Multiple sequence alignment - TraesCS2B01G171100

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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 TraesCS2B01G171100 chr2B 100.000 6002 0 0 1 6002 144426688 144432689 0.000000e+00 11084.0
1 TraesCS2B01G171100 chr2B 88.095 84 2 5 4459 4536 432132957 432133038 6.410000e-15 93.5
2 TraesCS2B01G171100 chr2D 94.270 1658 64 16 869 2504 92914072 92915720 0.000000e+00 2507.0
3 TraesCS2B01G171100 chr2D 92.786 1109 44 13 3192 4287 92915713 92916798 0.000000e+00 1572.0
4 TraesCS2B01G171100 chr2D 92.623 854 63 0 1 854 483639553 483638700 0.000000e+00 1229.0
5 TraesCS2B01G171100 chr2D 91.547 698 38 13 4530 5214 92918302 92918991 0.000000e+00 942.0
6 TraesCS2B01G171100 chr2D 89.882 761 36 20 5278 6002 92919109 92919864 0.000000e+00 941.0
7 TraesCS2B01G171100 chr2D 95.455 176 7 1 4280 4454 92918049 92918224 4.580000e-71 279.0
8 TraesCS2B01G171100 chr2D 89.157 83 2 3 4459 4536 445733668 445733748 4.950000e-16 97.1
9 TraesCS2B01G171100 chr2A 93.584 1652 79 17 869 2502 90589257 90590899 0.000000e+00 2438.0
10 TraesCS2B01G171100 chr2A 94.836 794 25 6 3663 4454 90592453 90593232 0.000000e+00 1225.0
11 TraesCS2B01G171100 chr2A 91.691 698 35 17 4530 5214 90593317 90594004 0.000000e+00 946.0
12 TraesCS2B01G171100 chr2A 89.951 617 34 18 5409 6002 90595178 90595789 0.000000e+00 771.0
13 TraesCS2B01G171100 chr2A 92.828 488 21 5 3192 3668 90590894 90591378 0.000000e+00 695.0
14 TraesCS2B01G171100 chr2A 88.063 444 31 12 2626 3049 40960170 40960611 1.930000e-139 507.0
15 TraesCS2B01G171100 chr2A 86.486 259 34 1 2936 3194 361252127 361251870 3.540000e-72 283.0
16 TraesCS2B01G171100 chr2A 91.034 145 5 3 5278 5414 90594261 90594405 7.940000e-44 189.0
17 TraesCS2B01G171100 chr2A 100.000 28 0 0 5252 5279 333342394 333342421 1.100000e-02 52.8
18 TraesCS2B01G171100 chr2A 100.000 28 0 0 5252 5279 333354390 333354417 1.100000e-02 52.8
19 TraesCS2B01G171100 chr4A 89.482 1331 88 28 869 2190 232003008 232004295 0.000000e+00 1635.0
20 TraesCS2B01G171100 chr4A 89.167 240 22 3 2504 2741 28168778 28168541 4.550000e-76 296.0
21 TraesCS2B01G171100 chr5B 95.571 858 36 1 1 856 505789569 505790426 0.000000e+00 1373.0
22 TraesCS2B01G171100 chr5B 80.080 753 80 22 2504 3191 518705872 518706619 4.180000e-136 496.0
23 TraesCS2B01G171100 chr5B 84.314 102 7 5 4439 4532 199658298 199658198 2.300000e-14 91.6
24 TraesCS2B01G171100 chr5B 100.000 28 0 0 5252 5279 591582642 591582615 1.100000e-02 52.8
25 TraesCS2B01G171100 chr5B 100.000 28 0 0 5252 5279 594135872 594135899 1.100000e-02 52.8
26 TraesCS2B01G171100 chr6B 93.326 854 57 0 1 854 711329469 711328616 0.000000e+00 1262.0
27 TraesCS2B01G171100 chr6B 80.319 752 76 27 2505 3191 83159648 83160392 2.500000e-138 503.0
28 TraesCS2B01G171100 chr6B 86.264 182 25 0 5788 5969 200005969 200006150 1.320000e-46 198.0
29 TraesCS2B01G171100 chrUn 90.654 856 80 0 1 856 313653624 313652769 0.000000e+00 1138.0
30 TraesCS2B01G171100 chr7A 90.654 856 80 0 1 856 1761026 1761881 0.000000e+00 1138.0
31 TraesCS2B01G171100 chr7A 88.785 107 6 3 2735 2835 113039179 113039285 6.320000e-25 126.0
32 TraesCS2B01G171100 chr1A 90.398 854 82 0 1 854 468465997 468465144 0.000000e+00 1123.0
33 TraesCS2B01G171100 chr1A 90.281 854 83 0 1 854 468414823 468413970 0.000000e+00 1118.0
34 TraesCS2B01G171100 chr1A 82.036 334 36 11 2505 2820 40933300 40933627 4.610000e-66 263.0
35 TraesCS2B01G171100 chr1A 100.000 28 0 0 5252 5279 561333772 561333799 1.100000e-02 52.8
36 TraesCS2B01G171100 chr5A 90.164 854 84 0 1 854 502834546 502835399 0.000000e+00 1112.0
37 TraesCS2B01G171100 chr5A 81.848 303 24 13 2672 2959 20228342 20228056 6.050000e-55 226.0
38 TraesCS2B01G171100 chr3A 89.720 856 88 0 1 856 688417304 688418159 0.000000e+00 1094.0
39 TraesCS2B01G171100 chr3A 87.500 88 4 5 4454 4536 28077437 28077352 1.780000e-15 95.3
40 TraesCS2B01G171100 chr4B 92.980 698 20 6 2504 3191 242801709 242801031 0.000000e+00 990.0
41 TraesCS2B01G171100 chr7B 91.501 706 43 10 2504 3193 666817540 666818244 0.000000e+00 955.0
42 TraesCS2B01G171100 chr1D 90.806 707 41 11 2505 3191 200446939 200446237 0.000000e+00 924.0
43 TraesCS2B01G171100 chr3D 89.016 437 29 11 2625 3049 36551470 36551899 1.920000e-144 523.0
44 TraesCS2B01G171100 chr3D 88.559 236 26 1 2959 3194 576408988 576408754 9.850000e-73 285.0
45 TraesCS2B01G171100 chr3D 88.889 234 21 3 2508 2741 576409521 576409293 3.540000e-72 283.0
46 TraesCS2B01G171100 chr3D 89.157 83 2 3 4459 4536 437961281 437961361 4.950000e-16 97.1
47 TraesCS2B01G171100 chr7D 89.453 256 26 1 2936 3191 385633651 385633397 7.500000e-84 322.0
48 TraesCS2B01G171100 chr7D 90.476 231 18 2 2511 2741 25628801 25628575 9.780000e-78 302.0
49 TraesCS2B01G171100 chr7D 88.983 236 22 2 2506 2741 385634152 385633921 7.610000e-74 289.0
50 TraesCS2B01G171100 chr7D 88.095 84 3 4 4458 4536 94123051 94122970 6.410000e-15 93.5
51 TraesCS2B01G171100 chr5D 84.273 337 29 7 2505 2820 393395656 393395323 2.100000e-79 307.0
52 TraesCS2B01G171100 chr5D 88.285 239 23 3 2506 2743 391819060 391819294 1.270000e-71 281.0
53 TraesCS2B01G171100 chr5D 88.235 85 3 4 4457 4536 151671543 151671625 1.780000e-15 95.3
54 TraesCS2B01G171100 chr5D 88.095 84 3 4 4459 4536 541938326 541938244 6.410000e-15 93.5
55 TraesCS2B01G171100 chr3B 88.327 257 27 3 2936 3192 573284298 573284551 7.560000e-79 305.0
56 TraesCS2B01G171100 chr1B 87.891 256 28 3 2936 3191 550965318 550965066 1.260000e-76 298.0
57 TraesCS2B01G171100 chr1B 82.388 335 36 10 2504 2820 681006355 681006026 2.760000e-68 270.0
58 TraesCS2B01G171100 chr1B 100.000 28 0 0 5252 5279 17382303 17382330 1.100000e-02 52.8
59 TraesCS2B01G171100 chr6D 86.264 182 25 0 5788 5969 111059400 111059581 1.320000e-46 198.0
60 TraesCS2B01G171100 chr6A 86.264 182 25 0 5788 5969 135558589 135558770 1.320000e-46 198.0
61 TraesCS2B01G171100 chr4D 85.870 92 5 4 4455 4541 355565120 355565208 2.300000e-14 91.6


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 TraesCS2B01G171100 chr2B 144426688 144432689 6001 False 11084.0 11084 100.000000 1 6002 1 chr2B.!!$F1 6001
1 TraesCS2B01G171100 chr2D 92914072 92919864 5792 False 1248.2 2507 92.788000 869 6002 5 chr2D.!!$F2 5133
2 TraesCS2B01G171100 chr2D 483638700 483639553 853 True 1229.0 1229 92.623000 1 854 1 chr2D.!!$R1 853
3 TraesCS2B01G171100 chr2A 90589257 90595789 6532 False 1044.0 2438 92.320667 869 6002 6 chr2A.!!$F4 5133
4 TraesCS2B01G171100 chr4A 232003008 232004295 1287 False 1635.0 1635 89.482000 869 2190 1 chr4A.!!$F1 1321
5 TraesCS2B01G171100 chr5B 505789569 505790426 857 False 1373.0 1373 95.571000 1 856 1 chr5B.!!$F1 855
6 TraesCS2B01G171100 chr5B 518705872 518706619 747 False 496.0 496 80.080000 2504 3191 1 chr5B.!!$F2 687
7 TraesCS2B01G171100 chr6B 711328616 711329469 853 True 1262.0 1262 93.326000 1 854 1 chr6B.!!$R1 853
8 TraesCS2B01G171100 chr6B 83159648 83160392 744 False 503.0 503 80.319000 2505 3191 1 chr6B.!!$F1 686
9 TraesCS2B01G171100 chrUn 313652769 313653624 855 True 1138.0 1138 90.654000 1 856 1 chrUn.!!$R1 855
10 TraesCS2B01G171100 chr7A 1761026 1761881 855 False 1138.0 1138 90.654000 1 856 1 chr7A.!!$F1 855
11 TraesCS2B01G171100 chr1A 468465144 468465997 853 True 1123.0 1123 90.398000 1 854 1 chr1A.!!$R2 853
12 TraesCS2B01G171100 chr1A 468413970 468414823 853 True 1118.0 1118 90.281000 1 854 1 chr1A.!!$R1 853
13 TraesCS2B01G171100 chr5A 502834546 502835399 853 False 1112.0 1112 90.164000 1 854 1 chr5A.!!$F1 853
14 TraesCS2B01G171100 chr3A 688417304 688418159 855 False 1094.0 1094 89.720000 1 856 1 chr3A.!!$F1 855
15 TraesCS2B01G171100 chr4B 242801031 242801709 678 True 990.0 990 92.980000 2504 3191 1 chr4B.!!$R1 687
16 TraesCS2B01G171100 chr7B 666817540 666818244 704 False 955.0 955 91.501000 2504 3193 1 chr7B.!!$F1 689
17 TraesCS2B01G171100 chr1D 200446237 200446939 702 True 924.0 924 90.806000 2505 3191 1 chr1D.!!$R1 686
18 TraesCS2B01G171100 chr3D 576408754 576409521 767 True 284.0 285 88.724000 2508 3194 2 chr3D.!!$R1 686
19 TraesCS2B01G171100 chr7D 385633397 385634152 755 True 305.5 322 89.218000 2506 3191 2 chr7D.!!$R3 685

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
959 967 0.035630 CTTGGGCCCTTGACTGAGAG 60.036 60.0 25.7 3.04 0.0 3.20 F
1288 1298 0.246360 CGGGTTTTGAATTGGAGGCC 59.754 55.0 0.0 0.00 0.0 5.19 F
3194 3363 0.573791 TATATGCCCACCCCTACCCA 59.426 55.0 0.0 0.00 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2839 2951 1.919240 TCTCTCCCTACAAGACGCAA 58.081 50.00 0.0 0.0 0.00 4.85 R
3246 3416 4.390264 TGTGTGGTCACGAATAAATTCCA 58.610 39.13 0.0 0.0 46.49 3.53 R
5161 7710 0.037447 TGGCATCGGGTTCAACATCA 59.963 50.00 0.0 0.0 0.00 3.07 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
128 129 2.736144 AAAGCACCGAGAACGATACA 57.264 45.000 0.00 0.00 42.66 2.29
133 134 1.471287 CACCGAGAACGATACAGACCA 59.529 52.381 0.00 0.00 42.66 4.02
213 214 2.911484 CCTGCAAGTAATCCCACTCTC 58.089 52.381 0.00 0.00 0.00 3.20
215 216 1.291132 GCAAGTAATCCCACTCTCGC 58.709 55.000 0.00 0.00 0.00 5.03
348 351 2.957402 ATGTCTTCCTGGCACAAAGA 57.043 45.000 3.34 3.34 38.70 2.52
350 353 0.868406 GTCTTCCTGGCACAAAGACG 59.132 55.000 16.90 0.00 43.36 4.18
355 358 0.320374 CCTGGCACAAAGACGGACTA 59.680 55.000 0.00 0.00 38.70 2.59
359 362 2.301870 TGGCACAAAGACGGACTATTCT 59.698 45.455 0.00 0.00 31.92 2.40
373 376 9.535878 GACGGACTATTCTTCTGAAATAATCTT 57.464 33.333 0.00 0.00 35.63 2.40
572 575 0.965866 CTACCTCCGTCACCTCAGCA 60.966 60.000 0.00 0.00 0.00 4.41
748 751 4.641094 TGGTACACAATTGAGAACCGTTTT 59.359 37.500 13.59 0.00 0.00 2.43
762 765 4.911514 ACCGTTTTCATGTTGCTAACTT 57.088 36.364 0.00 0.00 0.00 2.66
856 859 4.074970 GTCCCAAGAGAATTTTGCAGAGA 58.925 43.478 0.00 0.00 0.00 3.10
857 860 4.704057 GTCCCAAGAGAATTTTGCAGAGAT 59.296 41.667 0.00 0.00 0.00 2.75
858 861 5.882557 GTCCCAAGAGAATTTTGCAGAGATA 59.117 40.000 0.00 0.00 0.00 1.98
859 862 6.038050 GTCCCAAGAGAATTTTGCAGAGATAG 59.962 42.308 0.00 0.00 0.00 2.08
860 863 6.070021 TCCCAAGAGAATTTTGCAGAGATAGA 60.070 38.462 0.00 0.00 0.00 1.98
861 864 6.260493 CCCAAGAGAATTTTGCAGAGATAGAG 59.740 42.308 0.00 0.00 0.00 2.43
862 865 7.046652 CCAAGAGAATTTTGCAGAGATAGAGA 58.953 38.462 0.00 0.00 0.00 3.10
863 866 7.716123 CCAAGAGAATTTTGCAGAGATAGAGAT 59.284 37.037 0.00 0.00 0.00 2.75
864 867 9.761504 CAAGAGAATTTTGCAGAGATAGAGATA 57.238 33.333 0.00 0.00 0.00 1.98
865 868 9.985730 AAGAGAATTTTGCAGAGATAGAGATAG 57.014 33.333 0.00 0.00 0.00 2.08
866 869 9.365906 AGAGAATTTTGCAGAGATAGAGATAGA 57.634 33.333 0.00 0.00 0.00 1.98
867 870 9.630098 GAGAATTTTGCAGAGATAGAGATAGAG 57.370 37.037 0.00 0.00 0.00 2.43
876 879 7.756722 GCAGAGATAGAGATAGAGATTTGCTTC 59.243 40.741 0.00 0.00 0.00 3.86
953 961 0.178990 AACAGTCTTGGGCCCTTGAC 60.179 55.000 28.68 28.68 0.00 3.18
955 963 0.607489 CAGTCTTGGGCCCTTGACTG 60.607 60.000 38.25 38.25 46.45 3.51
959 967 0.035630 CTTGGGCCCTTGACTGAGAG 60.036 60.000 25.70 3.04 0.00 3.20
960 968 0.473694 TTGGGCCCTTGACTGAGAGA 60.474 55.000 25.70 0.00 0.00 3.10
961 969 0.906756 TGGGCCCTTGACTGAGAGAG 60.907 60.000 25.70 0.00 0.00 3.20
962 970 1.220477 GGCCCTTGACTGAGAGAGC 59.780 63.158 0.00 0.00 0.00 4.09
963 971 1.548357 GGCCCTTGACTGAGAGAGCA 61.548 60.000 0.00 0.00 0.00 4.26
964 972 0.390998 GCCCTTGACTGAGAGAGCAC 60.391 60.000 0.00 0.00 0.00 4.40
999 1007 2.360852 TCGTCTCGGGTGGACTCC 60.361 66.667 0.00 0.00 0.00 3.85
1008 1016 1.674980 GGTGGACTCCGTCGTCTCT 60.675 63.158 0.00 0.00 34.38 3.10
1037 1045 2.659244 GACCGACCGAAACGCACA 60.659 61.111 0.00 0.00 0.00 4.57
1188 1196 0.977395 CGTAATCCATCTCCTCCCCC 59.023 60.000 0.00 0.00 0.00 5.40
1223 1231 0.329261 CCTGTTTCCTGAGCATGGGA 59.671 55.000 0.00 0.00 0.00 4.37
1288 1298 0.246360 CGGGTTTTGAATTGGAGGCC 59.754 55.000 0.00 0.00 0.00 5.19
1359 1370 6.235231 TGTTGATTGGACTAATCCTAGGTC 57.765 41.667 9.08 0.00 46.43 3.85
1418 1429 2.430367 GTTGGTTCTGGCGACCCT 59.570 61.111 0.00 0.00 36.30 4.34
1475 1486 2.930950 TCTTGGAAGTGTTGGTCTTGG 58.069 47.619 0.00 0.00 0.00 3.61
1480 1491 1.876156 GAAGTGTTGGTCTTGGAGCAG 59.124 52.381 0.00 0.00 41.12 4.24
1511 1522 4.872691 AGCTCACAAGATGTAAATCTTCCG 59.127 41.667 5.08 0.37 38.73 4.30
1548 1559 9.553064 GAACATCAGATCCACAAGTAATTATCT 57.447 33.333 0.00 0.00 0.00 1.98
1696 1720 6.937465 TGTGTATGTATTTGTGTCCTAGCAAA 59.063 34.615 0.00 0.00 38.68 3.68
1722 1746 1.251251 ATGGCAACTCTTTGTCTGGC 58.749 50.000 0.00 0.00 38.25 4.85
1767 1791 4.624913 TCCCAGATTCCATCAGTTACTCT 58.375 43.478 0.00 0.00 0.00 3.24
1831 1857 4.021104 TCTCCTGTCCTGTGTCATTAAGTG 60.021 45.833 0.00 0.00 0.00 3.16
1928 1954 8.219546 TCTTTCAAATAGTGTGTTTGTCATGA 57.780 30.769 0.00 0.00 37.70 3.07
1978 2004 4.450080 CCTGTGGTTAAGAGACGGTTAAAC 59.550 45.833 0.00 0.00 0.00 2.01
2253 2283 2.453521 ACACGAGCTCAGGTATGGTTA 58.546 47.619 15.40 0.00 0.00 2.85
2295 2325 8.405531 TGCTGCCTGATTATACTTGAAAATAAC 58.594 33.333 0.00 0.00 0.00 1.89
2342 2372 8.084684 CAGGAGATAAAAGGAACCAAAAAGAAG 58.915 37.037 0.00 0.00 0.00 2.85
2370 2400 6.013466 TGCAGAAGGTATATGGATCAGCATTA 60.013 38.462 0.00 0.00 29.28 1.90
2416 2446 9.653287 TTTTACCAGAGTTACATCTCATAACTG 57.347 33.333 2.27 0.00 41.80 3.16
2556 2590 1.568025 GTTCGGTGCTTCGGTGTTC 59.432 57.895 0.01 0.00 0.00 3.18
2606 2640 3.204597 CCGATCGGTCTCTAGCAATAC 57.795 52.381 26.35 0.00 0.00 1.89
3194 3363 0.573791 TATATGCCCACCCCTACCCA 59.426 55.000 0.00 0.00 0.00 4.51
3195 3364 1.065997 ATATGCCCACCCCTACCCAC 61.066 60.000 0.00 0.00 0.00 4.61
3196 3365 2.494151 TATGCCCACCCCTACCCACA 62.494 60.000 0.00 0.00 0.00 4.17
3197 3366 3.021263 GCCCACCCCTACCCACAT 61.021 66.667 0.00 0.00 0.00 3.21
3198 3367 3.056754 GCCCACCCCTACCCACATC 62.057 68.421 0.00 0.00 0.00 3.06
3210 3379 3.448277 ACCCACATCCCTATCCCTAAA 57.552 47.619 0.00 0.00 0.00 1.85
3246 3416 1.322538 GCATGCATCCCCGAACCTTT 61.323 55.000 14.21 0.00 0.00 3.11
3340 3510 3.914312 TGGCTTTCGTCTTTAGTCTCAG 58.086 45.455 0.00 0.00 0.00 3.35
3367 3537 8.091952 TCTTCCTCTCACTAGTCTACTTCATA 57.908 38.462 0.00 0.00 0.00 2.15
3388 3558 8.281212 TCATAGAATTTTGTTCCTTCTAAGGC 57.719 34.615 3.73 0.00 46.06 4.35
3495 3665 5.471456 TGTTTGCACTTTTGACCACATTTTT 59.529 32.000 0.00 0.00 0.00 1.94
3569 3748 2.815478 CTAACTGAGGAACATCTCGGC 58.185 52.381 0.00 0.00 42.37 5.54
3581 3760 3.305720 ACATCTCGGCCCTATCAACTTA 58.694 45.455 0.00 0.00 0.00 2.24
3861 5121 1.135972 GCTTATGCACACTTCCACACG 60.136 52.381 0.00 0.00 39.41 4.49
3905 5166 2.440599 GGGAAGCCAGGGCAAGAA 59.559 61.111 13.63 0.00 44.88 2.52
3961 5222 3.610637 CAAATGTTTGGTGGGGCAG 57.389 52.632 0.00 0.00 34.59 4.85
4026 5287 3.826157 CCCAACCAACAAGAAATAGCAGA 59.174 43.478 0.00 0.00 0.00 4.26
4027 5288 4.280677 CCCAACCAACAAGAAATAGCAGAA 59.719 41.667 0.00 0.00 0.00 3.02
4028 5289 5.221422 CCCAACCAACAAGAAATAGCAGAAA 60.221 40.000 0.00 0.00 0.00 2.52
4029 5290 6.279882 CCAACCAACAAGAAATAGCAGAAAA 58.720 36.000 0.00 0.00 0.00 2.29
4030 5291 6.930722 CCAACCAACAAGAAATAGCAGAAAAT 59.069 34.615 0.00 0.00 0.00 1.82
4031 5292 8.087750 CCAACCAACAAGAAATAGCAGAAAATA 58.912 33.333 0.00 0.00 0.00 1.40
4032 5293 8.915654 CAACCAACAAGAAATAGCAGAAAATAC 58.084 33.333 0.00 0.00 0.00 1.89
4033 5294 8.409358 ACCAACAAGAAATAGCAGAAAATACT 57.591 30.769 0.00 0.00 0.00 2.12
4034 5295 9.515226 ACCAACAAGAAATAGCAGAAAATACTA 57.485 29.630 0.00 0.00 0.00 1.82
4139 5400 4.876107 TCTATTCCTGCGGAAATTGAAGAC 59.124 41.667 12.83 0.00 45.41 3.01
4454 6975 2.158385 AGCCCTACTGCAGCTATCTAGT 60.158 50.000 15.27 0.00 34.38 2.57
4456 6977 3.442273 GCCCTACTGCAGCTATCTAGTAG 59.558 52.174 15.27 6.08 41.27 2.57
4458 6979 5.317808 CCCTACTGCAGCTATCTAGTAGAA 58.682 45.833 15.27 0.00 43.20 2.10
4459 6980 5.949354 CCCTACTGCAGCTATCTAGTAGAAT 59.051 44.000 15.27 0.00 43.20 2.40
4460 6981 7.113437 CCCTACTGCAGCTATCTAGTAGAATA 58.887 42.308 15.27 0.00 43.20 1.75
4461 6982 7.777910 CCCTACTGCAGCTATCTAGTAGAATAT 59.222 40.741 15.27 0.00 43.20 1.28
4465 6986 9.391006 ACTGCAGCTATCTAGTAGAATATACTC 57.609 37.037 15.27 0.00 31.71 2.59
4466 6987 8.740123 TGCAGCTATCTAGTAGAATATACTCC 57.260 38.462 3.45 0.00 31.71 3.85
4468 6989 7.996644 GCAGCTATCTAGTAGAATATACTCCCT 59.003 40.741 3.45 0.00 31.71 4.20
4469 6990 9.555727 CAGCTATCTAGTAGAATATACTCCCTC 57.444 40.741 3.45 0.00 31.71 4.30
4470 6991 8.720537 AGCTATCTAGTAGAATATACTCCCTCC 58.279 40.741 3.45 0.00 31.71 4.30
4471 6992 7.658575 GCTATCTAGTAGAATATACTCCCTCCG 59.341 44.444 3.45 0.00 31.71 4.63
4475 6996 5.323581 AGTAGAATATACTCCCTCCGTTCC 58.676 45.833 0.00 0.00 0.00 3.62
4477 6998 5.595814 AGAATATACTCCCTCCGTTCCTA 57.404 43.478 0.00 0.00 0.00 2.94
4478 6999 5.961897 AGAATATACTCCCTCCGTTCCTAA 58.038 41.667 0.00 0.00 0.00 2.69
4479 7000 6.379579 AGAATATACTCCCTCCGTTCCTAAA 58.620 40.000 0.00 0.00 0.00 1.85
4480 7001 7.017531 AGAATATACTCCCTCCGTTCCTAAAT 58.982 38.462 0.00 0.00 0.00 1.40
4482 7003 8.912614 AATATACTCCCTCCGTTCCTAAATAT 57.087 34.615 0.00 0.00 0.00 1.28
4485 7006 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
4486 7007 5.011840 ACTCCCTCCGTTCCTAAATATAAGC 59.988 44.000 0.00 0.00 0.00 3.09
4487 7008 4.285260 TCCCTCCGTTCCTAAATATAAGCC 59.715 45.833 0.00 0.00 0.00 4.35
4489 7010 5.221864 CCCTCCGTTCCTAAATATAAGCCTT 60.222 44.000 0.00 0.00 0.00 4.35
4492 7013 6.655930 TCCGTTCCTAAATATAAGCCTTTGT 58.344 36.000 0.00 0.00 0.00 2.83
4494 7015 7.929785 TCCGTTCCTAAATATAAGCCTTTGTAG 59.070 37.037 0.00 0.00 0.00 2.74
4495 7016 7.929785 CCGTTCCTAAATATAAGCCTTTGTAGA 59.070 37.037 0.00 0.00 0.00 2.59
4503 7024 8.910351 AATATAAGCCTTTGTAGAGATTCCAC 57.090 34.615 0.00 0.00 0.00 4.02
4504 7025 4.917906 AAGCCTTTGTAGAGATTCCACT 57.082 40.909 0.00 0.00 0.00 4.00
4505 7026 7.676683 ATAAGCCTTTGTAGAGATTCCACTA 57.323 36.000 0.00 0.00 0.00 2.74
4506 7027 6.374417 AAGCCTTTGTAGAGATTCCACTAA 57.626 37.500 0.00 0.00 0.00 2.24
4507 7028 6.567602 AGCCTTTGTAGAGATTCCACTAAT 57.432 37.500 0.00 0.00 0.00 1.73
4524 7045 5.799960 CACTAATGGACTACGAGCAAAATG 58.200 41.667 0.00 0.00 0.00 2.32
4525 7046 5.580691 CACTAATGGACTACGAGCAAAATGA 59.419 40.000 0.00 0.00 0.00 2.57
4527 7048 3.678056 TGGACTACGAGCAAAATGAGT 57.322 42.857 0.00 0.00 0.00 3.41
4528 7049 3.325870 TGGACTACGAGCAAAATGAGTG 58.674 45.455 0.00 0.00 0.00 3.51
4545 7075 6.687081 ATGAGTGTACTCTAGTGCTTACTC 57.313 41.667 12.75 10.03 43.25 2.59
4677 7208 3.649502 TCTCTTTTCCCGGAACCTACTTT 59.350 43.478 0.73 0.00 0.00 2.66
4679 7210 3.136992 TCTTTTCCCGGAACCTACTTTGT 59.863 43.478 0.73 0.00 0.00 2.83
4680 7211 4.347583 TCTTTTCCCGGAACCTACTTTGTA 59.652 41.667 0.73 0.00 0.00 2.41
4681 7212 3.683365 TTCCCGGAACCTACTTTGTAC 57.317 47.619 0.73 0.00 0.00 2.90
4690 7221 6.020360 CGGAACCTACTTTGTACTAATAACGC 60.020 42.308 0.00 0.00 0.00 4.84
4691 7222 6.813152 GGAACCTACTTTGTACTAATAACGCA 59.187 38.462 0.00 0.00 0.00 5.24
4807 7338 2.502947 TGCCTACAAGAGCTGATGATGT 59.497 45.455 0.00 0.00 0.00 3.06
4880 7411 7.226128 TGCTGAAGATGTGATGATGTTAAGATC 59.774 37.037 5.66 5.66 0.00 2.75
4911 7442 4.021102 TCCTTTGTGGTTCTCATCTTCC 57.979 45.455 0.00 0.00 37.07 3.46
5110 7641 3.602390 ATATACACAAATTGCCGCGAC 57.398 42.857 8.23 0.00 0.00 5.19
5126 7657 2.905010 GCGACGTTGCAGATGGTACAG 61.905 57.143 23.02 0.00 36.77 2.74
5194 7743 2.353704 CGATGCCACCATATACGGATGT 60.354 50.000 0.00 0.00 0.00 3.06
5198 7747 3.006430 TGCCACCATATACGGATGTACAG 59.994 47.826 0.33 0.00 32.26 2.74
5214 7763 5.772521 ATGTACAGCATCTTGGAACAAAAC 58.227 37.500 0.33 0.00 36.88 2.43
5216 7765 6.183360 ATGTACAGCATCTTGGAACAAAACAA 60.183 34.615 0.33 0.00 36.88 2.83
5236 7988 5.113383 ACAATTATATCGAACTTGCCACGA 58.887 37.500 0.00 0.00 40.18 4.35
5237 7989 5.006358 ACAATTATATCGAACTTGCCACGAC 59.994 40.000 0.00 0.00 38.79 4.34
5240 7992 2.765250 ATCGAACTTGCCACGACGCT 62.765 55.000 0.00 0.00 38.79 5.07
5241 7993 2.551270 GAACTTGCCACGACGCTG 59.449 61.111 0.00 0.00 0.00 5.18
5242 7994 3.579626 GAACTTGCCACGACGCTGC 62.580 63.158 0.00 0.00 0.00 5.25
5243 7995 4.908687 ACTTGCCACGACGCTGCA 62.909 61.111 7.70 7.70 0.00 4.41
5244 7996 3.648982 CTTGCCACGACGCTGCAA 61.649 61.111 19.47 19.47 42.28 4.08
5246 7998 3.252665 TTGCCACGACGCTGCAATG 62.253 57.895 17.51 0.00 39.86 2.82
5247 7999 4.465512 GCCACGACGCTGCAATGG 62.466 66.667 0.00 2.30 0.00 3.16
5249 8001 2.174107 CACGACGCTGCAATGGTG 59.826 61.111 0.00 0.98 0.00 4.17
5264 8016 4.414852 CAATGGTGCTCTATTTTGGAACG 58.585 43.478 0.00 0.00 0.00 3.95
5265 8017 2.432444 TGGTGCTCTATTTTGGAACGG 58.568 47.619 0.00 0.00 0.00 4.44
5266 8018 2.039216 TGGTGCTCTATTTTGGAACGGA 59.961 45.455 0.00 0.00 0.00 4.69
5267 8019 2.678336 GGTGCTCTATTTTGGAACGGAG 59.322 50.000 0.00 0.00 0.00 4.63
5268 8020 2.678336 GTGCTCTATTTTGGAACGGAGG 59.322 50.000 0.00 0.00 0.00 4.30
5269 8021 2.289565 GCTCTATTTTGGAACGGAGGG 58.710 52.381 0.00 0.00 0.00 4.30
5270 8022 2.093128 GCTCTATTTTGGAACGGAGGGA 60.093 50.000 0.00 0.00 0.00 4.20
5271 8023 3.798202 CTCTATTTTGGAACGGAGGGAG 58.202 50.000 0.00 0.00 0.00 4.30
5272 8024 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
5273 8025 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
5274 8026 3.629142 ATTTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
5275 8027 2.314071 TTTGGAACGGAGGGAGTAGA 57.686 50.000 0.00 0.00 0.00 2.59
5276 8028 2.544844 TTGGAACGGAGGGAGTAGAT 57.455 50.000 0.00 0.00 0.00 1.98
5300 8052 9.383519 GATTGTTTCTTCCAGTTCACTGATATA 57.616 33.333 8.61 0.00 46.59 0.86
5301 8053 8.547967 TTGTTTCTTCCAGTTCACTGATATAC 57.452 34.615 8.61 0.55 46.59 1.47
5373 8132 1.138036 CATGCACATTGGCGACTGG 59.862 57.895 0.00 0.00 36.28 4.00
5394 8153 1.895798 TCGATCCTTGCTCACACTCTT 59.104 47.619 0.00 0.00 0.00 2.85
5404 8163 2.475487 GCTCACACTCTTTTCGTGGTAC 59.525 50.000 0.00 0.00 36.71 3.34
5417 8955 9.005777 TCTTTTCGTGGTACTTTAATTAGCATT 57.994 29.630 0.00 0.00 30.09 3.56
5433 8971 8.895932 AATTAGCATTATGACGAGAACAAAAC 57.104 30.769 0.00 0.00 0.00 2.43
5451 8989 7.288810 ACAAAACTCGAACCGGGTATATATA 57.711 36.000 6.32 0.00 40.83 0.86
5453 8991 8.370182 ACAAAACTCGAACCGGGTATATATATT 58.630 33.333 6.32 0.00 40.83 1.28
5455 8993 9.783081 AAAACTCGAACCGGGTATATATATTTT 57.217 29.630 6.32 0.00 40.83 1.82
5456 8994 8.767478 AACTCGAACCGGGTATATATATTTTG 57.233 34.615 6.32 0.00 40.83 2.44
5517 9056 1.592223 CTTCGCTCGGAGGTCCTTT 59.408 57.895 7.20 0.00 0.00 3.11
5704 9243 1.144298 TGGCATCATCCTTCATCCTGG 59.856 52.381 0.00 0.00 0.00 4.45
5716 9261 3.051940 TCATCCTGGTCAAGATAGCCT 57.948 47.619 0.00 0.00 0.00 4.58
5722 9267 0.530870 GGTCAAGATAGCCTGCCGTC 60.531 60.000 0.00 0.00 0.00 4.79
5761 9306 8.417106 TCATAACTCTTACAGCTCAATAAGGAG 58.583 37.037 8.40 7.45 37.97 3.69
5762 9307 6.613153 AACTCTTACAGCTCAATAAGGAGT 57.387 37.500 8.40 7.88 37.24 3.85
5763 9308 7.719871 AACTCTTACAGCTCAATAAGGAGTA 57.280 36.000 8.40 0.00 37.24 2.59
5764 9309 7.341445 ACTCTTACAGCTCAATAAGGAGTAG 57.659 40.000 8.40 3.09 37.24 2.57
5765 9310 6.322712 ACTCTTACAGCTCAATAAGGAGTAGG 59.677 42.308 8.40 0.00 37.24 3.18
5766 9311 3.828875 ACAGCTCAATAAGGAGTAGGC 57.171 47.619 0.00 0.00 37.24 3.93
5767 9312 3.107601 ACAGCTCAATAAGGAGTAGGCA 58.892 45.455 0.00 0.00 37.24 4.75
5770 9315 4.514441 CAGCTCAATAAGGAGTAGGCAATG 59.486 45.833 0.00 0.00 37.24 2.82
5772 9317 4.712476 CTCAATAAGGAGTAGGCAATGCT 58.288 43.478 4.82 0.00 0.00 3.79
5773 9318 5.743130 GCTCAATAAGGAGTAGGCAATGCTA 60.743 44.000 4.82 0.00 37.24 3.49
5774 9319 5.858381 TCAATAAGGAGTAGGCAATGCTAG 58.142 41.667 4.82 0.00 0.00 3.42
5775 9320 2.629336 AAGGAGTAGGCAATGCTAGC 57.371 50.000 8.10 8.10 0.00 3.42
5776 9321 1.799933 AGGAGTAGGCAATGCTAGCT 58.200 50.000 17.23 0.21 0.00 3.32
5777 9322 1.415659 AGGAGTAGGCAATGCTAGCTG 59.584 52.381 17.23 8.00 0.00 4.24
5780 9325 3.065655 GAGTAGGCAATGCTAGCTGATG 58.934 50.000 17.23 12.75 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.935203 CTCTTTTTAATCGCAGCAGAGGA 59.065 43.478 0.00 0.00 0.00 3.71
128 129 5.178096 TCATTATGAACATGGTGTGGTCT 57.822 39.130 0.00 0.00 45.16 3.85
133 134 7.147915 GGGTACAAATCATTATGAACATGGTGT 60.148 37.037 0.00 0.91 0.00 4.16
213 214 2.874086 TGATGAAAGCATATGACAGGCG 59.126 45.455 6.97 0.00 39.49 5.52
348 351 9.892130 AAAGATTATTTCAGAAGAATAGTCCGT 57.108 29.630 0.00 0.00 32.89 4.69
355 358 9.759473 TTCTCCCAAAGATTATTTCAGAAGAAT 57.241 29.630 0.00 0.00 32.82 2.40
359 362 9.182214 CAGATTCTCCCAAAGATTATTTCAGAA 57.818 33.333 0.00 0.00 32.82 3.02
373 376 4.263639 ACAGATTGAAGCAGATTCTCCCAA 60.264 41.667 0.00 0.00 38.83 4.12
572 575 3.008835 CATCATTGGGAGATGTGTGGT 57.991 47.619 0.00 0.00 38.40 4.16
646 649 1.349026 TCAAGACAGCCCTCTTTCAGG 59.651 52.381 0.00 0.00 43.01 3.86
748 751 4.323028 CCTCTGAGGAAGTTAGCAACATGA 60.323 45.833 19.13 0.00 37.67 3.07
856 859 5.337169 GCCCGAAGCAAATCTCTATCTCTAT 60.337 44.000 0.00 0.00 42.97 1.98
857 860 4.021894 GCCCGAAGCAAATCTCTATCTCTA 60.022 45.833 0.00 0.00 42.97 2.43
858 861 3.244044 GCCCGAAGCAAATCTCTATCTCT 60.244 47.826 0.00 0.00 42.97 3.10
859 862 3.063485 GCCCGAAGCAAATCTCTATCTC 58.937 50.000 0.00 0.00 42.97 2.75
860 863 2.224402 GGCCCGAAGCAAATCTCTATCT 60.224 50.000 0.00 0.00 46.50 1.98
861 864 2.147150 GGCCCGAAGCAAATCTCTATC 58.853 52.381 0.00 0.00 46.50 2.08
862 865 1.541233 CGGCCCGAAGCAAATCTCTAT 60.541 52.381 0.00 0.00 46.50 1.98
863 866 0.179084 CGGCCCGAAGCAAATCTCTA 60.179 55.000 0.00 0.00 46.50 2.43
864 867 1.450312 CGGCCCGAAGCAAATCTCT 60.450 57.895 0.00 0.00 46.50 3.10
865 868 1.432270 CTCGGCCCGAAGCAAATCTC 61.432 60.000 7.50 0.00 46.50 2.75
866 869 1.450312 CTCGGCCCGAAGCAAATCT 60.450 57.895 7.50 0.00 46.50 2.40
867 870 1.432270 CTCTCGGCCCGAAGCAAATC 61.432 60.000 7.50 0.00 46.50 2.17
932 940 1.063266 TCAAGGGCCCAAGACTGTTTT 60.063 47.619 27.56 2.23 0.00 2.43
937 945 0.768221 TCAGTCAAGGGCCCAAGACT 60.768 55.000 32.25 32.25 41.70 3.24
953 961 1.624865 GCTTGTGCGTGCTCTCTCAG 61.625 60.000 0.00 0.00 0.00 3.35
955 963 3.163655 GCTTGTGCGTGCTCTCTC 58.836 61.111 0.00 0.00 0.00 3.20
999 1007 1.459975 TCGAACTCAGAAGAGACGACG 59.540 52.381 12.25 0.00 44.98 5.12
1188 1196 5.163353 GGAAACAGGAGAGAATTAGAGGAGG 60.163 48.000 0.00 0.00 0.00 4.30
1228 1237 1.948635 GCGCCGCAAACACACAAAT 60.949 52.632 3.15 0.00 0.00 2.32
1281 1291 1.221840 GCGATTTCTCTGGCCTCCA 59.778 57.895 3.32 0.00 0.00 3.86
1288 1298 2.444351 GGCAAAATCGCGATTTCTCTG 58.556 47.619 38.58 32.82 39.88 3.35
1359 1370 0.029834 GCCATATTCCAAGCGCACAG 59.970 55.000 11.47 0.00 0.00 3.66
1418 1429 2.923655 CAGAAGCTTCGCGTGATCTAAA 59.076 45.455 20.43 0.00 0.00 1.85
1447 1458 1.800805 ACACTTCCAAGATCAGCGTG 58.199 50.000 0.00 0.00 0.00 5.34
1475 1486 2.203181 GAGCTCCATGGGCTGCTC 60.203 66.667 26.43 26.67 40.40 4.26
1480 1491 0.106819 ATCTTGTGAGCTCCATGGGC 60.107 55.000 13.02 14.33 0.00 5.36
1511 1522 2.143122 TCTGATGTTCGCCTTGTTGAC 58.857 47.619 0.00 0.00 0.00 3.18
1584 1608 4.905456 AGTCCTTTAACGGGATATGGATGA 59.095 41.667 0.00 0.00 35.15 2.92
1696 1720 6.449698 CAGACAAAGAGTTGCCATTTATGTT 58.550 36.000 0.00 0.00 38.39 2.71
1722 1746 7.281100 GGGAAATTCAGAAGTACAGACAATAGG 59.719 40.741 0.00 0.00 0.00 2.57
1767 1791 2.910319 TGCTTTGAGGGGCTAGAAGTAA 59.090 45.455 0.00 0.00 0.00 2.24
1945 1971 5.724854 TCTCTTAACCACAGGGCTATAACTT 59.275 40.000 0.00 0.00 37.90 2.66
1978 2004 7.061905 CACTTTCTATTTATATACGTGAGCCCG 59.938 40.741 0.00 0.00 0.00 6.13
2102 2132 3.007635 CCTACCATGTTTCCTTCGGTTC 58.992 50.000 0.00 0.00 0.00 3.62
2295 2325 2.555199 CAAGAAATAGCCCCGTCAGAG 58.445 52.381 0.00 0.00 0.00 3.35
2342 2372 3.008375 TGATCCATATACCTTCTGCAGCC 59.992 47.826 9.47 0.00 0.00 4.85
2416 2446 2.009774 CAGATGATGTGGTTCCGGAAC 58.990 52.381 34.71 34.71 40.45 3.62
2839 2951 1.919240 TCTCTCCCTACAAGACGCAA 58.081 50.000 0.00 0.00 0.00 4.85
2840 2952 1.919240 TTCTCTCCCTACAAGACGCA 58.081 50.000 0.00 0.00 0.00 5.24
3194 3363 5.043005 AGGCTATTTAGGGATAGGGATGT 57.957 43.478 0.00 0.00 31.62 3.06
3195 3364 6.903534 TCTAAGGCTATTTAGGGATAGGGATG 59.096 42.308 0.00 0.00 32.66 3.51
3196 3365 7.069902 TCTAAGGCTATTTAGGGATAGGGAT 57.930 40.000 0.00 0.00 32.66 3.85
3197 3366 6.494429 TCTAAGGCTATTTAGGGATAGGGA 57.506 41.667 0.00 0.00 32.66 4.20
3198 3367 7.136203 AGATCTAAGGCTATTTAGGGATAGGG 58.864 42.308 0.00 0.00 32.66 3.53
3210 3379 5.022122 TGCATGCTAGAGATCTAAGGCTAT 58.978 41.667 20.33 0.00 0.00 2.97
3246 3416 4.390264 TGTGTGGTCACGAATAAATTCCA 58.610 39.130 0.00 0.00 46.49 3.53
3340 3510 6.655848 TGAAGTAGACTAGTGAGAGGAAGAAC 59.344 42.308 0.00 0.00 0.00 3.01
3605 3784 7.148755 GCTCAAGAACGCAATTCATAACAAATT 60.149 33.333 0.92 0.00 40.09 1.82
3627 3806 5.711506 ACCTGAATGAACATTATGTTGCTCA 59.288 36.000 15.83 12.65 41.28 4.26
3861 5121 3.698040 TCTCGGTTAACCTCTATGACCAC 59.302 47.826 22.12 0.00 0.00 4.16
3905 5166 1.205655 TCAAGCGCACTCTCTGCTATT 59.794 47.619 11.47 0.00 44.64 1.73
3971 5232 6.447162 CCTCTGTTATTCCTTGTTTGGTTTC 58.553 40.000 0.00 0.00 0.00 2.78
4035 5296 9.944376 TTAGCAGTGATAACTGAGTCTATTTTT 57.056 29.630 14.96 0.00 39.99 1.94
4054 5315 3.440173 GTGTGTTATGGCATGTTAGCAGT 59.560 43.478 10.98 0.00 35.83 4.40
4139 5400 1.808411 TACCTTTTTCTCAGCAGCCG 58.192 50.000 0.00 0.00 0.00 5.52
4384 6904 1.173043 TATCCAACAAAGGCCAAGCG 58.827 50.000 5.01 0.00 0.00 4.68
4454 6975 5.595814 AGGAACGGAGGGAGTATATTCTA 57.404 43.478 0.00 0.00 0.00 2.10
4456 6977 6.661304 TTTAGGAACGGAGGGAGTATATTC 57.339 41.667 0.00 0.00 0.00 1.75
4459 6980 9.471702 CTTATATTTAGGAACGGAGGGAGTATA 57.528 37.037 0.00 0.00 0.00 1.47
4460 6981 7.093421 GCTTATATTTAGGAACGGAGGGAGTAT 60.093 40.741 0.00 0.00 0.00 2.12
4461 6982 6.210185 GCTTATATTTAGGAACGGAGGGAGTA 59.790 42.308 0.00 0.00 0.00 2.59
4463 6984 5.480205 GCTTATATTTAGGAACGGAGGGAG 58.520 45.833 0.00 0.00 0.00 4.30
4464 6985 4.285260 GGCTTATATTTAGGAACGGAGGGA 59.715 45.833 0.00 0.00 0.00 4.20
4465 6986 4.286291 AGGCTTATATTTAGGAACGGAGGG 59.714 45.833 0.00 0.00 0.00 4.30
4466 6987 5.485209 AGGCTTATATTTAGGAACGGAGG 57.515 43.478 0.00 0.00 0.00 4.30
4468 6989 6.655930 ACAAAGGCTTATATTTAGGAACGGA 58.344 36.000 0.00 0.00 0.00 4.69
4469 6990 6.937436 ACAAAGGCTTATATTTAGGAACGG 57.063 37.500 0.00 0.00 0.00 4.44
4470 6991 8.882415 TCTACAAAGGCTTATATTTAGGAACG 57.118 34.615 0.00 0.00 0.00 3.95
4477 6998 9.343539 GTGGAATCTCTACAAAGGCTTATATTT 57.656 33.333 0.00 0.00 0.00 1.40
4478 6999 8.718656 AGTGGAATCTCTACAAAGGCTTATATT 58.281 33.333 0.00 0.00 29.47 1.28
4479 7000 8.268878 AGTGGAATCTCTACAAAGGCTTATAT 57.731 34.615 0.00 0.00 29.47 0.86
4480 7001 7.676683 AGTGGAATCTCTACAAAGGCTTATA 57.323 36.000 0.00 0.00 29.47 0.98
4482 7003 7.490657 TTAGTGGAATCTCTACAAAGGCTTA 57.509 36.000 0.00 0.00 29.47 3.09
4483 7004 4.917906 AGTGGAATCTCTACAAAGGCTT 57.082 40.909 0.00 0.00 29.47 4.35
4484 7005 6.352516 CATTAGTGGAATCTCTACAAAGGCT 58.647 40.000 0.00 0.00 29.47 4.58
4485 7006 6.610741 CATTAGTGGAATCTCTACAAAGGC 57.389 41.667 0.00 0.00 29.47 4.35
4501 7022 5.580691 TCATTTTGCTCGTAGTCCATTAGTG 59.419 40.000 0.00 0.00 0.00 2.74
4503 7024 5.812642 ACTCATTTTGCTCGTAGTCCATTAG 59.187 40.000 0.00 0.00 0.00 1.73
4504 7025 5.580691 CACTCATTTTGCTCGTAGTCCATTA 59.419 40.000 0.00 0.00 0.00 1.90
4505 7026 4.393062 CACTCATTTTGCTCGTAGTCCATT 59.607 41.667 0.00 0.00 0.00 3.16
4506 7027 3.935203 CACTCATTTTGCTCGTAGTCCAT 59.065 43.478 0.00 0.00 0.00 3.41
4507 7028 3.244078 ACACTCATTTTGCTCGTAGTCCA 60.244 43.478 0.00 0.00 0.00 4.02
4512 7033 5.386958 AGAGTACACTCATTTTGCTCGTA 57.613 39.130 11.75 0.00 45.21 3.43
4516 7037 4.932200 GCACTAGAGTACACTCATTTTGCT 59.068 41.667 11.75 0.00 45.21 3.91
4518 7039 7.815068 AGTAAGCACTAGAGTACACTCATTTTG 59.185 37.037 11.75 4.54 45.21 2.44
4519 7040 7.897864 AGTAAGCACTAGAGTACACTCATTTT 58.102 34.615 11.75 0.00 45.21 1.82
4520 7041 7.394923 AGAGTAAGCACTAGAGTACACTCATTT 59.605 37.037 11.75 0.00 39.24 2.32
4521 7042 6.887545 AGAGTAAGCACTAGAGTACACTCATT 59.112 38.462 11.75 0.00 39.24 2.57
4523 7044 5.806818 AGAGTAAGCACTAGAGTACACTCA 58.193 41.667 11.75 0.00 39.24 3.41
4524 7045 6.036735 CAGAGAGTAAGCACTAGAGTACACTC 59.963 46.154 0.00 0.91 37.99 3.51
4525 7046 5.878116 CAGAGAGTAAGCACTAGAGTACACT 59.122 44.000 0.00 0.00 34.21 3.55
4527 7048 6.051179 TCAGAGAGTAAGCACTAGAGTACA 57.949 41.667 0.00 0.00 34.21 2.90
4528 7049 7.414436 CAATCAGAGAGTAAGCACTAGAGTAC 58.586 42.308 0.00 0.00 34.21 2.73
4677 7208 7.520451 AGATGGTAGATGCGTTATTAGTACA 57.480 36.000 0.00 0.00 0.00 2.90
4679 7210 8.857098 AGAAAGATGGTAGATGCGTTATTAGTA 58.143 33.333 0.00 0.00 0.00 1.82
4680 7211 7.727181 AGAAAGATGGTAGATGCGTTATTAGT 58.273 34.615 0.00 0.00 0.00 2.24
4681 7212 8.594881 AAGAAAGATGGTAGATGCGTTATTAG 57.405 34.615 0.00 0.00 0.00 1.73
4690 7221 4.133078 GCCAGGAAGAAAGATGGTAGATG 58.867 47.826 0.00 0.00 35.17 2.90
4691 7222 3.181461 CGCCAGGAAGAAAGATGGTAGAT 60.181 47.826 0.00 0.00 35.17 1.98
4880 7411 6.881065 TGAGAACCACAAAGGAAATATCAGAG 59.119 38.462 0.00 0.00 41.22 3.35
4911 7442 0.370273 GCTGTCTACATGGTTTCGCG 59.630 55.000 0.00 0.00 0.00 5.87
5091 7622 1.325037 CGTCGCGGCAATTTGTGTATA 59.675 47.619 12.89 0.00 0.00 1.47
5093 7624 1.222766 ACGTCGCGGCAATTTGTGTA 61.223 50.000 12.89 0.00 0.00 2.90
5095 7626 1.369930 AACGTCGCGGCAATTTGTG 60.370 52.632 12.89 0.00 0.00 3.33
5097 7628 2.706123 GCAACGTCGCGGCAATTTG 61.706 57.895 12.89 11.88 0.00 2.32
5099 7630 3.593551 CTGCAACGTCGCGGCAATT 62.594 57.895 12.89 0.33 37.06 2.32
5100 7631 4.088762 CTGCAACGTCGCGGCAAT 62.089 61.111 12.89 0.00 37.06 3.56
5103 7634 4.505217 CATCTGCAACGTCGCGGC 62.505 66.667 6.13 1.93 38.22 6.53
5104 7635 3.853330 CCATCTGCAACGTCGCGG 61.853 66.667 6.13 0.00 39.79 6.46
5105 7636 1.803922 TACCATCTGCAACGTCGCG 60.804 57.895 0.00 0.00 33.35 5.87
5106 7637 1.011968 TGTACCATCTGCAACGTCGC 61.012 55.000 0.00 0.00 0.00 5.19
5110 7641 3.896648 AAAACTGTACCATCTGCAACG 57.103 42.857 0.00 0.00 0.00 4.10
5150 7699 3.184178 GGTTCAACATCACGGCAAATTTG 59.816 43.478 14.03 14.03 0.00 2.32
5151 7700 3.389221 GGTTCAACATCACGGCAAATTT 58.611 40.909 0.00 0.00 0.00 1.82
5154 7703 0.671251 GGGTTCAACATCACGGCAAA 59.329 50.000 0.00 0.00 0.00 3.68
5161 7710 0.037447 TGGCATCGGGTTCAACATCA 59.963 50.000 0.00 0.00 0.00 3.07
5164 7713 1.602323 GGTGGCATCGGGTTCAACA 60.602 57.895 0.00 0.00 0.00 3.33
5194 7743 5.843673 TTGTTTTGTTCCAAGATGCTGTA 57.156 34.783 0.00 0.00 0.00 2.74
5198 7747 8.745837 CGATATAATTGTTTTGTTCCAAGATGC 58.254 33.333 0.00 0.00 0.00 3.91
5214 7763 5.432157 GTCGTGGCAAGTTCGATATAATTG 58.568 41.667 0.00 0.00 36.08 2.32
5216 7765 3.734231 CGTCGTGGCAAGTTCGATATAAT 59.266 43.478 12.65 0.00 36.08 1.28
5219 7971 1.556564 CGTCGTGGCAAGTTCGATAT 58.443 50.000 12.65 0.00 36.08 1.63
5222 7974 3.033764 GCGTCGTGGCAAGTTCGA 61.034 61.111 18.86 8.92 0.00 3.71
5242 7994 4.414852 CGTTCCAAAATAGAGCACCATTG 58.585 43.478 0.00 0.00 0.00 2.82
5243 7995 3.443681 CCGTTCCAAAATAGAGCACCATT 59.556 43.478 0.00 0.00 0.00 3.16
5244 7996 3.016736 CCGTTCCAAAATAGAGCACCAT 58.983 45.455 0.00 0.00 0.00 3.55
5246 7998 2.678336 CTCCGTTCCAAAATAGAGCACC 59.322 50.000 0.00 0.00 0.00 5.01
5247 7999 2.678336 CCTCCGTTCCAAAATAGAGCAC 59.322 50.000 0.00 0.00 0.00 4.40
5249 8001 2.093128 TCCCTCCGTTCCAAAATAGAGC 60.093 50.000 0.00 0.00 0.00 4.09
5251 8003 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
5252 8004 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
5253 8005 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
5255 8007 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
5256 8008 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
5257 8009 2.500098 CAATCTACTCCCTCCGTTCCAA 59.500 50.000 0.00 0.00 0.00 3.53
5258 8010 2.108168 CAATCTACTCCCTCCGTTCCA 58.892 52.381 0.00 0.00 0.00 3.53
5259 8011 2.108970 ACAATCTACTCCCTCCGTTCC 58.891 52.381 0.00 0.00 0.00 3.62
5260 8012 3.889520 AACAATCTACTCCCTCCGTTC 57.110 47.619 0.00 0.00 0.00 3.95
5264 8016 4.225267 TGGAAGAAACAATCTACTCCCTCC 59.775 45.833 0.00 0.00 37.42 4.30
5265 8017 5.046231 ACTGGAAGAAACAATCTACTCCCTC 60.046 44.000 0.00 0.00 37.42 4.30
5266 8018 4.846940 ACTGGAAGAAACAATCTACTCCCT 59.153 41.667 0.00 0.00 37.42 4.20
5267 8019 5.167303 ACTGGAAGAAACAATCTACTCCC 57.833 43.478 0.00 0.00 37.42 4.30
5268 8020 6.147985 GTGAACTGGAAGAAACAATCTACTCC 59.852 42.308 0.00 0.00 37.42 3.85
5269 8021 6.931840 AGTGAACTGGAAGAAACAATCTACTC 59.068 38.462 0.00 0.00 37.42 2.59
5270 8022 6.708054 CAGTGAACTGGAAGAAACAATCTACT 59.292 38.462 2.35 0.00 37.61 2.57
5271 8023 6.706270 TCAGTGAACTGGAAGAAACAATCTAC 59.294 38.462 10.45 0.00 43.91 2.59
5272 8024 6.826668 TCAGTGAACTGGAAGAAACAATCTA 58.173 36.000 10.45 0.00 43.91 1.98
5273 8025 5.684704 TCAGTGAACTGGAAGAAACAATCT 58.315 37.500 10.45 0.00 43.91 2.40
5274 8026 6.566197 ATCAGTGAACTGGAAGAAACAATC 57.434 37.500 10.45 0.00 43.91 2.67
5275 8027 9.167311 GTATATCAGTGAACTGGAAGAAACAAT 57.833 33.333 10.45 0.00 43.91 2.71
5276 8028 8.154203 TGTATATCAGTGAACTGGAAGAAACAA 58.846 33.333 10.45 0.00 43.91 2.83
5300 8052 5.670485 TCCAGATAATGTATTCGCACTTGT 58.330 37.500 0.00 0.00 0.00 3.16
5301 8053 5.755375 ACTCCAGATAATGTATTCGCACTTG 59.245 40.000 0.00 0.00 0.00 3.16
5337 8096 3.346315 CATGGCATACTGTGTTTCTGGA 58.654 45.455 0.00 0.00 0.00 3.86
5373 8132 1.203523 AGAGTGTGAGCAAGGATCGAC 59.796 52.381 0.00 0.00 0.00 4.20
5433 8971 6.814644 TGCAAAATATATATACCCGGTTCGAG 59.185 38.462 0.00 0.00 0.00 4.04
5451 8989 9.217278 TGATGCTTTATTATTTGTGTGCAAAAT 57.783 25.926 0.00 0.00 46.23 1.82
5455 8993 7.545489 TGATGATGCTTTATTATTTGTGTGCA 58.455 30.769 0.00 0.00 0.00 4.57
5456 8994 7.306399 GCTGATGATGCTTTATTATTTGTGTGC 60.306 37.037 0.00 0.00 0.00 4.57
5469 9008 1.945394 GGATCGTGCTGATGATGCTTT 59.055 47.619 0.00 0.00 37.47 3.51
5517 9056 1.103803 CGTCGGGGAAGATTCTGAGA 58.896 55.000 0.00 0.00 0.00 3.27
5704 9243 0.872021 CGACGGCAGGCTATCTTGAC 60.872 60.000 0.00 0.00 0.00 3.18
5716 9261 3.591023 TGATGATTTCTTAACGACGGCA 58.409 40.909 0.00 0.00 0.00 5.69
5756 9301 2.122768 AGCTAGCATTGCCTACTCCTT 58.877 47.619 18.83 0.00 0.00 3.36
5761 9306 1.534595 GCATCAGCTAGCATTGCCTAC 59.465 52.381 18.83 0.00 37.91 3.18
5762 9307 1.888215 GCATCAGCTAGCATTGCCTA 58.112 50.000 18.83 0.00 37.91 3.93
5763 9308 2.716814 GCATCAGCTAGCATTGCCT 58.283 52.632 18.83 0.00 37.91 4.75
5774 9319 1.002366 CGTGAGTACCAAGCATCAGC 58.998 55.000 0.00 0.00 42.56 4.26
5775 9320 1.645034 CCGTGAGTACCAAGCATCAG 58.355 55.000 0.00 0.00 0.00 2.90
5776 9321 0.249120 CCCGTGAGTACCAAGCATCA 59.751 55.000 0.00 0.00 0.00 3.07
5777 9322 0.535335 TCCCGTGAGTACCAAGCATC 59.465 55.000 0.00 0.00 0.00 3.91
5780 9325 1.445582 CGTCCCGTGAGTACCAAGC 60.446 63.158 0.00 0.00 0.00 4.01
5867 9434 2.284190 GAGCTCATCAAGTACAAGGGC 58.716 52.381 9.40 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.