Multiple sequence alignment - TraesCS2A01G508200

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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 TraesCS2A01G508200 chr2A 100.000 7402 0 0 1 7402 734885883 734893284 0.000000e+00 13670.0
1 TraesCS2A01G508200 chr2A 83.954 966 103 29 6462 7402 734912155 734913093 0.000000e+00 878.0
2 TraesCS2A01G508200 chr2A 90.363 633 60 1 6771 7402 735398342 735397710 0.000000e+00 830.0
3 TraesCS2A01G508200 chr2A 85.627 327 42 3 4060 4386 731544355 731544676 9.200000e-89 339.0
4 TraesCS2A01G508200 chr2A 83.942 137 17 4 3288 3423 731544084 731544216 7.800000e-25 126.0
5 TraesCS2A01G508200 chr2D 92.926 2375 120 31 3595 5944 601598951 601601302 0.000000e+00 3411.0
6 TraesCS2A01G508200 chr2D 95.688 1461 59 4 5946 7402 601601352 601602812 0.000000e+00 2346.0
7 TraesCS2A01G508200 chr2D 89.665 1432 78 32 353 1750 601595817 601597212 0.000000e+00 1760.0
8 TraesCS2A01G508200 chr2D 87.633 849 97 7 6557 7402 601657397 601658240 0.000000e+00 979.0
9 TraesCS2A01G508200 chr2D 87.834 748 55 21 1742 2477 601597239 601597962 0.000000e+00 845.0
10 TraesCS2A01G508200 chr2D 88.075 696 72 9 6716 7400 601962935 601963630 0.000000e+00 815.0
11 TraesCS2A01G508200 chr2D 91.436 362 24 3 1 360 601595277 601595633 2.400000e-134 490.0
12 TraesCS2A01G508200 chr2D 84.424 443 30 15 2519 2936 601598096 601598524 4.160000e-107 399.0
13 TraesCS2A01G508200 chr2D 81.944 288 19 9 3008 3274 601598655 601598930 5.820000e-51 213.0
14 TraesCS2A01G508200 chr2B 93.985 1995 90 18 3971 5944 731892984 731894969 0.000000e+00 2992.0
15 TraesCS2A01G508200 chr2B 94.494 1471 63 7 5946 7402 731895019 731896485 0.000000e+00 2252.0
16 TraesCS2A01G508200 chr2B 91.901 1457 68 23 15 1442 731888974 731890409 0.000000e+00 1991.0
17 TraesCS2A01G508200 chr2B 83.295 1736 119 73 1633 3274 731890548 731892206 0.000000e+00 1441.0
18 TraesCS2A01G508200 chr2B 86.627 845 92 13 6561 7402 732012197 732013023 0.000000e+00 915.0
19 TraesCS2A01G508200 chr2B 86.052 846 96 13 6561 7402 732016963 732017790 0.000000e+00 889.0
20 TraesCS2A01G508200 chr2B 91.304 621 51 2 6771 7391 732038688 732039305 0.000000e+00 845.0
21 TraesCS2A01G508200 chr2B 84.882 635 57 14 3273 3892 731892380 731892990 8.210000e-169 604.0
22 TraesCS2A01G508200 chr2B 81.790 637 59 16 3273 3872 523684221 523684837 1.440000e-131 481.0
23 TraesCS2A01G508200 chr2B 95.652 46 2 0 3273 3318 523684185 523684230 2.860000e-09 75.0
24 TraesCS2A01G508200 chrUn 91.009 634 52 3 6771 7402 379978999 379978369 0.000000e+00 850.0
25 TraesCS2A01G508200 chrUn 87.844 691 78 5 6714 7402 15279790 15279104 0.000000e+00 806.0
26 TraesCS2A01G508200 chr7B 83.790 839 109 12 5000 5817 674306577 674307409 0.000000e+00 771.0
27 TraesCS2A01G508200 chr7B 84.006 619 59 18 3273 3872 31062205 31062802 6.490000e-155 558.0
28 TraesCS2A01G508200 chr7B 83.529 340 51 4 4245 4584 674305954 674306288 5.580000e-81 313.0
29 TraesCS2A01G508200 chr7B 87.160 257 33 0 1143 1399 674304234 674304490 7.260000e-75 292.0
30 TraesCS2A01G508200 chr7B 81.734 323 54 4 6234 6555 674310020 674310338 1.580000e-66 265.0
31 TraesCS2A01G508200 chr7B 80.217 369 46 13 2129 2478 674305363 674305723 1.230000e-62 252.0
32 TraesCS2A01G508200 chr7B 84.483 232 32 3 4676 4905 674306326 674306555 7.470000e-55 226.0
33 TraesCS2A01G508200 chr7D 82.936 838 116 15 5000 5817 596237882 596238712 0.000000e+00 730.0
34 TraesCS2A01G508200 chr7D 87.302 252 32 0 1148 1399 596234340 596234591 9.400000e-74 289.0
35 TraesCS2A01G508200 chr7D 82.243 321 53 3 6235 6555 596241021 596241337 2.630000e-69 274.0
36 TraesCS2A01G508200 chr7D 84.211 266 35 5 4676 4939 596237622 596237882 1.230000e-62 252.0
37 TraesCS2A01G508200 chr7D 84.956 226 28 3 1794 2013 596235160 596235385 2.690000e-54 224.0
38 TraesCS2A01G508200 chr7D 77.747 364 54 12 2132 2477 596235489 596235843 1.630000e-46 198.0
39 TraesCS2A01G508200 chr7D 93.878 49 3 0 1346 1394 51428912 51428960 2.860000e-09 75.0
40 TraesCS2A01G508200 chr7A 82.966 816 117 10 5017 5814 689320372 689321183 0.000000e+00 717.0
41 TraesCS2A01G508200 chr7A 88.492 252 29 0 1148 1399 689315823 689316074 9.330000e-79 305.0
42 TraesCS2A01G508200 chr7A 83.835 266 36 5 4676 4939 689320097 689320357 5.740000e-61 246.0
43 TraesCS2A01G508200 chr7A 78.904 365 50 13 2132 2478 689316988 689317343 9.670000e-54 222.0
44 TraesCS2A01G508200 chr7A 93.878 49 3 0 1346 1394 53906854 53906902 2.860000e-09 75.0
45 TraesCS2A01G508200 chr4D 81.304 230 35 7 1797 2022 446137936 446138161 5.900000e-41 180.0
46 TraesCS2A01G508200 chr4D 76.020 196 33 11 1211 1397 446137580 446137770 1.020000e-13 89.8
47 TraesCS2A01G508200 chr4A 80.973 226 36 7 1800 2022 21219907 21219686 9.870000e-39 172.0
48 TraesCS2A01G508200 chr4A 75.648 193 39 7 1211 1397 21220238 21220048 1.020000e-13 89.8
49 TraesCS2A01G508200 chr4A 93.878 49 3 0 1346 1394 665628434 665628386 2.860000e-09 75.0
50 TraesCS2A01G508200 chr4B 80.531 226 37 6 1800 2022 558044762 558044983 4.590000e-37 167.0
51 TraesCS2A01G508200 chr4B 76.166 193 38 7 1211 1397 558044402 558044592 2.200000e-15 95.3
52 TraesCS2A01G508200 chr3D 76.596 188 37 7 1214 1397 397213427 397213243 6.110000e-16 97.1


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 TraesCS2A01G508200 chr2A 734885883 734893284 7401 False 13670.000000 13670 100.00000 1 7402 1 chr2A.!!$F1 7401
1 TraesCS2A01G508200 chr2A 734912155 734913093 938 False 878.000000 878 83.95400 6462 7402 1 chr2A.!!$F2 940
2 TraesCS2A01G508200 chr2A 735397710 735398342 632 True 830.000000 830 90.36300 6771 7402 1 chr2A.!!$R1 631
3 TraesCS2A01G508200 chr2A 731544084 731544676 592 False 232.500000 339 84.78450 3288 4386 2 chr2A.!!$F3 1098
4 TraesCS2A01G508200 chr2D 601595277 601602812 7535 False 1352.000000 3411 89.13100 1 7402 7 chr2D.!!$F3 7401
5 TraesCS2A01G508200 chr2D 601657397 601658240 843 False 979.000000 979 87.63300 6557 7402 1 chr2D.!!$F1 845
6 TraesCS2A01G508200 chr2D 601962935 601963630 695 False 815.000000 815 88.07500 6716 7400 1 chr2D.!!$F2 684
7 TraesCS2A01G508200 chr2B 731888974 731896485 7511 False 1856.000000 2992 89.71140 15 7402 5 chr2B.!!$F3 7387
8 TraesCS2A01G508200 chr2B 732012197 732017790 5593 False 902.000000 915 86.33950 6561 7402 2 chr2B.!!$F4 841
9 TraesCS2A01G508200 chr2B 732038688 732039305 617 False 845.000000 845 91.30400 6771 7391 1 chr2B.!!$F1 620
10 TraesCS2A01G508200 chr2B 523684185 523684837 652 False 278.000000 481 88.72100 3273 3872 2 chr2B.!!$F2 599
11 TraesCS2A01G508200 chrUn 379978369 379978999 630 True 850.000000 850 91.00900 6771 7402 1 chrUn.!!$R2 631
12 TraesCS2A01G508200 chrUn 15279104 15279790 686 True 806.000000 806 87.84400 6714 7402 1 chrUn.!!$R1 688
13 TraesCS2A01G508200 chr7B 31062205 31062802 597 False 558.000000 558 84.00600 3273 3872 1 chr7B.!!$F1 599
14 TraesCS2A01G508200 chr7B 674304234 674310338 6104 False 353.166667 771 83.48550 1143 6555 6 chr7B.!!$F2 5412
15 TraesCS2A01G508200 chr7D 596234340 596241337 6997 False 327.833333 730 83.23250 1148 6555 6 chr7D.!!$F2 5407
16 TraesCS2A01G508200 chr7A 689315823 689321183 5360 False 372.500000 717 83.54925 1148 5814 4 chr7A.!!$F2 4666

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
144 146 0.036294 AAGGGCGCTCTAACCTGTTC 60.036 55.0 11.98 0.0 34.17 3.18 F
2065 2640 0.031449 GGCCACGTCTCTCTCATAGC 59.969 60.0 0.00 0.0 0.00 2.97 F
2649 3371 0.455633 GTTCCGCTCAAATGCTGCTG 60.456 55.0 0.00 0.0 0.00 4.41 F
3085 4610 0.037605 GAAAAGAGACCGCGGGAGAA 60.038 55.0 31.76 0.0 0.00 2.87 F
3394 5970 0.106015 AAGCCCTTGAGCCACACTTT 60.106 50.0 0.00 0.0 0.00 2.66 F
3563 6149 0.813821 GGGTGCTGGCTTGAGAAATC 59.186 55.0 0.00 0.0 0.00 2.17 F
5237 7909 0.237761 GAGCAATCATCATCGCTGCC 59.762 55.0 0.00 0.0 34.12 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2644 0.031043 GTGCATGCACACACACACAT 59.969 50.0 39.12 0.00 45.53 3.21 R
2908 4371 0.539901 ATCTACCCATCGTCCTCCCG 60.540 60.0 0.00 0.00 0.00 5.14 R
3928 6556 0.588252 CGGTTGCAAGAGTGAGTTGG 59.412 55.0 0.00 0.00 0.00 3.77 R
5041 7709 0.813821 GCCATCAAGCTTTGGACCTC 59.186 55.0 19.41 0.00 34.81 3.85 R
5237 7909 1.143305 GATCGATCAGGCCAATGACG 58.857 55.0 20.52 7.95 30.46 4.35 R
5489 8181 3.147629 CTGAATCATCATCCTTGGCCTC 58.852 50.0 3.32 0.00 34.37 4.70 R
7054 12377 0.251354 GGCTGAAGATGCTGAGGTGA 59.749 55.0 0.00 0.00 0.00 4.02 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
25 27 8.888579 CCTTTTGAAGTTTCTTGTAGAGACTA 57.111 34.615 0.93 0.00 38.55 2.59
144 146 0.036294 AAGGGCGCTCTAACCTGTTC 60.036 55.000 11.98 0.00 34.17 3.18
198 200 5.234752 ACAACGACAATTGAGCTACATGTA 58.765 37.500 13.59 5.25 33.57 2.29
202 204 5.120208 ACGACAATTGAGCTACATGTAACAC 59.880 40.000 13.59 1.87 0.00 3.32
205 207 5.997746 ACAATTGAGCTACATGTAACACACT 59.002 36.000 13.59 0.00 0.00 3.55
311 314 5.518848 TTCCAAATCCGTAGATTAGCGTA 57.481 39.130 0.00 0.00 42.03 4.42
313 316 4.823442 TCCAAATCCGTAGATTAGCGTAGA 59.177 41.667 0.00 0.00 42.03 2.59
314 317 5.048921 TCCAAATCCGTAGATTAGCGTAGAG 60.049 44.000 0.00 0.00 42.03 2.43
315 318 5.278364 CCAAATCCGTAGATTAGCGTAGAGT 60.278 44.000 0.00 0.00 42.03 3.24
363 369 7.155328 CGCTTTATAGACCATTTGACTATCCT 58.845 38.462 0.00 0.00 0.00 3.24
367 565 8.798975 TTATAGACCATTTGACTATCCTCCTT 57.201 34.615 0.00 0.00 0.00 3.36
380 578 1.913419 TCCTCCTTTCCCGCTAATTGT 59.087 47.619 0.00 0.00 0.00 2.71
397 595 2.613026 TGTGTGTCGGATCAAAGTGT 57.387 45.000 0.00 0.00 0.00 3.55
398 596 2.209273 TGTGTGTCGGATCAAAGTGTG 58.791 47.619 0.00 0.00 0.00 3.82
488 693 8.888579 ATAGATGACACCGGAAATAACTAAAG 57.111 34.615 9.46 0.00 0.00 1.85
518 723 7.433537 AGGTAAAATATATATAGCGGCAGGT 57.566 36.000 1.45 0.00 0.00 4.00
632 837 1.062587 GCGGTGAATGTTTCTCCATCG 59.937 52.381 8.56 0.00 42.09 3.84
714 919 6.286758 TCTGTGCTTTTTGCCAAATTATTGA 58.713 32.000 0.00 0.00 42.00 2.57
727 932 1.502527 TTATTGAACGCCCCCACCCT 61.503 55.000 0.00 0.00 0.00 4.34
764 969 2.627863 TGTGTTGTCTTGTGTTGTGC 57.372 45.000 0.00 0.00 0.00 4.57
765 970 1.135831 TGTGTTGTCTTGTGTTGTGCG 60.136 47.619 0.00 0.00 0.00 5.34
766 971 1.135803 GTGTTGTCTTGTGTTGTGCGT 60.136 47.619 0.00 0.00 0.00 5.24
767 972 1.135831 TGTTGTCTTGTGTTGTGCGTG 60.136 47.619 0.00 0.00 0.00 5.34
911 1140 0.594028 CATATACGGACACACGCGCT 60.594 55.000 5.73 0.00 37.37 5.92
965 1198 1.875963 CTAGCAACAACCAAGGCCG 59.124 57.895 0.00 0.00 0.00 6.13
1008 1243 1.039856 AATAATTCCGCATGGTGGGC 58.960 50.000 0.00 0.00 36.30 5.36
1026 1261 3.550431 ATGAGCGGCGCCTATGGT 61.550 61.111 30.40 15.16 0.00 3.55
1107 1342 2.064581 GGAGGCCGTGATAGTGGGT 61.065 63.158 0.00 0.00 0.00 4.51
1332 1582 3.081409 TTGCCCGGCTACTCCCTC 61.081 66.667 11.61 0.00 0.00 4.30
1400 1650 2.389449 CCATCCCCCAGGCATGTCT 61.389 63.158 0.00 0.00 0.00 3.41
1424 1685 0.735471 CTCGATCTCCGCTCACTGAA 59.265 55.000 0.00 0.00 38.37 3.02
1439 1700 1.141053 ACTGAATAATCACTCCCGCCC 59.859 52.381 0.00 0.00 0.00 6.13
1440 1701 1.140852 CTGAATAATCACTCCCGCCCA 59.859 52.381 0.00 0.00 0.00 5.36
1451 1712 1.405463 CTCCCGCCCAAAAAGATTAGC 59.595 52.381 0.00 0.00 0.00 3.09
1459 1720 3.508762 CCAAAAAGATTAGCTGCTGCAG 58.491 45.455 24.80 24.80 42.74 4.41
1482 1743 7.462462 GCAGTTTCGGTCTAAATAGTCTTTACG 60.462 40.741 0.00 0.00 0.00 3.18
1489 1750 7.378995 CGGTCTAAATAGTCTTTACGAATGAGG 59.621 40.741 0.00 0.00 0.00 3.86
1500 1761 1.265905 ACGAATGAGGTTTGCGTTTCC 59.734 47.619 0.00 0.00 0.00 3.13
1514 1775 1.627879 GTTTCCGGTCGCACGTATAA 58.372 50.000 0.00 0.00 0.00 0.98
1542 1803 5.693961 TCCAAATGAGATATTTAGGCTGCA 58.306 37.500 0.50 0.00 0.00 4.41
1543 1804 5.766670 TCCAAATGAGATATTTAGGCTGCAG 59.233 40.000 10.11 10.11 0.00 4.41
1620 1884 3.656045 CAACCCGTGACCAACCGC 61.656 66.667 0.00 0.00 0.00 5.68
1710 1976 3.181499 CCGATCATAGGCCTATGTACGTC 60.181 52.174 38.03 31.56 42.57 4.34
1712 1978 4.201832 CGATCATAGGCCTATGTACGTCTC 60.202 50.000 39.33 27.02 42.57 3.36
1713 1979 3.072211 TCATAGGCCTATGTACGTCTCG 58.928 50.000 39.33 19.88 42.57 4.04
1715 1981 2.627515 AGGCCTATGTACGTCTCGTA 57.372 50.000 1.29 0.00 41.54 3.43
1718 1984 3.999663 AGGCCTATGTACGTCTCGTATAC 59.000 47.826 1.29 0.00 44.12 1.47
1734 2264 7.435488 GTCTCGTATACACATACATGCTTTTCT 59.565 37.037 3.32 0.00 37.47 2.52
1753 2318 8.697960 GCTTTTCTATTTATACCTAGCGTGTAC 58.302 37.037 0.00 0.00 0.00 2.90
1774 2339 4.882351 CGCGTACGTGCAAATAATTAAC 57.118 40.909 16.78 0.00 34.15 2.01
1779 2344 6.406042 GCGTACGTGCAAATAATTAACTGTAC 59.594 38.462 17.90 7.77 34.15 2.90
1784 2349 8.457866 CGTGCAAATAATTAACTGTACGTATG 57.542 34.615 21.78 0.00 41.18 2.39
1785 2350 8.111836 CGTGCAAATAATTAACTGTACGTATGT 58.888 33.333 21.78 0.00 41.18 2.29
2034 2609 2.562912 CGTACGTACGTGGCCTGT 59.437 61.111 33.95 5.22 44.13 4.00
2035 2610 1.512734 CGTACGTACGTGGCCTGTC 60.513 63.158 33.95 10.46 44.13 3.51
2036 2611 1.512734 GTACGTACGTGGCCTGTCG 60.513 63.158 30.25 9.18 0.00 4.35
2037 2612 2.689785 TACGTACGTGGCCTGTCGG 61.690 63.158 30.25 1.00 0.00 4.79
2038 2613 4.047059 CGTACGTGGCCTGTCGGT 62.047 66.667 7.22 0.00 0.00 4.69
2040 2615 2.598099 TACGTGGCCTGTCGGTCA 60.598 61.111 3.32 0.00 44.23 4.02
2064 2639 0.309302 CGGCCACGTCTCTCTCATAG 59.691 60.000 2.24 0.00 34.81 2.23
2065 2640 0.031449 GGCCACGTCTCTCTCATAGC 59.969 60.000 0.00 0.00 0.00 2.97
2066 2641 0.031449 GCCACGTCTCTCTCATAGCC 59.969 60.000 0.00 0.00 0.00 3.93
2069 2644 2.293170 CACGTCTCTCTCATAGCCTCA 58.707 52.381 0.00 0.00 0.00 3.86
2126 2704 4.009675 ACACGATAACAATGGATGTGCTT 58.990 39.130 0.00 0.00 42.99 3.91
2127 2705 4.142622 ACACGATAACAATGGATGTGCTTG 60.143 41.667 0.00 0.00 42.99 4.01
2316 2913 2.683933 AACGAGGTCCGGCCATCT 60.684 61.111 15.92 0.00 43.93 2.90
2317 2914 2.722201 AACGAGGTCCGGCCATCTC 61.722 63.158 15.92 5.60 43.93 2.75
2321 2918 1.306141 AGGTCCGGCCATCTCTCAA 60.306 57.895 15.92 0.00 40.61 3.02
2337 2951 4.099419 TCTCTCAACCGTACACATGCATAT 59.901 41.667 0.00 0.00 0.00 1.78
2367 2981 3.880846 GCACGGTGCATGCCTAGC 61.881 66.667 27.10 6.16 44.26 3.42
2368 2982 2.124983 CACGGTGCATGCCTAGCT 60.125 61.111 16.68 0.00 0.00 3.32
2370 2984 0.877649 CACGGTGCATGCCTAGCTAG 60.878 60.000 16.68 14.20 0.00 3.42
2371 2985 1.043116 ACGGTGCATGCCTAGCTAGA 61.043 55.000 22.70 3.20 0.00 2.43
2507 3207 2.515057 GTGGTGCACCGTTGACCA 60.515 61.111 30.07 8.73 39.43 4.02
2627 3349 4.853050 GATCGGCCTGCTGCTGCT 62.853 66.667 17.00 0.00 46.56 4.24
2632 3354 3.292936 GCCTGCTGCTGCTGTGTT 61.293 61.111 17.00 0.00 40.48 3.32
2633 3355 2.952245 CCTGCTGCTGCTGTGTTC 59.048 61.111 17.00 0.00 40.48 3.18
2636 3358 4.395583 GCTGCTGCTGTGTTCCGC 62.396 66.667 8.53 0.00 36.03 5.54
2637 3359 2.667536 CTGCTGCTGTGTTCCGCT 60.668 61.111 0.00 0.00 0.00 5.52
2638 3360 2.666190 TGCTGCTGTGTTCCGCTC 60.666 61.111 0.00 0.00 0.00 5.03
2642 3364 0.877071 CTGCTGTGTTCCGCTCAAAT 59.123 50.000 0.00 0.00 0.00 2.32
2643 3365 0.592637 TGCTGTGTTCCGCTCAAATG 59.407 50.000 0.00 0.00 0.00 2.32
2645 3367 0.877071 CTGTGTTCCGCTCAAATGCT 59.123 50.000 0.00 0.00 0.00 3.79
2646 3368 0.592637 TGTGTTCCGCTCAAATGCTG 59.407 50.000 0.00 0.00 0.00 4.41
2647 3369 0.730494 GTGTTCCGCTCAAATGCTGC 60.730 55.000 0.00 0.00 0.00 5.25
2648 3370 0.890542 TGTTCCGCTCAAATGCTGCT 60.891 50.000 0.00 0.00 0.00 4.24
2649 3371 0.455633 GTTCCGCTCAAATGCTGCTG 60.456 55.000 0.00 0.00 0.00 4.41
2650 3372 2.202570 CCGCTCAAATGCTGCTGC 60.203 61.111 8.89 8.89 40.20 5.25
2652 3374 1.514228 CGCTCAAATGCTGCTGCTG 60.514 57.895 17.00 7.03 40.48 4.41
2653 3375 1.805945 GCTCAAATGCTGCTGCTGC 60.806 57.895 22.51 22.51 40.48 5.25
2740 3559 3.673746 ATCATTATTGCGTTGTCCGTG 57.326 42.857 0.00 0.00 39.32 4.94
2798 4231 4.088762 GTACGTGCCGTCGGTCGA 62.089 66.667 27.64 14.42 41.54 4.20
2852 4311 1.507141 GCCAGGCCACATATGTACGC 61.507 60.000 8.32 12.75 0.00 4.42
2869 4332 1.403225 CGCATGTGGTCGTAGTCGTG 61.403 60.000 0.00 0.00 38.33 4.35
2908 4371 1.409064 TGCATATCTCACTCCGTCCAC 59.591 52.381 0.00 0.00 0.00 4.02
2970 4460 1.705337 GGTGAACGGATGGATGCACG 61.705 60.000 0.00 0.00 0.00 5.34
2977 4467 4.552365 ATGGATGCACGCCTCCGG 62.552 66.667 8.55 0.00 39.22 5.14
2996 4486 2.096119 CGGCAGTGTTTTACTTTACCCG 60.096 50.000 0.00 0.00 37.60 5.28
3077 4600 2.471743 GTCGTGTTCAGAAAAGAGACCG 59.528 50.000 0.00 0.00 0.00 4.79
3085 4610 0.037605 GAAAAGAGACCGCGGGAGAA 60.038 55.000 31.76 0.00 0.00 2.87
3090 4615 1.636570 GAGACCGCGGGAGAAAAAGC 61.637 60.000 31.76 6.61 0.00 3.51
3146 4689 0.320771 AAGTGGTCATCCGCAGTGAC 60.321 55.000 0.00 4.93 45.81 3.67
3200 4743 1.617947 CCACTCCCAGTCCCAGCTAC 61.618 65.000 0.00 0.00 0.00 3.58
3203 4746 1.965754 CTCCCAGTCCCAGCTACTGC 61.966 65.000 9.27 0.00 42.47 4.40
3212 4755 0.737715 CCAGCTACTGCGACCTTCAC 60.738 60.000 0.00 0.00 45.42 3.18
3228 4771 2.245159 TCACTTCACTGAACCTGCAG 57.755 50.000 6.78 6.78 41.63 4.41
3229 4772 0.590195 CACTTCACTGAACCTGCAGC 59.410 55.000 8.66 0.00 39.51 5.25
3230 4773 0.181114 ACTTCACTGAACCTGCAGCA 59.819 50.000 8.66 0.00 39.51 4.41
3231 4774 1.202855 ACTTCACTGAACCTGCAGCAT 60.203 47.619 8.66 0.00 39.51 3.79
3232 4775 1.884579 CTTCACTGAACCTGCAGCATT 59.115 47.619 8.66 4.47 39.51 3.56
3233 4776 1.527034 TCACTGAACCTGCAGCATTC 58.473 50.000 17.66 17.66 39.51 2.67
3234 4777 1.072806 TCACTGAACCTGCAGCATTCT 59.927 47.619 22.33 7.39 39.51 2.40
3235 4778 2.302733 TCACTGAACCTGCAGCATTCTA 59.697 45.455 22.33 12.38 39.51 2.10
3236 4779 3.076621 CACTGAACCTGCAGCATTCTAA 58.923 45.455 22.33 8.73 39.51 2.10
3264 4807 2.148768 TGCACAGCTGAATCACTGAAG 58.851 47.619 23.35 10.49 37.35 3.02
3274 4817 9.299963 CAGCTGAATCACTGAAGCTATATATAC 57.700 37.037 8.42 0.00 44.00 1.47
3275 4818 9.253832 AGCTGAATCACTGAAGCTATATATACT 57.746 33.333 2.40 0.00 44.00 2.12
3320 5857 3.475566 TTGCTCTGTACTTCTGCAGTT 57.524 42.857 14.67 1.95 36.88 3.16
3325 5862 4.564769 GCTCTGTACTTCTGCAGTTACATC 59.435 45.833 14.67 8.30 36.88 3.06
3361 5937 7.175641 ACTGACCTCTTTCCAAATGAAATACTG 59.824 37.037 0.00 0.00 41.96 2.74
3368 5944 5.004361 TCCAAATGAAATACTGGTTGGGA 57.996 39.130 0.00 0.00 36.88 4.37
3378 5954 2.171003 ACTGGTTGGGAATAGCAAAGC 58.829 47.619 0.00 0.00 0.00 3.51
3387 5963 1.406898 GAATAGCAAAGCCCTTGAGCC 59.593 52.381 0.40 0.00 37.17 4.70
3388 5964 0.332632 ATAGCAAAGCCCTTGAGCCA 59.667 50.000 0.40 0.00 37.17 4.75
3390 5966 2.202395 GCAAAGCCCTTGAGCCACA 61.202 57.895 0.40 0.00 37.17 4.17
3391 5967 1.662044 CAAAGCCCTTGAGCCACAC 59.338 57.895 0.00 0.00 37.17 3.82
3394 5970 0.106015 AAGCCCTTGAGCCACACTTT 60.106 50.000 0.00 0.00 0.00 2.66
3395 5971 0.106015 AGCCCTTGAGCCACACTTTT 60.106 50.000 0.00 0.00 0.00 2.27
3396 5972 1.144913 AGCCCTTGAGCCACACTTTTA 59.855 47.619 0.00 0.00 0.00 1.52
3398 5974 2.562738 GCCCTTGAGCCACACTTTTAAT 59.437 45.455 0.00 0.00 0.00 1.40
3399 5975 3.761752 GCCCTTGAGCCACACTTTTAATA 59.238 43.478 0.00 0.00 0.00 0.98
3400 5976 4.142381 GCCCTTGAGCCACACTTTTAATAG 60.142 45.833 0.00 0.00 0.00 1.73
3401 5977 4.142381 CCCTTGAGCCACACTTTTAATAGC 60.142 45.833 0.00 0.00 0.00 2.97
3402 5978 4.142381 CCTTGAGCCACACTTTTAATAGCC 60.142 45.833 0.00 0.00 0.00 3.93
3405 5981 4.010349 GAGCCACACTTTTAATAGCCAGT 58.990 43.478 0.00 0.00 0.00 4.00
3430 6006 1.966451 GGCAACCCTGTCCAACTCG 60.966 63.158 0.00 0.00 0.00 4.18
3470 6048 1.702401 TGCTATGGGTTGGTCAGTTGA 59.298 47.619 0.00 0.00 0.00 3.18
3472 6050 2.684881 GCTATGGGTTGGTCAGTTGATG 59.315 50.000 0.00 0.00 0.00 3.07
3473 6051 2.978156 ATGGGTTGGTCAGTTGATGT 57.022 45.000 0.00 0.00 0.00 3.06
3474 6052 4.625324 GCTATGGGTTGGTCAGTTGATGTA 60.625 45.833 0.00 0.00 0.00 2.29
3475 6053 3.134574 TGGGTTGGTCAGTTGATGTAC 57.865 47.619 0.00 0.00 0.00 2.90
3476 6054 2.708861 TGGGTTGGTCAGTTGATGTACT 59.291 45.455 0.00 0.00 0.00 2.73
3477 6055 3.244422 TGGGTTGGTCAGTTGATGTACTC 60.244 47.826 0.00 0.00 0.00 2.59
3478 6056 3.008049 GGGTTGGTCAGTTGATGTACTCT 59.992 47.826 0.00 0.00 0.00 3.24
3479 6057 3.997021 GGTTGGTCAGTTGATGTACTCTG 59.003 47.826 0.00 0.00 0.00 3.35
3492 6070 5.301805 TGATGTACTCTGAAACTGACAGACA 59.698 40.000 10.08 5.63 39.10 3.41
3494 6072 5.348986 TGTACTCTGAAACTGACAGACAAC 58.651 41.667 10.08 2.90 39.10 3.32
3539 6125 4.656041 GCATTCTTGCTGTATGACTGAAC 58.344 43.478 3.90 0.00 45.77 3.18
3563 6149 0.813821 GGGTGCTGGCTTGAGAAATC 59.186 55.000 0.00 0.00 0.00 2.17
3690 6302 0.879090 ATTTCGGTTCCTCGGCAAAC 59.121 50.000 0.00 0.00 0.00 2.93
3777 6389 4.020751 TCTGCAGCTACATCTTCTTTCAGT 60.021 41.667 9.47 0.00 0.00 3.41
3795 6407 4.957296 TCAGTACTGACCTCTTTCCAAAC 58.043 43.478 21.74 0.00 34.14 2.93
3799 6411 3.467803 ACTGACCTCTTTCCAAACGAAG 58.532 45.455 0.00 0.00 0.00 3.79
3801 6413 4.202367 ACTGACCTCTTTCCAAACGAAGAT 60.202 41.667 0.00 0.00 31.97 2.40
3803 6415 4.755123 TGACCTCTTTCCAAACGAAGATTC 59.245 41.667 0.00 0.00 31.97 2.52
3834 6446 8.951243 AGAATAATAAAAGGTCTTGAGCACTTC 58.049 33.333 2.64 0.00 0.00 3.01
3928 6556 8.173542 TCCATTTCCAGAACCTAAAACTAAAC 57.826 34.615 0.00 0.00 0.00 2.01
3995 6623 2.924105 GCTGCTGGCAACCTTGTCC 61.924 63.158 0.00 0.00 41.35 4.02
3997 6625 1.521450 CTGCTGGCAACCTTGTCCAG 61.521 60.000 17.42 17.42 46.18 3.86
3999 6627 2.203480 TGGCAACCTTGTCCAGCC 60.203 61.111 0.00 0.00 45.41 4.85
4011 6639 1.026718 GTCCAGCCCGGTTCATTCTG 61.027 60.000 0.00 0.00 35.57 3.02
4037 6665 7.548967 AGTAGTAGTAAAGTTCTTGAGGCATC 58.451 38.462 0.00 0.00 0.00 3.91
4040 6668 4.583871 AGTAAAGTTCTTGAGGCATCCTG 58.416 43.478 0.00 0.00 31.76 3.86
4041 6669 3.515602 AAAGTTCTTGAGGCATCCTGT 57.484 42.857 0.00 0.00 31.76 4.00
4042 6670 4.640771 AAAGTTCTTGAGGCATCCTGTA 57.359 40.909 0.00 0.00 31.76 2.74
4043 6671 3.618690 AGTTCTTGAGGCATCCTGTAC 57.381 47.619 0.00 0.00 31.76 2.90
4044 6672 3.177228 AGTTCTTGAGGCATCCTGTACT 58.823 45.455 0.00 0.00 31.76 2.73
4063 6704 7.707035 CCTGTACTTACCTACTTTGATAGCAAG 59.293 40.741 0.00 0.00 35.04 4.01
4129 6771 5.330455 TGTCTATGCTGAAACTGGTAGAG 57.670 43.478 0.00 0.00 0.00 2.43
4142 6784 8.977412 TGAAACTGGTAGAGAATTTTCCTTTTT 58.023 29.630 0.00 0.00 0.00 1.94
4237 6883 0.855349 GTCTGATATTCTGCGTGCGG 59.145 55.000 0.00 0.00 0.00 5.69
4288 6934 2.613133 GTTCTTCTGGATCTCAGCATGC 59.387 50.000 10.51 10.51 43.06 4.06
4312 6958 1.431488 CCTTGGCATCCGTCATCGTG 61.431 60.000 0.00 0.00 35.01 4.35
4451 7099 9.754382 GATGGCAAACAACAAATATATGAATCT 57.246 29.630 0.00 0.00 0.00 2.40
4587 7235 1.611977 TCATCTCCCTTACGGTATGCG 59.388 52.381 0.00 0.00 0.00 4.73
4660 7321 7.973944 ACTCTAACACACTTCAAATTGGAAAAC 59.026 33.333 0.00 0.00 0.00 2.43
4769 7437 1.403679 CTCTGACAGGAAGGAGTAGCG 59.596 57.143 1.81 0.00 0.00 4.26
4888 7556 2.923655 CGTGCTATGTGACAACAGGTAG 59.076 50.000 0.00 0.00 40.39 3.18
4943 7611 4.478206 TCCTCTTGCATTCCTTGTAGAG 57.522 45.455 1.54 1.54 36.66 2.43
4965 7633 5.189180 AGAAACTGAAGGATCAATACCTGC 58.811 41.667 0.00 0.00 37.85 4.85
4970 7638 3.069586 TGAAGGATCAATACCTGCGTAGG 59.930 47.826 18.97 18.97 40.46 3.18
5041 7709 5.320607 CATCATACGATGCACACAACTAG 57.679 43.478 0.00 0.00 42.54 2.57
5066 7738 2.840038 TCCAAAGCTTGATGGCTCTCTA 59.160 45.455 11.71 0.00 42.24 2.43
5237 7909 0.237761 GAGCAATCATCATCGCTGCC 59.762 55.000 0.00 0.00 34.12 4.85
5267 7939 1.372748 GATCGATCTCCCTGCTGCG 60.373 63.158 18.29 0.00 0.00 5.18
5489 8181 5.749596 TTAGGGTATTGATGCAAATCACG 57.250 39.130 0.00 0.00 0.00 4.35
5516 8208 3.895656 CAAGGATGATGATTCAGGGCAAT 59.104 43.478 0.00 0.00 34.73 3.56
5519 8211 5.507637 AGGATGATGATTCAGGGCAATATC 58.492 41.667 0.00 0.00 34.73 1.63
5645 8337 7.633789 ACACCAACTATCTGAATGAAAGGTAT 58.366 34.615 0.00 0.00 0.00 2.73
5771 8463 8.754080 TGAAAGTTCTTCAGGGAATAAACAAAA 58.246 29.630 0.00 0.00 0.00 2.44
5825 8517 3.560668 GGTTAGTGACCCCCGAGATTTTT 60.561 47.826 0.00 0.00 43.06 1.94
5826 8518 2.200373 AGTGACCCCCGAGATTTTTG 57.800 50.000 0.00 0.00 0.00 2.44
5827 8519 1.423921 AGTGACCCCCGAGATTTTTGT 59.576 47.619 0.00 0.00 0.00 2.83
5831 8523 3.068873 TGACCCCCGAGATTTTTGTTTTG 59.931 43.478 0.00 0.00 0.00 2.44
6059 11331 2.344592 TCCCTTTTTCAGCTGTCCCTA 58.655 47.619 14.67 0.00 0.00 3.53
6222 11506 8.311109 TCACAAGCTATCAGTTAAGTTATGTGA 58.689 33.333 4.46 4.46 39.70 3.58
6308 11596 5.006746 GGAGAAAATACAACGAGCGAATGAT 59.993 40.000 0.00 0.00 0.00 2.45
6333 11621 2.821378 CACAATCATTTCAGGCCAGACA 59.179 45.455 5.01 0.00 0.00 3.41
6350 11638 2.371841 AGACAGCCTGTATTTGACCACA 59.628 45.455 0.00 0.00 0.00 4.17
6411 11699 3.383505 GGCAACACCTTAGAGTGGTTTTT 59.616 43.478 5.98 0.00 42.28 1.94
6413 11701 4.338400 GCAACACCTTAGAGTGGTTTTTCT 59.662 41.667 5.98 0.00 42.28 2.52
6906 12229 3.616956 TGCTTCCCTTGTATGACTGAG 57.383 47.619 0.00 0.00 0.00 3.35
6918 12241 7.307632 CCTTGTATGACTGAGCATTTATAGCAC 60.308 40.741 0.00 0.00 0.00 4.40
7035 12358 9.744468 TTTCTTCACCTTTTAAACTTAAGCATC 57.256 29.630 1.29 0.00 0.00 3.91
7054 12377 3.777106 TCCTTCTGTGAGTCTTGCAAT 57.223 42.857 0.00 0.00 0.00 3.56
7145 12468 9.967451 TTATCCCTTATAAGTGACACAAAATGA 57.033 29.630 11.50 0.00 0.00 2.57
7260 12583 0.098025 GCTCTTCTCCGTGAGTCGAG 59.902 60.000 0.00 12.77 42.86 4.04
7275 12598 6.089283 CGTGAGTCGAGTGGTATAGTAGTATC 59.911 46.154 0.00 0.00 42.86 2.24
7393 12716 7.921786 TTGCTGTTAAAGTATCAGTAAGCAT 57.078 32.000 0.00 0.00 37.90 3.79
7394 12717 9.443323 TTTGCTGTTAAAGTATCAGTAAGCATA 57.557 29.630 0.00 0.00 37.90 3.14
7395 12718 9.613428 TTGCTGTTAAAGTATCAGTAAGCATAT 57.387 29.630 0.00 0.00 37.90 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 27 1.884464 CATGCGCACATACGAGGCT 60.884 57.895 14.90 0.00 33.67 4.58
144 146 1.102154 TGTTGGGCTTGTTCACACAG 58.898 50.000 0.00 0.00 33.22 3.66
198 200 3.632145 GGATCTTGTGGTTTCAGTGTGTT 59.368 43.478 0.00 0.00 0.00 3.32
202 204 3.077359 GAGGGATCTTGTGGTTTCAGTG 58.923 50.000 0.00 0.00 0.00 3.66
205 207 4.387026 AATGAGGGATCTTGTGGTTTCA 57.613 40.909 0.00 0.00 0.00 2.69
311 314 0.687354 AGGTGTTTCGGCATGACTCT 59.313 50.000 0.00 0.00 0.00 3.24
313 316 1.523758 GAAGGTGTTTCGGCATGACT 58.476 50.000 0.00 0.00 0.00 3.41
336 342 5.353394 AGTCAAATGGTCTATAAAGCGGA 57.647 39.130 0.00 0.00 0.00 5.54
363 369 2.224670 ACACACAATTAGCGGGAAAGGA 60.225 45.455 0.00 0.00 0.00 3.36
367 565 1.434555 CGACACACAATTAGCGGGAA 58.565 50.000 0.00 0.00 0.00 3.97
380 578 2.102420 AGACACACTTTGATCCGACACA 59.898 45.455 0.00 0.00 0.00 3.72
488 693 9.857957 GCCGCTATATATATTTTACCTATCTCC 57.142 37.037 0.00 0.00 0.00 3.71
502 707 4.381612 GCTTCACACCTGCCGCTATATATA 60.382 45.833 0.00 0.00 0.00 0.86
510 715 3.058160 ATGCTTCACACCTGCCGC 61.058 61.111 0.00 0.00 0.00 6.53
515 720 5.301551 TGAAAATTACACATGCTTCACACCT 59.698 36.000 0.00 0.00 0.00 4.00
518 723 7.036996 TCTTGAAAATTACACATGCTTCACA 57.963 32.000 0.00 0.00 0.00 3.58
632 837 1.947597 TTGATGCCGCCAATCCTTGC 61.948 55.000 0.00 0.00 0.00 4.01
643 848 1.265095 CGATCCTTGGATTTGATGCCG 59.735 52.381 3.43 0.00 0.00 5.69
672 877 6.093633 AGCACAGATAAATTCGTAGTTTTCCC 59.906 38.462 0.00 0.00 0.00 3.97
727 932 1.364269 CAACACAAGGGGGTAGGGTA 58.636 55.000 0.00 0.00 0.00 3.69
764 969 4.310769 AGAGAAGAATCAAAGGTGACACG 58.689 43.478 0.00 0.00 36.31 4.49
765 970 4.693095 GGAGAGAAGAATCAAAGGTGACAC 59.307 45.833 0.00 0.00 36.31 3.67
766 971 4.263068 GGGAGAGAAGAATCAAAGGTGACA 60.263 45.833 0.00 0.00 36.31 3.58
767 972 4.019771 AGGGAGAGAAGAATCAAAGGTGAC 60.020 45.833 0.00 0.00 36.31 3.67
955 1188 1.893919 GAGAGAGCTCGGCCTTGGTT 61.894 60.000 8.37 0.00 34.09 3.67
965 1198 2.202730 GCTGTGCCGAGAGAGCTC 60.203 66.667 5.27 5.27 37.81 4.09
985 1218 2.287788 CCACCATGCGGAATTATTGCTC 60.288 50.000 0.00 0.00 35.59 4.26
1008 1243 3.046087 CCATAGGCGCCGCTCATG 61.046 66.667 23.20 21.12 0.00 3.07
1332 1582 0.533032 GGTCGGACTTGAAGAGGGAG 59.467 60.000 8.23 0.00 0.00 4.30
1400 1650 3.758088 GAGCGGAGATCGAGCGCAA 62.758 63.158 11.47 0.00 42.43 4.85
1424 1685 2.818751 TTTTGGGCGGGAGTGATTAT 57.181 45.000 0.00 0.00 0.00 1.28
1439 1700 4.170292 ACTGCAGCAGCTAATCTTTTTG 57.830 40.909 23.05 0.00 42.74 2.44
1440 1701 4.861102 AACTGCAGCAGCTAATCTTTTT 57.139 36.364 23.05 2.73 42.74 1.94
1451 1712 1.795768 TTAGACCGAAACTGCAGCAG 58.204 50.000 21.54 21.54 37.52 4.24
1459 1720 8.452989 TTCGTAAAGACTATTTAGACCGAAAC 57.547 34.615 0.00 0.00 0.00 2.78
1500 1761 1.124297 GATGCATTATACGTGCGACCG 59.876 52.381 0.00 0.00 45.37 4.79
1514 1775 6.952358 AGCCTAAATATCTCATTTGGATGCAT 59.048 34.615 0.00 0.00 33.14 3.96
1542 1803 3.878778 CACAGGCTAGCTTCCAAATACT 58.121 45.455 15.72 0.00 0.00 2.12
1543 1804 2.356069 GCACAGGCTAGCTTCCAAATAC 59.644 50.000 15.72 0.00 36.96 1.89
1620 1884 1.521010 CAGGAGAGCACCATCAGCG 60.521 63.158 0.00 0.00 37.01 5.18
1710 1976 7.700322 AGAAAAGCATGTATGTGTATACGAG 57.300 36.000 0.00 0.00 41.68 4.18
1753 2318 4.428853 CAGTTAATTATTTGCACGTACGCG 59.571 41.667 16.72 3.53 44.93 6.01
1755 2320 6.616769 CGTACAGTTAATTATTTGCACGTACG 59.383 38.462 15.01 15.01 41.37 3.67
1780 2345 2.661675 CTGAGCACACACACGTACATAC 59.338 50.000 0.00 0.00 0.00 2.39
1782 2347 1.339929 TCTGAGCACACACACGTACAT 59.660 47.619 0.00 0.00 0.00 2.29
1783 2348 0.741915 TCTGAGCACACACACGTACA 59.258 50.000 0.00 0.00 0.00 2.90
1784 2349 2.065993 ATCTGAGCACACACACGTAC 57.934 50.000 0.00 0.00 0.00 3.67
1785 2350 2.672714 GAATCTGAGCACACACACGTA 58.327 47.619 0.00 0.00 0.00 3.57
1786 2351 1.502231 GAATCTGAGCACACACACGT 58.498 50.000 0.00 0.00 0.00 4.49
1787 2352 0.436150 CGAATCTGAGCACACACACG 59.564 55.000 0.00 0.00 0.00 4.49
1788 2353 1.723542 CTCGAATCTGAGCACACACAC 59.276 52.381 0.00 0.00 0.00 3.82
1789 2354 2.070262 CTCGAATCTGAGCACACACA 57.930 50.000 0.00 0.00 0.00 3.72
1797 2365 0.919981 GCACGAAGCTCGAATCTGAG 59.080 55.000 11.64 0.00 43.74 3.35
2024 2599 3.991051 CTGACCGACAGGCCACGT 61.991 66.667 5.01 0.00 42.39 4.49
2043 2618 4.500116 GAGAGAGACGTGGCCGGC 62.500 72.222 21.18 21.18 44.68 6.13
2046 2621 0.031449 GCTATGAGAGAGACGTGGCC 59.969 60.000 0.00 0.00 0.00 5.36
2064 2639 1.283793 GCACACACACACATGAGGC 59.716 57.895 0.00 0.00 0.00 4.70
2065 2640 1.068816 CATGCACACACACACATGAGG 60.069 52.381 0.00 0.00 41.93 3.86
2066 2641 1.664874 GCATGCACACACACACATGAG 60.665 52.381 14.21 0.00 41.93 2.90
2069 2644 0.031043 GTGCATGCACACACACACAT 59.969 50.000 39.12 0.00 45.53 3.21
2126 2704 0.618458 GATGAACCCCAGCCTACACA 59.382 55.000 0.00 0.00 0.00 3.72
2127 2705 0.618458 TGATGAACCCCAGCCTACAC 59.382 55.000 0.00 0.00 0.00 2.90
2310 2907 1.067142 TGTGTACGGTTGAGAGATGGC 60.067 52.381 0.00 0.00 0.00 4.40
2313 2910 2.233676 TGCATGTGTACGGTTGAGAGAT 59.766 45.455 0.00 0.00 0.00 2.75
2316 2913 2.760634 ATGCATGTGTACGGTTGAGA 57.239 45.000 0.00 0.00 0.00 3.27
2317 2914 3.303329 GCATATGCATGTGTACGGTTGAG 60.303 47.826 22.84 0.00 41.59 3.02
2367 2981 9.495754 GCACAAAAGAAAACATTAGCTATCTAG 57.504 33.333 0.00 0.00 0.00 2.43
2368 2982 9.008965 TGCACAAAAGAAAACATTAGCTATCTA 57.991 29.630 0.00 0.00 0.00 1.98
2370 2984 8.693542 ATGCACAAAAGAAAACATTAGCTATC 57.306 30.769 0.00 0.00 0.00 2.08
2371 2985 9.573133 GTATGCACAAAAGAAAACATTAGCTAT 57.427 29.630 0.00 0.00 0.00 2.97
2478 3108 2.986290 CACCACAGTGGCGGGATA 59.014 61.111 20.48 0.00 42.67 2.59
2617 3339 2.952245 GGAACACAGCAGCAGCAG 59.048 61.111 3.17 0.00 45.49 4.24
2618 3340 2.974148 CGGAACACAGCAGCAGCA 60.974 61.111 3.17 0.00 45.49 4.41
2619 3341 4.395583 GCGGAACACAGCAGCAGC 62.396 66.667 0.00 0.00 42.56 5.25
2620 3342 2.667536 AGCGGAACACAGCAGCAG 60.668 61.111 0.00 0.00 35.48 4.24
2621 3343 2.666190 GAGCGGAACACAGCAGCA 60.666 61.111 0.00 0.00 35.48 4.41
2622 3344 1.785041 TTTGAGCGGAACACAGCAGC 61.785 55.000 0.00 0.00 35.48 5.25
2623 3345 0.877071 ATTTGAGCGGAACACAGCAG 59.123 50.000 0.00 0.00 35.48 4.24
2624 3346 0.592637 CATTTGAGCGGAACACAGCA 59.407 50.000 0.00 0.00 35.48 4.41
2625 3347 0.730494 GCATTTGAGCGGAACACAGC 60.730 55.000 0.00 0.00 0.00 4.40
2627 3349 0.592637 CAGCATTTGAGCGGAACACA 59.407 50.000 0.00 0.00 40.15 3.72
2628 3350 0.730494 GCAGCATTTGAGCGGAACAC 60.730 55.000 0.00 0.00 40.15 3.32
2629 3351 0.890542 AGCAGCATTTGAGCGGAACA 60.891 50.000 0.00 0.00 40.15 3.18
2630 3352 0.455633 CAGCAGCATTTGAGCGGAAC 60.456 55.000 0.00 0.00 40.15 3.62
2631 3353 1.878070 CAGCAGCATTTGAGCGGAA 59.122 52.632 0.00 0.00 40.15 4.30
2632 3354 2.693762 GCAGCAGCATTTGAGCGGA 61.694 57.895 0.00 0.00 41.58 5.54
2633 3355 2.202570 GCAGCAGCATTTGAGCGG 60.203 61.111 0.00 0.00 41.58 5.52
2636 3358 0.456824 CAGCAGCAGCAGCATTTGAG 60.457 55.000 12.92 0.00 45.49 3.02
2637 3359 1.584495 CAGCAGCAGCAGCATTTGA 59.416 52.632 12.92 0.00 45.49 2.69
2638 3360 4.169102 CAGCAGCAGCAGCATTTG 57.831 55.556 12.92 0.00 45.49 2.32
2650 3372 2.459421 GAACACAGCAGCAGCAGCAG 62.459 60.000 12.92 6.60 45.49 4.24
2652 3374 2.254651 GAACACAGCAGCAGCAGC 59.745 61.111 3.17 0.46 45.49 5.25
2653 3375 2.952245 GGAACACAGCAGCAGCAG 59.048 61.111 3.17 0.00 45.49 4.24
2852 4311 0.242825 ACCACGACTACGACCACATG 59.757 55.000 0.00 0.00 42.66 3.21
2857 4316 0.727122 CAACGACCACGACTACGACC 60.727 60.000 0.00 0.00 42.66 4.79
2858 4317 0.235665 TCAACGACCACGACTACGAC 59.764 55.000 0.00 0.00 42.66 4.34
2859 4318 1.135888 CATCAACGACCACGACTACGA 60.136 52.381 0.00 0.00 42.66 3.43
2869 4332 1.524355 CATCTCGCATCATCAACGACC 59.476 52.381 0.00 0.00 0.00 4.79
2908 4371 0.539901 ATCTACCCATCGTCCTCCCG 60.540 60.000 0.00 0.00 0.00 5.14
2920 4383 4.340381 ACTCCGTATTGTACACATCTACCC 59.660 45.833 0.00 0.00 0.00 3.69
2977 4467 2.291190 TGCGGGTAAAGTAAAACACTGC 59.709 45.455 0.00 0.00 37.63 4.40
3077 4600 4.116328 GCCCGCTTTTTCTCCCGC 62.116 66.667 0.00 0.00 0.00 6.13
3146 4689 1.300620 TTGCAGTGAACGTCCCTCG 60.301 57.895 0.00 0.00 46.00 4.63
3200 4743 1.143305 CAGTGAAGTGAAGGTCGCAG 58.857 55.000 0.00 0.00 0.00 5.18
3203 4746 2.135933 GGTTCAGTGAAGTGAAGGTCG 58.864 52.381 5.62 0.00 37.12 4.79
3212 4755 1.531423 ATGCTGCAGGTTCAGTGAAG 58.469 50.000 17.12 0.00 36.49 3.02
3228 4771 2.941064 TGTGCAGCTGAGATTAGAATGC 59.059 45.455 20.43 0.00 34.45 3.56
3229 4772 4.797693 CTGTGCAGCTGAGATTAGAATG 57.202 45.455 20.43 0.00 0.00 2.67
3245 4788 1.135746 GCTTCAGTGATTCAGCTGTGC 60.136 52.381 14.67 4.98 34.57 4.57
3257 4800 8.920665 GTTGCAGAAGTATATATAGCTTCAGTG 58.079 37.037 22.90 17.89 40.57 3.66
3264 4807 9.706691 TTTGTAGGTTGCAGAAGTATATATAGC 57.293 33.333 0.00 0.00 0.00 2.97
3274 4817 4.380531 TGAGACTTTGTAGGTTGCAGAAG 58.619 43.478 0.00 0.00 0.00 2.85
3275 4818 4.415881 TGAGACTTTGTAGGTTGCAGAA 57.584 40.909 0.00 0.00 0.00 3.02
3277 4820 4.130118 AGTTGAGACTTTGTAGGTTGCAG 58.870 43.478 0.00 0.00 29.87 4.41
3320 5857 4.973168 AGGTCAGTGCTGAAAAAGATGTA 58.027 39.130 3.19 0.00 41.85 2.29
3325 5862 4.261363 GGAAAGAGGTCAGTGCTGAAAAAG 60.261 45.833 3.19 0.00 41.85 2.27
3361 5937 0.824109 GGGCTTTGCTATTCCCAACC 59.176 55.000 0.00 0.00 38.62 3.77
3368 5944 1.272648 TGGCTCAAGGGCTTTGCTATT 60.273 47.619 4.20 0.00 41.48 1.73
3378 5954 4.142381 GCTATTAAAAGTGTGGCTCAAGGG 60.142 45.833 0.00 0.00 0.00 3.95
3424 6000 4.452455 AGCAGTTAAGAATGAACCGAGTTG 59.548 41.667 0.00 0.00 25.56 3.16
3430 6006 5.532557 AGCAAAAGCAGTTAAGAATGAACC 58.467 37.500 0.00 0.00 25.56 3.62
3454 6032 2.978156 ACATCAACTGACCAACCCAT 57.022 45.000 0.00 0.00 0.00 4.00
3455 6033 2.708861 AGTACATCAACTGACCAACCCA 59.291 45.455 0.00 0.00 0.00 4.51
3462 6040 6.216569 TCAGTTTCAGAGTACATCAACTGAC 58.783 40.000 16.10 5.55 43.15 3.51
3470 6048 5.791336 TGTCTGTCAGTTTCAGAGTACAT 57.209 39.130 0.00 0.00 41.66 2.29
3472 6050 5.593010 AGTTGTCTGTCAGTTTCAGAGTAC 58.407 41.667 0.00 0.00 41.66 2.73
3473 6051 5.854010 AGTTGTCTGTCAGTTTCAGAGTA 57.146 39.130 0.00 0.00 41.66 2.59
3474 6052 4.744795 AGTTGTCTGTCAGTTTCAGAGT 57.255 40.909 0.00 0.00 41.66 3.24
3475 6053 6.092670 TGAAAAGTTGTCTGTCAGTTTCAGAG 59.907 38.462 9.00 0.00 41.66 3.35
3476 6054 5.937540 TGAAAAGTTGTCTGTCAGTTTCAGA 59.062 36.000 9.00 0.00 39.25 3.27
3477 6055 6.182039 TGAAAAGTTGTCTGTCAGTTTCAG 57.818 37.500 9.00 0.00 32.99 3.02
3478 6056 6.757897 ATGAAAAGTTGTCTGTCAGTTTCA 57.242 33.333 13.39 13.39 37.45 2.69
3479 6057 7.970614 AGAAATGAAAAGTTGTCTGTCAGTTTC 59.029 33.333 0.00 2.51 31.63 2.78
3492 6070 9.468532 GCAGACTTGATTTAGAAATGAAAAGTT 57.531 29.630 0.00 0.00 30.02 2.66
3494 6072 9.635520 ATGCAGACTTGATTTAGAAATGAAAAG 57.364 29.630 0.00 0.00 0.00 2.27
3539 6125 3.072468 CAAGCCAGCACCCATGGG 61.072 66.667 30.23 30.23 38.33 4.00
3704 6316 1.882912 TGCGCATGTGAGTTTCTTCT 58.117 45.000 5.66 0.00 0.00 2.85
3720 6332 3.890385 AGTTCAGACTTTGCAGGTTGCG 61.890 50.000 0.00 0.00 38.59 4.85
3777 6389 4.342951 TCTTCGTTTGGAAAGAGGTCAGTA 59.657 41.667 0.00 0.00 33.34 2.74
3799 6411 8.576936 AGACCTTTTATTATTCTCGACGAATC 57.423 34.615 11.69 0.00 41.36 2.52
3801 6413 8.030692 TCAAGACCTTTTATTATTCTCGACGAA 58.969 33.333 0.00 0.79 35.78 3.85
3803 6415 7.515371 GCTCAAGACCTTTTATTATTCTCGACG 60.515 40.741 0.00 0.00 0.00 5.12
3804 6416 7.277981 TGCTCAAGACCTTTTATTATTCTCGAC 59.722 37.037 0.00 0.00 0.00 4.20
3805 6417 7.277981 GTGCTCAAGACCTTTTATTATTCTCGA 59.722 37.037 0.00 0.00 0.00 4.04
3806 6418 7.278868 AGTGCTCAAGACCTTTTATTATTCTCG 59.721 37.037 0.00 0.00 0.00 4.04
3807 6419 8.499403 AGTGCTCAAGACCTTTTATTATTCTC 57.501 34.615 0.00 0.00 0.00 2.87
3808 6420 8.870075 AAGTGCTCAAGACCTTTTATTATTCT 57.130 30.769 0.00 0.00 0.00 2.40
3810 6422 8.635765 TGAAGTGCTCAAGACCTTTTATTATT 57.364 30.769 0.00 0.00 0.00 1.40
3812 6424 7.224297 ACTGAAGTGCTCAAGACCTTTTATTA 58.776 34.615 0.00 0.00 32.17 0.98
3813 6425 6.064717 ACTGAAGTGCTCAAGACCTTTTATT 58.935 36.000 0.00 0.00 32.17 1.40
3815 6427 5.036117 ACTGAAGTGCTCAAGACCTTTTA 57.964 39.130 0.00 0.00 32.17 1.52
3816 6428 3.891049 ACTGAAGTGCTCAAGACCTTTT 58.109 40.909 0.00 0.00 32.17 2.27
3928 6556 0.588252 CGGTTGCAAGAGTGAGTTGG 59.412 55.000 0.00 0.00 0.00 3.77
4011 6639 6.921914 TGCCTCAAGAACTTTACTACTACTC 58.078 40.000 0.00 0.00 0.00 2.59
4037 6665 7.108841 TGCTATCAAAGTAGGTAAGTACAGG 57.891 40.000 0.00 0.00 0.00 4.00
4040 6668 6.479331 GGCTTGCTATCAAAGTAGGTAAGTAC 59.521 42.308 0.00 0.00 0.00 2.73
4041 6669 6.383147 AGGCTTGCTATCAAAGTAGGTAAGTA 59.617 38.462 0.00 0.00 0.00 2.24
4042 6670 5.189934 AGGCTTGCTATCAAAGTAGGTAAGT 59.810 40.000 0.00 0.00 0.00 2.24
4043 6671 5.525378 CAGGCTTGCTATCAAAGTAGGTAAG 59.475 44.000 0.00 0.00 0.00 2.34
4044 6672 5.428253 CAGGCTTGCTATCAAAGTAGGTAA 58.572 41.667 0.00 0.00 0.00 2.85
4063 6704 2.926778 ATGAAGTGAGATAGGCAGGC 57.073 50.000 0.00 0.00 0.00 4.85
4288 6934 4.473520 ACGGATGCCAAGGGAGCG 62.474 66.667 0.00 0.00 0.00 5.03
4312 6958 1.079750 GAAGACGAGCAGGGTGGAC 60.080 63.158 0.00 0.00 0.00 4.02
4587 7235 2.093500 TGCAGTGTGAGGGTCATATGTC 60.093 50.000 1.90 0.00 0.00 3.06
4672 7336 7.408756 TGCAGCTACTTAATTCCAATTTGAT 57.591 32.000 0.00 0.00 0.00 2.57
4769 7437 1.534163 GAAGCAAACGTCCTACCAACC 59.466 52.381 0.00 0.00 0.00 3.77
4888 7556 5.904362 ATTTCAAGTCCAGAAATGTAGGC 57.096 39.130 0.00 0.00 42.39 3.93
4943 7611 4.034510 CGCAGGTATTGATCCTTCAGTTTC 59.965 45.833 0.00 0.00 32.37 2.78
5041 7709 0.813821 GCCATCAAGCTTTGGACCTC 59.186 55.000 19.41 0.00 34.81 3.85
5066 7738 7.655328 CGAGAGAATGCTCCTGTTAGAAATAAT 59.345 37.037 0.00 0.00 42.30 1.28
5237 7909 1.143305 GATCGATCAGGCCAATGACG 58.857 55.000 20.52 7.95 30.46 4.35
5393 8085 8.049721 AGCAATTAAAGTAGCAACTTCCTCTAT 58.950 33.333 0.00 0.00 45.37 1.98
5489 8181 3.147629 CTGAATCATCATCCTTGGCCTC 58.852 50.000 3.32 0.00 34.37 4.70
5516 8208 6.555738 TCCGGTAAATATCTGTTCCCTTGATA 59.444 38.462 0.00 0.00 0.00 2.15
5519 8211 5.031066 TCCGGTAAATATCTGTTCCCTTG 57.969 43.478 0.00 0.00 0.00 3.61
5771 8463 4.695455 CCAAGATTACAACACGGAGTTCAT 59.305 41.667 0.00 0.00 41.61 2.57
5825 8517 5.231147 GCTAAAATGTGAAGCGAACAAAACA 59.769 36.000 0.00 0.00 0.00 2.83
5826 8518 5.231147 TGCTAAAATGTGAAGCGAACAAAAC 59.769 36.000 0.00 0.00 39.14 2.43
5827 8519 5.344066 TGCTAAAATGTGAAGCGAACAAAA 58.656 33.333 0.00 0.00 39.14 2.44
5831 8523 5.393962 AGAATGCTAAAATGTGAAGCGAAC 58.606 37.500 0.00 0.00 39.14 3.95
5938 11149 4.253685 GCCTGATCTAACACTTAGTTGCA 58.746 43.478 0.00 0.00 41.50 4.08
5944 11155 8.956426 CATTTTTAAGGCCTGATCTAACACTTA 58.044 33.333 5.69 0.00 0.00 2.24
6011 11283 4.061596 TGTATGATGCGTCAGTGAAAACA 58.938 39.130 15.04 8.44 37.87 2.83
6059 11331 3.057315 GCTATGCCACTTGTGTCAATTGT 60.057 43.478 5.13 0.00 0.00 2.71
6222 11506 7.255486 CGAAGGGAGAGAAAAAGGTAAATTTGT 60.255 37.037 0.00 0.00 0.00 2.83
6308 11596 1.273048 GGCCTGAAATGATTGTGTGCA 59.727 47.619 0.00 0.00 0.00 4.57
6411 11699 6.378848 TCAGATGATCAAAATGGCAATTCAGA 59.621 34.615 0.00 0.00 0.00 3.27
6413 11701 6.532988 TCAGATGATCAAAATGGCAATTCA 57.467 33.333 0.00 0.00 0.00 2.57
6789 12109 3.074412 GCTTACATGGTGTAGTGTTGCT 58.926 45.455 0.00 0.00 33.92 3.91
6798 12118 6.392354 CAAGATGATTTTGCTTACATGGTGT 58.608 36.000 0.00 0.00 0.00 4.16
6906 12229 4.878397 AGTGAACCAGAGTGCTATAAATGC 59.122 41.667 0.00 0.00 0.00 3.56
7035 12358 3.188048 GTGATTGCAAGACTCACAGAAGG 59.812 47.826 21.28 0.00 39.24 3.46
7054 12377 0.251354 GGCTGAAGATGCTGAGGTGA 59.749 55.000 0.00 0.00 0.00 4.02
7145 12468 1.271656 GAAAGCACAAGCCTTGCATCT 59.728 47.619 3.88 0.00 42.83 2.90
7260 12583 7.122948 CCTTGATCCTGGATACTACTATACCAC 59.877 44.444 9.66 0.00 37.61 4.16
7275 12598 5.373812 ACTTATGGTTACCTTGATCCTGG 57.626 43.478 2.07 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.