Multiple sequence alignment - TraesCS4B01G023700

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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 TraesCS4B01G023700 chr4B 100.000 3074 0 0 1 3074 17082255 17085328 0.000000e+00 5677.0
1 TraesCS4B01G023700 chr4B 99.306 576 4 0 2499 3074 147078471 147079046 0.000000e+00 1042.0
2 TraesCS4B01G023700 chr4B 75.988 658 128 24 1407 2048 407808075 407807432 2.300000e-81 313.0
3 TraesCS4B01G023700 chr4A 90.684 1535 61 39 763 2270 594270893 594269414 0.000000e+00 1967.0
4 TraesCS4B01G023700 chr4A 99.222 514 2 2 2276 2788 115901261 115901773 0.000000e+00 926.0
5 TraesCS4B01G023700 chr4A 99.022 511 3 2 2279 2788 740126428 740126937 0.000000e+00 915.0
6 TraesCS4B01G023700 chr4A 87.895 190 13 7 2091 2280 594222735 594222556 6.680000e-52 215.0
7 TraesCS4B01G023700 chr4A 81.773 203 11 11 105 292 594272448 594272257 2.470000e-31 147.0
8 TraesCS4B01G023700 chr4A 95.455 44 2 0 2049 2092 594222806 594222763 1.530000e-08 71.3
9 TraesCS4B01G023700 chr4D 89.003 1555 98 40 753 2277 9205977 9207488 0.000000e+00 1857.0
10 TraesCS4B01G023700 chr4D 92.547 161 8 2 107 266 9204642 9204799 8.570000e-56 228.0
11 TraesCS4B01G023700 chr1B 99.126 801 6 1 2275 3074 38842516 38843316 0.000000e+00 1439.0
12 TraesCS4B01G023700 chr2A 98.373 799 9 4 2279 3074 724040846 724040049 0.000000e+00 1400.0
13 TraesCS4B01G023700 chr2A 98.828 512 4 2 2278 2788 194166166 194166676 0.000000e+00 911.0
14 TraesCS4B01G023700 chr2A 92.118 203 16 0 549 751 26932983 26933185 1.390000e-73 287.0
15 TraesCS4B01G023700 chr5B 99.306 576 4 0 2499 3074 21407597 21408172 0.000000e+00 1042.0
16 TraesCS4B01G023700 chr5B 99.306 576 4 0 2499 3074 678301818 678302393 0.000000e+00 1042.0
17 TraesCS4B01G023700 chr5B 99.022 511 3 2 2279 2788 52920157 52919648 0.000000e+00 915.0
18 TraesCS4B01G023700 chr7B 99.306 576 3 1 2499 3074 603979516 603980090 0.000000e+00 1040.0
19 TraesCS4B01G023700 chr6B 99.476 573 2 1 2502 3074 470926431 470925860 0.000000e+00 1040.0
20 TraesCS4B01G023700 chr6A 99.476 573 2 1 2502 3074 362710889 362710318 0.000000e+00 1040.0
21 TraesCS4B01G023700 chr7A 97.830 599 10 3 2279 2876 148648792 148649388 0.000000e+00 1031.0
22 TraesCS4B01G023700 chr7A 76.750 843 142 43 1199 2014 159558252 159557437 3.660000e-114 422.0
23 TraesCS4B01G023700 chr7A 93.299 194 12 1 557 750 10423141 10422949 5.020000e-73 285.0
24 TraesCS4B01G023700 chr3B 98.646 517 5 2 2273 2788 654427702 654428217 0.000000e+00 915.0
25 TraesCS4B01G023700 chr3B 93.333 195 13 0 557 751 92330253 92330447 3.880000e-74 289.0
26 TraesCS4B01G023700 chr3A 98.638 514 5 2 2276 2788 650004786 650005298 0.000000e+00 909.0
27 TraesCS4B01G023700 chr7D 76.303 844 144 45 1199 2014 159062901 159063716 1.720000e-107 399.0
28 TraesCS4B01G023700 chr7D 93.434 198 12 1 557 753 162984875 162984678 3.000000e-75 292.0
29 TraesCS4B01G023700 chr7D 93.333 195 10 3 557 750 2260423 2260231 5.020000e-73 285.0
30 TraesCS4B01G023700 chr2D 94.845 194 9 1 557 750 645666176 645666368 4.980000e-78 302.0
31 TraesCS4B01G023700 chr1D 94.359 195 11 0 557 751 66380825 66381019 1.790000e-77 300.0
32 TraesCS4B01G023700 chr1D 91.080 213 17 1 545 755 394818351 394818563 1.390000e-73 287.0
33 TraesCS4B01G023700 chr3D 92.537 201 14 1 549 749 56362393 56362592 1.390000e-73 287.0
34 TraesCS4B01G023700 chr2B 73.010 867 184 41 1208 2043 552340920 552340073 3.040000e-65 259.0


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 TraesCS4B01G023700 chr4B 17082255 17085328 3073 False 5677.0 5677 100.0000 1 3074 1 chr4B.!!$F1 3073
1 TraesCS4B01G023700 chr4B 147078471 147079046 575 False 1042.0 1042 99.3060 2499 3074 1 chr4B.!!$F2 575
2 TraesCS4B01G023700 chr4B 407807432 407808075 643 True 313.0 313 75.9880 1407 2048 1 chr4B.!!$R1 641
3 TraesCS4B01G023700 chr4A 594269414 594272448 3034 True 1057.0 1967 86.2285 105 2270 2 chr4A.!!$R2 2165
4 TraesCS4B01G023700 chr4A 115901261 115901773 512 False 926.0 926 99.2220 2276 2788 1 chr4A.!!$F1 512
5 TraesCS4B01G023700 chr4A 740126428 740126937 509 False 915.0 915 99.0220 2279 2788 1 chr4A.!!$F2 509
6 TraesCS4B01G023700 chr4D 9204642 9207488 2846 False 1042.5 1857 90.7750 107 2277 2 chr4D.!!$F1 2170
7 TraesCS4B01G023700 chr1B 38842516 38843316 800 False 1439.0 1439 99.1260 2275 3074 1 chr1B.!!$F1 799
8 TraesCS4B01G023700 chr2A 724040049 724040846 797 True 1400.0 1400 98.3730 2279 3074 1 chr2A.!!$R1 795
9 TraesCS4B01G023700 chr2A 194166166 194166676 510 False 911.0 911 98.8280 2278 2788 1 chr2A.!!$F2 510
10 TraesCS4B01G023700 chr5B 21407597 21408172 575 False 1042.0 1042 99.3060 2499 3074 1 chr5B.!!$F1 575
11 TraesCS4B01G023700 chr5B 678301818 678302393 575 False 1042.0 1042 99.3060 2499 3074 1 chr5B.!!$F2 575
12 TraesCS4B01G023700 chr5B 52919648 52920157 509 True 915.0 915 99.0220 2279 2788 1 chr5B.!!$R1 509
13 TraesCS4B01G023700 chr7B 603979516 603980090 574 False 1040.0 1040 99.3060 2499 3074 1 chr7B.!!$F1 575
14 TraesCS4B01G023700 chr6B 470925860 470926431 571 True 1040.0 1040 99.4760 2502 3074 1 chr6B.!!$R1 572
15 TraesCS4B01G023700 chr6A 362710318 362710889 571 True 1040.0 1040 99.4760 2502 3074 1 chr6A.!!$R1 572
16 TraesCS4B01G023700 chr7A 148648792 148649388 596 False 1031.0 1031 97.8300 2279 2876 1 chr7A.!!$F1 597
17 TraesCS4B01G023700 chr7A 159557437 159558252 815 True 422.0 422 76.7500 1199 2014 1 chr7A.!!$R2 815
18 TraesCS4B01G023700 chr3B 654427702 654428217 515 False 915.0 915 98.6460 2273 2788 1 chr3B.!!$F2 515
19 TraesCS4B01G023700 chr3A 650004786 650005298 512 False 909.0 909 98.6380 2276 2788 1 chr3A.!!$F1 512
20 TraesCS4B01G023700 chr7D 159062901 159063716 815 False 399.0 399 76.3030 1199 2014 1 chr7D.!!$F1 815
21 TraesCS4B01G023700 chr2B 552340073 552340920 847 True 259.0 259 73.0100 1208 2043 1 chr2B.!!$R1 835

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
851 2275 0.035458 CACGCTTTTCCTCTGGTCCT 59.965 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 3927 1.069668 AGGGTGACGCGAAACTAAACT 59.93 47.619 15.93 5.32 0.0 2.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.480224 GCCGACACAGCGTACTATAA 57.520 50.000 0.00 0.00 0.00 0.98
35 36 2.801063 GCCGACACAGCGTACTATAAA 58.199 47.619 0.00 0.00 0.00 1.40
36 37 3.378339 GCCGACACAGCGTACTATAAAT 58.622 45.455 0.00 0.00 0.00 1.40
37 38 3.424529 GCCGACACAGCGTACTATAAATC 59.575 47.826 0.00 0.00 0.00 2.17
38 39 4.792057 GCCGACACAGCGTACTATAAATCT 60.792 45.833 0.00 0.00 0.00 2.40
39 40 5.279384 CCGACACAGCGTACTATAAATCTT 58.721 41.667 0.00 0.00 0.00 2.40
40 41 5.398711 CCGACACAGCGTACTATAAATCTTC 59.601 44.000 0.00 0.00 0.00 2.87
41 42 5.113678 CGACACAGCGTACTATAAATCTTCG 59.886 44.000 0.00 0.00 0.00 3.79
42 43 6.127810 ACACAGCGTACTATAAATCTTCGA 57.872 37.500 0.00 0.00 0.00 3.71
43 44 5.970023 ACACAGCGTACTATAAATCTTCGAC 59.030 40.000 0.00 0.00 0.00 4.20
44 45 6.183360 ACACAGCGTACTATAAATCTTCGACT 60.183 38.462 0.00 0.00 0.00 4.18
45 46 6.140895 CACAGCGTACTATAAATCTTCGACTG 59.859 42.308 0.00 0.00 0.00 3.51
46 47 5.115773 CAGCGTACTATAAATCTTCGACTGC 59.884 44.000 0.00 0.00 0.00 4.40
47 48 4.382160 GCGTACTATAAATCTTCGACTGCC 59.618 45.833 0.00 0.00 0.00 4.85
48 49 4.611782 CGTACTATAAATCTTCGACTGCCG 59.388 45.833 0.00 0.00 40.25 5.69
49 50 3.381949 ACTATAAATCTTCGACTGCCGC 58.618 45.455 0.00 0.00 38.37 6.53
50 51 1.209128 ATAAATCTTCGACTGCCGCG 58.791 50.000 0.00 0.00 38.37 6.46
51 52 1.418342 TAAATCTTCGACTGCCGCGC 61.418 55.000 0.00 0.00 38.37 6.86
78 79 2.652496 GCCTCGCGAGTCACGATC 60.652 66.667 32.41 10.11 45.77 3.69
79 80 2.024871 CCTCGCGAGTCACGATCC 59.975 66.667 32.41 0.00 45.77 3.36
80 81 2.761195 CCTCGCGAGTCACGATCCA 61.761 63.158 32.41 0.00 45.77 3.41
81 82 1.136774 CTCGCGAGTCACGATCCAA 59.863 57.895 27.79 0.00 45.77 3.53
82 83 1.134530 CTCGCGAGTCACGATCCAAC 61.135 60.000 27.79 0.00 45.77 3.77
83 84 2.497092 CGCGAGTCACGATCCAACG 61.497 63.158 0.00 0.00 45.77 4.10
84 85 2.789203 GCGAGTCACGATCCAACGC 61.789 63.158 0.00 0.00 45.77 4.84
85 86 1.154016 CGAGTCACGATCCAACGCT 60.154 57.895 0.00 0.00 45.77 5.07
86 87 1.406219 CGAGTCACGATCCAACGCTG 61.406 60.000 0.00 0.00 45.77 5.18
87 88 0.109272 GAGTCACGATCCAACGCTGA 60.109 55.000 0.00 0.00 36.70 4.26
88 89 0.532573 AGTCACGATCCAACGCTGAT 59.467 50.000 0.00 0.00 36.70 2.90
89 90 1.066858 AGTCACGATCCAACGCTGATT 60.067 47.619 0.00 0.00 36.70 2.57
90 91 1.732259 GTCACGATCCAACGCTGATTT 59.268 47.619 0.00 0.00 36.70 2.17
91 92 2.159627 GTCACGATCCAACGCTGATTTT 59.840 45.455 0.00 0.00 36.70 1.82
92 93 2.415168 TCACGATCCAACGCTGATTTTC 59.585 45.455 0.00 0.00 36.70 2.29
93 94 1.737793 ACGATCCAACGCTGATTTTCC 59.262 47.619 0.00 0.00 36.70 3.13
94 95 1.737236 CGATCCAACGCTGATTTTCCA 59.263 47.619 0.00 0.00 0.00 3.53
95 96 2.161410 CGATCCAACGCTGATTTTCCAA 59.839 45.455 0.00 0.00 0.00 3.53
96 97 3.728864 CGATCCAACGCTGATTTTCCAAG 60.729 47.826 0.00 0.00 0.00 3.61
97 98 2.857483 TCCAACGCTGATTTTCCAAGA 58.143 42.857 0.00 0.00 0.00 3.02
98 99 3.420893 TCCAACGCTGATTTTCCAAGAT 58.579 40.909 0.00 0.00 0.00 2.40
99 100 3.440173 TCCAACGCTGATTTTCCAAGATC 59.560 43.478 0.00 0.00 0.00 2.75
100 101 3.419915 CAACGCTGATTTTCCAAGATCG 58.580 45.455 0.00 0.00 0.00 3.69
101 102 1.398390 ACGCTGATTTTCCAAGATCGC 59.602 47.619 0.00 0.00 0.00 4.58
102 103 1.268234 CGCTGATTTTCCAAGATCGCC 60.268 52.381 0.00 0.00 0.00 5.54
103 104 1.745087 GCTGATTTTCCAAGATCGCCA 59.255 47.619 0.00 0.00 0.00 5.69
160 171 3.869272 CGCGAGCCTGGACATTGC 61.869 66.667 0.00 0.00 0.00 3.56
247 263 4.760047 CTTGACCGGGTCCCGCAG 62.760 72.222 25.88 14.87 46.86 5.18
287 303 2.279918 ACGTGTCACCCAACGCTC 60.280 61.111 0.00 0.00 0.00 5.03
292 308 4.717629 TCACCCAACGCTCGCTCG 62.718 66.667 0.00 0.00 0.00 5.03
299 315 2.126812 ACGCTCGCTCGTTCTCAC 60.127 61.111 0.00 0.00 40.07 3.51
312 375 2.543031 CGTTCTCACTTCTCACCGACAA 60.543 50.000 0.00 0.00 0.00 3.18
314 377 3.812156 TCTCACTTCTCACCGACAAAA 57.188 42.857 0.00 0.00 0.00 2.44
315 378 4.131649 TCTCACTTCTCACCGACAAAAA 57.868 40.909 0.00 0.00 0.00 1.94
325 388 2.730928 CACCGACAAAAACATTGATGCC 59.269 45.455 0.00 0.00 0.00 4.40
330 393 1.994779 CAAAAACATTGATGCCGGAGC 59.005 47.619 5.05 0.00 40.48 4.70
376 439 2.550101 GCGATCTTCCTGCCCATGC 61.550 63.158 0.00 0.00 38.26 4.06
392 455 2.554806 ATGCTGCACATGAATGAACG 57.445 45.000 3.57 0.00 37.70 3.95
393 456 1.521580 TGCTGCACATGAATGAACGA 58.478 45.000 0.00 0.00 0.00 3.85
394 457 2.086094 TGCTGCACATGAATGAACGAT 58.914 42.857 0.00 0.00 0.00 3.73
395 458 2.159490 TGCTGCACATGAATGAACGATG 60.159 45.455 0.00 0.00 0.00 3.84
396 459 2.793585 GCTGCACATGAATGAACGATGG 60.794 50.000 0.00 0.00 0.00 3.51
414 950 3.283684 CCCGGAGTGCGTTGCAAA 61.284 61.111 0.73 0.00 41.47 3.68
430 966 4.718858 TGCAAACATGTACGAGTGTAAC 57.281 40.909 0.00 0.00 30.94 2.50
458 994 9.592196 TTTTTCTCTAGGGTAGTAGTAGACAAA 57.408 33.333 0.00 0.00 0.00 2.83
460 996 8.572855 TTCTCTAGGGTAGTAGTAGACAAAAC 57.427 38.462 0.00 0.00 0.00 2.43
461 997 7.693132 TCTCTAGGGTAGTAGTAGACAAAACA 58.307 38.462 0.00 0.00 0.00 2.83
462 998 8.334734 TCTCTAGGGTAGTAGTAGACAAAACAT 58.665 37.037 0.00 0.00 0.00 2.71
466 1002 7.834803 AGGGTAGTAGTAGACAAAACATGTAC 58.165 38.462 0.00 0.00 44.12 2.90
467 1003 7.673082 AGGGTAGTAGTAGACAAAACATGTACT 59.327 37.037 0.00 0.00 44.12 2.73
469 1005 9.780413 GGTAGTAGTAGACAAAACATGTACTAC 57.220 37.037 18.73 18.73 45.86 2.73
473 1009 9.557338 GTAGTAGACAAAACATGTACTACTCTG 57.443 37.037 18.95 5.37 44.00 3.35
476 1718 3.994392 ACAAAACATGTACTACTCTGGCG 59.006 43.478 0.00 0.00 41.63 5.69
479 1721 4.530710 AACATGTACTACTCTGGCGAAA 57.469 40.909 0.00 0.00 0.00 3.46
480 1722 3.846360 ACATGTACTACTCTGGCGAAAC 58.154 45.455 0.00 0.00 0.00 2.78
482 1724 2.522185 TGTACTACTCTGGCGAAACCT 58.478 47.619 0.00 0.00 40.22 3.50
485 1727 5.439721 TGTACTACTCTGGCGAAACCTATA 58.560 41.667 0.00 0.00 40.22 1.31
487 1744 2.865343 ACTCTGGCGAAACCTATACG 57.135 50.000 0.00 0.00 40.22 3.06
488 1745 2.097825 ACTCTGGCGAAACCTATACGT 58.902 47.619 0.00 0.00 40.22 3.57
496 1753 5.106038 TGGCGAAACCTATACGTATATCCAG 60.106 44.000 15.42 5.97 40.22 3.86
500 1757 7.201767 GCGAAACCTATACGTATATCCAGGTAT 60.202 40.741 22.24 12.95 31.13 2.73
505 1763 7.718753 ACCTATACGTATATCCAGGTATACTGC 59.281 40.741 21.13 0.00 46.14 4.40
507 1765 5.899120 ACGTATATCCAGGTATACTGCAG 57.101 43.478 13.48 13.48 46.14 4.41
513 1771 1.000843 CCAGGTATACTGCAGCGCATA 59.999 52.381 15.27 6.40 46.14 3.14
514 1772 2.061773 CAGGTATACTGCAGCGCATAC 58.938 52.381 15.27 17.45 40.97 2.39
515 1773 1.686587 AGGTATACTGCAGCGCATACA 59.313 47.619 24.05 3.10 38.13 2.29
522 1793 0.657312 TGCAGCGCATACATACAAGC 59.343 50.000 11.47 0.00 31.71 4.01
524 1795 1.333524 GCAGCGCATACATACAAGCAG 60.334 52.381 11.47 0.00 0.00 4.24
535 1806 7.388776 GCATACATACAAGCAGAATGGAAGATA 59.611 37.037 0.00 0.00 35.86 1.98
536 1807 9.276590 CATACATACAAGCAGAATGGAAGATAA 57.723 33.333 0.00 0.00 35.86 1.75
537 1808 7.559590 ACATACAAGCAGAATGGAAGATAAC 57.440 36.000 0.00 0.00 35.86 1.89
538 1809 6.543831 ACATACAAGCAGAATGGAAGATAACC 59.456 38.462 0.00 0.00 35.86 2.85
540 1811 4.702131 ACAAGCAGAATGGAAGATAACCAC 59.298 41.667 0.00 0.00 40.36 4.16
541 1812 3.535561 AGCAGAATGGAAGATAACCACG 58.464 45.455 0.00 0.00 40.36 4.94
542 1813 3.055094 AGCAGAATGGAAGATAACCACGT 60.055 43.478 0.00 0.00 40.36 4.49
545 1816 5.681437 GCAGAATGGAAGATAACCACGTAGA 60.681 44.000 0.00 0.00 40.36 2.59
546 1817 6.516718 CAGAATGGAAGATAACCACGTAGAT 58.483 40.000 0.00 0.00 40.36 1.98
547 1818 7.658261 CAGAATGGAAGATAACCACGTAGATA 58.342 38.462 0.00 0.00 40.36 1.98
548 1819 8.141909 CAGAATGGAAGATAACCACGTAGATAA 58.858 37.037 0.00 0.00 40.36 1.75
549 1820 8.142551 AGAATGGAAGATAACCACGTAGATAAC 58.857 37.037 0.00 0.00 40.36 1.89
552 1823 7.844009 TGGAAGATAACCACGTAGATAACTTT 58.156 34.615 0.00 0.00 32.03 2.66
553 1824 7.977853 TGGAAGATAACCACGTAGATAACTTTC 59.022 37.037 0.00 0.00 32.03 2.62
554 1825 8.196103 GGAAGATAACCACGTAGATAACTTTCT 58.804 37.037 0.00 0.00 0.00 2.52
559 1830 9.798994 ATAACCACGTAGATAACTTTCTAACTG 57.201 33.333 0.00 0.00 30.25 3.16
560 1831 7.224522 ACCACGTAGATAACTTTCTAACTGT 57.775 36.000 0.00 0.00 30.25 3.55
561 1832 7.311408 ACCACGTAGATAACTTTCTAACTGTC 58.689 38.462 0.00 0.00 30.25 3.51
562 1833 7.176340 ACCACGTAGATAACTTTCTAACTGTCT 59.824 37.037 0.00 0.00 30.25 3.41
563 1834 8.671921 CCACGTAGATAACTTTCTAACTGTCTA 58.328 37.037 0.00 0.00 30.25 2.59
580 1851 7.625828 ACTGTCTATTACAATAAGGTTTGCC 57.374 36.000 0.00 0.00 37.74 4.52
581 1852 6.602009 ACTGTCTATTACAATAAGGTTTGCCC 59.398 38.462 0.00 0.00 37.74 5.36
582 1853 5.587043 TGTCTATTACAATAAGGTTTGCCCG 59.413 40.000 0.00 0.00 34.63 6.13
583 1854 5.818857 GTCTATTACAATAAGGTTTGCCCGA 59.181 40.000 0.00 0.00 38.74 5.14
584 1855 4.976224 ATTACAATAAGGTTTGCCCGAC 57.024 40.909 0.00 0.00 38.74 4.79
585 1856 2.579410 ACAATAAGGTTTGCCCGACT 57.421 45.000 0.00 0.00 38.74 4.18
586 1857 2.433436 ACAATAAGGTTTGCCCGACTC 58.567 47.619 0.00 0.00 38.74 3.36
587 1858 1.743394 CAATAAGGTTTGCCCGACTCC 59.257 52.381 0.00 0.00 38.74 3.85
588 1859 0.107848 ATAAGGTTTGCCCGACTCCG 60.108 55.000 0.00 0.00 38.74 4.63
598 1869 4.814900 CGACTCCGGTGATGAAGG 57.185 61.111 11.17 0.00 0.00 3.46
599 1870 1.141881 CGACTCCGGTGATGAAGGG 59.858 63.158 11.17 0.00 0.00 3.95
600 1871 1.522569 GACTCCGGTGATGAAGGGG 59.477 63.158 11.17 0.00 0.00 4.79
601 1872 2.190578 CTCCGGTGATGAAGGGGC 59.809 66.667 0.00 0.00 0.00 5.80
602 1873 3.740128 CTCCGGTGATGAAGGGGCG 62.740 68.421 0.00 0.00 0.00 6.13
603 1874 3.781307 CCGGTGATGAAGGGGCGA 61.781 66.667 0.00 0.00 0.00 5.54
605 1876 1.889105 CGGTGATGAAGGGGCGATG 60.889 63.158 0.00 0.00 0.00 3.84
606 1877 1.526887 GGTGATGAAGGGGCGATGA 59.473 57.895 0.00 0.00 0.00 2.92
607 1878 0.815615 GGTGATGAAGGGGCGATGAC 60.816 60.000 0.00 0.00 0.00 3.06
608 1879 1.143838 TGATGAAGGGGCGATGACG 59.856 57.895 0.00 0.00 42.93 4.35
609 1880 1.595382 GATGAAGGGGCGATGACGG 60.595 63.158 0.00 0.00 40.15 4.79
631 1902 3.858989 GCGCCTTCTGCTCGCTTC 61.859 66.667 0.00 0.00 44.79 3.86
632 1903 2.433145 CGCCTTCTGCTCGCTTCA 60.433 61.111 0.00 0.00 38.05 3.02
633 1904 2.029288 CGCCTTCTGCTCGCTTCAA 61.029 57.895 0.00 0.00 38.05 2.69
634 1905 1.364626 CGCCTTCTGCTCGCTTCAAT 61.365 55.000 0.00 0.00 38.05 2.57
635 1906 0.098376 GCCTTCTGCTCGCTTCAATG 59.902 55.000 0.00 0.00 36.87 2.82
636 1907 0.098376 CCTTCTGCTCGCTTCAATGC 59.902 55.000 0.00 0.00 0.00 3.56
637 1908 1.085091 CTTCTGCTCGCTTCAATGCT 58.915 50.000 0.00 0.00 0.00 3.79
638 1909 1.467734 CTTCTGCTCGCTTCAATGCTT 59.532 47.619 0.00 0.00 0.00 3.91
639 1910 0.800631 TCTGCTCGCTTCAATGCTTG 59.199 50.000 0.00 0.00 0.00 4.01
640 1911 0.520404 CTGCTCGCTTCAATGCTTGT 59.480 50.000 0.00 0.00 0.00 3.16
641 1912 1.733912 CTGCTCGCTTCAATGCTTGTA 59.266 47.619 0.00 0.00 0.00 2.41
642 1913 1.733912 TGCTCGCTTCAATGCTTGTAG 59.266 47.619 0.00 0.00 0.00 2.74
643 1914 1.734465 GCTCGCTTCAATGCTTGTAGT 59.266 47.619 0.00 0.00 31.53 2.73
644 1915 2.222908 GCTCGCTTCAATGCTTGTAGTC 60.223 50.000 0.00 0.00 31.53 2.59
645 1916 1.992667 TCGCTTCAATGCTTGTAGTCG 59.007 47.619 0.00 0.44 33.03 4.18
646 1917 1.726791 CGCTTCAATGCTTGTAGTCGT 59.273 47.619 0.00 0.00 31.53 4.34
647 1918 2.222596 CGCTTCAATGCTTGTAGTCGTC 60.223 50.000 0.00 0.00 31.53 4.20
648 1919 2.222596 GCTTCAATGCTTGTAGTCGTCG 60.223 50.000 0.00 0.00 31.53 5.12
649 1920 1.346365 TCAATGCTTGTAGTCGTCGC 58.654 50.000 0.00 0.00 0.00 5.19
650 1921 1.067846 TCAATGCTTGTAGTCGTCGCT 60.068 47.619 0.00 0.00 0.00 4.93
651 1922 2.162809 TCAATGCTTGTAGTCGTCGCTA 59.837 45.455 0.00 0.00 0.00 4.26
652 1923 2.476873 ATGCTTGTAGTCGTCGCTAG 57.523 50.000 0.00 0.00 0.00 3.42
653 1924 1.445871 TGCTTGTAGTCGTCGCTAGA 58.554 50.000 0.00 0.00 0.00 2.43
654 1925 2.014857 TGCTTGTAGTCGTCGCTAGAT 58.985 47.619 0.00 0.00 0.00 1.98
655 1926 2.223272 TGCTTGTAGTCGTCGCTAGATG 60.223 50.000 0.00 0.00 34.75 2.90
656 1927 2.855187 GCTTGTAGTCGTCGCTAGATGG 60.855 54.545 0.00 0.00 34.23 3.51
657 1928 2.034104 TGTAGTCGTCGCTAGATGGT 57.966 50.000 0.00 0.00 34.23 3.55
658 1929 1.938577 TGTAGTCGTCGCTAGATGGTC 59.061 52.381 0.00 0.00 34.23 4.02
659 1930 1.263752 GTAGTCGTCGCTAGATGGTCC 59.736 57.143 0.00 0.00 34.23 4.46
660 1931 0.393944 AGTCGTCGCTAGATGGTCCA 60.394 55.000 0.00 0.00 34.23 4.02
661 1932 0.669077 GTCGTCGCTAGATGGTCCAT 59.331 55.000 3.26 3.26 34.23 3.41
662 1933 1.878088 GTCGTCGCTAGATGGTCCATA 59.122 52.381 3.72 0.00 34.23 2.74
663 1934 2.095668 GTCGTCGCTAGATGGTCCATAG 60.096 54.545 3.72 0.36 34.23 2.23
664 1935 2.152016 CGTCGCTAGATGGTCCATAGA 58.848 52.381 3.72 0.00 0.00 1.98
665 1936 2.095668 CGTCGCTAGATGGTCCATAGAC 60.096 54.545 3.72 8.67 42.73 2.59
712 1983 3.261643 TGTGTTCTCTGTACTGCCATGAT 59.738 43.478 0.00 0.00 0.00 2.45
713 1984 3.868077 GTGTTCTCTGTACTGCCATGATC 59.132 47.826 0.00 0.00 0.00 2.92
717 1988 3.005155 TCTCTGTACTGCCATGATCGATG 59.995 47.826 0.54 0.00 0.00 3.84
719 1990 3.384467 TCTGTACTGCCATGATCGATGAA 59.616 43.478 0.54 0.00 33.31 2.57
721 1992 5.243730 TCTGTACTGCCATGATCGATGAATA 59.756 40.000 0.54 0.00 33.31 1.75
723 1994 4.879197 ACTGCCATGATCGATGAATAGA 57.121 40.909 0.54 0.00 33.31 1.98
724 1995 5.417754 ACTGCCATGATCGATGAATAGAT 57.582 39.130 0.54 0.00 33.31 1.98
725 1996 5.802465 ACTGCCATGATCGATGAATAGATT 58.198 37.500 0.54 0.00 33.31 2.40
727 1998 5.797051 TGCCATGATCGATGAATAGATTGA 58.203 37.500 0.54 0.00 33.31 2.57
728 1999 6.232692 TGCCATGATCGATGAATAGATTGAA 58.767 36.000 0.54 0.00 33.31 2.69
730 2001 7.229106 TGCCATGATCGATGAATAGATTGAAAA 59.771 33.333 0.54 0.00 33.31 2.29
731 2002 8.242053 GCCATGATCGATGAATAGATTGAAAAT 58.758 33.333 0.54 0.00 33.31 1.82
804 2222 2.853705 TCACCCGGTTTTCTTTACCAG 58.146 47.619 0.00 0.00 35.31 4.00
805 2223 2.438763 TCACCCGGTTTTCTTTACCAGA 59.561 45.455 0.00 0.00 35.31 3.86
840 2264 4.497608 CGTTACACATTCAAACACGCTTTT 59.502 37.500 0.00 0.00 0.00 2.27
842 2266 3.443976 ACACATTCAAACACGCTTTTCC 58.556 40.909 0.00 0.00 0.00 3.13
845 2269 3.632145 ACATTCAAACACGCTTTTCCTCT 59.368 39.130 0.00 0.00 0.00 3.69
847 2271 1.946768 TCAAACACGCTTTTCCTCTGG 59.053 47.619 0.00 0.00 0.00 3.86
848 2272 1.676006 CAAACACGCTTTTCCTCTGGT 59.324 47.619 0.00 0.00 0.00 4.00
850 2274 0.250338 ACACGCTTTTCCTCTGGTCC 60.250 55.000 0.00 0.00 0.00 4.46
851 2275 0.035458 CACGCTTTTCCTCTGGTCCT 59.965 55.000 0.00 0.00 0.00 3.85
852 2276 1.275291 CACGCTTTTCCTCTGGTCCTA 59.725 52.381 0.00 0.00 0.00 2.94
866 2291 1.276622 GTCCTAACCCTCTCCAAGCA 58.723 55.000 0.00 0.00 0.00 3.91
876 2301 2.089980 CTCTCCAAGCATTTGACCCAG 58.910 52.381 0.00 0.00 36.36 4.45
892 2317 1.299648 CAGATTTGACGCCTCCCCA 59.700 57.895 0.00 0.00 0.00 4.96
998 2433 3.582120 CCACCGCACACACACACC 61.582 66.667 0.00 0.00 0.00 4.16
999 2434 3.935872 CACCGCACACACACACCG 61.936 66.667 0.00 0.00 0.00 4.94
1007 2455 1.194547 CACACACACACCGATGCTTAC 59.805 52.381 0.00 0.00 0.00 2.34
1110 2567 2.617274 GCCGCACTTCACCAACTCC 61.617 63.158 0.00 0.00 0.00 3.85
1320 2777 4.689549 TTCCTCACCTCCGCCGGA 62.690 66.667 5.05 5.37 0.00 5.14
1337 2794 4.070265 ATCACCCTCCCGGACGGA 62.070 66.667 13.13 0.00 38.83 4.69
1487 2947 4.537433 GCGCTCCTACCTGGCCAG 62.537 72.222 26.87 26.87 35.26 4.85
1548 3008 2.747822 CGACGTCGTCCTCACCGAT 61.748 63.158 29.08 0.00 36.62 4.18
2043 3521 1.153823 CAAGTACGACCTGCTCCGG 60.154 63.158 0.00 0.00 0.00 5.14
2078 3556 1.352156 GACGCCGTCTTGTGATGACC 61.352 60.000 10.56 0.00 0.00 4.02
2081 3559 0.460284 GCCGTCTTGTGATGACCGAT 60.460 55.000 0.00 0.00 0.00 4.18
2083 3561 1.135112 CCGTCTTGTGATGACCGATGA 60.135 52.381 0.00 0.00 0.00 2.92
2088 3566 0.594796 TGTGATGACCGATGATCGCG 60.595 55.000 9.74 0.00 38.82 5.87
2112 3601 2.674796 TTTTTGGTCGGTTTGGTTGG 57.325 45.000 0.00 0.00 0.00 3.77
2126 3615 6.056236 GGTTTGGTTGGATTAGGAGATACTC 58.944 44.000 0.00 0.00 0.00 2.59
2127 3616 6.352737 GGTTTGGTTGGATTAGGAGATACTCA 60.353 42.308 0.00 0.00 31.08 3.41
2128 3617 5.871396 TGGTTGGATTAGGAGATACTCAC 57.129 43.478 0.00 0.00 31.08 3.51
2130 3619 6.679542 TGGTTGGATTAGGAGATACTCACTA 58.320 40.000 0.00 0.00 31.08 2.74
2131 3620 6.778069 TGGTTGGATTAGGAGATACTCACTAG 59.222 42.308 0.00 0.00 31.08 2.57
2132 3621 7.005296 GGTTGGATTAGGAGATACTCACTAGA 58.995 42.308 0.00 0.00 31.08 2.43
2133 3622 7.672239 GGTTGGATTAGGAGATACTCACTAGAT 59.328 40.741 0.00 0.00 31.08 1.98
2134 3623 8.519526 GTTGGATTAGGAGATACTCACTAGATG 58.480 40.741 0.00 0.00 31.08 2.90
2135 3624 7.990055 TGGATTAGGAGATACTCACTAGATGA 58.010 38.462 0.00 0.00 35.45 2.92
2136 3625 8.619281 TGGATTAGGAGATACTCACTAGATGAT 58.381 37.037 0.00 0.00 36.48 2.45
2137 3626 9.120538 GGATTAGGAGATACTCACTAGATGATC 57.879 40.741 0.00 0.00 36.48 2.92
2138 3627 9.679661 GATTAGGAGATACTCACTAGATGATCA 57.320 37.037 0.00 0.00 36.48 2.92
2139 3628 9.685276 ATTAGGAGATACTCACTAGATGATCAG 57.315 37.037 0.09 0.00 36.48 2.90
2140 3629 5.945784 AGGAGATACTCACTAGATGATCAGC 59.054 44.000 1.78 1.78 36.48 4.26
2141 3630 5.945784 GGAGATACTCACTAGATGATCAGCT 59.054 44.000 18.88 18.88 36.48 4.24
2173 3662 7.117523 CCTTCTTTTGTTGATTGTTGTTGTCAA 59.882 33.333 0.00 0.00 0.00 3.18
2232 3724 5.234757 GTGTACATAGTGTTTGGACGAACAA 59.765 40.000 6.69 0.00 40.86 2.83
2233 3725 5.992829 TGTACATAGTGTTTGGACGAACAAT 59.007 36.000 9.90 9.90 40.86 2.71
2234 3726 6.483974 TGTACATAGTGTTTGGACGAACAATT 59.516 34.615 10.22 3.99 40.86 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.480224 TTATAGTACGCTGTGTCGGC 57.520 50.000 0.00 0.00 0.00 5.54
16 17 4.856664 AGATTTATAGTACGCTGTGTCGG 58.143 43.478 0.00 0.00 0.00 4.79
17 18 5.113678 CGAAGATTTATAGTACGCTGTGTCG 59.886 44.000 0.00 0.00 0.00 4.35
18 19 6.140422 GTCGAAGATTTATAGTACGCTGTGTC 59.860 42.308 0.00 0.00 40.67 3.67
19 20 5.970023 GTCGAAGATTTATAGTACGCTGTGT 59.030 40.000 0.00 0.00 40.67 3.72
20 21 6.140895 CAGTCGAAGATTTATAGTACGCTGTG 59.859 42.308 0.00 0.00 40.67 3.66
21 22 6.200100 CAGTCGAAGATTTATAGTACGCTGT 58.800 40.000 0.00 0.00 40.67 4.40
22 23 5.115773 GCAGTCGAAGATTTATAGTACGCTG 59.884 44.000 0.00 0.00 40.67 5.18
23 24 5.213675 GCAGTCGAAGATTTATAGTACGCT 58.786 41.667 0.00 0.00 40.67 5.07
24 25 4.382160 GGCAGTCGAAGATTTATAGTACGC 59.618 45.833 0.00 0.00 40.67 4.42
25 26 4.611782 CGGCAGTCGAAGATTTATAGTACG 59.388 45.833 0.00 0.00 40.67 3.67
26 27 4.382160 GCGGCAGTCGAAGATTTATAGTAC 59.618 45.833 0.00 0.00 40.67 2.73
27 28 4.543692 GCGGCAGTCGAAGATTTATAGTA 58.456 43.478 0.00 0.00 40.67 1.82
28 29 3.381949 GCGGCAGTCGAAGATTTATAGT 58.618 45.455 0.00 0.00 40.67 2.12
29 30 2.405357 CGCGGCAGTCGAAGATTTATAG 59.595 50.000 0.00 0.00 40.67 1.31
30 31 2.390938 CGCGGCAGTCGAAGATTTATA 58.609 47.619 0.00 0.00 40.67 0.98
31 32 1.209128 CGCGGCAGTCGAAGATTTAT 58.791 50.000 0.00 0.00 40.67 1.40
32 33 1.418342 GCGCGGCAGTCGAAGATTTA 61.418 55.000 8.83 0.00 40.67 1.40
33 34 2.740714 GCGCGGCAGTCGAAGATTT 61.741 57.895 8.83 0.00 40.67 2.17
34 35 3.188786 GCGCGGCAGTCGAAGATT 61.189 61.111 8.83 0.00 40.67 2.40
65 66 2.497092 CGTTGGATCGTGACTCGCG 61.497 63.158 0.00 0.00 39.67 5.87
66 67 2.789203 GCGTTGGATCGTGACTCGC 61.789 63.158 0.00 0.00 39.67 5.03
67 68 1.154016 AGCGTTGGATCGTGACTCG 60.154 57.895 0.00 0.00 41.41 4.18
68 69 0.109272 TCAGCGTTGGATCGTGACTC 60.109 55.000 0.00 0.00 0.00 3.36
69 70 0.532573 ATCAGCGTTGGATCGTGACT 59.467 50.000 0.00 0.00 0.00 3.41
70 71 1.359848 AATCAGCGTTGGATCGTGAC 58.640 50.000 0.00 0.00 0.00 3.67
71 72 2.093306 AAATCAGCGTTGGATCGTGA 57.907 45.000 0.00 0.00 0.00 4.35
72 73 2.476185 GGAAAATCAGCGTTGGATCGTG 60.476 50.000 0.00 0.00 0.00 4.35
73 74 1.737793 GGAAAATCAGCGTTGGATCGT 59.262 47.619 0.00 0.00 0.00 3.73
74 75 1.737236 TGGAAAATCAGCGTTGGATCG 59.263 47.619 0.00 0.00 0.00 3.69
75 76 3.440173 TCTTGGAAAATCAGCGTTGGATC 59.560 43.478 0.00 0.00 0.00 3.36
76 77 3.420893 TCTTGGAAAATCAGCGTTGGAT 58.579 40.909 0.00 0.00 0.00 3.41
77 78 2.857483 TCTTGGAAAATCAGCGTTGGA 58.143 42.857 0.00 0.00 0.00 3.53
78 79 3.728864 CGATCTTGGAAAATCAGCGTTGG 60.729 47.826 0.00 0.00 0.00 3.77
79 80 3.419915 CGATCTTGGAAAATCAGCGTTG 58.580 45.455 0.00 0.00 0.00 4.10
80 81 2.159517 GCGATCTTGGAAAATCAGCGTT 60.160 45.455 0.00 0.00 0.00 4.84
81 82 1.398390 GCGATCTTGGAAAATCAGCGT 59.602 47.619 0.00 0.00 0.00 5.07
82 83 1.268234 GGCGATCTTGGAAAATCAGCG 60.268 52.381 0.00 0.00 0.00 5.18
83 84 1.745087 TGGCGATCTTGGAAAATCAGC 59.255 47.619 0.00 0.00 0.00 4.26
84 85 4.357142 CAATGGCGATCTTGGAAAATCAG 58.643 43.478 0.00 0.00 0.00 2.90
85 86 3.130869 CCAATGGCGATCTTGGAAAATCA 59.869 43.478 5.70 0.00 43.83 2.57
86 87 3.491447 CCCAATGGCGATCTTGGAAAATC 60.491 47.826 11.95 0.00 43.83 2.17
87 88 2.431782 CCCAATGGCGATCTTGGAAAAT 59.568 45.455 11.95 0.00 43.83 1.82
88 89 1.824230 CCCAATGGCGATCTTGGAAAA 59.176 47.619 11.95 0.00 43.83 2.29
89 90 1.473258 CCCAATGGCGATCTTGGAAA 58.527 50.000 11.95 0.00 43.83 3.13
90 91 3.189568 CCCAATGGCGATCTTGGAA 57.810 52.632 11.95 0.00 43.83 3.53
91 92 4.984194 CCCAATGGCGATCTTGGA 57.016 55.556 11.95 0.00 43.83 3.53
101 102 1.153005 GGAGAGCTCTGCCCAATGG 60.153 63.158 23.91 0.00 0.00 3.16
102 103 0.747283 GTGGAGAGCTCTGCCCAATG 60.747 60.000 29.71 0.00 32.95 2.82
103 104 1.606531 GTGGAGAGCTCTGCCCAAT 59.393 57.895 29.71 0.30 32.95 3.16
160 171 1.880340 GCGAGCGAATCCTCTGGTG 60.880 63.158 0.00 0.00 0.00 4.17
226 242 2.582978 GGGACCCGGTCAAGTAGC 59.417 66.667 19.43 0.41 33.68 3.58
227 243 2.890371 CGGGACCCGGTCAAGTAG 59.110 66.667 26.15 1.75 44.15 2.57
264 280 2.368011 TTGGGTGACACGTGGTCCA 61.368 57.895 21.57 17.29 46.38 4.02
265 281 1.890510 GTTGGGTGACACGTGGTCC 60.891 63.158 21.57 17.41 46.38 4.46
269 285 2.587753 AGCGTTGGGTGACACGTG 60.588 61.111 15.48 15.48 0.00 4.49
287 303 1.332178 GTGAGAAGTGAGAACGAGCG 58.668 55.000 0.00 0.00 0.00 5.03
292 308 2.795175 TGTCGGTGAGAAGTGAGAAC 57.205 50.000 0.00 0.00 0.00 3.01
293 309 3.812156 TTTGTCGGTGAGAAGTGAGAA 57.188 42.857 0.00 0.00 0.00 2.87
295 311 3.621268 TGTTTTTGTCGGTGAGAAGTGAG 59.379 43.478 0.00 0.00 0.00 3.51
296 312 3.601435 TGTTTTTGTCGGTGAGAAGTGA 58.399 40.909 0.00 0.00 0.00 3.41
299 315 5.168526 TCAATGTTTTTGTCGGTGAGAAG 57.831 39.130 0.00 0.00 0.00 2.85
312 375 1.255882 TGCTCCGGCATCAATGTTTT 58.744 45.000 0.00 0.00 44.28 2.43
314 377 4.740922 TGCTCCGGCATCAATGTT 57.259 50.000 0.00 0.00 44.28 2.71
325 388 2.249557 GATTGCACTGCACTGCTCCG 62.250 60.000 17.53 0.00 38.71 4.63
330 393 3.570926 AGAAATGATTGCACTGCACTG 57.429 42.857 2.26 0.00 38.71 3.66
331 394 3.125829 CGTAGAAATGATTGCACTGCACT 59.874 43.478 2.26 0.00 38.71 4.40
332 395 3.419915 CGTAGAAATGATTGCACTGCAC 58.580 45.455 2.26 0.00 38.71 4.57
333 396 2.159531 GCGTAGAAATGATTGCACTGCA 60.160 45.455 0.00 0.00 36.47 4.41
334 397 2.444351 GCGTAGAAATGATTGCACTGC 58.556 47.619 0.00 0.00 0.00 4.40
335 398 2.537529 CGGCGTAGAAATGATTGCACTG 60.538 50.000 0.00 0.00 0.00 3.66
360 423 1.453762 GCAGCATGGGCAGGAAGATC 61.454 60.000 0.00 0.00 44.61 2.75
361 424 1.455217 GCAGCATGGGCAGGAAGAT 60.455 57.895 0.00 0.00 44.61 2.40
376 439 2.793585 GCCATCGTTCATTCATGTGCAG 60.794 50.000 0.00 0.00 0.00 4.41
392 455 4.778143 AACGCACTCCGGGCCATC 62.778 66.667 4.39 0.00 42.52 3.51
407 943 3.602390 ACACTCGTACATGTTTGCAAC 57.398 42.857 2.30 0.00 0.00 4.17
408 944 4.812091 AGTTACACTCGTACATGTTTGCAA 59.188 37.500 2.30 0.00 0.00 4.08
432 968 9.592196 TTTGTCTACTACTACCCTAGAGAAAAA 57.408 33.333 0.00 0.00 30.77 1.94
435 971 8.166061 TGTTTTGTCTACTACTACCCTAGAGAA 58.834 37.037 0.00 0.00 0.00 2.87
439 975 8.064336 ACATGTTTTGTCTACTACTACCCTAG 57.936 38.462 0.00 0.00 30.89 3.02
440 976 8.960591 GTACATGTTTTGTCTACTACTACCCTA 58.039 37.037 2.30 0.00 39.87 3.53
441 977 6.930068 ACATGTTTTGTCTACTACTACCCT 57.070 37.500 0.00 0.00 30.89 4.34
442 978 7.834803 AGTACATGTTTTGTCTACTACTACCC 58.165 38.462 2.30 0.00 39.87 3.69
443 979 9.780413 GTAGTACATGTTTTGTCTACTACTACC 57.220 37.037 18.95 4.75 42.26 3.18
447 983 9.557338 CAGAGTAGTACATGTTTTGTCTACTAC 57.443 37.037 18.73 18.73 44.06 2.73
448 984 8.737175 CCAGAGTAGTACATGTTTTGTCTACTA 58.263 37.037 2.30 0.49 42.66 1.82
449 985 7.603651 CCAGAGTAGTACATGTTTTGTCTACT 58.396 38.462 2.30 13.73 43.81 2.57
450 986 6.310711 GCCAGAGTAGTACATGTTTTGTCTAC 59.689 42.308 2.30 9.59 39.87 2.59
452 988 5.238583 GCCAGAGTAGTACATGTTTTGTCT 58.761 41.667 2.30 0.00 39.87 3.41
453 989 4.091509 CGCCAGAGTAGTACATGTTTTGTC 59.908 45.833 2.30 0.00 39.87 3.18
454 990 3.994392 CGCCAGAGTAGTACATGTTTTGT 59.006 43.478 2.30 0.00 42.62 2.83
455 991 4.242475 TCGCCAGAGTAGTACATGTTTTG 58.758 43.478 2.30 0.00 0.00 2.44
456 992 4.530710 TCGCCAGAGTAGTACATGTTTT 57.469 40.909 2.30 0.00 0.00 2.43
457 993 4.530710 TTCGCCAGAGTAGTACATGTTT 57.469 40.909 2.30 0.00 0.00 2.83
458 994 4.243270 GTTTCGCCAGAGTAGTACATGTT 58.757 43.478 2.30 0.00 0.00 2.71
460 996 3.119101 AGGTTTCGCCAGAGTAGTACATG 60.119 47.826 2.52 0.96 40.61 3.21
461 997 3.097614 AGGTTTCGCCAGAGTAGTACAT 58.902 45.455 2.52 0.00 40.61 2.29
462 998 2.522185 AGGTTTCGCCAGAGTAGTACA 58.478 47.619 2.52 0.00 40.61 2.90
464 1000 4.512944 CGTATAGGTTTCGCCAGAGTAGTA 59.487 45.833 0.00 0.00 40.61 1.82
466 1002 3.314635 ACGTATAGGTTTCGCCAGAGTAG 59.685 47.826 0.00 0.00 40.61 2.57
467 1003 3.282021 ACGTATAGGTTTCGCCAGAGTA 58.718 45.455 0.00 0.00 40.61 2.59
469 1005 2.865343 ACGTATAGGTTTCGCCAGAG 57.135 50.000 0.00 0.00 40.61 3.35
472 1008 4.766373 TGGATATACGTATAGGTTTCGCCA 59.234 41.667 19.40 13.78 40.61 5.69
473 1009 5.314923 TGGATATACGTATAGGTTTCGCC 57.685 43.478 19.40 11.87 37.58 5.54
479 1721 7.718753 GCAGTATACCTGGATATACGTATAGGT 59.281 40.741 24.24 24.24 41.19 3.08
480 1722 7.718314 TGCAGTATACCTGGATATACGTATAGG 59.282 40.741 19.40 18.15 41.19 2.57
482 1724 7.228108 GCTGCAGTATACCTGGATATACGTATA 59.772 40.741 17.24 17.24 41.10 1.47
485 1727 4.158025 GCTGCAGTATACCTGGATATACGT 59.842 45.833 16.64 0.00 41.10 3.57
487 1744 4.673441 CGCTGCAGTATACCTGGATATAC 58.327 47.826 16.64 9.15 41.10 1.47
488 1745 3.130516 GCGCTGCAGTATACCTGGATATA 59.869 47.826 16.64 0.00 41.10 0.86
496 1753 2.148916 TGTATGCGCTGCAGTATACC 57.851 50.000 23.09 6.78 43.65 2.73
500 1757 2.880963 TGTATGTATGCGCTGCAGTA 57.119 45.000 16.64 2.57 43.65 2.74
505 1763 2.204237 TCTGCTTGTATGTATGCGCTG 58.796 47.619 9.73 0.00 0.00 5.18
507 1765 3.548587 CATTCTGCTTGTATGTATGCGC 58.451 45.455 0.00 0.00 0.00 6.09
513 1771 6.543831 GGTTATCTTCCATTCTGCTTGTATGT 59.456 38.462 0.00 0.00 0.00 2.29
514 1772 6.543465 TGGTTATCTTCCATTCTGCTTGTATG 59.457 38.462 0.00 0.00 0.00 2.39
515 1773 6.543831 GTGGTTATCTTCCATTCTGCTTGTAT 59.456 38.462 0.00 0.00 37.30 2.29
522 1793 5.902681 TCTACGTGGTTATCTTCCATTCTG 58.097 41.667 0.00 0.00 37.30 3.02
524 1795 8.142551 AGTTATCTACGTGGTTATCTTCCATTC 58.857 37.037 0.00 0.00 37.30 2.67
535 1806 7.664758 ACAGTTAGAAAGTTATCTACGTGGTT 58.335 34.615 0.00 0.00 31.78 3.67
536 1807 7.176340 AGACAGTTAGAAAGTTATCTACGTGGT 59.824 37.037 0.00 0.00 31.78 4.16
537 1808 7.536855 AGACAGTTAGAAAGTTATCTACGTGG 58.463 38.462 0.00 0.00 31.78 4.94
554 1825 9.169592 GGCAAACCTTATTGTAATAGACAGTTA 57.830 33.333 0.00 0.00 39.88 2.24
555 1826 7.122204 GGGCAAACCTTATTGTAATAGACAGTT 59.878 37.037 0.00 0.00 36.27 3.16
556 1827 6.602009 GGGCAAACCTTATTGTAATAGACAGT 59.398 38.462 0.00 0.00 36.27 3.55
557 1828 6.238374 CGGGCAAACCTTATTGTAATAGACAG 60.238 42.308 0.00 0.00 36.79 3.51
558 1829 5.587043 CGGGCAAACCTTATTGTAATAGACA 59.413 40.000 0.00 0.00 36.97 3.41
559 1830 5.818857 TCGGGCAAACCTTATTGTAATAGAC 59.181 40.000 0.00 0.00 36.97 2.59
560 1831 5.818857 GTCGGGCAAACCTTATTGTAATAGA 59.181 40.000 0.00 0.00 36.97 1.98
561 1832 5.820947 AGTCGGGCAAACCTTATTGTAATAG 59.179 40.000 0.00 0.00 36.97 1.73
562 1833 5.747342 AGTCGGGCAAACCTTATTGTAATA 58.253 37.500 0.00 0.00 36.97 0.98
563 1834 4.595986 AGTCGGGCAAACCTTATTGTAAT 58.404 39.130 0.00 0.00 36.97 1.89
564 1835 4.004982 GAGTCGGGCAAACCTTATTGTAA 58.995 43.478 0.00 0.00 36.97 2.41
565 1836 3.602483 GAGTCGGGCAAACCTTATTGTA 58.398 45.455 0.00 0.00 36.97 2.41
566 1837 2.433436 GAGTCGGGCAAACCTTATTGT 58.567 47.619 0.00 0.00 36.97 2.71
568 1839 1.677820 CGGAGTCGGGCAAACCTTATT 60.678 52.381 0.00 0.00 36.97 1.40
569 1840 0.107848 CGGAGTCGGGCAAACCTTAT 60.108 55.000 0.00 0.00 36.97 1.73
570 1841 1.294138 CGGAGTCGGGCAAACCTTA 59.706 57.895 0.00 0.00 36.97 2.69
581 1852 1.141881 CCCTTCATCACCGGAGTCG 59.858 63.158 9.46 0.00 0.00 4.18
582 1853 1.522569 CCCCTTCATCACCGGAGTC 59.477 63.158 9.46 0.00 0.00 3.36
583 1854 2.670148 GCCCCTTCATCACCGGAGT 61.670 63.158 9.46 0.00 0.00 3.85
584 1855 2.190578 GCCCCTTCATCACCGGAG 59.809 66.667 9.46 0.00 0.00 4.63
585 1856 3.781307 CGCCCCTTCATCACCGGA 61.781 66.667 9.46 0.00 0.00 5.14
586 1857 3.106986 ATCGCCCCTTCATCACCGG 62.107 63.158 0.00 0.00 0.00 5.28
587 1858 1.889105 CATCGCCCCTTCATCACCG 60.889 63.158 0.00 0.00 0.00 4.94
588 1859 0.815615 GTCATCGCCCCTTCATCACC 60.816 60.000 0.00 0.00 0.00 4.02
589 1860 1.154205 CGTCATCGCCCCTTCATCAC 61.154 60.000 0.00 0.00 0.00 3.06
591 1862 1.595382 CCGTCATCGCCCCTTCATC 60.595 63.158 0.00 0.00 35.54 2.92
592 1863 2.505982 CCGTCATCGCCCCTTCAT 59.494 61.111 0.00 0.00 35.54 2.57
593 1864 4.467084 GCCGTCATCGCCCCTTCA 62.467 66.667 0.00 0.00 35.54 3.02
616 1887 0.098376 CATTGAAGCGAGCAGAAGGC 59.902 55.000 0.00 0.00 45.30 4.35
617 1888 0.098376 GCATTGAAGCGAGCAGAAGG 59.902 55.000 0.00 0.00 0.00 3.46
618 1889 1.085091 AGCATTGAAGCGAGCAGAAG 58.915 50.000 0.00 0.00 40.15 2.85
619 1890 1.527034 AAGCATTGAAGCGAGCAGAA 58.473 45.000 0.00 0.00 40.15 3.02
620 1891 3.238232 AAGCATTGAAGCGAGCAGA 57.762 47.368 0.00 0.00 40.15 4.26
632 1903 2.422479 TCTAGCGACGACTACAAGCATT 59.578 45.455 0.00 0.00 0.00 3.56
633 1904 2.014857 TCTAGCGACGACTACAAGCAT 58.985 47.619 0.00 0.00 0.00 3.79
634 1905 1.445871 TCTAGCGACGACTACAAGCA 58.554 50.000 0.00 0.00 0.00 3.91
635 1906 2.376956 CATCTAGCGACGACTACAAGC 58.623 52.381 0.00 0.00 0.00 4.01
636 1907 2.355132 ACCATCTAGCGACGACTACAAG 59.645 50.000 0.00 0.00 0.00 3.16
637 1908 2.353889 GACCATCTAGCGACGACTACAA 59.646 50.000 0.00 0.00 0.00 2.41
638 1909 1.938577 GACCATCTAGCGACGACTACA 59.061 52.381 0.00 0.00 0.00 2.74
639 1910 1.263752 GGACCATCTAGCGACGACTAC 59.736 57.143 0.00 0.00 0.00 2.73
640 1911 1.134310 TGGACCATCTAGCGACGACTA 60.134 52.381 0.00 0.00 0.00 2.59
641 1912 0.393944 TGGACCATCTAGCGACGACT 60.394 55.000 0.00 0.00 0.00 4.18
642 1913 0.669077 ATGGACCATCTAGCGACGAC 59.331 55.000 0.00 0.00 0.00 4.34
643 1914 2.152016 CTATGGACCATCTAGCGACGA 58.848 52.381 11.17 0.00 0.00 4.20
644 1915 2.095668 GTCTATGGACCATCTAGCGACG 60.096 54.545 11.17 0.00 36.53 5.12
645 1916 3.562567 GTCTATGGACCATCTAGCGAC 57.437 52.381 11.17 7.50 36.53 5.19
680 1951 8.191446 GCAGTACAGAGAACACAAGAGATAATA 58.809 37.037 0.00 0.00 0.00 0.98
681 1952 7.038659 GCAGTACAGAGAACACAAGAGATAAT 58.961 38.462 0.00 0.00 0.00 1.28
682 1953 6.390721 GCAGTACAGAGAACACAAGAGATAA 58.609 40.000 0.00 0.00 0.00 1.75
683 1954 5.105716 GGCAGTACAGAGAACACAAGAGATA 60.106 44.000 0.00 0.00 0.00 1.98
684 1955 4.322349 GGCAGTACAGAGAACACAAGAGAT 60.322 45.833 0.00 0.00 0.00 2.75
685 1956 3.005897 GGCAGTACAGAGAACACAAGAGA 59.994 47.826 0.00 0.00 0.00 3.10
686 1957 3.243873 TGGCAGTACAGAGAACACAAGAG 60.244 47.826 0.00 0.00 0.00 2.85
687 1958 2.698274 TGGCAGTACAGAGAACACAAGA 59.302 45.455 0.00 0.00 0.00 3.02
688 1959 3.111853 TGGCAGTACAGAGAACACAAG 57.888 47.619 0.00 0.00 0.00 3.16
689 1960 3.070878 TCATGGCAGTACAGAGAACACAA 59.929 43.478 0.00 0.00 0.00 3.33
690 1961 2.632512 TCATGGCAGTACAGAGAACACA 59.367 45.455 0.00 0.00 0.00 3.72
691 1962 3.319137 TCATGGCAGTACAGAGAACAC 57.681 47.619 0.00 0.00 0.00 3.32
692 1963 3.429410 CGATCATGGCAGTACAGAGAACA 60.429 47.826 0.00 0.00 0.00 3.18
693 1964 3.119291 CGATCATGGCAGTACAGAGAAC 58.881 50.000 0.00 0.00 0.00 3.01
695 1966 2.654863 TCGATCATGGCAGTACAGAGA 58.345 47.619 0.00 0.00 0.00 3.10
698 1969 3.375782 TCATCGATCATGGCAGTACAG 57.624 47.619 0.00 0.00 32.64 2.74
700 1971 5.714047 TCTATTCATCGATCATGGCAGTAC 58.286 41.667 0.00 0.00 32.64 2.73
702 1973 4.879197 TCTATTCATCGATCATGGCAGT 57.121 40.909 0.00 0.00 32.64 4.40
703 1974 5.873164 TCAATCTATTCATCGATCATGGCAG 59.127 40.000 0.00 0.00 32.64 4.85
746 2017 6.025280 GTCAAACATGTCTACGTGTGTTTTT 58.975 36.000 8.65 0.00 44.64 1.94
750 2021 3.128349 GGTCAAACATGTCTACGTGTGT 58.872 45.455 8.65 0.49 44.64 3.72
751 2022 3.390135 AGGTCAAACATGTCTACGTGTG 58.610 45.455 8.65 0.00 44.64 3.82
847 2271 1.276622 TGCTTGGAGAGGGTTAGGAC 58.723 55.000 0.00 0.00 0.00 3.85
848 2272 2.270434 ATGCTTGGAGAGGGTTAGGA 57.730 50.000 0.00 0.00 0.00 2.94
850 2274 3.691609 GTCAAATGCTTGGAGAGGGTTAG 59.308 47.826 0.00 0.00 33.01 2.34
851 2275 3.561313 GGTCAAATGCTTGGAGAGGGTTA 60.561 47.826 0.00 0.00 33.01 2.85
852 2276 2.519013 GTCAAATGCTTGGAGAGGGTT 58.481 47.619 0.00 0.00 33.01 4.11
866 2291 1.818674 GGCGTCAAATCTGGGTCAAAT 59.181 47.619 0.00 0.00 0.00 2.32
876 2301 1.025041 GAATGGGGAGGCGTCAAATC 58.975 55.000 8.91 0.00 0.00 2.17
920 2345 0.374410 CGTGTTTTTATACGGGCCGG 59.626 55.000 31.78 12.53 36.71 6.13
921 2346 3.881783 CGTGTTTTTATACGGGCCG 57.118 52.632 27.06 27.06 36.71 6.13
994 2429 1.739035 CGACATGGTAAGCATCGGTGT 60.739 52.381 0.00 0.00 0.00 4.16
995 2430 0.930310 CGACATGGTAAGCATCGGTG 59.070 55.000 0.00 0.00 0.00 4.94
996 2431 0.810031 GCGACATGGTAAGCATCGGT 60.810 55.000 0.00 0.00 33.45 4.69
998 2433 1.559814 CGCGACATGGTAAGCATCG 59.440 57.895 0.00 0.00 35.91 3.84
999 2434 1.276844 GCGCGACATGGTAAGCATC 59.723 57.895 12.10 0.00 0.00 3.91
1386 2846 3.313007 CTCGTCGAACGGGTACGCA 62.313 63.158 10.84 0.00 46.04 5.24
2099 3588 3.007635 CTCCTAATCCAACCAAACCGAC 58.992 50.000 0.00 0.00 0.00 4.79
2111 3600 9.120538 GATCATCTAGTGAGTATCTCCTAATCC 57.879 40.741 0.00 0.00 40.92 3.01
2112 3601 9.679661 TGATCATCTAGTGAGTATCTCCTAATC 57.320 37.037 0.00 0.00 40.92 1.75
2126 3615 3.305539 GGAGCTGAGCTGATCATCTAGTG 60.306 52.174 13.71 0.00 39.88 2.74
2127 3616 2.892852 GGAGCTGAGCTGATCATCTAGT 59.107 50.000 13.71 0.00 39.88 2.57
2128 3617 3.159472 AGGAGCTGAGCTGATCATCTAG 58.841 50.000 13.71 0.00 39.88 2.43
2130 3619 2.091098 AGGAGCTGAGCTGATCATCT 57.909 50.000 13.71 0.00 39.88 2.90
2131 3620 2.366266 AGAAGGAGCTGAGCTGATCATC 59.634 50.000 13.71 3.96 39.88 2.92
2132 3621 2.400573 AGAAGGAGCTGAGCTGATCAT 58.599 47.619 13.71 0.00 39.88 2.45
2133 3622 1.863325 AGAAGGAGCTGAGCTGATCA 58.137 50.000 13.71 0.00 39.88 2.92
2134 3623 2.985957 AAGAAGGAGCTGAGCTGATC 57.014 50.000 13.71 7.17 39.88 2.92
2135 3624 3.244840 ACAAAAGAAGGAGCTGAGCTGAT 60.245 43.478 13.71 0.00 39.88 2.90
2136 3625 2.105477 ACAAAAGAAGGAGCTGAGCTGA 59.895 45.455 13.71 0.00 39.88 4.26
2137 3626 2.502295 ACAAAAGAAGGAGCTGAGCTG 58.498 47.619 13.71 0.00 39.88 4.24
2138 3627 2.883386 CAACAAAAGAAGGAGCTGAGCT 59.117 45.455 6.69 6.69 43.88 4.09
2139 3628 2.880890 TCAACAAAAGAAGGAGCTGAGC 59.119 45.455 0.00 0.00 0.00 4.26
2140 3629 5.009410 ACAATCAACAAAAGAAGGAGCTGAG 59.991 40.000 0.00 0.00 0.00 3.35
2141 3630 4.889409 ACAATCAACAAAAGAAGGAGCTGA 59.111 37.500 0.00 0.00 0.00 4.26
2173 3662 8.995220 TGCACGAACACTCTAATTAATTAAAGT 58.005 29.630 8.16 8.16 0.00 2.66
2270 3766 8.927675 TCCATTAGGAGTAGAGATTAAGAGAC 57.072 38.462 0.00 0.00 39.61 3.36
2429 3927 1.069668 AGGGTGACGCGAAACTAAACT 59.930 47.619 15.93 5.32 0.00 2.66


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

AutoCloner maintained by Alex Coulton.