Multiple sequence alignment - TraesCS4A01G484800

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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 TraesCS4A01G484800 chr4A 100.000 5781 0 0 1 5781 738891615 738885835 0.000000e+00 10676.0
1 TraesCS4A01G484800 chr4A 81.024 859 150 9 2317 3165 739273627 739274482 0.000000e+00 671.0
2 TraesCS4A01G484800 chr4A 77.858 691 144 8 4068 4753 739312947 739313633 2.490000e-113 420.0
3 TraesCS4A01G484800 chr4A 78.419 658 128 14 4078 4728 739080576 739081226 3.220000e-112 416.0
4 TraesCS4A01G484800 chr4A 94.382 89 5 0 1345 1433 739310609 739310697 2.810000e-28 137.0
5 TraesCS4A01G484800 chr7A 92.490 2197 112 19 3251 5415 4627540 4629715 0.000000e+00 3094.0
6 TraesCS4A01G484800 chr7A 89.973 1476 102 32 277 1733 4624594 4626042 0.000000e+00 1864.0
7 TraesCS4A01G484800 chr7A 87.052 1506 105 41 1775 3245 4626043 4627493 0.000000e+00 1618.0
8 TraesCS4A01G484800 chr7A 81.024 859 150 11 2317 3166 4069960 4069106 0.000000e+00 671.0
9 TraesCS4A01G484800 chr7A 78.520 689 142 6 4077 4762 3983851 3983166 1.140000e-121 448.0
10 TraesCS4A01G484800 chr7A 78.528 652 116 22 4089 4728 4328554 4327915 1.940000e-109 407.0
11 TraesCS4A01G484800 chr7A 77.056 693 142 12 4077 4762 29786052 29786734 3.270000e-102 383.0
12 TraesCS4A01G484800 chr7A 76.349 630 139 10 4104 4728 4206926 4206302 4.320000e-86 329.0
13 TraesCS4A01G484800 chr7A 88.618 246 16 4 4937 5177 4630934 4631172 7.330000e-74 289.0
14 TraesCS4A01G484800 chr7A 79.021 286 41 13 3 275 4624745 4625024 1.660000e-40 178.0
15 TraesCS4A01G484800 chr7A 89.796 98 10 0 1333 1430 29665099 29665002 6.080000e-25 126.0
16 TraesCS4A01G484800 chr7A 88.776 98 11 0 1333 1430 4254755 4254658 2.830000e-23 121.0
17 TraesCS4A01G484800 chr7D 94.319 1373 65 5 3992 5355 4796066 4797434 0.000000e+00 2091.0
18 TraesCS4A01G484800 chr7D 90.105 1526 78 22 526 2008 4792322 4793817 0.000000e+00 1914.0
19 TraesCS4A01G484800 chr7D 97.558 942 22 1 2316 3256 4794076 4795017 0.000000e+00 1611.0
20 TraesCS4A01G484800 chr7D 91.353 717 31 15 3251 3940 4795045 4795757 0.000000e+00 952.0
21 TraesCS4A01G484800 chr7D 90.373 509 44 4 5 511 4791762 4792267 0.000000e+00 664.0
22 TraesCS4A01G484800 chr7D 79.580 857 159 12 2317 3162 4291472 4290621 2.980000e-167 599.0
23 TraesCS4A01G484800 chr7D 79.102 646 123 12 4089 4728 4502152 4501513 8.900000e-118 435.0
24 TraesCS4A01G484800 chr7D 77.147 722 150 11 4047 4762 29551924 29552636 6.980000e-109 405.0
25 TraesCS4A01G484800 chr7D 77.576 330 46 19 385 701 4791718 4792032 2.140000e-39 174.0
26 TraesCS4A01G484800 chr7D 81.921 177 17 12 111 275 4792322 4792495 1.010000e-27 135.0
27 TraesCS4A01G484800 chr7D 92.135 89 7 0 1345 1433 29550326 29550414 6.080000e-25 126.0
28 TraesCS4A01G484800 chr7D 88.776 98 11 0 1333 1430 29405394 29405297 2.830000e-23 121.0
29 TraesCS4A01G484800 chr3D 90.349 373 24 3 5420 5781 98565461 98565090 4.050000e-131 479.0
30 TraesCS4A01G484800 chr3D 87.733 375 32 5 5420 5781 563419651 563420024 5.350000e-115 425.0
31 TraesCS4A01G484800 chr3A 90.489 368 28 5 5420 5781 545251459 545251093 4.050000e-131 479.0
32 TraesCS4A01G484800 chr3A 79.715 281 47 6 892 1169 362555938 362556211 1.640000e-45 195.0
33 TraesCS4A01G484800 chrUn 90.296 371 24 3 5420 5778 97329421 97329791 5.240000e-130 475.0
34 TraesCS4A01G484800 chrUn 90.027 371 25 3 5420 5778 97227790 97228160 2.440000e-128 470.0
35 TraesCS4A01G484800 chr5D 90.107 374 25 3 5420 5781 537735587 537735960 5.240000e-130 475.0
36 TraesCS4A01G484800 chr5A 89.362 376 26 4 5420 5781 41460532 41460157 1.470000e-125 460.0
37 TraesCS4A01G484800 chr5A 82.400 125 18 4 3027 3149 687150854 687150976 7.920000e-19 106.0
38 TraesCS4A01G484800 chr1A 89.182 379 24 4 5420 5781 20250470 20250848 1.900000e-124 457.0
39 TraesCS4A01G484800 chr7B 88.978 372 29 3 5422 5781 729127432 729127061 3.180000e-122 449.0
40 TraesCS4A01G484800 chr6D 80.662 574 99 8 2317 2884 10103702 10103135 8.900000e-118 435.0
41 TraesCS4A01G484800 chr6D 74.175 697 160 15 4077 4757 10119902 10119210 7.380000e-69 272.0
42 TraesCS4A01G484800 chr6D 81.569 255 47 0 2908 3162 10044938 10044684 1.630000e-50 211.0
43 TraesCS4A01G484800 chr6D 81.457 151 25 3 1277 1427 10122059 10121912 2.830000e-23 121.0
44 TraesCS4A01G484800 chr6B 80.348 575 102 7 2311 2879 18593654 18594223 5.350000e-115 425.0
45 TraesCS4A01G484800 chr6B 79.658 585 100 14 2311 2885 18648052 18647477 2.510000e-108 403.0
46 TraesCS4A01G484800 chr6B 74.085 683 161 12 4077 4745 18595430 18596110 3.430000e-67 267.0
47 TraesCS4A01G484800 chr6B 81.712 257 47 0 2906 3162 18657714 18657458 1.260000e-51 215.0
48 TraesCS4A01G484800 chr6A 79.310 580 105 11 2311 2882 11590394 11589822 5.430000e-105 392.0
49 TraesCS4A01G484800 chr6A 73.458 697 165 15 4077 4757 11588640 11587948 1.610000e-60 244.0
50 TraesCS4A01G484800 chr6A 80.934 257 49 0 2906 3162 11570453 11570197 2.730000e-48 204.0
51 TraesCS4A01G484800 chr2B 85.342 307 20 12 3589 3876 143244143 143244443 1.580000e-75 294.0
52 TraesCS4A01G484800 chr2B 93.878 49 2 1 3875 3922 143244463 143244511 8.040000e-09 73.1
53 TraesCS4A01G484800 chr3B 80.172 232 34 8 1204 1435 80091205 80091424 4.640000e-36 163.0
54 TraesCS4A01G484800 chr4D 82.576 132 19 4 3020 3149 502710359 502710488 4.730000e-21 113.0
55 TraesCS4A01G484800 chr4B 81.818 132 20 4 3020 3149 647624655 647624784 2.200000e-19 108.0
56 TraesCS4A01G484800 chr1D 93.878 49 2 1 3875 3922 69688542 69688494 8.040000e-09 73.1


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 TraesCS4A01G484800 chr4A 738885835 738891615 5780 True 10676.000000 10676 100.000000 1 5781 1 chr4A.!!$R1 5780
1 TraesCS4A01G484800 chr4A 739273627 739274482 855 False 671.000000 671 81.024000 2317 3165 1 chr4A.!!$F2 848
2 TraesCS4A01G484800 chr4A 739080576 739081226 650 False 416.000000 416 78.419000 4078 4728 1 chr4A.!!$F1 650
3 TraesCS4A01G484800 chr4A 739310609 739313633 3024 False 278.500000 420 86.120000 1345 4753 2 chr4A.!!$F3 3408
4 TraesCS4A01G484800 chr7A 4624594 4631172 6578 False 1408.600000 3094 87.430800 3 5415 5 chr7A.!!$F2 5412
5 TraesCS4A01G484800 chr7A 4069106 4069960 854 True 671.000000 671 81.024000 2317 3166 1 chr7A.!!$R2 849
6 TraesCS4A01G484800 chr7A 3983166 3983851 685 True 448.000000 448 78.520000 4077 4762 1 chr7A.!!$R1 685
7 TraesCS4A01G484800 chr7A 4327915 4328554 639 True 407.000000 407 78.528000 4089 4728 1 chr7A.!!$R5 639
8 TraesCS4A01G484800 chr7A 29786052 29786734 682 False 383.000000 383 77.056000 4077 4762 1 chr7A.!!$F1 685
9 TraesCS4A01G484800 chr7A 4206302 4206926 624 True 329.000000 329 76.349000 4104 4728 1 chr7A.!!$R3 624
10 TraesCS4A01G484800 chr7D 4791718 4797434 5716 False 1077.285714 2091 89.029286 5 5355 7 chr7D.!!$F1 5350
11 TraesCS4A01G484800 chr7D 4290621 4291472 851 True 599.000000 599 79.580000 2317 3162 1 chr7D.!!$R1 845
12 TraesCS4A01G484800 chr7D 4501513 4502152 639 True 435.000000 435 79.102000 4089 4728 1 chr7D.!!$R2 639
13 TraesCS4A01G484800 chr7D 29550326 29552636 2310 False 265.500000 405 84.641000 1345 4762 2 chr7D.!!$F2 3417
14 TraesCS4A01G484800 chr6D 10103135 10103702 567 True 435.000000 435 80.662000 2317 2884 1 chr6D.!!$R2 567
15 TraesCS4A01G484800 chr6B 18647477 18648052 575 True 403.000000 403 79.658000 2311 2885 1 chr6B.!!$R1 574
16 TraesCS4A01G484800 chr6B 18593654 18596110 2456 False 346.000000 425 77.216500 2311 4745 2 chr6B.!!$F1 2434
17 TraesCS4A01G484800 chr6A 11587948 11590394 2446 True 318.000000 392 76.384000 2311 4757 2 chr6A.!!$R2 2446

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
438 480 0.037303 AAGTGGGTGTGCATGGAGAG 59.963 55.000 0.00 0.00 0.00 3.20 F
711 798 0.250467 AATGGATCCGCCGATCTTGG 60.250 55.000 13.62 0.00 43.90 3.61 F
808 898 0.250727 CTTTTCCTTGCCGTCCCTGA 60.251 55.000 0.00 0.00 0.00 3.86 F
810 900 0.322456 TTTCCTTGCCGTCCCTGATG 60.322 55.000 0.00 0.00 0.00 3.07 F
2076 2289 0.796927 TGTTGTTGTTGTCGTTGCGA 59.203 45.000 0.00 0.00 0.00 5.10 F
2077 2290 1.197036 TGTTGTTGTTGTCGTTGCGAA 59.803 42.857 0.00 0.00 37.72 4.70 F
3402 3928 0.381089 CCGGTCGTGATCACCTACTC 59.619 60.000 20.03 10.93 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2372 0.105224 CGTTGGCGGACCCACATATA 59.895 55.000 0.00 0.00 45.34 0.86 R
2216 2429 1.143073 GGTGGCGGATTAGGGAAGATT 59.857 52.381 0.00 0.00 0.00 2.40 R
2314 2598 1.303561 TAGTACACGGGACCTGCGT 60.304 57.895 0.00 0.00 0.00 5.24 R
2738 3025 2.258726 GCCGTGGTTGTCCTTGGAC 61.259 63.158 12.54 12.54 32.87 4.02 R
3023 3382 0.620556 ACTTGCCCCAGTCATACCTG 59.379 55.000 0.00 0.00 0.00 4.00 R
3972 4525 1.501582 TGGAAACAAAAACCTGGGGG 58.498 50.000 0.00 0.00 37.44 5.40 R
5356 6316 0.251430 CCCCTACCCCGCAAAAAGAA 60.251 55.000 0.00 0.00 0.00 2.52 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
44 85 6.356186 AGTTAGAGACCAATAAAAGTCCGT 57.644 37.500 0.00 0.00 33.29 4.69
49 90 5.011329 AGAGACCAATAAAAGTCCGTGTGTA 59.989 40.000 0.00 0.00 33.29 2.90
53 94 5.824097 ACCAATAAAAGTCCGTGTGTAGTTT 59.176 36.000 0.00 0.00 0.00 2.66
56 97 8.013378 CCAATAAAAGTCCGTGTGTAGTTTTAG 58.987 37.037 0.00 0.00 35.22 1.85
57 98 5.996669 AAAAGTCCGTGTGTAGTTTTAGG 57.003 39.130 0.00 0.00 0.00 2.69
60 101 4.625028 AGTCCGTGTGTAGTTTTAGGAAC 58.375 43.478 0.00 0.00 0.00 3.62
86 127 0.802607 GTAGGCAAGTCGAAGCGAGG 60.803 60.000 0.00 0.00 36.23 4.63
101 142 3.471680 AGCGAGGATAGGAAAGAAATGC 58.528 45.455 0.00 0.00 0.00 3.56
147 188 1.135315 GCGCGTGCACATGAAGAAT 59.865 52.632 17.66 0.00 42.15 2.40
152 193 2.855180 CGTGCACATGAAGAATCAACC 58.145 47.619 18.64 0.00 39.49 3.77
156 197 3.503363 TGCACATGAAGAATCAACCTGTC 59.497 43.478 0.00 0.00 39.49 3.51
185 226 2.017049 GCCATGATCCTGGTTGTACAC 58.983 52.381 17.21 0.00 38.63 2.90
191 232 4.832248 TGATCCTGGTTGTACACATTCTC 58.168 43.478 0.00 0.00 0.00 2.87
241 282 3.116096 AGGGTGTCTAGCAATGGACTA 57.884 47.619 0.00 0.00 34.01 2.59
246 287 4.541779 GTGTCTAGCAATGGACTAGATCG 58.458 47.826 0.00 0.00 45.80 3.69
247 288 3.004839 TGTCTAGCAATGGACTAGATCGC 59.995 47.826 0.00 0.00 45.80 4.58
260 301 4.462133 ACTAGATCGCAGCTACTTTCCTA 58.538 43.478 0.00 0.00 0.00 2.94
308 349 5.433855 CGAAAACGAAACCGATAAAACTCA 58.566 37.500 0.00 0.00 0.00 3.41
309 350 5.902981 CGAAAACGAAACCGATAAAACTCAA 59.097 36.000 0.00 0.00 0.00 3.02
315 356 7.918643 ACGAAACCGATAAAACTCAAGTAAAA 58.081 30.769 0.00 0.00 0.00 1.52
350 391 6.958193 CACGATTACATCTTCTTTGAGCTTTC 59.042 38.462 0.00 0.00 0.00 2.62
356 397 4.345859 TCTTCTTTGAGCTTTCGGGTTA 57.654 40.909 0.00 0.00 0.00 2.85
383 424 2.432146 AGCCATGACTTTAGATGCTCGA 59.568 45.455 0.00 0.00 0.00 4.04
422 464 0.745128 TTCGTGGCGGTTGTCAAAGT 60.745 50.000 0.00 0.00 0.00 2.66
438 480 0.037303 AAGTGGGTGTGCATGGAGAG 59.963 55.000 0.00 0.00 0.00 3.20
463 505 5.163437 ACCGGTAGCTAGAGACCAATAAAAG 60.163 44.000 4.49 0.00 35.26 2.27
470 512 1.730064 GAGACCAATAAAAGCACGCGA 59.270 47.619 15.93 0.00 0.00 5.87
486 528 2.542595 ACGCGAGTGGTTGTAAAAGAAG 59.457 45.455 15.93 0.00 46.97 2.85
529 585 3.281727 AGAAATGCCCGAAAGCTATCA 57.718 42.857 0.00 0.00 0.00 2.15
577 661 2.027625 CGCGGAGAACCAACCTGTC 61.028 63.158 0.00 0.00 35.59 3.51
595 679 4.307432 CTGTCGTTGGATGATACATACCC 58.693 47.826 0.00 0.00 0.00 3.69
603 687 0.679505 TGATACATACCCGGAGCTGC 59.320 55.000 0.73 0.00 0.00 5.25
608 692 0.681733 CATACCCGGAGCTGCATACT 59.318 55.000 0.73 0.00 0.00 2.12
611 695 2.304221 ACCCGGAGCTGCATACTATA 57.696 50.000 0.73 0.00 0.00 1.31
612 696 2.605257 ACCCGGAGCTGCATACTATAA 58.395 47.619 0.73 0.00 0.00 0.98
618 705 6.348540 CCCGGAGCTGCATACTATAATTTTTC 60.349 42.308 0.73 0.00 0.00 2.29
626 713 8.908786 TGCATACTATAATTTTTCCCTCTCTG 57.091 34.615 0.00 0.00 0.00 3.35
638 725 2.024273 TCCCTCTCTGTTCGGAACCTAT 60.024 50.000 17.62 0.00 0.00 2.57
710 797 1.532868 GAAATGGATCCGCCGATCTTG 59.467 52.381 13.62 0.00 43.90 3.02
711 798 0.250467 AATGGATCCGCCGATCTTGG 60.250 55.000 13.62 0.00 43.90 3.61
723 810 1.679944 CGATCTTGGTGGGTCAATGCT 60.680 52.381 0.00 0.00 0.00 3.79
748 835 3.632645 CCCTACCCTTGATCCAGTTCCTA 60.633 52.174 0.00 0.00 0.00 2.94
788 877 7.826744 GTGGAATGGAAAATAAAAATGGCCTTA 59.173 33.333 3.32 0.00 0.00 2.69
801 891 0.526211 GGCCTTACTTTTCCTTGCCG 59.474 55.000 0.00 0.00 0.00 5.69
808 898 0.250727 CTTTTCCTTGCCGTCCCTGA 60.251 55.000 0.00 0.00 0.00 3.86
810 900 0.322456 TTTCCTTGCCGTCCCTGATG 60.322 55.000 0.00 0.00 0.00 3.07
934 1024 1.073897 GGGAGCCATGCCTATCCAC 59.926 63.158 6.20 0.00 33.20 4.02
938 1028 1.073897 GCCATGCCTATCCACTCCC 59.926 63.158 0.00 0.00 0.00 4.30
977 1067 1.499049 GCCGGAACCGATTCATAGAC 58.501 55.000 15.07 0.00 42.83 2.59
1446 1536 1.065109 TACGTGCACGATCCATCCG 59.935 57.895 42.94 16.07 43.02 4.18
1451 1541 2.237751 GCACGATCCATCCGTTCCG 61.238 63.158 0.00 0.00 38.29 4.30
1452 1542 1.141019 CACGATCCATCCGTTCCGT 59.859 57.895 0.00 0.00 38.29 4.69
1504 1597 9.245962 GATTCAGATTCACATGAATTTCCATTC 57.754 33.333 8.47 0.00 44.18 2.67
1695 1822 6.809196 GGATAGAATATTCCTACTTGAGCGTG 59.191 42.308 11.92 0.00 0.00 5.34
1758 1885 2.941891 ATTTACACAGTCAACGTGCG 57.058 45.000 0.00 0.00 37.93 5.34
1777 1904 6.258727 ACGTGCGAAATGAGATGAGATTATTT 59.741 34.615 0.00 0.00 0.00 1.40
1793 1920 8.088981 TGAGATTATTTTTACCGATCTAGAGGC 58.911 37.037 0.00 0.00 0.00 4.70
1814 1943 4.637534 GGCAGATAACTCAAGCATCTTTGA 59.362 41.667 0.00 0.00 35.83 2.69
1832 1965 7.325660 TCTTTGAATATTGACTGAATCTGGC 57.674 36.000 0.00 0.00 0.00 4.85
1870 2004 1.944709 ACGGCAAGTTAGTTGGTTGTC 59.055 47.619 1.75 0.00 36.56 3.18
1871 2005 1.944024 CGGCAAGTTAGTTGGTTGTCA 59.056 47.619 1.75 0.00 36.56 3.58
1919 2063 1.132849 ACCGGTAGATGGATGGATGGA 60.133 52.381 4.49 0.00 0.00 3.41
1999 2164 3.877559 AGGTAGTAATAAAACCGGCCAC 58.122 45.455 0.00 0.00 38.37 5.01
2074 2287 2.320367 TGTTGTTGTTGTTGTCGTTGC 58.680 42.857 0.00 0.00 0.00 4.17
2075 2288 1.316152 GTTGTTGTTGTTGTCGTTGCG 59.684 47.619 0.00 0.00 0.00 4.85
2076 2289 0.796927 TGTTGTTGTTGTCGTTGCGA 59.203 45.000 0.00 0.00 0.00 5.10
2077 2290 1.197036 TGTTGTTGTTGTCGTTGCGAA 59.803 42.857 0.00 0.00 37.72 4.70
2078 2291 2.159503 TGTTGTTGTTGTCGTTGCGAAT 60.160 40.909 0.00 0.00 37.72 3.34
2081 2294 3.609475 TGTTGTTGTCGTTGCGAATTAC 58.391 40.909 0.00 0.00 37.72 1.89
2098 2311 9.589111 TGCGAATTACTACATATGTTCAAACTA 57.411 29.630 14.77 0.00 0.00 2.24
2144 2357 4.913784 AGGTCATGCATGCACATCATATA 58.086 39.130 25.37 0.00 33.19 0.86
2145 2358 5.506708 AGGTCATGCATGCACATCATATAT 58.493 37.500 25.37 0.00 33.19 0.86
2146 2359 6.655930 AGGTCATGCATGCACATCATATATA 58.344 36.000 25.37 0.00 33.19 0.86
2147 2360 7.287810 AGGTCATGCATGCACATCATATATAT 58.712 34.615 25.37 0.00 33.19 0.86
2148 2361 7.228706 AGGTCATGCATGCACATCATATATATG 59.771 37.037 25.37 15.47 33.19 1.78
2152 2365 4.581409 GCATGCACATCATATATATGGCCA 59.419 41.667 20.18 8.56 34.50 5.36
2153 2366 5.243060 GCATGCACATCATATATATGGCCAT 59.757 40.000 24.45 24.45 34.50 4.40
2154 2367 6.431852 GCATGCACATCATATATATGGCCATA 59.568 38.462 27.36 27.36 34.50 2.74
2155 2368 7.122204 GCATGCACATCATATATATGGCCATAT 59.878 37.037 34.76 34.76 34.72 1.78
2156 2369 9.675464 CATGCACATCATATATATGGCCATATA 57.325 33.333 36.31 36.31 35.81 0.86
2214 2427 2.063266 GCCAACAAAGCACACATGATG 58.937 47.619 0.00 0.00 0.00 3.07
2215 2428 2.288334 GCCAACAAAGCACACATGATGA 60.288 45.455 0.00 0.00 0.00 2.92
2216 2429 3.799574 GCCAACAAAGCACACATGATGAA 60.800 43.478 0.00 0.00 0.00 2.57
2224 2437 3.698040 AGCACACATGATGAAATCTTCCC 59.302 43.478 0.00 0.00 45.81 3.97
2242 2465 3.673956 CTAATCCGCCACCCACGCA 62.674 63.158 0.00 0.00 0.00 5.24
2250 2475 1.901820 CCACCCACGCACCTACATA 59.098 57.895 0.00 0.00 0.00 2.29
2837 3130 2.681778 CTCCTCCACAGCGTCCCT 60.682 66.667 0.00 0.00 0.00 4.20
3023 3382 2.340443 GATGTCGGGATCGGGCTC 59.660 66.667 0.00 0.00 36.95 4.70
3217 3667 2.041966 GCAATATAGTCGTCGGTGTCG 58.958 52.381 0.00 0.00 37.82 4.35
3331 3854 2.127869 TAGCTAGGTCGCTGCTGGG 61.128 63.158 0.00 0.85 41.12 4.45
3402 3928 0.381089 CCGGTCGTGATCACCTACTC 59.619 60.000 20.03 10.93 0.00 2.59
3422 3948 8.971073 CCTACTCCAATTTACTGGAAAAATGAT 58.029 33.333 3.78 0.00 44.97 2.45
3423 3949 9.793252 CTACTCCAATTTACTGGAAAAATGATG 57.207 33.333 3.78 0.33 44.97 3.07
3424 3950 8.421249 ACTCCAATTTACTGGAAAAATGATGA 57.579 30.769 3.78 0.00 44.97 2.92
3449 3975 4.402851 ACGTGCATGCATGTTCCT 57.597 50.000 34.50 16.29 42.86 3.36
3454 3981 2.331194 GTGCATGCATGTTCCTTCAAC 58.669 47.619 25.64 8.24 35.28 3.18
3513 4046 3.300066 CGCGTAGTACTTTTTCTTCTCCG 59.700 47.826 0.00 0.00 0.00 4.63
3543 4076 5.252547 ACAAGTTTGCCCTTTTTGTCAATT 58.747 33.333 0.00 0.00 0.00 2.32
3628 4161 1.938585 TATCTATTAGGCCGGCTGCT 58.061 50.000 28.56 18.64 40.92 4.24
3649 4182 4.333926 GCTTTTGCTCTGATCGATAGGTTT 59.666 41.667 0.00 0.00 43.35 3.27
3653 4186 3.181475 TGCTCTGATCGATAGGTTTGGTC 60.181 47.826 0.00 0.00 0.00 4.02
3785 4318 9.905713 GTGCCTTAGATAAATATATGGATTGGA 57.094 33.333 1.80 0.00 0.00 3.53
3814 4347 1.599542 GTTGCTATGATTGAGGGACGC 59.400 52.381 0.00 0.00 0.00 5.19
3867 4400 4.082733 GGCTAACCACCAAATTCAGACTTC 60.083 45.833 0.00 0.00 35.26 3.01
3872 4405 3.254166 CCACCAAATTCAGACTTCCTGTG 59.746 47.826 0.00 0.00 43.38 3.66
3873 4406 2.887152 ACCAAATTCAGACTTCCTGTGC 59.113 45.455 0.00 0.00 43.38 4.57
3922 4475 2.796557 TGATCGTGCAACCCCATTTTA 58.203 42.857 0.00 0.00 0.00 1.52
3932 4485 7.308891 CGTGCAACCCCATTTTATATGCTTATA 60.309 37.037 0.00 0.00 33.66 0.98
4019 4829 7.322938 CGTGCATTGTTCATGATTGATTAGATC 59.677 37.037 0.00 0.00 34.31 2.75
4087 5020 3.644966 TTTGTCATACAGTCCATCCCC 57.355 47.619 0.00 0.00 0.00 4.81
4099 5032 2.124085 ATCCCCAGGACGGTGGAA 59.876 61.111 2.47 0.00 40.44 3.53
4433 5378 1.592400 CTTCTACGTGTCGAGGGGCA 61.592 60.000 0.00 0.00 0.00 5.36
4913 5858 3.741249 TGGAGATGGAGTACTAGCTACG 58.259 50.000 0.00 0.00 0.00 3.51
4914 5859 3.136077 TGGAGATGGAGTACTAGCTACGT 59.864 47.826 0.00 0.00 0.00 3.57
4915 5860 4.346127 TGGAGATGGAGTACTAGCTACGTA 59.654 45.833 0.00 0.00 0.00 3.57
4916 5861 4.690280 GGAGATGGAGTACTAGCTACGTAC 59.310 50.000 18.29 18.29 37.96 3.67
4998 5943 9.827411 GTTTTTGGTGAGATGAATTAGTTAGAC 57.173 33.333 0.00 0.00 0.00 2.59
5010 5955 4.914312 TTAGTTAGACGATTTGTTGGCG 57.086 40.909 0.00 0.00 0.00 5.69
5016 5961 1.312371 ACGATTTGTTGGCGGGATGG 61.312 55.000 0.00 0.00 0.00 3.51
5246 6200 4.509970 TCACAATTTAATATCCGCTGTCCG 59.490 41.667 0.00 0.00 0.00 4.79
5303 6261 5.617528 TTGGTGTAACTAGGACAGTTTCA 57.382 39.130 0.00 0.00 45.54 2.69
5306 6264 7.305813 TGGTGTAACTAGGACAGTTTCATTA 57.694 36.000 0.00 0.00 45.54 1.90
5314 6272 9.793259 AACTAGGACAGTTTCATTATTTCTGAA 57.207 29.630 0.00 0.00 45.54 3.02
5355 6315 0.323816 CTTGGGGCCCCTTCTTCTTC 60.324 60.000 40.66 12.40 36.94 2.87
5356 6316 0.776080 TTGGGGCCCCTTCTTCTTCT 60.776 55.000 40.66 0.00 36.94 2.85
5357 6317 0.776080 TGGGGCCCCTTCTTCTTCTT 60.776 55.000 40.66 0.00 36.94 2.52
5366 6326 4.540824 CCCTTCTTCTTCTTCTTTTTGCG 58.459 43.478 0.00 0.00 0.00 4.85
5395 6355 4.217767 GGGGCGTAGATGAAAAAGAAAACT 59.782 41.667 0.00 0.00 0.00 2.66
5402 6362 9.710979 CGTAGATGAAAAAGAAAACTGTTAACA 57.289 29.630 8.28 8.28 0.00 2.41
5415 6375 5.695851 ACTGTTAACAAAGCAAGGAGATG 57.304 39.130 10.03 0.00 0.00 2.90
5416 6376 5.133221 ACTGTTAACAAAGCAAGGAGATGT 58.867 37.500 10.03 0.00 0.00 3.06
5417 6377 5.239525 ACTGTTAACAAAGCAAGGAGATGTC 59.760 40.000 10.03 0.00 0.00 3.06
5418 6378 4.213270 TGTTAACAAAGCAAGGAGATGTCG 59.787 41.667 5.64 0.00 0.00 4.35
5419 6379 1.160137 ACAAAGCAAGGAGATGTCGC 58.840 50.000 0.00 0.00 0.00 5.19
5420 6380 0.449388 CAAAGCAAGGAGATGTCGCC 59.551 55.000 0.00 0.00 35.95 5.54
5421 6381 0.678048 AAAGCAAGGAGATGTCGCCC 60.678 55.000 0.00 0.00 36.39 6.13
5424 6384 0.249657 GCAAGGAGATGTCGCCCTAG 60.250 60.000 0.00 0.00 36.39 3.02
5428 6388 3.850095 GAGATGTCGCCCTAGCCGC 62.850 68.421 0.00 0.00 34.57 6.53
5429 6389 4.971125 GATGTCGCCCTAGCCGCC 62.971 72.222 0.00 0.00 34.57 6.13
5455 6415 3.787001 CGGCCTTCCTCCACCCTC 61.787 72.222 0.00 0.00 0.00 4.30
5456 6416 3.412408 GGCCTTCCTCCACCCTCC 61.412 72.222 0.00 0.00 0.00 4.30
5458 6418 2.692741 CCTTCCTCCACCCTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
5460 6420 1.690985 CTTCCTCCACCCTCCCCTC 60.691 68.421 0.00 0.00 0.00 4.30
5461 6421 3.268647 TTCCTCCACCCTCCCCTCC 62.269 68.421 0.00 0.00 0.00 4.30
5462 6422 4.825679 CCTCCACCCTCCCCTCCC 62.826 77.778 0.00 0.00 0.00 4.30
5463 6423 4.825679 CTCCACCCTCCCCTCCCC 62.826 77.778 0.00 0.00 0.00 4.81
5466 6426 4.825679 CACCCTCCCCTCCCCCTC 62.826 77.778 0.00 0.00 0.00 4.30
5468 6428 4.825679 CCCTCCCCTCCCCCTCAC 62.826 77.778 0.00 0.00 0.00 3.51
5469 6429 4.825679 CCTCCCCTCCCCCTCACC 62.826 77.778 0.00 0.00 0.00 4.02
5491 6451 2.437359 CCGAGAGCCAAAGCCCAG 60.437 66.667 0.00 0.00 41.25 4.45
5492 6452 2.437359 CGAGAGCCAAAGCCCAGG 60.437 66.667 0.00 0.00 41.25 4.45
5493 6453 2.044551 GAGAGCCAAAGCCCAGGG 60.045 66.667 0.00 0.00 41.25 4.45
5494 6454 2.532715 AGAGCCAAAGCCCAGGGA 60.533 61.111 10.89 0.00 41.25 4.20
5496 6456 2.860971 AGCCAAAGCCCAGGGAGT 60.861 61.111 10.89 0.00 41.25 3.85
5497 6457 2.677875 GCCAAAGCCCAGGGAGTG 60.678 66.667 10.89 2.79 0.00 3.51
5498 6458 2.846532 CCAAAGCCCAGGGAGTGT 59.153 61.111 10.89 0.00 0.00 3.55
5499 6459 1.303643 CCAAAGCCCAGGGAGTGTC 60.304 63.158 10.89 0.00 0.00 3.67
5500 6460 1.763770 CAAAGCCCAGGGAGTGTCT 59.236 57.895 10.89 0.00 0.00 3.41
5501 6461 0.607489 CAAAGCCCAGGGAGTGTCTG 60.607 60.000 10.89 0.00 0.00 3.51
5502 6462 2.417558 AAAGCCCAGGGAGTGTCTGC 62.418 60.000 10.89 0.00 0.00 4.26
5504 6464 4.087892 CCCAGGGAGTGTCTGCGG 62.088 72.222 0.00 0.00 0.00 5.69
5505 6465 4.767255 CCAGGGAGTGTCTGCGGC 62.767 72.222 0.00 0.00 0.00 6.53
5542 6502 3.896479 CGCAGCTTCCCTTCTTCC 58.104 61.111 0.00 0.00 0.00 3.46
5544 6504 0.742635 CGCAGCTTCCCTTCTTCCTC 60.743 60.000 0.00 0.00 0.00 3.71
5546 6506 0.742635 CAGCTTCCCTTCTTCCTCGC 60.743 60.000 0.00 0.00 0.00 5.03
5547 6507 1.811679 GCTTCCCTTCTTCCTCGCG 60.812 63.158 0.00 0.00 0.00 5.87
5548 6508 1.153549 CTTCCCTTCTTCCTCGCGG 60.154 63.158 6.13 0.00 0.00 6.46
5549 6509 3.310860 TTCCCTTCTTCCTCGCGGC 62.311 63.158 6.13 0.00 0.00 6.53
5555 6515 4.508128 CTTCCTCGCGGCGGCTTA 62.508 66.667 23.46 1.39 36.88 3.09
5556 6516 4.508128 TTCCTCGCGGCGGCTTAG 62.508 66.667 23.46 12.11 36.88 2.18
5559 6519 4.492160 CTCGCGGCGGCTTAGTCA 62.492 66.667 23.46 0.00 36.88 3.41
5561 6521 4.796231 CGCGGCGGCTTAGTCACT 62.796 66.667 15.84 0.00 36.88 3.41
5562 6522 2.886124 GCGGCGGCTTAGTCACTC 60.886 66.667 9.78 0.00 35.83 3.51
5563 6523 2.202756 CGGCGGCTTAGTCACTCC 60.203 66.667 7.61 0.00 0.00 3.85
5564 6524 2.187163 GGCGGCTTAGTCACTCCC 59.813 66.667 0.00 0.00 0.00 4.30
5565 6525 2.202756 GCGGCTTAGTCACTCCCG 60.203 66.667 7.02 7.02 41.72 5.14
5566 6526 2.494918 CGGCTTAGTCACTCCCGG 59.505 66.667 0.00 0.00 35.54 5.73
5567 6527 2.348888 CGGCTTAGTCACTCCCGGT 61.349 63.158 0.00 0.00 35.54 5.28
5568 6528 1.218316 GGCTTAGTCACTCCCGGTG 59.782 63.158 0.00 0.00 46.60 4.94
5569 6529 1.218316 GCTTAGTCACTCCCGGTGG 59.782 63.158 0.00 0.00 45.38 4.61
5573 6533 2.358737 GTCACTCCCGGTGGCTTG 60.359 66.667 0.00 0.00 46.12 4.01
5574 6534 3.636231 TCACTCCCGGTGGCTTGG 61.636 66.667 0.00 0.00 45.38 3.61
5576 6536 3.953775 ACTCCCGGTGGCTTGGTG 61.954 66.667 0.00 0.00 0.00 4.17
5577 6537 4.722700 CTCCCGGTGGCTTGGTGG 62.723 72.222 0.00 0.00 0.00 4.61
5598 6558 2.815647 GGCGCTTCGAACCTCCAG 60.816 66.667 7.64 0.00 0.00 3.86
5599 6559 3.491652 GCGCTTCGAACCTCCAGC 61.492 66.667 0.00 0.00 0.00 4.85
5601 6561 2.815647 GCTTCGAACCTCCAGCGG 60.816 66.667 0.00 0.00 0.00 5.52
5602 6562 2.657237 CTTCGAACCTCCAGCGGT 59.343 61.111 0.00 0.00 39.48 5.68
5603 6563 1.738099 CTTCGAACCTCCAGCGGTG 60.738 63.158 7.86 7.86 37.36 4.94
5622 6582 3.041940 CTCGTTTCGCGGCAGGTT 61.042 61.111 6.13 0.00 41.72 3.50
5623 6583 3.295228 CTCGTTTCGCGGCAGGTTG 62.295 63.158 6.13 0.00 41.72 3.77
5625 6585 2.975799 GTTTCGCGGCAGGTTGGA 60.976 61.111 6.13 0.00 0.00 3.53
5626 6586 2.668212 TTTCGCGGCAGGTTGGAG 60.668 61.111 6.13 0.00 0.00 3.86
5627 6587 4.697756 TTCGCGGCAGGTTGGAGG 62.698 66.667 6.13 0.00 0.00 4.30
5631 6591 4.431131 CGGCAGGTTGGAGGGCAT 62.431 66.667 0.00 0.00 0.00 4.40
5633 6593 2.036256 GCAGGTTGGAGGGCATGT 59.964 61.111 0.00 0.00 0.00 3.21
5635 6595 1.598701 GCAGGTTGGAGGGCATGTTC 61.599 60.000 0.00 0.00 0.00 3.18
5636 6596 0.967380 CAGGTTGGAGGGCATGTTCC 60.967 60.000 0.00 0.25 0.00 3.62
5645 6605 2.040544 GGCATGTTCCCGTCTGGTG 61.041 63.158 0.00 0.00 34.77 4.17
5646 6606 2.040544 GCATGTTCCCGTCTGGTGG 61.041 63.158 0.00 0.00 34.77 4.61
5647 6607 1.374947 CATGTTCCCGTCTGGTGGT 59.625 57.895 0.00 0.00 34.77 4.16
5648 6608 0.955428 CATGTTCCCGTCTGGTGGTG 60.955 60.000 0.00 0.00 34.77 4.17
5649 6609 2.668550 GTTCCCGTCTGGTGGTGC 60.669 66.667 0.00 0.00 34.77 5.01
5650 6610 3.948719 TTCCCGTCTGGTGGTGCC 61.949 66.667 0.00 0.00 34.77 5.01
5657 6617 3.390521 CTGGTGGTGCCGCCTAGA 61.391 66.667 20.11 1.23 46.12 2.43
5659 6619 3.702048 GGTGGTGCCGCCTAGACA 61.702 66.667 13.23 0.00 42.89 3.41
5662 6622 4.840005 GGTGCCGCCTAGACAGCC 62.840 72.222 0.00 0.00 0.00 4.85
5665 6625 3.775654 GCCGCCTAGACAGCCACT 61.776 66.667 0.00 0.00 0.00 4.00
5666 6626 2.423898 GCCGCCTAGACAGCCACTA 61.424 63.158 0.00 0.00 0.00 2.74
5667 6627 1.437986 CCGCCTAGACAGCCACTAC 59.562 63.158 0.00 0.00 0.00 2.73
5668 6628 1.064296 CGCCTAGACAGCCACTACG 59.936 63.158 0.00 0.00 0.00 3.51
5669 6629 1.437986 GCCTAGACAGCCACTACGG 59.562 63.158 0.00 0.00 38.11 4.02
5686 6646 2.911928 GCCTAGGGCTCTTGACCC 59.088 66.667 11.72 0.00 46.69 4.46
5691 6651 3.746957 GGGCTCTTGACCCCAGAT 58.253 61.111 0.00 0.00 42.01 2.90
5694 6654 0.394899 GGCTCTTGACCCCAGATTGG 60.395 60.000 0.00 0.00 37.25 3.16
5696 6656 1.213926 GCTCTTGACCCCAGATTGGAT 59.786 52.381 0.00 0.00 40.96 3.41
5697 6657 2.747799 GCTCTTGACCCCAGATTGGATC 60.748 54.545 0.00 0.00 40.96 3.36
5706 6666 3.890527 AGATTGGATCTGGTGGTGC 57.109 52.632 0.00 0.00 38.44 5.01
5708 6668 1.211457 AGATTGGATCTGGTGGTGCTC 59.789 52.381 0.00 0.00 38.44 4.26
5709 6669 0.107508 ATTGGATCTGGTGGTGCTCG 60.108 55.000 0.00 0.00 0.00 5.03
5710 6670 2.184020 TTGGATCTGGTGGTGCTCGG 62.184 60.000 0.00 0.00 0.00 4.63
5711 6671 2.187946 GATCTGGTGGTGCTCGGG 59.812 66.667 0.00 0.00 0.00 5.14
5712 6672 4.101448 ATCTGGTGGTGCTCGGGC 62.101 66.667 0.00 0.00 39.26 6.13
5775 6735 2.503061 CCTCTGGGCATCGTGGAG 59.497 66.667 0.00 0.00 0.00 3.86
5776 6736 2.503061 CTCTGGGCATCGTGGAGG 59.497 66.667 0.00 0.00 0.00 4.30
5778 6738 2.124983 CTGGGCATCGTGGAGGTG 60.125 66.667 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.629596 ACTACCGGTCTCTCCATCCA 59.370 55.000 12.40 0.00 35.57 3.41
6 7 3.816523 CTCTAACTACCGGTCTCTCCATC 59.183 52.174 12.40 0.00 35.57 3.51
7 8 3.458857 TCTCTAACTACCGGTCTCTCCAT 59.541 47.826 12.40 0.00 35.57 3.41
8 9 2.842496 TCTCTAACTACCGGTCTCTCCA 59.158 50.000 12.40 0.00 35.57 3.86
49 90 7.253905 TGCCTACTATCTTGTTCCTAAAACT 57.746 36.000 0.00 0.00 0.00 2.66
53 94 6.405508 CGACTTGCCTACTATCTTGTTCCTAA 60.406 42.308 0.00 0.00 0.00 2.69
56 97 4.113354 CGACTTGCCTACTATCTTGTTCC 58.887 47.826 0.00 0.00 0.00 3.62
57 98 4.995124 TCGACTTGCCTACTATCTTGTTC 58.005 43.478 0.00 0.00 0.00 3.18
60 101 3.799420 GCTTCGACTTGCCTACTATCTTG 59.201 47.826 0.00 0.00 0.00 3.02
86 127 5.359292 AGCTTTCTGGCATTTCTTTCCTATC 59.641 40.000 0.00 0.00 34.17 2.08
210 251 9.725019 CATTGCTAGACACCCTATATTAATTCA 57.275 33.333 0.00 0.00 0.00 2.57
241 282 4.737855 TTTAGGAAAGTAGCTGCGATCT 57.262 40.909 0.00 0.00 0.00 2.75
246 287 5.352643 TTTCGTTTTAGGAAAGTAGCTGC 57.647 39.130 0.00 0.00 29.79 5.25
247 288 7.129109 TCATTTCGTTTTAGGAAAGTAGCTG 57.871 36.000 0.00 0.00 35.75 4.24
260 301 6.405842 GGAAATAGCTGGGATCATTTCGTTTT 60.406 38.462 0.00 0.00 37.96 2.43
308 349 8.316214 TGTAATCGTGAGGGAATAGTTTTACTT 58.684 33.333 0.00 0.00 0.00 2.24
309 350 7.844009 TGTAATCGTGAGGGAATAGTTTTACT 58.156 34.615 0.00 0.00 0.00 2.24
356 397 4.467769 CATCTAAAGTCATGGCTTGGGAT 58.532 43.478 14.47 16.13 0.00 3.85
367 408 1.202302 CGGCTCGAGCATCTAAAGTCA 60.202 52.381 36.27 0.00 44.36 3.41
422 464 1.679311 GTCTCTCCATGCACACCCA 59.321 57.895 0.00 0.00 0.00 4.51
438 480 1.760192 TTGGTCTCTAGCTACCGGTC 58.240 55.000 12.40 0.00 38.70 4.79
463 505 0.305313 TTTTACAACCACTCGCGTGC 59.695 50.000 5.77 0.00 39.86 5.34
483 525 6.696148 TCGATTCGCCTACTATTTTCTTCTTC 59.304 38.462 0.00 0.00 0.00 2.87
486 528 6.696148 TCTTCGATTCGCCTACTATTTTCTTC 59.304 38.462 0.00 0.00 0.00 2.87
496 538 2.032808 GGCATTTCTTCGATTCGCCTAC 60.033 50.000 0.00 0.00 35.17 3.18
554 638 1.702491 GGTTGGTTCTCCGCGTATGC 61.702 60.000 4.92 0.00 36.30 3.14
560 644 2.027625 CGACAGGTTGGTTCTCCGC 61.028 63.158 0.00 0.00 36.30 5.54
561 645 0.249741 AACGACAGGTTGGTTCTCCG 60.250 55.000 0.00 0.00 37.50 4.63
577 661 2.297880 TCCGGGTATGTATCATCCAACG 59.702 50.000 0.00 0.00 0.00 4.10
588 672 0.393077 GTATGCAGCTCCGGGTATGT 59.607 55.000 0.00 0.00 0.00 2.29
589 673 0.681733 AGTATGCAGCTCCGGGTATG 59.318 55.000 0.00 0.00 0.00 2.39
595 679 6.348540 GGGAAAAATTATAGTATGCAGCTCCG 60.349 42.308 0.00 0.00 0.00 4.63
608 692 7.190335 TCCGAACAGAGAGGGAAAAATTATA 57.810 36.000 0.00 0.00 0.00 0.98
611 695 4.367039 TCCGAACAGAGAGGGAAAAATT 57.633 40.909 0.00 0.00 0.00 1.82
612 696 4.072839 GTTCCGAACAGAGAGGGAAAAAT 58.927 43.478 6.38 0.00 40.03 1.82
618 705 1.848652 TAGGTTCCGAACAGAGAGGG 58.151 55.000 13.23 0.00 0.00 4.30
626 713 8.152898 ACACCCTATATTAAATAGGTTCCGAAC 58.847 37.037 16.18 2.37 39.55 3.95
638 725 8.154856 GTCCATTGCTAGACACCCTATATTAAA 58.845 37.037 0.00 0.00 33.08 1.52
710 797 3.662117 GGGGGAGCATTGACCCACC 62.662 68.421 17.11 10.02 46.56 4.61
711 798 2.043953 GGGGGAGCATTGACCCAC 60.044 66.667 17.11 12.04 46.56 4.61
723 810 0.030092 CTGGATCAAGGGTAGGGGGA 60.030 60.000 0.00 0.00 0.00 4.81
788 877 0.537371 CAGGGACGGCAAGGAAAAGT 60.537 55.000 0.00 0.00 0.00 2.66
801 891 1.678970 GGCCAACCACATCAGGGAC 60.679 63.158 0.00 0.00 35.26 4.46
934 1024 3.391382 GTGGACGGGTGGAGGGAG 61.391 72.222 0.00 0.00 0.00 4.30
938 1028 3.075005 ATCGGTGGACGGGTGGAG 61.075 66.667 0.00 0.00 44.45 3.86
965 1055 6.985188 TCCAAGAAAAAGTCTATGAATCGG 57.015 37.500 0.00 0.00 34.56 4.18
977 1067 3.614588 GACGACGGTTTCCAAGAAAAAG 58.385 45.455 0.00 0.00 0.00 2.27
1150 1240 2.666190 CACGACCAGCACCACCAG 60.666 66.667 0.00 0.00 0.00 4.00
1446 1536 3.118000 AGGAAGGGATTAATGGACGGAAC 60.118 47.826 0.00 0.00 0.00 3.62
1451 1541 4.338400 CCGAAAAGGAAGGGATTAATGGAC 59.662 45.833 0.00 0.00 45.00 4.02
1452 1542 4.532834 CCGAAAAGGAAGGGATTAATGGA 58.467 43.478 0.00 0.00 45.00 3.41
1504 1597 3.168193 GGATTAACAACGCGTGGAAATG 58.832 45.455 23.00 13.87 0.00 2.32
1777 1904 6.069331 AGTTATCTGCCTCTAGATCGGTAAA 58.931 40.000 0.00 0.00 38.35 2.01
1791 1918 4.637534 TCAAAGATGCTTGAGTTATCTGCC 59.362 41.667 0.00 0.00 31.89 4.85
1792 1919 5.808042 TCAAAGATGCTTGAGTTATCTGC 57.192 39.130 0.00 0.00 31.89 4.26
1814 1943 5.282055 TCGAGCCAGATTCAGTCAATATT 57.718 39.130 0.00 0.00 0.00 1.28
1832 1965 1.546834 GTTGGTAACGCTAGCTCGAG 58.453 55.000 13.93 8.45 42.51 4.04
1843 1976 3.304190 CCAACTAACTTGCCGTTGGTAAC 60.304 47.826 11.22 0.00 45.22 2.50
1870 2004 3.558418 TCTCCGTTCGGTTTCTTTTTCTG 59.442 43.478 11.04 0.00 0.00 3.02
1871 2005 3.800531 TCTCCGTTCGGTTTCTTTTTCT 58.199 40.909 11.04 0.00 0.00 2.52
1919 2063 4.012554 CGCACGCGTTCTATCCAT 57.987 55.556 10.22 0.00 34.35 3.41
1999 2164 1.808343 CACACATGATCACCACTGTGG 59.192 52.381 24.80 24.80 45.02 4.17
2007 2199 2.677199 ACACGAGACACACATGATCAC 58.323 47.619 0.00 0.00 0.00 3.06
2066 2279 6.037726 ACATATGTAGTAATTCGCAACGACA 58.962 36.000 6.56 0.00 34.89 4.35
2067 2280 6.506464 ACATATGTAGTAATTCGCAACGAC 57.494 37.500 6.56 0.00 34.89 4.34
2069 2282 6.928820 TGAACATATGTAGTAATTCGCAACG 58.071 36.000 9.21 0.00 0.00 4.10
2070 2283 8.995906 GTTTGAACATATGTAGTAATTCGCAAC 58.004 33.333 9.21 5.65 0.00 4.17
2107 2320 5.106712 TGCATGACCTATCGAGTTTTTGAAC 60.107 40.000 0.00 0.00 0.00 3.18
2111 2324 4.201950 GCATGCATGACCTATCGAGTTTTT 60.202 41.667 30.64 0.00 0.00 1.94
2112 2325 3.313526 GCATGCATGACCTATCGAGTTTT 59.686 43.478 30.64 0.00 0.00 2.43
2145 2358 9.279233 GGACCCACATATATATATATGGCCATA 57.721 37.037 32.03 27.36 46.13 2.74
2146 2359 7.092891 CGGACCCACATATATATATATGGCCAT 60.093 40.741 32.03 24.45 46.13 4.40
2147 2360 6.212589 CGGACCCACATATATATATATGGCCA 59.787 42.308 32.03 8.56 46.13 5.36
2148 2361 6.640518 CGGACCCACATATATATATATGGCC 58.359 44.000 32.03 24.65 46.13 5.36
2152 2365 7.524863 CGTTGGCGGACCCACATATATATATAT 60.525 40.741 9.12 9.12 45.34 0.86
2153 2366 6.239092 CGTTGGCGGACCCACATATATATATA 60.239 42.308 4.90 4.92 45.34 0.86
2154 2367 5.452776 CGTTGGCGGACCCACATATATATAT 60.453 44.000 0.00 0.00 45.34 0.86
2155 2368 4.142116 CGTTGGCGGACCCACATATATATA 60.142 45.833 0.00 0.00 45.34 0.86
2156 2369 3.369052 CGTTGGCGGACCCACATATATAT 60.369 47.826 0.00 0.00 45.34 0.86
2157 2370 2.028839 CGTTGGCGGACCCACATATATA 60.029 50.000 0.00 0.00 45.34 0.86
2158 2371 1.270625 CGTTGGCGGACCCACATATAT 60.271 52.381 0.00 0.00 45.34 0.86
2159 2372 0.105224 CGTTGGCGGACCCACATATA 59.895 55.000 0.00 0.00 45.34 0.86
2160 2373 1.153249 CGTTGGCGGACCCACATAT 60.153 57.895 0.00 0.00 45.34 1.78
2161 2374 2.266372 CGTTGGCGGACCCACATA 59.734 61.111 0.00 0.00 45.34 2.29
2207 2420 6.000219 CGGATTAGGGAAGATTTCATCATGT 59.000 40.000 0.00 0.00 0.00 3.21
2214 2427 2.879026 GTGGCGGATTAGGGAAGATTTC 59.121 50.000 0.00 0.00 0.00 2.17
2215 2428 2.422945 GGTGGCGGATTAGGGAAGATTT 60.423 50.000 0.00 0.00 0.00 2.17
2216 2429 1.143073 GGTGGCGGATTAGGGAAGATT 59.857 52.381 0.00 0.00 0.00 2.40
2224 2437 2.895372 GCGTGGGTGGCGGATTAG 60.895 66.667 0.00 0.00 0.00 1.73
2242 2465 5.836898 TCGTTGATTAGGTGGATATGTAGGT 59.163 40.000 0.00 0.00 0.00 3.08
2250 2475 4.665833 TCGATTCGTTGATTAGGTGGAT 57.334 40.909 5.89 0.00 0.00 3.41
2305 2533 1.891919 GGACCTGCGTTGCAACAGA 60.892 57.895 28.01 13.18 38.41 3.41
2314 2598 1.303561 TAGTACACGGGACCTGCGT 60.304 57.895 0.00 0.00 0.00 5.24
2738 3025 2.258726 GCCGTGGTTGTCCTTGGAC 61.259 63.158 12.54 12.54 32.87 4.02
2894 3253 2.130272 TCATCACGTACAGCTCCTCT 57.870 50.000 0.00 0.00 0.00 3.69
3023 3382 0.620556 ACTTGCCCCAGTCATACCTG 59.379 55.000 0.00 0.00 0.00 4.00
3217 3667 5.106277 CCAATCCATATGCATGACAGTGATC 60.106 44.000 10.16 0.00 33.67 2.92
3331 3854 8.680903 TCATCTTAAAGCTGAAGATTTCAATCC 58.319 33.333 17.49 0.00 40.83 3.01
3422 3948 3.632855 TGCATGCACGTTTACAAATCA 57.367 38.095 18.46 0.00 0.00 2.57
3423 3949 3.919804 ACATGCATGCACGTTTACAAATC 59.080 39.130 25.37 0.00 0.00 2.17
3424 3950 3.911868 ACATGCATGCACGTTTACAAAT 58.088 36.364 25.37 0.00 0.00 2.32
3429 3955 2.158559 AGGAACATGCATGCACGTTTA 58.841 42.857 30.29 4.45 32.27 2.01
3449 3975 7.762159 GTCAACTGGAATTAACAAAAGGTTGAA 59.238 33.333 12.60 1.98 40.92 2.69
3454 3981 6.155475 TGGTCAACTGGAATTAACAAAAGG 57.845 37.500 0.00 0.00 0.00 3.11
3513 4046 5.453567 AAAAGGGCAAACTTGTACAGATC 57.546 39.130 0.00 0.00 0.00 2.75
3543 4076 2.667481 CGCGTACCACGAGGATTAAAAA 59.333 45.455 5.68 0.00 46.05 1.94
3628 4161 4.635765 CCAAACCTATCGATCAGAGCAAAA 59.364 41.667 0.00 0.00 0.00 2.44
3649 4182 3.340928 CTTGATCTGCACTCATTGACCA 58.659 45.455 0.00 0.00 0.00 4.02
3653 4186 2.355132 GAGGCTTGATCTGCACTCATTG 59.645 50.000 12.02 0.00 32.20 2.82
3785 4318 4.260985 TCAATCATAGCAACGGTCAACAT 58.739 39.130 0.00 0.00 0.00 2.71
3814 4347 4.495184 GGACAAATTAAGATACGGTTGCGG 60.495 45.833 0.00 0.00 0.00 5.69
3867 4400 5.353394 TGATTTAAGTAGGGTAGCACAGG 57.647 43.478 0.00 0.00 0.00 4.00
3904 4457 4.261994 GCATATAAAATGGGGTTGCACGAT 60.262 41.667 0.00 0.00 0.00 3.73
3972 4525 1.501582 TGGAAACAAAAACCTGGGGG 58.498 50.000 0.00 0.00 37.44 5.40
4019 4829 9.694520 CAGATAAATCATTCTGTCACTTTTACG 57.305 33.333 0.00 0.00 35.66 3.18
4060 4964 3.501828 TGGACTGTATGACAAATGCACAC 59.498 43.478 0.00 0.00 0.00 3.82
4087 5020 1.004918 GTCCAGTTCCACCGTCCTG 60.005 63.158 0.00 0.00 0.00 3.86
4099 5032 1.977544 CCGGGTCTTCTCGTCCAGT 60.978 63.158 0.00 0.00 0.00 4.00
4286 5219 4.047059 GTCGGCCTCGTTGACGGA 62.047 66.667 0.00 0.00 40.29 4.69
4433 5378 2.851102 CTGGAGGCCCCCATCGAT 60.851 66.667 6.38 0.00 35.33 3.59
4913 5858 5.354792 ACGAACAGGAAGATGACTAGAGTAC 59.645 44.000 0.00 0.00 0.00 2.73
4914 5859 5.498393 ACGAACAGGAAGATGACTAGAGTA 58.502 41.667 0.00 0.00 0.00 2.59
4915 5860 4.337145 ACGAACAGGAAGATGACTAGAGT 58.663 43.478 0.00 0.00 0.00 3.24
4916 5861 4.974368 ACGAACAGGAAGATGACTAGAG 57.026 45.455 0.00 0.00 0.00 2.43
4998 5943 1.312371 ACCATCCCGCCAACAAATCG 61.312 55.000 0.00 0.00 0.00 3.34
5010 5955 0.623723 TGGAAGGCAGTAACCATCCC 59.376 55.000 2.61 0.00 45.29 3.85
5016 5961 4.386711 AGTTACACTTGGAAGGCAGTAAC 58.613 43.478 16.13 16.13 39.89 2.50
5163 6117 8.477256 AGTTGGAAGTCAGAAAATTTCATTTCA 58.523 29.630 8.55 0.14 40.89 2.69
5314 6272 8.478877 CCAAGAGAATACAGTACCAATAAGACT 58.521 37.037 0.00 0.00 0.00 3.24
5355 6315 1.173913 CCCTACCCCGCAAAAAGAAG 58.826 55.000 0.00 0.00 0.00 2.85
5356 6316 0.251430 CCCCTACCCCGCAAAAAGAA 60.251 55.000 0.00 0.00 0.00 2.52
5357 6317 1.381076 CCCCTACCCCGCAAAAAGA 59.619 57.895 0.00 0.00 0.00 2.52
5366 6326 0.761702 TTCATCTACGCCCCTACCCC 60.762 60.000 0.00 0.00 0.00 4.95
5380 6340 9.689075 GCTTTGTTAACAGTTTTCTTTTTCATC 57.311 29.630 8.56 0.00 0.00 2.92
5395 6355 4.213270 CGACATCTCCTTGCTTTGTTAACA 59.787 41.667 3.59 3.59 0.00 2.41
5402 6362 0.678048 GGGCGACATCTCCTTGCTTT 60.678 55.000 0.00 0.00 0.00 3.51
5438 6398 3.787001 GAGGGTGGAGGAAGGCCG 61.787 72.222 0.00 0.00 39.96 6.13
5439 6399 3.412408 GGAGGGTGGAGGAAGGCC 61.412 72.222 0.00 0.00 0.00 5.19
5440 6400 3.412408 GGGAGGGTGGAGGAAGGC 61.412 72.222 0.00 0.00 0.00 4.35
5441 6401 2.692741 GGGGAGGGTGGAGGAAGG 60.693 72.222 0.00 0.00 0.00 3.46
5445 6405 4.825679 GGGAGGGGAGGGTGGAGG 62.826 77.778 0.00 0.00 0.00 4.30
5449 6409 4.825679 GAGGGGGAGGGGAGGGTG 62.826 77.778 0.00 0.00 0.00 4.61
5452 6412 4.825679 GGTGAGGGGGAGGGGAGG 62.826 77.778 0.00 0.00 0.00 4.30
5473 6433 4.722700 TGGGCTTTGGCTCTCGGC 62.723 66.667 0.00 0.00 40.19 5.54
5474 6434 2.437359 CTGGGCTTTGGCTCTCGG 60.437 66.667 0.00 0.00 40.19 4.63
5475 6435 2.437359 CCTGGGCTTTGGCTCTCG 60.437 66.667 0.00 0.00 40.19 4.04
5476 6436 2.044551 CCCTGGGCTTTGGCTCTC 60.045 66.667 0.00 0.00 40.19 3.20
5477 6437 2.532715 TCCCTGGGCTTTGGCTCT 60.533 61.111 8.22 0.00 40.19 4.09
5478 6438 2.044551 CTCCCTGGGCTTTGGCTC 60.045 66.667 8.22 0.00 39.89 4.70
5479 6439 2.860971 ACTCCCTGGGCTTTGGCT 60.861 61.111 8.22 0.00 38.73 4.75
5481 6441 1.303643 GACACTCCCTGGGCTTTGG 60.304 63.158 8.22 0.00 0.00 3.28
5484 6444 2.900106 GCAGACACTCCCTGGGCTT 61.900 63.158 8.22 0.00 32.51 4.35
5485 6445 3.325753 GCAGACACTCCCTGGGCT 61.326 66.667 8.22 0.00 32.51 5.19
5486 6446 4.767255 CGCAGACACTCCCTGGGC 62.767 72.222 8.22 0.00 37.68 5.36
5487 6447 4.087892 CCGCAGACACTCCCTGGG 62.088 72.222 6.33 6.33 42.17 4.45
5488 6448 4.767255 GCCGCAGACACTCCCTGG 62.767 72.222 0.00 0.00 32.51 4.45
5521 6481 3.130160 GAAGGGAAGCTGCGCCAG 61.130 66.667 4.18 3.40 34.12 4.85
5523 6483 2.360475 AAGAAGGGAAGCTGCGCC 60.360 61.111 4.18 6.10 0.00 6.53
5524 6484 2.402572 GGAAGAAGGGAAGCTGCGC 61.403 63.158 0.00 0.00 0.00 6.09
5525 6485 0.742635 GAGGAAGAAGGGAAGCTGCG 60.743 60.000 0.00 0.00 0.00 5.18
5526 6486 0.742635 CGAGGAAGAAGGGAAGCTGC 60.743 60.000 0.00 0.00 0.00 5.25
5527 6487 0.742635 GCGAGGAAGAAGGGAAGCTG 60.743 60.000 0.00 0.00 0.00 4.24
5528 6488 1.599576 GCGAGGAAGAAGGGAAGCT 59.400 57.895 0.00 0.00 0.00 3.74
5529 6489 1.811679 CGCGAGGAAGAAGGGAAGC 60.812 63.158 0.00 0.00 0.00 3.86
5530 6490 4.504132 CGCGAGGAAGAAGGGAAG 57.496 61.111 0.00 0.00 0.00 3.46
5542 6502 4.492160 TGACTAAGCCGCCGCGAG 62.492 66.667 15.93 5.96 41.18 5.03
5544 6504 4.796231 AGTGACTAAGCCGCCGCG 62.796 66.667 5.59 5.59 41.18 6.46
5546 6506 2.202756 GGAGTGACTAAGCCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
5547 6507 2.187163 GGGAGTGACTAAGCCGCC 59.813 66.667 0.00 0.00 0.00 6.13
5548 6508 2.202756 CGGGAGTGACTAAGCCGC 60.203 66.667 0.00 0.00 0.00 6.53
5549 6509 2.348888 ACCGGGAGTGACTAAGCCG 61.349 63.158 6.32 0.00 0.00 5.52
5550 6510 3.709567 ACCGGGAGTGACTAAGCC 58.290 61.111 6.32 0.00 0.00 4.35
5559 6519 3.953775 CACCAAGCCACCGGGAGT 61.954 66.667 6.32 0.00 35.59 3.85
5584 6544 2.815647 CCGCTGGAGGTTCGAAGC 60.816 66.667 19.40 19.40 0.00 3.86
5586 6546 2.342279 CACCGCTGGAGGTTCGAA 59.658 61.111 0.00 0.00 43.00 3.71
5587 6547 3.691342 CCACCGCTGGAGGTTCGA 61.691 66.667 0.00 0.00 43.00 3.71
5589 6549 4.021925 AGCCACCGCTGGAGGTTC 62.022 66.667 0.00 0.00 46.19 3.62
5607 6567 4.383602 CCAACCTGCCGCGAAACG 62.384 66.667 8.23 0.00 43.15 3.60
5608 6568 2.966309 CTCCAACCTGCCGCGAAAC 61.966 63.158 8.23 0.00 0.00 2.78
5610 6570 4.697756 CCTCCAACCTGCCGCGAA 62.698 66.667 8.23 0.00 0.00 4.70
5614 6574 4.431131 ATGCCCTCCAACCTGCCG 62.431 66.667 0.00 0.00 0.00 5.69
5616 6576 1.598701 GAACATGCCCTCCAACCTGC 61.599 60.000 0.00 0.00 0.00 4.85
5617 6577 0.967380 GGAACATGCCCTCCAACCTG 60.967 60.000 0.00 0.00 0.00 4.00
5618 6578 1.384191 GGAACATGCCCTCCAACCT 59.616 57.895 0.00 0.00 0.00 3.50
5619 6579 1.682344 GGGAACATGCCCTCCAACC 60.682 63.158 10.37 0.00 45.12 3.77
5620 6580 2.046285 CGGGAACATGCCCTCCAAC 61.046 63.158 6.81 0.00 46.44 3.77
5621 6581 2.354729 CGGGAACATGCCCTCCAA 59.645 61.111 6.81 0.00 46.44 3.53
5622 6582 2.933287 ACGGGAACATGCCCTCCA 60.933 61.111 6.81 0.00 46.44 3.86
5623 6583 2.124695 GACGGGAACATGCCCTCC 60.125 66.667 6.81 4.03 46.44 4.30
5625 6585 2.671070 CAGACGGGAACATGCCCT 59.329 61.111 6.81 0.00 46.44 5.19
5626 6586 2.438434 CCAGACGGGAACATGCCC 60.438 66.667 0.00 0.00 45.10 5.36
5627 6587 2.040544 CACCAGACGGGAACATGCC 61.041 63.158 0.00 0.00 41.15 4.40
5628 6588 2.040544 CCACCAGACGGGAACATGC 61.041 63.158 0.00 0.00 41.15 4.06
5629 6589 0.955428 CACCACCAGACGGGAACATG 60.955 60.000 0.00 0.00 41.15 3.21
5630 6590 1.374947 CACCACCAGACGGGAACAT 59.625 57.895 0.00 0.00 41.15 2.71
5631 6591 2.825982 CACCACCAGACGGGAACA 59.174 61.111 0.00 0.00 41.15 3.18
5633 6593 3.948719 GGCACCACCAGACGGGAA 61.949 66.667 0.00 0.00 41.15 3.97
5638 6598 3.665675 CTAGGCGGCACCACCAGAC 62.666 68.421 13.08 0.00 43.14 3.51
5640 6600 3.390521 TCTAGGCGGCACCACCAG 61.391 66.667 13.08 0.00 43.14 4.00
5641 6601 3.702048 GTCTAGGCGGCACCACCA 61.702 66.667 13.08 0.00 43.14 4.17
5645 6605 4.840005 GGCTGTCTAGGCGGCACC 62.840 72.222 28.46 9.51 42.25 5.01
5676 6636 0.620556 TCCAATCTGGGGTCAAGAGC 59.379 55.000 0.00 0.00 38.32 4.09
5688 6648 1.211457 GAGCACCACCAGATCCAATCT 59.789 52.381 0.00 0.00 41.15 2.40
5689 6649 1.673168 GAGCACCACCAGATCCAATC 58.327 55.000 0.00 0.00 0.00 2.67
5690 6650 0.107508 CGAGCACCACCAGATCCAAT 60.108 55.000 0.00 0.00 0.00 3.16
5691 6651 1.296392 CGAGCACCACCAGATCCAA 59.704 57.895 0.00 0.00 0.00 3.53
5694 6654 2.187946 CCCGAGCACCACCAGATC 59.812 66.667 0.00 0.00 0.00 2.75
5758 6718 2.503061 CTCCACGATGCCCAGAGG 59.497 66.667 0.00 0.00 0.00 3.69
5760 6720 2.284625 ACCTCCACGATGCCCAGA 60.285 61.111 0.00 0.00 0.00 3.86
5761 6721 2.124983 CACCTCCACGATGCCCAG 60.125 66.667 0.00 0.00 0.00 4.45
5762 6722 4.408821 GCACCTCCACGATGCCCA 62.409 66.667 0.00 0.00 33.06 5.36


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

AutoCloner maintained by Alex Coulton.