGCTCACTCTTTCTCTCTCAAATCT 59.519 40.000 0.00 0.00 0.00 2.40
5506 6042 6.014327 AGCTCACTCTTTCTCTCTCAAATCTT 60.014 38.462 0.00 0.00 0.00 2.40
5507 6043 6.091169 GCTCACTCTTTCTCTCTCAAATCTTG 59.909 42.308 0.00 0.00 0.00 3.02
5508 6044 6.462500 TCACTCTTTCTCTCTCAAATCTTGG 58.538 40.000 0.00 0.00 0.00 3.61
5509 6045 6.268617 TCACTCTTTCTCTCTCAAATCTTGGA 59.731 38.462 0.00 0.00 0.00 3.53
5510 6046 6.933521 CACTCTTTCTCTCTCAAATCTTGGAA 59.066 38.462 0.00 0.00 0.00 3.53
5511 6047 7.443575 CACTCTTTCTCTCTCAAATCTTGGAAA 59.556 37.037 0.00 0.00 0.00 3.13
5512 6048 7.443879 ACTCTTTCTCTCTCAAATCTTGGAAAC 59.556 37.037 0.00 0.00 0.00 2.78
5513 6049 7.282585 TCTTTCTCTCTCAAATCTTGGAAACA 58.717 34.615 0.00 0.00 39.83 2.83
5514 6050 7.941238 TCTTTCTCTCTCAAATCTTGGAAACAT 59.059 33.333 0.00 0.00 42.32 2.71
5515 6051 7.444629 TTCTCTCTCAAATCTTGGAAACATG 57.555 36.000 0.00 0.00 42.32 3.21
5516 6052 6.772605 TCTCTCTCAAATCTTGGAAACATGA 58.227 36.000 0.00 0.00 46.98 3.07
5524 6060 3.765381 TCTTGGAAACATGATGCCTTCA 58.235 40.909 0.00 0.00 42.32 3.02
5525 6061 4.346730 TCTTGGAAACATGATGCCTTCAT 58.653 39.130 0.00 0.00 46.27 2.57
5539 6075 8.706492 TGATGCCTTCATGTTAAAAATTGATC 57.294 30.769 0.00 0.00 31.96 2.92
5540 6076 8.533657 TGATGCCTTCATGTTAAAAATTGATCT 58.466 29.630 0.00 0.00 31.96 2.75
5541 6077 9.374838 GATGCCTTCATGTTAAAAATTGATCTT 57.625 29.630 0.00 0.00 31.96 2.40
5542 6078 8.537049 TGCCTTCATGTTAAAAATTGATCTTG 57.463 30.769 0.00 0.00 0.00 3.02
5543 6079 7.118101 TGCCTTCATGTTAAAAATTGATCTTGC 59.882 33.333 0.00 0.00 0.00 4.01
5544 6080 7.332678 GCCTTCATGTTAAAAATTGATCTTGCT 59.667 33.333 0.00 0.00 0.00 3.91
5545 6081 9.859427 CCTTCATGTTAAAAATTGATCTTGCTA 57.141 29.630 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.096001 AGGGTGTACTCGTTATAGTTTACTGG 59.904 42.308 0.00 0.00 0.00 4.00
15 16 6.319911 GGAGGGTGTACTCGTTATAGTTTACT 59.680 42.308 0.00 0.00 38.39 2.24
26 27 1.975407 CGGTGGAGGGTGTACTCGT 60.975 63.158 0.00 0.00 38.39 4.18
27 28 1.930908 GACGGTGGAGGGTGTACTCG 61.931 65.000 0.00 0.00 38.39 4.18
28 29 1.888736 GACGGTGGAGGGTGTACTC 59.111 63.158 0.00 0.00 36.76 2.59
29 30 1.975407 CGACGGTGGAGGGTGTACT 60.975 63.158 0.00 0.00 0.00 2.73
30 31 2.570181 CGACGGTGGAGGGTGTAC 59.430 66.667 0.00 0.00 0.00 2.90
95 104 4.090057 GACGAGGCAAGTTGCGGC 62.090 66.667 21.11 14.06 46.21 6.53
158 172 3.721706 AGAAGGAAGGGCGGCTGG 61.722 66.667 9.56 0.00 0.00 4.85
159 173 2.437359 CAGAAGGAAGGGCGGCTG 60.437 66.667 9.56 0.00 0.00 4.85
160 174 4.416738 GCAGAAGGAAGGGCGGCT 62.417 66.667 9.56 0.00 0.00 5.52
237 278 2.877691 GGCATTTCCCGTGCAGAC 59.122 61.111 0.00 0.00 44.25 3.51
252 293 0.615827 AGAAGGCTGGGAAATTGGGC 60.616 55.000 0.00 0.00 0.00 5.36
335 376 1.576356 GGAAATAGCTGGACTGCGAG 58.424 55.000 0.00 0.00 38.13 5.03
537 615 1.569708 GAGCTCATCTCTTTCTGGCG 58.430 55.000 9.40 0.00 38.78 5.69
596 674 2.653702 GCTCGCCTCTCTGTGTGT 59.346 61.111 0.00 0.00 0.00 3.72
597 675 2.505777 CGCTCGCCTCTCTGTGTG 60.506 66.667 0.00 0.00 0.00 3.82
598 676 3.753434 CCGCTCGCCTCTCTGTGT 61.753 66.667 0.00 0.00 0.00 3.72
599 677 3.753434 ACCGCTCGCCTCTCTGTG 61.753 66.667 0.00 0.00 0.00 3.66
600 678 3.753434 CACCGCTCGCCTCTCTGT 61.753 66.667 0.00 0.00 0.00 3.41
800 930 0.185901 CTGGCCTAGAGAGAGAGCCT 59.814 60.000 3.32 0.00 44.19 4.58
801 931 0.827507 CCTGGCCTAGAGAGAGAGCC 60.828 65.000 3.32 0.00 44.13 4.70
802 932 0.827507 CCCTGGCCTAGAGAGAGAGC 60.828 65.000 3.32 0.00 0.00 4.09
803 933 0.555769 ACCCTGGCCTAGAGAGAGAG 59.444 60.000 3.32 0.00 0.00 3.20
804 934 0.260230 CACCCTGGCCTAGAGAGAGA 59.740 60.000 3.32 0.00 0.00 3.10
805 935 0.758685 CCACCCTGGCCTAGAGAGAG 60.759 65.000 3.32 0.00 0.00 3.20
806 936 1.311403 CCACCCTGGCCTAGAGAGA 59.689 63.158 3.32 0.00 0.00 3.10
807 937 1.764054 CCCACCCTGGCCTAGAGAG 60.764 68.421 3.32 0.00 35.79 3.20
808 938 2.368594 CCCACCCTGGCCTAGAGA 59.631 66.667 3.32 0.00 35.79 3.10
809 939 2.041265 ACCCACCCTGGCCTAGAG 59.959 66.667 3.32 0.00 35.79 2.43
810 940 2.285368 CACCCACCCTGGCCTAGA 60.285 66.667 3.32 0.00 35.79 2.43
811 941 3.411517 CCACCCACCCTGGCCTAG 61.412 72.222 3.32 0.00 35.79 3.02
860 990 2.768492 CGCCCCAATCAAGCAGCTC 61.768 63.158 0.00 0.00 0.00 4.09
878 1008 4.610714 GATCTCCCGCCCGGCTTC 62.611 72.222 8.05 0.00 0.00 3.86
908 1038 1.692042 CAGGGGATCTGCAGGTCCT 60.692 63.158 38.34 22.17 36.60 3.85
1116 1252 1.894756 CGAGGCGGAGGAGGAGTAG 60.895 68.421 0.00 0.00 0.00 2.57
1386 1522 4.710695 TGTACGCGTGGCTGGTCG 62.711 66.667 24.59 0.00 0.00 4.79
1860 2310 0.767446 AGGATCCTGCAGATGAGGGG 60.767 60.000 15.29 0.00 34.42 4.79
1866 2316 1.969923 GCTAGTGAGGATCCTGCAGAT 59.030 52.381 22.02 6.84 38.17 2.90
1898 2348 1.084289 ACTCGGGCGCTTATGTTTTC 58.916 50.000 7.64 0.00 0.00 2.29
1908 2358 1.361793 TACATTTAACACTCGGGCGC 58.638 50.000 0.00 0.00 0.00 6.53
1942 2392 7.010275 CGTCTAGGACTGGCTAAATTTAGAAAC 59.990 40.741 26.00 15.83 32.47 2.78
1959 2409 4.036971 ACTGTAATGAGCATCGTCTAGGAC 59.963 45.833 0.00 0.00 38.61 3.85
2236 2686 1.117150 CCTGCCCATTCCCAATCTTG 58.883 55.000 0.00 0.00 0.00 3.02
2329 2779 1.765904 TGGCCCTCTGATACGCAATAA 59.234 47.619 0.00 0.00 0.00 1.40
2422 2872 9.807649 GATGCAAATAAAAGAACCACTATGATT 57.192 29.630 0.00 0.00 0.00 2.57
2538 2988 0.968901 TGACCCTCGTACGCCAATCT 60.969 55.000 11.24 0.00 0.00 2.40
2635 3085 5.339200 CCACACTAGTTCAGGGGATTAATGT 60.339 44.000 0.00 0.00 28.64 2.71
2800 3250 7.379529 ACAACTGAAAAATCGCATAGAAACAAG 59.620 33.333 0.00 0.00 0.00 3.16
2925 3378 1.808411 ATGTTCCCATGACACGTGTC 58.192 50.000 36.01 36.01 44.97 3.67
2958 3411 0.244721 GCAATGGCTGTCTTTGGACC 59.755 55.000 9.51 0.00 41.47 4.46
2968 3421 2.490509 TGACTGAAGATTGCAATGGCTG 59.509 45.455 18.59 11.52 41.91 4.85
3099 3556 9.606631 ACAACTCCAAAAGAATATAGATCAGAC 57.393 33.333 0.00 0.00 0.00 3.51
3168 3625 1.523258 CTCATCTCCAAGCGGCTGG 60.523 63.158 1.81 7.71 37.87 4.85
3332 3790 8.362464 AGCCAGATAATACGATAGGTCAATTA 57.638 34.615 0.00 0.00 43.77 1.40
3423 3882 9.841295 TCTAAGTAACATAACCAAACTTCAACT 57.159 29.630 0.00 0.00 32.85 3.16
3498 4023 7.611467 ACCTCAACAGCTATATTGATCAACAAA 59.389 33.333 11.07 0.00 42.03 2.83
3570 4097 5.043732 AGGGAAAGAGGTGATCTAGAGAAGA 60.044 44.000 0.00 0.00 37.23 2.87
3729 4256 2.952310 AGTTGGAACTTTTCAGCTCACC 59.048 45.455 0.00 0.00 35.21 4.02
3760 4287 4.412207 GTTGCCCACTTTCTATAAAAGCG 58.588 43.478 0.00 0.00 0.00 4.68
3838 4365 2.289257 TGACTCACCACAGCATGAAGAG 60.289 50.000 0.00 0.00 39.69 2.85
3871 4398 6.039829 GTCCCTGTTTTCTCAAGTTCTCATTT 59.960 38.462 0.00 0.00 0.00 2.32
3872 4399 5.532779 GTCCCTGTTTTCTCAAGTTCTCATT 59.467 40.000 0.00 0.00 0.00 2.57
3910 4442 9.448438 TCCATTTATGCTTATGTTCGCTAATAT 57.552 29.630 0.00 0.00 0.00 1.28
3911 4443 8.840833 TCCATTTATGCTTATGTTCGCTAATA 57.159 30.769 0.00 0.00 0.00 0.98
3912 4444 7.744087 TCCATTTATGCTTATGTTCGCTAAT 57.256 32.000 0.00 0.00 0.00 1.73
3913 4445 7.282224 AGTTCCATTTATGCTTATGTTCGCTAA 59.718 33.333 0.00 0.00 0.00 3.09
3918 4450 8.623903 TCATCAGTTCCATTTATGCTTATGTTC 58.376 33.333 0.00 0.00 0.00 3.18
3985 4517 5.112686 GCATTTAGACAGTAACCAGAGAGG 58.887 45.833 0.00 0.00 45.67 3.69
4089 4622 2.507110 CTTGCGAGAGAAAGGGCCGA 62.507 60.000 0.00 0.00 43.35 5.54
4128 4661 3.547513 GGGTCCGGAAGATCCCCG 61.548 72.222 15.62 15.08 40.31 5.73
4134 4667 1.756950 CATCCTCGGGTCCGGAAGA 60.757 63.158 5.23 5.45 40.25 2.87
4140 4673 0.326927 TGTTTTCCATCCTCGGGTCC 59.673 55.000 0.00 0.00 0.00 4.46
4143 4676 3.427503 CGAATTTGTTTTCCATCCTCGGG 60.428 47.826 0.00 0.00 0.00 5.14
4301 4834 6.530120 TCTTAGTCCTGTGCTGTCATTTAAA 58.470 36.000 0.00 0.00 0.00 1.52
4302 4835 6.109156 TCTTAGTCCTGTGCTGTCATTTAA 57.891 37.500 0.00 0.00 0.00 1.52
4303 4836 5.738619 TCTTAGTCCTGTGCTGTCATTTA 57.261 39.130 0.00 0.00 0.00 1.40
4327 4862 5.049828 GCAAAGGAAAATACATGGGCATAC 58.950 41.667 0.00 0.00 0.00 2.39
4352 4887 2.706190 GTGCTCTTACCACCTGGGATAT 59.294 50.000 0.00 0.00 41.15 1.63
4353 4888 2.116238 GTGCTCTTACCACCTGGGATA 58.884 52.381 0.00 0.00 41.15 2.59
4357 4892 0.036010 CCAGTGCTCTTACCACCTGG 60.036 60.000 0.00 0.00 42.17 4.45
4447 4982 1.040339 ACAGCCTGATCTCCTCGGTC 61.040 60.000 0.00 0.00 0.00 4.79
4547 5082 1.885388 CCGACGCCTGTTGTTCACA 60.885 57.895 0.00 0.00 0.00 3.58
4548 5083 1.828331 GACCGACGCCTGTTGTTCAC 61.828 60.000 0.00 0.00 0.00 3.18
4549 5084 1.593209 GACCGACGCCTGTTGTTCA 60.593 57.895 0.00 0.00 0.00 3.18
4550 5085 2.654912 CGACCGACGCCTGTTGTTC 61.655 63.158 0.00 0.00 34.51 3.18
4551 5086 2.660552 CGACCGACGCCTGTTGTT 60.661 61.111 0.00 0.00 34.51 2.83
4649 5184 1.278127 GACAAGGATTTCCGTCAGGGA 59.722 52.381 1.20 0.00 45.40 4.20
4658 5193 0.107165 CCGGGGAGGACAAGGATTTC 60.107 60.000 0.00 0.00 45.00 2.17
4681 5216 9.612066 TCCTGAAAGAATTGCAAAATTTACTTT 57.388 25.926 1.71 9.02 34.07 2.66
4682 5217 9.264719 CTCCTGAAAGAATTGCAAAATTTACTT 57.735 29.630 1.71 0.61 34.07 2.24
4711 5246 9.885934 GACAGAAAAGAAAGAAGGAATTTACTC 57.114 33.333 0.00 0.00 0.00 2.59
4752 5287 7.649057 CCGAAGTCTCTGTATTTTTCCTTTTT 58.351 34.615 0.00 0.00 0.00 1.94
4757 5292 4.254492 AGCCGAAGTCTCTGTATTTTTCC 58.746 43.478 0.00 0.00 0.00 3.13
4775 5310 3.003173 TGAGAACCCCTGGAGCCG 61.003 66.667 0.00 0.00 0.00 5.52
4790 5325 9.078990 CACCCATAATACAGTTACTCTATCTGA 57.921 37.037 0.00 0.00 33.93 3.27
4797 5332 7.625828 AAAAGCACCCATAATACAGTTACTC 57.374 36.000 0.00 0.00 0.00 2.59
4879 5414 0.547075 ACCGAGCTCTACTGCCTAGA 59.453 55.000 12.85 0.00 0.00 2.43
4880 5415 0.665835 CACCGAGCTCTACTGCCTAG 59.334 60.000 12.85 0.00 0.00 3.02
4881 5416 0.752009 CCACCGAGCTCTACTGCCTA 60.752 60.000 12.85 0.00 0.00 3.93
4882 5417 2.055042 CCACCGAGCTCTACTGCCT 61.055 63.158 12.85 0.00 0.00 4.75
4883 5418 2.496817 CCACCGAGCTCTACTGCC 59.503 66.667 12.85 0.00 0.00 4.85
4884 5419 1.889530 AACCCACCGAGCTCTACTGC 61.890 60.000 12.85 0.00 0.00 4.40
4885 5420 0.108615 CAACCCACCGAGCTCTACTG 60.109 60.000 12.85 3.77 0.00 2.74
4901 5436 2.109425 AATACAAGGCCCGAGTCAAC 57.891 50.000 0.00 0.00 0.00 3.18
4969 5505 2.806608 TAAGATCCACGGGATTACGC 57.193 50.000 6.85 0.00 43.27 4.42
5019 5555 1.830408 CCCACCGGCCTTTTGACAA 60.830 57.895 0.00 0.00 0.00 3.18
5020 5556 2.203422 CCCACCGGCCTTTTGACA 60.203 61.111 0.00 0.00 0.00 3.58
5021 5557 1.971695 CTCCCACCGGCCTTTTGAC 60.972 63.158 0.00 0.00 0.00 3.18
5022 5558 2.434331 CTCCCACCGGCCTTTTGA 59.566 61.111 0.00 0.00 0.00 2.69
5043 5579 2.976494 AAGTGGCAACGGGACAAGGG 62.976 60.000 0.00 0.00 35.15 3.95
5108 5644 2.816204 ATCTCAGCGATCCATCACAG 57.184 50.000 0.00 0.00 0.00 3.66
5109 5645 3.200483 CAAATCTCAGCGATCCATCACA 58.800 45.455 0.00 0.00 0.00 3.58
5300 5836 2.642311 TCCATAGGCACTTGAGGAACAA 59.358 45.455 0.00 0.00 41.75 2.83
5301 5837 2.265367 TCCATAGGCACTTGAGGAACA 58.735 47.619 0.00 0.00 41.75 3.18
5302 5838 3.567478 ATCCATAGGCACTTGAGGAAC 57.433 47.619 0.00 0.00 41.75 3.62
5303 5839 4.473196 TGTAATCCATAGGCACTTGAGGAA 59.527 41.667 0.00 0.00 41.75 3.36
5304 5840 4.037222 TGTAATCCATAGGCACTTGAGGA 58.963 43.478 0.00 0.00 41.75 3.71
5305 5841 4.384056 CTGTAATCCATAGGCACTTGAGG 58.616 47.826 0.00 0.00 41.75 3.86
5306 5842 4.384056 CCTGTAATCCATAGGCACTTGAG 58.616 47.826 0.00 0.00 41.75 3.02
5307 5843 4.422073 CCTGTAATCCATAGGCACTTGA 57.578 45.455 0.00 0.00 41.75 3.02
5314 5850 6.670027 AGACTAATAGGCCTGTAATCCATAGG 59.330 42.308 17.99 0.00 38.55 2.57
5315 5851 7.726033 AGACTAATAGGCCTGTAATCCATAG 57.274 40.000 17.99 8.80 0.00 2.23
5316 5852 8.375506 CAAAGACTAATAGGCCTGTAATCCATA 58.624 37.037 17.99 0.00 0.00 2.74
5317 5853 7.147302 ACAAAGACTAATAGGCCTGTAATCCAT 60.147 37.037 17.99 0.00 0.00 3.41
5318 5854 6.157994 ACAAAGACTAATAGGCCTGTAATCCA 59.842 38.462 17.99 0.00 0.00 3.41
5319 5855 6.592870 ACAAAGACTAATAGGCCTGTAATCC 58.407 40.000 17.99 0.26 0.00 3.01
5320 5856 9.780186 ATTACAAAGACTAATAGGCCTGTAATC 57.220 33.333 17.99 7.09 37.84 1.75
5321 5857 9.561069 CATTACAAAGACTAATAGGCCTGTAAT 57.439 33.333 17.99 18.33 40.54 1.89
5322 5858 8.545472 ACATTACAAAGACTAATAGGCCTGTAA 58.455 33.333 17.99 16.20 36.83 2.41
5323 5859 8.086143 ACATTACAAAGACTAATAGGCCTGTA 57.914 34.615 17.99 6.67 0.00 2.74
5324 5860 6.958767 ACATTACAAAGACTAATAGGCCTGT 58.041 36.000 17.99 5.57 0.00 4.00
5325 5861 7.336931 ACAACATTACAAAGACTAATAGGCCTG 59.663 37.037 17.99 0.00 0.00 4.85
5326 5862 7.402862 ACAACATTACAAAGACTAATAGGCCT 58.597 34.615 11.78 11.78 0.00 5.19
5327 5863 7.625828 ACAACATTACAAAGACTAATAGGCC 57.374 36.000 0.00 0.00 0.00 5.19
5354 5890 8.921353 AGCAAGAGATTTAGCAATGATCTTAT 57.079 30.769 0.00 0.00 29.60 1.73
5355 5891 9.836864 TTAGCAAGAGATTTAGCAATGATCTTA 57.163 29.630 0.00 0.00 29.60 2.10
5356 5892 8.619546 GTTAGCAAGAGATTTAGCAATGATCTT 58.380 33.333 0.00 0.00 30.25 2.40
5357 5893 7.772292 TGTTAGCAAGAGATTTAGCAATGATCT 59.228 33.333 0.00 0.00 33.05 2.75
5358 5894 7.923888 TGTTAGCAAGAGATTTAGCAATGATC 58.076 34.615 0.00 0.00 0.00 2.92
5359 5895 7.013083 CCTGTTAGCAAGAGATTTAGCAATGAT 59.987 37.037 0.00 0.00 0.00 2.45
5360 5896 6.317140 CCTGTTAGCAAGAGATTTAGCAATGA 59.683 38.462 0.00 0.00 0.00 2.57
5361 5897 6.317140 TCCTGTTAGCAAGAGATTTAGCAATG 59.683 38.462 0.00 0.00 0.00 2.82
5362 5898 6.418101 TCCTGTTAGCAAGAGATTTAGCAAT 58.582 36.000 0.00 0.00 0.00 3.56
5363 5899 5.804639 TCCTGTTAGCAAGAGATTTAGCAA 58.195 37.500 0.00 0.00 0.00 3.91
5364 5900 5.420725 TCCTGTTAGCAAGAGATTTAGCA 57.579 39.130 0.00 0.00 0.00 3.49
5365 5901 6.934048 AATCCTGTTAGCAAGAGATTTAGC 57.066 37.500 0.00 0.00 0.00 3.09
5367 5903 9.174166 GGTTTAATCCTGTTAGCAAGAGATTTA 57.826 33.333 5.04 0.00 0.00 1.40
5368 5904 7.890655 AGGTTTAATCCTGTTAGCAAGAGATTT 59.109 33.333 4.20 0.00 36.35 2.17
5369 5905 7.406104 AGGTTTAATCCTGTTAGCAAGAGATT 58.594 34.615 4.20 5.08 36.35 2.40
5370 5906 6.963322 AGGTTTAATCCTGTTAGCAAGAGAT 58.037 36.000 4.20 0.00 36.35 2.75
5371 5907 6.013725 TGAGGTTTAATCCTGTTAGCAAGAGA 60.014 38.462 9.89 0.00 38.02 3.10
5372 5908 6.092807 GTGAGGTTTAATCCTGTTAGCAAGAG 59.907 42.308 9.89 0.00 38.02 2.85
5373 5909 5.938125 GTGAGGTTTAATCCTGTTAGCAAGA 59.062 40.000 9.89 0.00 38.02 3.02
5374 5910 5.123979 GGTGAGGTTTAATCCTGTTAGCAAG 59.876 44.000 9.89 0.00 38.02 4.01
5375 5911 5.007682 GGTGAGGTTTAATCCTGTTAGCAA 58.992 41.667 9.89 0.00 38.02 3.91
5376 5912 4.288626 AGGTGAGGTTTAATCCTGTTAGCA 59.711 41.667 9.89 0.00 38.02 3.49
5377 5913 4.844884 AGGTGAGGTTTAATCCTGTTAGC 58.155 43.478 9.89 6.11 38.02 3.09
5378 5914 5.880887 GGAAGGTGAGGTTTAATCCTGTTAG 59.119 44.000 9.89 0.00 38.02 2.34
5379 5915 5.550403 AGGAAGGTGAGGTTTAATCCTGTTA 59.450 40.000 9.89 0.00 38.02 2.41
5380 5916 4.354087 AGGAAGGTGAGGTTTAATCCTGTT 59.646 41.667 9.89 0.00 38.02 3.16
5381 5917 3.916989 AGGAAGGTGAGGTTTAATCCTGT 59.083 43.478 9.89 0.00 38.02 4.00
5382 5918 4.265073 CAGGAAGGTGAGGTTTAATCCTG 58.735 47.826 9.89 5.77 44.43 3.86
5383 5919 4.175962 TCAGGAAGGTGAGGTTTAATCCT 58.824 43.478 4.69 4.69 40.97 3.24
5384 5920 4.569719 TCAGGAAGGTGAGGTTTAATCC 57.430 45.455 0.00 0.00 0.00 3.01
5388 5924 9.892444 TCTATATAATCAGGAAGGTGAGGTTTA 57.108 33.333 0.00 0.00 0.00 2.01
5389 5925 8.798975 TCTATATAATCAGGAAGGTGAGGTTT 57.201 34.615 0.00 0.00 0.00 3.27
5390 5926 8.980832 ATCTATATAATCAGGAAGGTGAGGTT 57.019 34.615 0.00 0.00 0.00 3.50
5391 5927 7.621683 GGATCTATATAATCAGGAAGGTGAGGT 59.378 40.741 0.00 0.00 0.00 3.85
5392 5928 7.843760 AGGATCTATATAATCAGGAAGGTGAGG 59.156 40.741 0.00 0.00 0.00 3.86
5393 5929 8.694540 CAGGATCTATATAATCAGGAAGGTGAG 58.305 40.741 0.00 0.00 0.00 3.51
5394 5930 7.124901 GCAGGATCTATATAATCAGGAAGGTGA 59.875 40.741 0.00 0.00 0.00 4.02
5395 5931 7.271511 GCAGGATCTATATAATCAGGAAGGTG 58.728 42.308 0.00 0.00 0.00 4.00
5396 5932 6.385467 GGCAGGATCTATATAATCAGGAAGGT 59.615 42.308 0.00 0.00 0.00 3.50
5397 5933 6.183361 GGGCAGGATCTATATAATCAGGAAGG 60.183 46.154 0.00 0.00 0.00 3.46
5398 5934 6.385176 TGGGCAGGATCTATATAATCAGGAAG 59.615 42.308 0.00 0.00 0.00 3.46
5399 5935 6.271537 TGGGCAGGATCTATATAATCAGGAA 58.728 40.000 0.00 0.00 0.00 3.36
5400 5936 5.853700 TGGGCAGGATCTATATAATCAGGA 58.146 41.667 0.00 0.00 0.00 3.86
5401 5937 6.070021 TGTTGGGCAGGATCTATATAATCAGG 60.070 42.308 0.00 1.89 0.00 3.86
5402 5938 6.950842 TGTTGGGCAGGATCTATATAATCAG 58.049 40.000 0.00 2.37 0.00 2.90
5403 5939 6.950842 CTGTTGGGCAGGATCTATATAATCA 58.049 40.000 0.00 0.00 41.42 2.57
5420 5956 1.547372 CCTCAATGAAAGCCTGTTGGG 59.453 52.381 0.00 0.00 38.36 4.12
5421 5957 1.547372 CCCTCAATGAAAGCCTGTTGG 59.453 52.381 0.00 0.00 0.00 3.77
5422 5958 2.242043 ACCCTCAATGAAAGCCTGTTG 58.758 47.619 0.00 0.00 0.00 3.33
5423 5959 2.683211 ACCCTCAATGAAAGCCTGTT 57.317 45.000 0.00 0.00 0.00 3.16
5424 5960 2.912956 TCTACCCTCAATGAAAGCCTGT 59.087 45.455 0.00 0.00 0.00 4.00
5425 5961 3.634397 TCTACCCTCAATGAAAGCCTG 57.366 47.619 0.00 0.00 0.00 4.85
5426 5962 3.846588 TCTTCTACCCTCAATGAAAGCCT 59.153 43.478 0.00 0.00 0.00 4.58
5427 5963 4.222124 TCTTCTACCCTCAATGAAAGCC 57.778 45.455 0.00 0.00 0.00 4.35
5428 5964 6.765915 AATTCTTCTACCCTCAATGAAAGC 57.234 37.500 0.00 0.00 0.00 3.51
5429 5965 8.887717 CACTAATTCTTCTACCCTCAATGAAAG 58.112 37.037 0.00 0.00 0.00 2.62
5430 5966 8.602424 TCACTAATTCTTCTACCCTCAATGAAA 58.398 33.333 0.00 0.00 0.00 2.69
5431 5967 8.146053 TCACTAATTCTTCTACCCTCAATGAA 57.854 34.615 0.00 0.00 0.00 2.57
5432 5968 7.733773 TCACTAATTCTTCTACCCTCAATGA 57.266 36.000 0.00 0.00 0.00 2.57
5461 5997 9.434420 GTGAGCTATCTCTTGAGCAATTATAAT 57.566 33.333 0.00 0.00 41.36 1.28
5462 5998 8.646004 AGTGAGCTATCTCTTGAGCAATTATAA 58.354 33.333 0.00 0.00 41.36 0.98
5463 5999 8.187913 AGTGAGCTATCTCTTGAGCAATTATA 57.812 34.615 0.00 0.00 41.36 0.98
5464 6000 7.015487 AGAGTGAGCTATCTCTTGAGCAATTAT 59.985 37.037 12.58 0.00 41.36 1.28
5465 6001 6.323482 AGAGTGAGCTATCTCTTGAGCAATTA 59.677 38.462 12.58 0.00 41.36 1.40
5466 6002 5.129155 AGAGTGAGCTATCTCTTGAGCAATT 59.871 40.000 12.58 0.00 41.36 2.32
5467 6003 4.650588 AGAGTGAGCTATCTCTTGAGCAAT 59.349 41.667 12.58 0.00 41.36 3.56
5468 6004 4.022603 AGAGTGAGCTATCTCTTGAGCAA 58.977 43.478 12.58 0.00 41.36 3.91
5469 6005 3.630168 AGAGTGAGCTATCTCTTGAGCA 58.370 45.455 12.58 0.00 41.36 4.26
5470 6006 4.654091 AAGAGTGAGCTATCTCTTGAGC 57.346 45.455 23.40 0.00 45.50 4.26
5471 6007 6.319658 AGAGAAAGAGTGAGCTATCTCTTGAG 59.680 42.308 24.22 0.00 46.20 3.02
5472 6008 6.186957 AGAGAAAGAGTGAGCTATCTCTTGA 58.813 40.000 24.22 0.00 46.20 3.02
5473 6009 6.319658 AGAGAGAAAGAGTGAGCTATCTCTTG 59.680 42.308 24.22 0.00 46.20 3.02
5475 6011 6.006275 AGAGAGAAAGAGTGAGCTATCTCT 57.994 41.667 12.58 12.58 41.98 3.10
5476 6012 5.822519 TGAGAGAGAAAGAGTGAGCTATCTC 59.177 44.000 0.00 0.00 42.82 2.75
5477 6013 5.754782 TGAGAGAGAAAGAGTGAGCTATCT 58.245 41.667 0.00 0.00 32.19 1.98
5478 6014 6.449635 TTGAGAGAGAAAGAGTGAGCTATC 57.550 41.667 0.00 0.00 0.00 2.08
5479 6015 6.849085 TTTGAGAGAGAAAGAGTGAGCTAT 57.151 37.500 0.00 0.00 0.00 2.97
5480 6016 6.663093 AGATTTGAGAGAGAAAGAGTGAGCTA 59.337 38.462 0.00 0.00 0.00 3.32
5481 6017 5.481473 AGATTTGAGAGAGAAAGAGTGAGCT 59.519 40.000 0.00 0.00 0.00 4.09
5482 6018 5.723295 AGATTTGAGAGAGAAAGAGTGAGC 58.277 41.667 0.00 0.00 0.00 4.26
5483 6019 6.591062 CCAAGATTTGAGAGAGAAAGAGTGAG 59.409 42.308 0.00 0.00 0.00 3.51
5484 6020 6.268617 TCCAAGATTTGAGAGAGAAAGAGTGA 59.731 38.462 0.00 0.00 0.00 3.41
5485 6021 6.462500 TCCAAGATTTGAGAGAGAAAGAGTG 58.538 40.000 0.00 0.00 0.00 3.51
5486 6022 6.678568 TCCAAGATTTGAGAGAGAAAGAGT 57.321 37.500 0.00 0.00 0.00 3.24
5487 6023 7.443575 TGTTTCCAAGATTTGAGAGAGAAAGAG 59.556 37.037 0.00 0.00 0.00 2.85
5488 6024 7.282585 TGTTTCCAAGATTTGAGAGAGAAAGA 58.717 34.615 0.00 0.00 0.00 2.52
5489 6025 7.502120 TGTTTCCAAGATTTGAGAGAGAAAG 57.498 36.000 0.00 0.00 0.00 2.62
5490 6026 7.720957 TCATGTTTCCAAGATTTGAGAGAGAAA 59.279 33.333 0.00 0.00 0.00 2.52
5491 6027 7.226441 TCATGTTTCCAAGATTTGAGAGAGAA 58.774 34.615 0.00 0.00 0.00 2.87
5492 6028 6.772605 TCATGTTTCCAAGATTTGAGAGAGA 58.227 36.000 0.00 0.00 0.00 3.10
5493 6029 7.473366 CATCATGTTTCCAAGATTTGAGAGAG 58.527 38.462 0.00 0.00 26.81 3.20
5494 6030 6.127814 GCATCATGTTTCCAAGATTTGAGAGA 60.128 38.462 0.00 0.00 26.81 3.10
5495 6031 6.034591 GCATCATGTTTCCAAGATTTGAGAG 58.965 40.000 0.00 0.00 26.81 3.20
5496 6032 5.105635 GGCATCATGTTTCCAAGATTTGAGA 60.106 40.000 0.00 0.00 26.81 3.27
5497 6033 5.105473 AGGCATCATGTTTCCAAGATTTGAG 60.105 40.000 0.00 0.00 26.81 3.02
5498 6034 4.773674 AGGCATCATGTTTCCAAGATTTGA 59.226 37.500 0.00 0.00 26.81 2.69
5499 6035 5.080969 AGGCATCATGTTTCCAAGATTTG 57.919 39.130 0.00 0.00 26.81 2.32
5500 6036 5.246656 TGAAGGCATCATGTTTCCAAGATTT 59.753 36.000 0.00 0.00 31.50 2.17
5501 6037 4.773674 TGAAGGCATCATGTTTCCAAGATT 59.226 37.500 0.00 0.00 31.50 2.40
5502 6038 4.346730 TGAAGGCATCATGTTTCCAAGAT 58.653 39.130 0.00 0.00 31.50 2.40
5503 6039 3.765381 TGAAGGCATCATGTTTCCAAGA 58.235 40.909 0.00 0.00 31.50 3.02
5514 6050 8.533657 AGATCAATTTTTAACATGAAGGCATCA 58.466 29.630 0.00 0.00 43.67 3.07
5515 6051 8.937634 AGATCAATTTTTAACATGAAGGCATC 57.062 30.769 0.00 0.00 30.68 3.91
5516 6052 9.158233 CAAGATCAATTTTTAACATGAAGGCAT 57.842 29.630 0.00 0.00 34.29 4.40
5517 6053 7.118101 GCAAGATCAATTTTTAACATGAAGGCA 59.882 33.333 0.00 0.00 0.00 4.75
5518 6054 7.332678 AGCAAGATCAATTTTTAACATGAAGGC 59.667 33.333 0.00 0.00 0.00 4.35
5519 6055 8.767478 AGCAAGATCAATTTTTAACATGAAGG 57.233 30.769 0.00 0.00 0.00 3.46



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

AutoCloner maintained by Alex Coulton.