Multiple sequence alignment - TraesCS4B01G217600

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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 TraesCS4B01G217600 chr4B 100.000 4283 0 0 3640 7922 459069807 459074089 0.000000e+00 7910
1 TraesCS4B01G217600 chr4B 100.000 3314 0 0 1 3314 459066168 459069481 0.000000e+00 6120
2 TraesCS4B01G217600 chr4B 92.299 909 62 5 1453 2356 646867506 646866601 0.000000e+00 1284
3 TraesCS4B01G217600 chr4D 95.631 3342 131 8 3640 6970 373643403 373640066 0.000000e+00 5349
4 TraesCS4B01G217600 chr4D 94.128 562 22 6 890 1444 373643968 373643411 0.000000e+00 845
5 TraesCS4B01G217600 chr4A 94.574 2101 94 11 4954 7040 90888543 90886449 0.000000e+00 3230
6 TraesCS4B01G217600 chr4A 93.184 983 59 6 3941 4916 90889634 90888653 0.000000e+00 1437
7 TraesCS4B01G217600 chr4A 89.220 872 63 15 7079 7922 90886441 90885573 0.000000e+00 1061
8 TraesCS4B01G217600 chr4A 95.910 489 19 1 956 1444 90890392 90889905 0.000000e+00 791
9 TraesCS4B01G217600 chr4A 81.623 419 49 13 110 500 642207081 642207499 9.920000e-84 322
10 TraesCS4B01G217600 chr4A 86.957 253 30 2 603 852 642207500 642207752 1.680000e-71 281
11 TraesCS4B01G217600 chr5B 88.529 1883 145 31 1452 3314 80605206 80603375 0.000000e+00 2215
12 TraesCS4B01G217600 chr5B 88.011 1885 154 33 1452 3314 80200728 80198894 0.000000e+00 2163
13 TraesCS4B01G217600 chr3B 88.157 1883 155 33 1449 3314 605450248 605452079 0.000000e+00 2180
14 TraesCS4B01G217600 chr6D 91.218 1355 100 7 1495 2836 6390262 6391610 0.000000e+00 1825
15 TraesCS4B01G217600 chr6D 87.307 323 32 8 2908 3224 6391608 6391927 2.100000e-95 361
16 TraesCS4B01G217600 chr5A 90.902 1363 97 12 1522 2870 32742371 32741022 0.000000e+00 1805
17 TraesCS4B01G217600 chr5A 88.421 190 19 1 3069 3255 32741016 32740827 8.000000e-55 226
18 TraesCS4B01G217600 chr2B 86.497 1570 170 22 1448 2991 742654000 742652447 0.000000e+00 1687
19 TraesCS4B01G217600 chr2B 78.584 565 79 30 1452 1999 763883457 763882918 1.270000e-87 335
20 TraesCS4B01G217600 chr2B 75.135 555 101 31 1452 1984 183513644 183514183 8.000000e-55 226
21 TraesCS4B01G217600 chr2D 85.449 1560 153 43 1452 2987 608801411 608799902 0.000000e+00 1555
22 TraesCS4B01G217600 chr3A 91.109 1091 89 5 1452 2536 584293902 584292814 0.000000e+00 1471
23 TraesCS4B01G217600 chr7A 86.098 1043 92 25 2279 3311 130163049 130164048 0.000000e+00 1074
24 TraesCS4B01G217600 chr7A 85.189 871 98 8 1 841 135918507 135919376 0.000000e+00 865
25 TraesCS4B01G217600 chr7A 72.941 425 96 19 435 850 700661309 700660895 6.450000e-26 130
26 TraesCS4B01G217600 chr7A 72.705 414 97 16 445 850 700643801 700643396 3.000000e-24 124
27 TraesCS4B01G217600 chr7A 72.535 426 98 19 435 851 700627090 700626675 3.880000e-23 121
28 TraesCS4B01G217600 chr7D 92.160 574 31 5 2423 2988 627106001 627105434 0.000000e+00 798
29 TraesCS4B01G217600 chr7D 80.412 194 18 6 3057 3247 627105437 627105261 6.450000e-26 130
30 TraesCS4B01G217600 chr5D 93.750 256 7 2 6637 6883 486915814 486916069 7.510000e-100 375
31 TraesCS4B01G217600 chr5D 90.681 279 14 2 6283 6558 486915506 486915775 2.100000e-95 361
32 TraesCS4B01G217600 chr5D 94.898 98 4 1 5996 6092 486915415 486915512 1.380000e-32 152
33 TraesCS4B01G217600 chr1D 85.479 365 38 11 2460 2816 122241066 122240709 4.520000e-97 366
34 TraesCS4B01G217600 chr1A 78.649 370 78 1 433 801 351888401 351888032 2.210000e-60 244
35 TraesCS4B01G217600 chr1A 75.406 431 98 7 428 853 133418977 133418550 1.350000e-47 202
36 TraesCS4B01G217600 chr2A 79.916 239 45 1 3022 3257 441143872 441143634 1.060000e-38 172
37 TraesCS4B01G217600 chr2A 72.664 428 102 15 433 852 771958076 771957656 2.320000e-25 128


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 TraesCS4B01G217600 chr4B 459066168 459074089 7921 False 7015.00 7910 100.000000 1 7922 2 chr4B.!!$F1 7921
1 TraesCS4B01G217600 chr4B 646866601 646867506 905 True 1284.00 1284 92.299000 1453 2356 1 chr4B.!!$R1 903
2 TraesCS4B01G217600 chr4D 373640066 373643968 3902 True 3097.00 5349 94.879500 890 6970 2 chr4D.!!$R1 6080
3 TraesCS4B01G217600 chr4A 90885573 90890392 4819 True 1629.75 3230 93.222000 956 7922 4 chr4A.!!$R1 6966
4 TraesCS4B01G217600 chr4A 642207081 642207752 671 False 301.50 322 84.290000 110 852 2 chr4A.!!$F1 742
5 TraesCS4B01G217600 chr5B 80603375 80605206 1831 True 2215.00 2215 88.529000 1452 3314 1 chr5B.!!$R2 1862
6 TraesCS4B01G217600 chr5B 80198894 80200728 1834 True 2163.00 2163 88.011000 1452 3314 1 chr5B.!!$R1 1862
7 TraesCS4B01G217600 chr3B 605450248 605452079 1831 False 2180.00 2180 88.157000 1449 3314 1 chr3B.!!$F1 1865
8 TraesCS4B01G217600 chr6D 6390262 6391927 1665 False 1093.00 1825 89.262500 1495 3224 2 chr6D.!!$F1 1729
9 TraesCS4B01G217600 chr5A 32740827 32742371 1544 True 1015.50 1805 89.661500 1522 3255 2 chr5A.!!$R1 1733
10 TraesCS4B01G217600 chr2B 742652447 742654000 1553 True 1687.00 1687 86.497000 1448 2991 1 chr2B.!!$R1 1543
11 TraesCS4B01G217600 chr2B 763882918 763883457 539 True 335.00 335 78.584000 1452 1999 1 chr2B.!!$R2 547
12 TraesCS4B01G217600 chr2B 183513644 183514183 539 False 226.00 226 75.135000 1452 1984 1 chr2B.!!$F1 532
13 TraesCS4B01G217600 chr2D 608799902 608801411 1509 True 1555.00 1555 85.449000 1452 2987 1 chr2D.!!$R1 1535
14 TraesCS4B01G217600 chr3A 584292814 584293902 1088 True 1471.00 1471 91.109000 1452 2536 1 chr3A.!!$R1 1084
15 TraesCS4B01G217600 chr7A 130163049 130164048 999 False 1074.00 1074 86.098000 2279 3311 1 chr7A.!!$F1 1032
16 TraesCS4B01G217600 chr7A 135918507 135919376 869 False 865.00 865 85.189000 1 841 1 chr7A.!!$F2 840
17 TraesCS4B01G217600 chr7D 627105261 627106001 740 True 464.00 798 86.286000 2423 3247 2 chr7D.!!$R1 824
18 TraesCS4B01G217600 chr5D 486915415 486916069 654 False 296.00 375 93.109667 5996 6883 3 chr5D.!!$F1 887

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
539 569 0.108186 TCCGTGAAGCTATGCCACTG 60.108 55.000 0.00 0.00 0.00 3.66 F
802 833 0.536724 ATAACCCGAACCGTGTACCC 59.463 55.000 0.00 0.00 0.00 3.69 F
1909 1996 0.179156 GACACTTGCGGCATCATTGG 60.179 55.000 2.28 0.00 0.00 3.16 F
2872 2973 0.169672 CTCACCAGAAATGCGCCAAG 59.830 55.000 4.18 0.00 0.00 3.61 F
3691 3813 0.954452 CACCCTGAGTTGGAACTTGC 59.046 55.000 0.00 0.00 39.88 4.01 F
3771 3893 1.274728 AGGTGCTACTGCTGTTCAGAG 59.725 52.381 0.09 0.00 45.72 3.35 F
3875 3999 1.766143 GCAGCATAGAACGAAGCGGG 61.766 60.000 0.00 0.00 0.00 6.13 F
5358 5565 4.837298 TGGACCAATCATTCAAATGTTCCA 59.163 37.500 0.00 5.92 37.65 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1724 0.037326 CTAGGCGTGCCTTGTCTTGA 60.037 55.000 20.08 0.00 45.70 3.02 R
2277 2369 0.255318 GACACCTCTCCCCTCTACGA 59.745 60.000 0.00 0.00 0.00 3.43 R
3737 3859 0.464554 GCACCTAACATCCCTGGAGC 60.465 60.000 0.00 0.00 0.00 4.70 R
3744 3866 2.093447 ACAGCAGTAGCACCTAACATCC 60.093 50.000 0.00 0.00 45.49 3.51 R
4562 4690 2.549754 CAGGGAAACATATCACCGCATC 59.450 50.000 0.00 0.00 0.00 3.91 R
5757 5964 7.011773 CACTCACATTGACAATAAGTTCTTCG 58.988 38.462 0.00 0.00 0.00 3.79 R
5799 6006 8.206867 TCCTCAACTATCTTGAACTCATTATGG 58.793 37.037 0.00 0.00 0.00 2.74 R
7313 7558 0.798776 AGTTACGGACCGTACTGTCG 59.201 55.000 26.03 8.88 42.13 4.35 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
19 20 0.803117 CAAGAGACATGCCTGCTGTG 59.197 55.000 0.00 0.00 0.00 3.66
20 21 0.959372 AAGAGACATGCCTGCTGTGC 60.959 55.000 0.00 0.00 0.00 4.57
21 22 2.360852 AGACATGCCTGCTGTGCC 60.361 61.111 0.00 0.00 0.00 5.01
22 23 3.807538 GACATGCCTGCTGTGCCG 61.808 66.667 0.00 0.00 0.00 5.69
37 40 2.758089 GCCGCTGCAAGGACTCATG 61.758 63.158 11.69 0.00 37.47 3.07
40 43 1.676635 GCTGCAAGGACTCATGGCA 60.677 57.895 0.00 0.00 0.00 4.92
59 62 0.396556 ATCATGCATTGCTGGCCTGA 60.397 50.000 14.77 0.26 39.60 3.86
68 71 1.279496 TGCTGGCCTGAACTATGTCT 58.721 50.000 14.77 0.00 0.00 3.41
71 74 1.751351 CTGGCCTGAACTATGTCTCGA 59.249 52.381 3.32 0.00 0.00 4.04
141 144 3.845781 ATATGGAAGTCAACGCCAGAT 57.154 42.857 0.00 0.00 34.74 2.90
170 173 5.173131 GCTGTTCGATTTGAATGAAACGTTT 59.827 36.000 14.57 14.57 39.21 3.60
178 181 7.060979 CGATTTGAATGAAACGTTTGATCATGT 59.939 33.333 20.10 10.43 34.21 3.21
227 230 5.509670 CCTGTGGTCTATTTGATATGCGAGA 60.510 44.000 0.00 0.00 0.00 4.04
257 260 8.954834 AGGCAATATATGAATCCATTTACCAA 57.045 30.769 0.00 0.00 34.31 3.67
266 269 6.310941 TGAATCCATTTACCAAAGTCCTCAA 58.689 36.000 0.00 0.00 0.00 3.02
267 270 6.953520 TGAATCCATTTACCAAAGTCCTCAAT 59.046 34.615 0.00 0.00 0.00 2.57
281 284 7.454260 AAGTCCTCAATAAACCACATCTTTC 57.546 36.000 0.00 0.00 0.00 2.62
285 288 5.445939 CCTCAATAAACCACATCTTTCGTCG 60.446 44.000 0.00 0.00 0.00 5.12
299 302 5.466819 TCTTTCGTCGACAACTACATCAAT 58.533 37.500 17.16 0.00 0.00 2.57
302 305 4.412207 TCGTCGACAACTACATCAATGAG 58.588 43.478 17.16 0.00 0.00 2.90
331 334 7.882791 TGGTCAATATGCGTTCAAGGATAATAT 59.117 33.333 0.00 0.00 0.00 1.28
381 410 5.392380 CCTTACTGGCAATGTCAAGATCAAC 60.392 44.000 0.00 0.00 0.00 3.18
382 411 3.489355 ACTGGCAATGTCAAGATCAACA 58.511 40.909 0.00 0.00 0.00 3.33
397 426 0.320683 CAACATGGACGGAGCAGTCA 60.321 55.000 0.00 0.00 42.62 3.41
398 427 0.615331 AACATGGACGGAGCAGTCAT 59.385 50.000 0.00 0.00 42.62 3.06
422 452 4.760047 CACCGGGAAGGAGTGGCG 62.760 72.222 6.32 0.00 45.00 5.69
440 470 1.016130 CGGCGACTGTTTGCAGAGAT 61.016 55.000 0.00 0.00 45.28 2.75
470 500 4.141482 GGTTTATACTTGGGATCCTCAGCA 60.141 45.833 12.58 0.00 0.00 4.41
488 518 2.108952 AGCACTGGTCTTTCAGGGAATT 59.891 45.455 0.00 0.00 40.45 2.17
500 530 5.434003 TTCAGGGAATTAGGGATCCTCTA 57.566 43.478 12.58 8.70 35.95 2.43
507 537 6.209589 GGGAATTAGGGATCCTCTAATTTTGC 59.790 42.308 29.54 22.38 43.42 3.68
514 544 5.891551 GGGATCCTCTAATTTTGCAAACCTA 59.108 40.000 12.39 5.36 0.00 3.08
516 546 6.377146 GGATCCTCTAATTTTGCAAACCTACA 59.623 38.462 12.39 0.00 0.00 2.74
520 550 7.232534 TCCTCTAATTTTGCAAACCTACACATT 59.767 33.333 12.39 9.56 0.00 2.71
523 553 3.634568 TTTGCAAACCTACACATTCCG 57.365 42.857 8.05 0.00 0.00 4.30
539 569 0.108186 TCCGTGAAGCTATGCCACTG 60.108 55.000 0.00 0.00 0.00 3.66
575 605 4.779475 CGGAGGATATGTGTGGCC 57.221 61.111 0.00 0.00 0.00 5.36
614 644 2.887152 GGTGAATGATATCAACAGGGGC 59.113 50.000 9.99 2.13 36.99 5.80
634 664 2.362889 CGGAGGCCCCAATGCTTT 60.363 61.111 0.00 0.00 34.14 3.51
641 671 1.410153 GGCCCCAATGCTTTGATAGTG 59.590 52.381 13.58 0.00 34.60 2.74
668 698 6.064717 GGAAATCCTGAGCCATTGTAATAGT 58.935 40.000 0.00 0.00 0.00 2.12
701 731 3.243177 GCTCTTTTATTCACGAGCGTAGG 59.757 47.826 0.00 0.00 39.39 3.18
782 813 6.933514 AACATATTTGGTTGGACAATCCTT 57.066 33.333 0.00 0.00 37.46 3.36
785 816 9.707957 AACATATTTGGTTGGACAATCCTTATA 57.292 29.630 0.00 0.00 37.46 0.98
802 833 0.536724 ATAACCCGAACCGTGTACCC 59.463 55.000 0.00 0.00 0.00 3.69
816 847 3.309682 CGTGTACCCATGACAATTGCTAG 59.690 47.826 5.05 0.00 0.00 3.42
826 857 7.365741 CCATGACAATTGCTAGGAATGAATAC 58.634 38.462 10.53 2.38 0.00 1.89
841 872 7.601886 AGGAATGAATACAGATAGCGAGATTTG 59.398 37.037 0.00 0.00 0.00 2.32
867 900 2.969443 AAAACACGCAGCAGTATCAC 57.031 45.000 0.00 0.00 0.00 3.06
868 901 0.790207 AAACACGCAGCAGTATCACG 59.210 50.000 0.00 0.00 0.00 4.35
869 902 1.014044 AACACGCAGCAGTATCACGG 61.014 55.000 0.00 0.00 0.00 4.94
870 903 2.509336 ACGCAGCAGTATCACGGC 60.509 61.111 0.00 0.00 39.63 5.68
871 904 2.509111 CGCAGCAGTATCACGGCA 60.509 61.111 4.34 0.00 41.80 5.69
872 905 2.802667 CGCAGCAGTATCACGGCAC 61.803 63.158 4.34 0.00 41.80 5.01
873 906 2.464459 GCAGCAGTATCACGGCACC 61.464 63.158 4.34 0.00 41.80 5.01
874 907 2.167219 CAGCAGTATCACGGCACCG 61.167 63.158 7.71 7.71 41.80 4.94
953 986 4.899239 GCACGATCCCCTGCCGAG 62.899 72.222 0.00 0.00 0.00 4.63
1021 1066 2.457598 TGGCGTCTCCTCTCATACTTT 58.542 47.619 0.00 0.00 35.26 2.66
1042 1087 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1304 1349 2.287427 CCATGAATCTTGAATCTGCGGC 60.287 50.000 0.00 0.00 0.00 6.53
1370 1415 9.168451 TCGTTTGATGCACTATTTCCTAATTTA 57.832 29.630 0.00 0.00 0.00 1.40
1413 1458 4.133820 TGCAATGATATTTGGTACTCCGG 58.866 43.478 0.00 0.00 36.30 5.14
1437 1482 8.148351 CGGGTCTAGTTTATGAGGATAAATGAA 58.852 37.037 0.00 0.00 0.00 2.57
1573 1632 4.034048 CCGGATCGAAAACCTAGACAATTG 59.966 45.833 3.24 3.24 0.00 2.32
1620 1693 3.868754 GCCGAAAACCATACAAGAGAGGT 60.869 47.826 0.00 0.00 35.47 3.85
1651 1724 4.157840 AGAGAAACCAAAACAAAAGACGCT 59.842 37.500 0.00 0.00 0.00 5.07
1795 1870 2.920384 TGCGTACCAGGCACCAGA 60.920 61.111 0.00 0.00 33.67 3.86
1892 1978 5.466432 GGAAACGATTAGCAAGTTAGGAC 57.534 43.478 0.00 0.00 0.00 3.85
1909 1996 0.179156 GACACTTGCGGCATCATTGG 60.179 55.000 2.28 0.00 0.00 3.16
1922 2009 3.118884 GCATCATTGGGCAAAGATGAACT 60.119 43.478 14.44 0.00 44.65 3.01
1939 2026 3.197766 TGAACTGAGACAACACCAAGAGT 59.802 43.478 0.00 0.00 0.00 3.24
1945 2032 5.924356 TGAGACAACACCAAGAGTATGAAA 58.076 37.500 0.00 0.00 0.00 2.69
1969 2056 4.012895 GCACCACAACGACAGCCG 62.013 66.667 0.00 0.00 45.44 5.52
2003 2092 3.977244 GCACAACAACAGGGGCGG 61.977 66.667 0.00 0.00 0.00 6.13
2076 2166 2.040330 CACCACCACCACCAACATG 58.960 57.895 0.00 0.00 0.00 3.21
2080 2170 2.203611 CCACCACCAACATGCCCA 60.204 61.111 0.00 0.00 0.00 5.36
2082 2172 1.531365 CACCACCAACATGCCCACT 60.531 57.895 0.00 0.00 0.00 4.00
2094 2184 2.912025 CCCACTGCAACACCCACC 60.912 66.667 0.00 0.00 0.00 4.61
2263 2355 2.028484 GTTGGTCGTCTGGTCGCA 59.972 61.111 0.00 0.00 0.00 5.10
2277 2369 1.077357 TCGCAACCCAACAACACCT 60.077 52.632 0.00 0.00 0.00 4.00
2300 2392 3.498841 CGTAGAGGGGAGAGGTGTCATAT 60.499 52.174 0.00 0.00 0.00 1.78
2372 2466 2.571653 TGGAAGAATCGAACCACTCCAT 59.428 45.455 0.00 0.00 0.00 3.41
2374 2468 3.118592 GGAAGAATCGAACCACTCCATCT 60.119 47.826 0.00 0.00 0.00 2.90
2455 2549 3.637273 GTCGACCCCCAGCCAGTT 61.637 66.667 3.51 0.00 0.00 3.16
2864 2965 2.677228 CCGCCCCTCACCAGAAAT 59.323 61.111 0.00 0.00 0.00 2.17
2870 2971 1.675310 CCTCACCAGAAATGCGCCA 60.675 57.895 4.18 0.00 0.00 5.69
2871 2972 1.243342 CCTCACCAGAAATGCGCCAA 61.243 55.000 4.18 0.00 0.00 4.52
2872 2973 0.169672 CTCACCAGAAATGCGCCAAG 59.830 55.000 4.18 0.00 0.00 3.61
3017 3135 4.988598 CGCCGACCCACAACAGCT 62.989 66.667 0.00 0.00 0.00 4.24
3018 3136 2.345991 GCCGACCCACAACAGCTA 59.654 61.111 0.00 0.00 0.00 3.32
3019 3137 1.741770 GCCGACCCACAACAGCTAG 60.742 63.158 0.00 0.00 0.00 3.42
3121 3239 4.741239 ACCGTCCCCAGCCTCCAT 62.741 66.667 0.00 0.00 0.00 3.41
3280 3401 4.446413 CGGCGGGGAGGTGTGTAC 62.446 72.222 0.00 0.00 0.00 2.90
3283 3405 2.580601 GCGGGGAGGTGTGTACAGT 61.581 63.158 0.00 0.00 0.00 3.55
3287 3409 1.125711 GGGAGGTGTGTACAGTGGGT 61.126 60.000 0.00 0.00 0.00 4.51
3690 3812 2.348411 ACACCCTGAGTTGGAACTTG 57.652 50.000 0.00 0.00 39.88 3.16
3691 3813 0.954452 CACCCTGAGTTGGAACTTGC 59.046 55.000 0.00 0.00 39.88 4.01
3706 3828 4.083003 GGAACTTGCCATTCGTGATGTAAA 60.083 41.667 1.96 0.00 33.71 2.01
3711 3833 5.493133 TGCCATTCGTGATGTAAAATACC 57.507 39.130 1.96 0.00 33.71 2.73
3718 3840 4.632251 TCGTGATGTAAAATACCGTGCAAT 59.368 37.500 0.00 0.00 0.00 3.56
3737 3859 7.512297 GTGCAATGATGTAAAATTTGGAACAG 58.488 34.615 0.00 0.00 42.39 3.16
3771 3893 1.274728 AGGTGCTACTGCTGTTCAGAG 59.725 52.381 0.09 0.00 45.72 3.35
3796 3918 6.206634 GTGGATGGTTTGTTTCATCTTGACTA 59.793 38.462 0.00 0.00 39.57 2.59
3804 3926 7.715265 TTGTTTCATCTTGACTAACTGTCTC 57.285 36.000 0.00 0.00 45.54 3.36
3805 3927 6.816136 TGTTTCATCTTGACTAACTGTCTCA 58.184 36.000 0.00 0.00 45.54 3.27
3875 3999 1.766143 GCAGCATAGAACGAAGCGGG 61.766 60.000 0.00 0.00 0.00 6.13
3990 4116 8.978539 GGTAGCTGGAAAATTTAAAAGTTGAAG 58.021 33.333 0.00 0.00 0.00 3.02
4190 4316 8.099537 AGATGGTATAAGAAGGAATATGCTGTG 58.900 37.037 0.00 0.00 0.00 3.66
4562 4690 9.734620 TTTTCAAGATGACTGTTTTAACTGATG 57.265 29.630 6.52 0.00 0.00 3.07
4728 4860 5.930837 TGAACAAATTTCCTTGTCACCTT 57.069 34.783 0.00 0.00 38.59 3.50
5358 5565 4.837298 TGGACCAATCATTCAAATGTTCCA 59.163 37.500 0.00 5.92 37.65 3.53
5637 5844 4.937620 GCAGTCTCTTTCATTGACCATACA 59.062 41.667 0.00 0.00 0.00 2.29
5757 5964 7.303634 TGATATAAACGCTCTTGTTTTCTCC 57.696 36.000 0.00 0.00 41.92 3.71
5799 6006 4.978580 GTGAGTGCAAGAGTTTTTGATTCC 59.021 41.667 0.00 0.00 0.00 3.01
5904 6111 7.545615 GCCAAGTGGAATTCTAAAAATTACAGG 59.454 37.037 5.23 0.00 37.39 4.00
5980 6187 5.345472 GGTAAGAAGACTTTAAGTGAGCGAC 59.655 44.000 0.93 0.00 37.53 5.19
6049 6256 7.185318 TGGCTCAACCATTTGATATTTGAAT 57.815 32.000 0.00 0.00 46.36 2.57
6109 6316 0.968405 TTTGGCCTTCACCATTCTGC 59.032 50.000 3.32 0.00 40.13 4.26
6206 6413 2.611800 ATCCCCTGTCCAGCAGCA 60.612 61.111 0.00 0.00 43.71 4.41
6571 6784 0.108138 AGATACAACCGCTGAGGCAC 60.108 55.000 0.00 0.00 46.52 5.01
6580 6793 2.949106 CTGAGGCACCACGCTTTG 59.051 61.111 0.00 0.00 41.91 2.77
6598 6811 1.352622 TGTGCCAGGTTCTCCAGGTT 61.353 55.000 0.00 0.00 41.70 3.50
6702 6919 1.629013 TTCTACTCGCGTGCTTGATG 58.371 50.000 5.77 0.00 0.00 3.07
6730 6947 5.643664 CCATGATACATTTGAAGGTGTGTG 58.356 41.667 0.00 0.00 0.00 3.82
6751 6973 3.271729 GTTTCTACTAGCCCAGCTTTCC 58.728 50.000 0.00 0.00 40.44 3.13
6887 7115 6.934645 TGGATGCCACTATTACTATTAAGTGC 59.065 38.462 0.00 0.00 38.39 4.40
6944 7172 4.174009 CGTAGAACCCAGAACTGTACATG 58.826 47.826 0.00 0.00 0.00 3.21
6946 7174 5.106038 CGTAGAACCCAGAACTGTACATGTA 60.106 44.000 0.08 0.08 0.00 2.29
6961 7189 6.521162 TGTACATGTATGAAGTGAACTGTGT 58.479 36.000 9.18 0.00 0.00 3.72
6965 7193 6.318648 ACATGTATGAAGTGAACTGTGTTTGT 59.681 34.615 0.00 0.00 0.00 2.83
6976 7204 5.353123 TGAACTGTGTTTGTGTACTTTCTCC 59.647 40.000 0.00 0.00 0.00 3.71
6983 7211 5.123186 TGTTTGTGTACTTTCTCCTGTTGTG 59.877 40.000 0.00 0.00 0.00 3.33
6984 7212 4.481368 TGTGTACTTTCTCCTGTTGTGT 57.519 40.909 0.00 0.00 0.00 3.72
6996 7224 4.901868 TCCTGTTGTGTACCCTTTACATC 58.098 43.478 0.00 0.00 0.00 3.06
6997 7225 4.348461 TCCTGTTGTGTACCCTTTACATCA 59.652 41.667 0.00 0.00 0.00 3.07
6999 7227 5.181245 CCTGTTGTGTACCCTTTACATCAAG 59.819 44.000 0.00 0.00 0.00 3.02
7000 7228 5.931294 TGTTGTGTACCCTTTACATCAAGA 58.069 37.500 0.00 0.00 0.00 3.02
7003 7231 7.504238 TGTTGTGTACCCTTTACATCAAGAAAT 59.496 33.333 0.00 0.00 0.00 2.17
7005 7233 9.575868 TTGTGTACCCTTTACATCAAGAAATTA 57.424 29.630 0.00 0.00 0.00 1.40
7006 7234 9.747898 TGTGTACCCTTTACATCAAGAAATTAT 57.252 29.630 0.00 0.00 0.00 1.28
7034 7262 5.957771 AGGTATGCTGGAGAATAAACTCA 57.042 39.130 0.00 0.00 38.51 3.41
7042 7270 8.635765 TGCTGGAGAATAAACTCATTTTAAGT 57.364 30.769 0.00 0.00 38.51 2.24
7043 7271 9.077885 TGCTGGAGAATAAACTCATTTTAAGTT 57.922 29.630 0.00 0.00 38.59 2.66
7044 7272 9.914131 GCTGGAGAATAAACTCATTTTAAGTTT 57.086 29.630 6.50 6.50 46.04 2.66
7074 7302 9.833917 AAAGGGAAGTTAGTATAAATCACTAGC 57.166 33.333 0.00 0.00 31.86 3.42
7094 7322 2.560981 GCTAAGCTAGGATCAGACCCTC 59.439 54.545 0.00 0.00 35.30 4.30
7107 7335 5.367945 TCAGACCCTCCATATAAAACCAC 57.632 43.478 0.00 0.00 0.00 4.16
7145 7374 4.042311 TGTTTCTTGTATCTTGGTGCCCTA 59.958 41.667 0.00 0.00 0.00 3.53
7162 7391 6.483640 GGTGCCCTATCAAACTAGTATGAAAG 59.516 42.308 0.00 0.00 0.00 2.62
7194 7439 1.463444 ACGACATGCTTAAAACCTCGC 59.537 47.619 0.00 0.00 0.00 5.03
7203 7448 0.596082 TAAAACCTCGCTTGCCTTGC 59.404 50.000 0.00 0.00 0.00 4.01
7271 7516 4.156008 CCTACTGTAAAAACTGTGGATGCC 59.844 45.833 1.46 0.00 0.00 4.40
7313 7558 5.376854 AACTTAGGAAACATGATGCACAC 57.623 39.130 0.00 0.00 0.00 3.82
7321 7566 2.337583 ACATGATGCACACGACAGTAC 58.662 47.619 0.00 0.00 0.00 2.73
7323 7568 0.388006 TGATGCACACGACAGTACGG 60.388 55.000 0.00 0.00 37.61 4.02
7327 7572 1.441515 CACACGACAGTACGGTCCG 60.442 63.158 18.69 10.48 37.61 4.79
7340 7585 3.940209 ACGGTCCGTAACTGAACATAA 57.060 42.857 17.19 0.00 38.73 1.90
7349 7594 6.762187 TCCGTAACTGAACATAACAAGTTTGA 59.238 34.615 0.00 0.00 0.00 2.69
7412 7657 5.359756 TGCTAACATAGAACCACAGCATAG 58.640 41.667 0.00 0.00 32.94 2.23
7415 7660 6.984474 GCTAACATAGAACCACAGCATAGTTA 59.016 38.462 0.00 0.00 0.00 2.24
7439 7685 3.079578 ACTGCATCAGTCATCACCAAAG 58.920 45.455 0.00 0.00 41.21 2.77
7444 7690 4.093998 GCATCAGTCATCACCAAAGTACTG 59.906 45.833 0.00 0.00 36.52 2.74
7447 7693 5.297547 TCAGTCATCACCAAAGTACTGAAC 58.702 41.667 0.00 0.00 40.10 3.18
7468 7714 9.409312 CTGAACAAAATGCATAACATAACTGAA 57.591 29.630 0.00 0.00 38.34 3.02
7521 7767 7.395190 AACTGAACATTGAAGCATAGCATAA 57.605 32.000 0.00 0.00 0.00 1.90
7522 7768 6.789262 ACTGAACATTGAAGCATAGCATAAC 58.211 36.000 0.00 0.00 0.00 1.89
7524 7770 6.788243 TGAACATTGAAGCATAGCATAACTG 58.212 36.000 0.00 0.00 0.00 3.16
7525 7771 5.762825 ACATTGAAGCATAGCATAACTGG 57.237 39.130 0.00 0.00 0.00 4.00
7526 7772 5.439721 ACATTGAAGCATAGCATAACTGGA 58.560 37.500 0.00 0.00 0.00 3.86
7527 7773 6.066690 ACATTGAAGCATAGCATAACTGGAT 58.933 36.000 0.00 0.00 0.00 3.41
7528 7774 6.206243 ACATTGAAGCATAGCATAACTGGATC 59.794 38.462 0.00 0.00 0.00 3.36
7530 7776 5.303165 TGAAGCATAGCATAACTGGATCAG 58.697 41.667 0.00 0.00 37.52 2.90
7533 7779 4.592351 AGCATAGCATAACTGGATCAGTCT 59.408 41.667 0.75 0.00 44.62 3.24
7538 7784 3.742640 GCATAACTGGATCAGTCTCACCC 60.743 52.174 0.75 0.00 44.62 4.61
7539 7785 1.280457 AACTGGATCAGTCTCACCCC 58.720 55.000 0.75 0.00 44.62 4.95
7540 7786 0.117140 ACTGGATCAGTCTCACCCCA 59.883 55.000 0.00 0.00 41.21 4.96
7542 7788 0.909610 TGGATCAGTCTCACCCCACC 60.910 60.000 0.00 0.00 0.00 4.61
7543 7789 0.909610 GGATCAGTCTCACCCCACCA 60.910 60.000 0.00 0.00 0.00 4.17
7545 7791 0.693049 ATCAGTCTCACCCCACCAAC 59.307 55.000 0.00 0.00 0.00 3.77
7546 7792 1.073199 CAGTCTCACCCCACCAACC 59.927 63.158 0.00 0.00 0.00 3.77
7559 7814 0.401738 ACCAACCAGGGACATCACAG 59.598 55.000 0.00 0.00 43.89 3.66
7562 7817 0.321671 AACCAGGGACATCACAGACG 59.678 55.000 0.00 0.00 0.00 4.18
7568 7823 1.409064 GGGACATCACAGACGCTGATA 59.591 52.381 12.77 2.26 35.18 2.15
7573 7828 1.485124 TCACAGACGCTGATACCCAT 58.515 50.000 12.77 0.00 35.18 4.00
7590 7845 4.897051 ACCCATCTACCTAGATTTCACCT 58.103 43.478 0.00 0.00 40.91 4.00
7596 7851 1.135083 ACCTAGATTTCACCTGACGCG 60.135 52.381 3.53 3.53 0.00 6.01
7640 7895 2.286523 CGACCTCCTTGGACTGCCT 61.287 63.158 0.00 0.00 39.71 4.75
7654 7909 1.596408 TGCCTAAGCAGCACGATGA 59.404 52.632 0.00 0.00 46.52 2.92
7662 7917 2.548875 AGCAGCACGATGATCTTCTTC 58.451 47.619 6.99 0.00 0.00 2.87
7684 7939 3.730761 GCTCACGCTTGGTGCCAG 61.731 66.667 0.00 0.00 46.56 4.85
7731 7986 1.364901 CACCCTTGCCAGCTTGTTG 59.635 57.895 0.00 0.00 0.00 3.33
7776 8031 0.693622 TCTCGAGGTCACTCTCCACT 59.306 55.000 13.56 0.00 41.71 4.00
7800 8055 3.220999 CTTGACGCCACGGAGGACA 62.221 63.158 0.00 0.00 41.22 4.02
7845 8100 2.315925 GGAGCACGATGATCTTCCAA 57.684 50.000 3.19 0.00 32.54 3.53
7851 8106 3.732212 CACGATGATCTTCCAATAGGCA 58.268 45.455 3.19 0.00 33.74 4.75
7856 8111 4.412796 TGATCTTCCAATAGGCAGTCAG 57.587 45.455 0.00 0.00 33.74 3.51
7875 8130 3.490759 CGCGCGCTCAGGTCAAAT 61.491 61.111 30.48 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.437359 ATGAGTCCTTGCAGCGGC 60.437 61.111 0.31 0.31 41.68 6.53
20 21 2.110967 CCATGAGTCCTTGCAGCGG 61.111 63.158 0.00 0.00 0.00 5.52
21 22 2.758089 GCCATGAGTCCTTGCAGCG 61.758 63.158 0.00 0.00 0.00 5.18
22 23 1.035932 ATGCCATGAGTCCTTGCAGC 61.036 55.000 0.00 0.00 0.00 5.25
23 24 1.022735 GATGCCATGAGTCCTTGCAG 58.977 55.000 0.00 0.00 0.00 4.41
24 25 0.328926 TGATGCCATGAGTCCTTGCA 59.671 50.000 0.00 0.00 0.00 4.08
25 26 1.688772 ATGATGCCATGAGTCCTTGC 58.311 50.000 0.00 0.00 0.00 4.01
37 40 1.594293 GCCAGCAATGCATGATGCC 60.594 57.895 17.68 0.00 44.14 4.40
40 43 0.396556 TCAGGCCAGCAATGCATGAT 60.397 50.000 8.35 0.00 43.73 2.45
59 62 4.501571 GCCCATACACATCGAGACATAGTT 60.502 45.833 0.00 0.00 0.00 2.24
68 71 0.313987 CTAGCGCCCATACACATCGA 59.686 55.000 2.29 0.00 0.00 3.59
71 74 0.250038 CTGCTAGCGCCCATACACAT 60.250 55.000 10.77 0.00 34.43 3.21
102 105 5.336610 CCATATTCTCAGTCATCTGCGAGAT 60.337 44.000 0.00 0.00 41.10 2.75
106 109 4.248691 TCCATATTCTCAGTCATCTGCG 57.751 45.455 0.00 0.00 41.10 5.18
141 144 5.193663 TCATTCAAATCGAACAGCCAAAA 57.806 34.783 0.00 0.00 36.12 2.44
152 155 6.909849 TGATCAAACGTTTCATTCAAATCG 57.090 33.333 11.37 0.00 0.00 3.34
155 158 9.179552 CTAACATGATCAAACGTTTCATTCAAA 57.820 29.630 11.37 0.00 0.00 2.69
170 173 5.164620 TCCTTGTGAAGCTAACATGATCA 57.835 39.130 13.80 0.00 0.00 2.92
178 181 2.375174 ACCACCATCCTTGTGAAGCTAA 59.625 45.455 0.00 0.00 35.74 3.09
218 221 2.882927 TTGCCTTACGTCTCGCATAT 57.117 45.000 0.00 0.00 0.00 1.78
227 230 8.635765 AAATGGATTCATATATTGCCTTACGT 57.364 30.769 0.00 0.00 32.44 3.57
257 260 6.149474 CGAAAGATGTGGTTTATTGAGGACTT 59.851 38.462 0.00 0.00 0.00 3.01
266 269 4.562082 TGTCGACGAAAGATGTGGTTTAT 58.438 39.130 11.62 0.00 0.00 1.40
267 270 3.979948 TGTCGACGAAAGATGTGGTTTA 58.020 40.909 11.62 0.00 0.00 2.01
281 284 3.000674 GCTCATTGATGTAGTTGTCGACG 60.001 47.826 11.62 0.00 0.00 5.12
285 288 4.697352 ACCAAGCTCATTGATGTAGTTGTC 59.303 41.667 0.00 0.00 41.83 3.18
299 302 2.401583 ACGCATATTGACCAAGCTCA 57.598 45.000 0.00 0.00 0.00 4.26
302 305 3.429085 CTTGAACGCATATTGACCAAGC 58.571 45.455 0.00 0.00 0.00 4.01
331 334 3.003173 CCACCTCTCCGGCCTTGA 61.003 66.667 0.00 0.00 35.61 3.02
357 386 4.264253 TGATCTTGACATTGCCAGTAAGG 58.736 43.478 0.00 0.00 41.84 2.69
359 388 5.069318 TGTTGATCTTGACATTGCCAGTAA 58.931 37.500 0.00 0.00 0.00 2.24
381 410 0.812811 CCATGACTGCTCCGTCCATG 60.813 60.000 0.00 0.00 32.97 3.66
382 411 0.977627 TCCATGACTGCTCCGTCCAT 60.978 55.000 0.00 0.00 32.97 3.41
397 426 1.137594 TCCTTCCCGGTGGTTTCCAT 61.138 55.000 0.00 0.00 35.28 3.41
398 427 1.770927 TCCTTCCCGGTGGTTTCCA 60.771 57.895 0.00 0.00 0.00 3.53
422 452 0.723981 GATCTCTGCAAACAGTCGCC 59.276 55.000 0.00 0.00 44.77 5.54
426 456 2.027377 CCTCCTGATCTCTGCAAACAGT 60.027 50.000 0.00 0.00 44.77 3.55
440 470 4.083080 TCCCAAGTATAAACCCTCCTGA 57.917 45.455 0.00 0.00 0.00 3.86
470 500 3.267031 CCCTAATTCCCTGAAAGACCAGT 59.733 47.826 0.00 0.00 34.07 4.00
488 518 5.891551 GGTTTGCAAAATTAGAGGATCCCTA 59.108 40.000 14.67 6.99 31.76 3.53
500 530 4.987912 CGGAATGTGTAGGTTTGCAAAATT 59.012 37.500 14.67 8.05 0.00 1.82
516 546 1.065491 TGGCATAGCTTCACGGAATGT 60.065 47.619 0.00 0.00 0.00 2.71
520 550 0.108186 CAGTGGCATAGCTTCACGGA 60.108 55.000 0.00 0.00 36.60 4.69
534 564 1.525923 CCAGATCCTCTGCCAGTGG 59.474 63.158 4.20 4.20 42.98 4.00
539 569 3.453070 GACCGCCAGATCCTCTGCC 62.453 68.421 0.00 0.00 42.98 4.85
542 572 2.835431 CGGACCGCCAGATCCTCT 60.835 66.667 0.00 0.00 32.33 3.69
544 574 4.458829 TCCGGACCGCCAGATCCT 62.459 66.667 8.86 0.00 32.33 3.24
549 579 1.908793 ATATCCTCCGGACCGCCAG 60.909 63.158 8.86 6.22 32.98 4.85
556 586 1.407656 GGCCACACATATCCTCCGGA 61.408 60.000 2.93 2.93 35.55 5.14
574 604 0.319728 CACCTCCTGACAGTCTGTGG 59.680 60.000 11.04 6.62 0.00 4.17
575 605 0.319728 CCACCTCCTGACAGTCTGTG 59.680 60.000 11.04 5.28 0.00 3.66
578 608 0.188587 TCACCACCTCCTGACAGTCT 59.811 55.000 1.31 0.00 0.00 3.24
654 684 9.533253 GCATGAAATAAAACTATTACAATGGCT 57.467 29.630 0.00 0.00 0.00 4.75
756 786 7.744733 AGGATTGTCCAACCAAATATGTTTTT 58.255 30.769 0.00 0.00 39.61 1.94
757 787 7.315066 AGGATTGTCCAACCAAATATGTTTT 57.685 32.000 0.00 0.00 39.61 2.43
774 805 3.198417 ACGGTTCGGGTTATAAGGATTGT 59.802 43.478 0.00 0.00 0.00 2.71
782 813 1.754226 GGGTACACGGTTCGGGTTATA 59.246 52.381 0.00 0.00 42.45 0.98
785 816 1.482748 ATGGGTACACGGTTCGGGTT 61.483 55.000 0.00 0.00 42.45 4.11
802 833 7.933396 TGTATTCATTCCTAGCAATTGTCATG 58.067 34.615 7.40 1.63 0.00 3.07
816 847 7.600375 TCAAATCTCGCTATCTGTATTCATTCC 59.400 37.037 0.00 0.00 0.00 3.01
852 885 2.802667 GCCGTGATACTGCTGCGTG 61.803 63.158 7.25 0.00 0.00 5.34
853 886 2.509336 GCCGTGATACTGCTGCGT 60.509 61.111 0.00 0.00 0.00 5.24
854 887 2.509111 TGCCGTGATACTGCTGCG 60.509 61.111 0.00 0.00 0.00 5.18
855 888 2.464459 GGTGCCGTGATACTGCTGC 61.464 63.158 0.00 0.00 0.00 5.25
856 889 2.167219 CGGTGCCGTGATACTGCTG 61.167 63.158 1.93 0.00 34.35 4.41
857 890 2.184322 CGGTGCCGTGATACTGCT 59.816 61.111 1.93 0.00 34.35 4.24
877 910 4.590918 TGCCGTGATACATAAGGGAAAAA 58.409 39.130 0.00 0.00 0.00 1.94
878 911 4.223556 TGCCGTGATACATAAGGGAAAA 57.776 40.909 0.00 0.00 0.00 2.29
879 912 3.916359 TGCCGTGATACATAAGGGAAA 57.084 42.857 0.00 0.00 0.00 3.13
880 913 3.554129 CGATGCCGTGATACATAAGGGAA 60.554 47.826 0.00 0.00 0.00 3.97
881 914 2.029380 CGATGCCGTGATACATAAGGGA 60.029 50.000 0.00 0.00 0.00 4.20
882 915 2.337583 CGATGCCGTGATACATAAGGG 58.662 52.381 0.00 0.00 0.00 3.95
910 943 2.526304 TGCCGTGATATACTTGAGGC 57.474 50.000 0.00 0.00 43.05 4.70
971 1004 4.257654 TCTTGCCGCCGGTGGAAA 62.258 61.111 38.08 32.06 0.00 3.13
1021 1066 2.015726 GGAGGAGGAGGAGGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
1304 1349 1.722751 CGAAAGCTGTAAAGCTGTGCG 60.723 52.381 8.57 8.92 45.54 5.34
1338 1383 6.907212 GGAAATAGTGCATCAAACGAACTATG 59.093 38.462 0.00 0.00 34.96 2.23
1478 1526 0.786435 ATTCAGGTGGGGAGCCTTTT 59.214 50.000 0.00 0.00 33.31 2.27
1651 1724 0.037326 CTAGGCGTGCCTTGTCTTGA 60.037 55.000 20.08 0.00 45.70 3.02
1794 1869 1.427592 GATGCTCCTCTGTTGCGCTC 61.428 60.000 9.73 2.14 0.00 5.03
1795 1870 1.449246 GATGCTCCTCTGTTGCGCT 60.449 57.895 9.73 0.00 0.00 5.92
1867 1949 2.467566 ACTTGCTAATCGTTTCCGGT 57.532 45.000 0.00 0.00 33.95 5.28
1868 1950 3.308866 CCTAACTTGCTAATCGTTTCCGG 59.691 47.826 0.00 0.00 33.95 5.14
1892 1978 1.140161 CCCAATGATGCCGCAAGTG 59.860 57.895 0.00 0.00 0.00 3.16
1909 1996 3.565482 TGTTGTCTCAGTTCATCTTTGCC 59.435 43.478 0.00 0.00 0.00 4.52
1922 2009 5.545063 TTCATACTCTTGGTGTTGTCTCA 57.455 39.130 0.00 0.00 0.00 3.27
1939 2026 1.017177 GTGGTGCGGCGAGTTTCATA 61.017 55.000 12.98 0.00 0.00 2.15
1969 2056 0.321919 TGCATGCTCAAGACCTCCAC 60.322 55.000 20.33 0.00 0.00 4.02
2003 2092 3.343421 GGTGGTGTTCGTCGGTGC 61.343 66.667 0.00 0.00 0.00 5.01
2076 2166 3.605664 GTGGGTGTTGCAGTGGGC 61.606 66.667 0.00 0.00 45.13 5.36
2080 2170 3.767630 GACGGGTGGGTGTTGCAGT 62.768 63.158 0.00 0.00 0.00 4.40
2082 2172 3.345607 TTGACGGGTGGGTGTTGCA 62.346 57.895 0.00 0.00 0.00 4.08
2094 2184 1.966451 GGGTCTGCTTGGTTGACGG 60.966 63.158 0.00 0.00 0.00 4.79
2195 2285 0.613777 GATGGAAGTTGAGACCCCGT 59.386 55.000 0.00 0.00 0.00 5.28
2263 2355 1.764134 TCTACGAGGTGTTGTTGGGTT 59.236 47.619 0.00 0.00 0.00 4.11
2277 2369 0.255318 GACACCTCTCCCCTCTACGA 59.745 60.000 0.00 0.00 0.00 3.43
2300 2392 0.406750 TCTGGACCACCTCGTTCCTA 59.593 55.000 0.00 0.00 37.04 2.94
2455 2549 2.115052 GATGGTGGTGGTGGTGCA 59.885 61.111 0.00 0.00 0.00 4.57
2616 2717 1.262640 TTACCTCCTTGGAGGCGTCC 61.263 60.000 29.93 18.69 46.05 4.79
2759 2860 0.610174 CTGCAGTGGACCTTGCTCTA 59.390 55.000 18.31 2.77 40.87 2.43
2829 2930 2.671070 CGTGGGCAGGTTGGATCT 59.329 61.111 0.00 0.00 0.00 2.75
2854 2955 1.865788 GCTTGGCGCATTTCTGGTGA 61.866 55.000 10.83 0.00 38.92 4.02
2923 3036 2.675056 CCTCTGCGTGTTCAGCTGC 61.675 63.158 9.47 0.00 34.19 5.25
3002 3120 1.741770 GCTAGCTGTTGTGGGTCGG 60.742 63.158 7.70 0.00 0.00 4.79
3076 3194 3.819920 CGCTCGCTGCTCTCTCCA 61.820 66.667 0.00 0.00 40.11 3.86
3274 3395 1.701031 CCACCCACCCACTGTACACA 61.701 60.000 0.00 0.00 0.00 3.72
3276 3397 2.150719 CCCACCCACCCACTGTACA 61.151 63.158 0.00 0.00 0.00 2.90
3278 3399 1.386200 AACCCACCCACCCACTGTA 60.386 57.895 0.00 0.00 0.00 2.74
3280 3401 2.203480 CAACCCACCCACCCACTG 60.203 66.667 0.00 0.00 0.00 3.66
3653 3775 9.967451 TCAGGGTGTTTAAATATATTTGACTCA 57.033 29.630 18.98 10.60 0.00 3.41
3669 3791 3.023832 CAAGTTCCAACTCAGGGTGTTT 58.976 45.455 0.00 0.00 38.57 2.83
3680 3802 1.606668 TCACGAATGGCAAGTTCCAAC 59.393 47.619 0.00 0.00 39.96 3.77
3690 3812 4.034742 ACGGTATTTTACATCACGAATGGC 59.965 41.667 0.00 0.00 39.90 4.40
3691 3813 5.498159 CACGGTATTTTACATCACGAATGG 58.502 41.667 0.00 0.00 39.90 3.16
3706 3828 7.277539 CCAAATTTTACATCATTGCACGGTATT 59.722 33.333 0.00 0.00 0.00 1.89
3711 3833 6.145209 TGTTCCAAATTTTACATCATTGCACG 59.855 34.615 0.00 0.00 0.00 5.34
3718 3840 6.024552 GGAGCTGTTCCAAATTTTACATCA 57.975 37.500 5.59 0.00 46.01 3.07
3737 3859 0.464554 GCACCTAACATCCCTGGAGC 60.465 60.000 0.00 0.00 0.00 4.70
3744 3866 2.093447 ACAGCAGTAGCACCTAACATCC 60.093 50.000 0.00 0.00 45.49 3.51
3771 3893 5.010012 AGTCAAGATGAAACAAACCATCCAC 59.990 40.000 0.00 0.00 39.85 4.02
3796 3918 8.466617 TTCTAAACTAGACTCTTGAGACAGTT 57.533 34.615 4.49 7.34 33.84 3.16
3825 3947 7.277174 AGTGAAGAATTAAAGGTCCACAAAG 57.723 36.000 0.00 0.00 0.00 2.77
3828 3950 5.163141 TGGAGTGAAGAATTAAAGGTCCACA 60.163 40.000 0.00 0.00 0.00 4.17
3958 4084 6.732896 TTAAATTTTCCAGCTACCACCAAA 57.267 33.333 0.00 0.00 0.00 3.28
3990 4116 3.689649 AGTAGGCCAACAATTCGATTCAC 59.310 43.478 5.01 0.00 0.00 3.18
4348 4474 8.421002 GCCTCTAATATCAAATATCCTCCTCTC 58.579 40.741 0.00 0.00 0.00 3.20
4562 4690 2.549754 CAGGGAAACATATCACCGCATC 59.450 50.000 0.00 0.00 0.00 3.91
4695 4827 9.695526 CAAGGAAATTTGTTCAAGATAATGTGA 57.304 29.630 0.00 0.00 0.00 3.58
4728 4860 7.867305 TGGAACATTAGTTTCTTGTTGTACA 57.133 32.000 0.00 0.00 38.30 2.90
5637 5844 7.373617 AGAAGTTTGGAATGGTTGGTTTAAT 57.626 32.000 0.00 0.00 0.00 1.40
5757 5964 7.011773 CACTCACATTGACAATAAGTTCTTCG 58.988 38.462 0.00 0.00 0.00 3.79
5799 6006 8.206867 TCCTCAACTATCTTGAACTCATTATGG 58.793 37.037 0.00 0.00 0.00 2.74
5890 6097 6.600882 AGACGGACTCCTGTAATTTTTAGA 57.399 37.500 0.00 0.00 30.59 2.10
5904 6111 2.406596 AGTGAGTAGGAGACGGACTC 57.593 55.000 0.00 0.00 44.07 3.36
5921 6128 3.128589 CACAAACACTTGCAACCAGTAGT 59.871 43.478 0.00 0.00 35.84 2.73
5980 6187 1.200020 GCCCTCAACTGAAAATGGTCG 59.800 52.381 0.00 0.00 0.00 4.79
6049 6256 5.984725 TCTATAAGCGTCTTCCCATTCAAA 58.015 37.500 0.00 0.00 0.00 2.69
6084 6291 4.463891 AGAATGGTGAAGGCCAAATTACTG 59.536 41.667 5.01 0.00 42.48 2.74
6109 6316 2.167075 GGATTTGGGGAATGAGCAACAG 59.833 50.000 0.00 0.00 0.00 3.16
6206 6413 2.307392 ACCAACCAAAACCAAGCCTTTT 59.693 40.909 0.00 0.00 0.00 2.27
6571 6784 2.406452 GAACCTGGCACAAAGCGTGG 62.406 60.000 0.00 0.00 46.45 4.94
6598 6811 6.814954 AGATAGGTTCATTAAAGCTCCTGA 57.185 37.500 0.00 0.00 44.43 3.86
6640 6853 4.022068 ACCACAAAATTTGATCAGCACGAT 60.022 37.500 13.19 0.00 36.91 3.73
6702 6919 3.003689 CCTTCAAATGTATCATGGCCGTC 59.996 47.826 0.00 0.00 0.00 4.79
6730 6947 3.271729 GGAAAGCTGGGCTAGTAGAAAC 58.728 50.000 0.00 0.00 38.25 2.78
6787 7015 4.924305 TTGAAGAAAGCTGCACAAAGAT 57.076 36.364 1.02 0.00 26.09 2.40
6887 7115 1.667724 GCATTGTACAGTAGGCAGCAG 59.332 52.381 0.00 0.00 0.00 4.24
6944 7172 6.119144 ACACAAACACAGTTCACTTCATAC 57.881 37.500 0.00 0.00 0.00 2.39
6946 7174 5.880332 AGTACACAAACACAGTTCACTTCAT 59.120 36.000 0.00 0.00 0.00 2.57
6961 7189 5.250200 ACACAACAGGAGAAAGTACACAAA 58.750 37.500 0.00 0.00 0.00 2.83
6965 7193 4.202284 GGGTACACAACAGGAGAAAGTACA 60.202 45.833 0.00 0.00 33.82 2.90
6976 7204 5.995282 TCTTGATGTAAAGGGTACACAACAG 59.005 40.000 0.00 0.00 0.00 3.16
6996 7224 9.903682 CCAGCATACCTATTCAATAATTTCTTG 57.096 33.333 0.00 0.00 0.00 3.02
6997 7225 9.866655 TCCAGCATACCTATTCAATAATTTCTT 57.133 29.630 0.00 0.00 0.00 2.52
6999 7227 9.507329 TCTCCAGCATACCTATTCAATAATTTC 57.493 33.333 0.00 0.00 0.00 2.17
7000 7228 9.866655 TTCTCCAGCATACCTATTCAATAATTT 57.133 29.630 0.00 0.00 0.00 1.82
7005 7233 9.289782 GTTTATTCTCCAGCATACCTATTCAAT 57.710 33.333 0.00 0.00 0.00 2.57
7006 7234 8.494433 AGTTTATTCTCCAGCATACCTATTCAA 58.506 33.333 0.00 0.00 0.00 2.69
7007 7235 8.034313 AGTTTATTCTCCAGCATACCTATTCA 57.966 34.615 0.00 0.00 0.00 2.57
7013 7241 7.573968 AAATGAGTTTATTCTCCAGCATACC 57.426 36.000 0.00 0.00 33.93 2.73
7048 7276 9.833917 GCTAGTGATTTATACTAACTTCCCTTT 57.166 33.333 0.00 0.00 30.82 3.11
7049 7277 9.214962 AGCTAGTGATTTATACTAACTTCCCTT 57.785 33.333 0.00 0.00 30.82 3.95
7050 7278 8.785184 AGCTAGTGATTTATACTAACTTCCCT 57.215 34.615 0.00 0.00 30.82 4.20
7071 7299 3.399644 AGGGTCTGATCCTAGCTTAGCTA 59.600 47.826 7.96 13.70 40.44 3.32
7072 7300 2.178984 AGGGTCTGATCCTAGCTTAGCT 59.821 50.000 12.67 12.67 43.41 3.32
7073 7301 2.560981 GAGGGTCTGATCCTAGCTTAGC 59.439 54.545 10.02 0.00 34.21 3.09
7074 7302 3.161866 GGAGGGTCTGATCCTAGCTTAG 58.838 54.545 10.02 0.00 34.21 2.18
7077 7305 0.937441 TGGAGGGTCTGATCCTAGCT 59.063 55.000 10.02 0.00 36.50 3.32
7084 7312 5.454755 CGTGGTTTTATATGGAGGGTCTGAT 60.455 44.000 0.00 0.00 0.00 2.90
7091 7319 5.240844 GGGATTTCGTGGTTTTATATGGAGG 59.759 44.000 0.00 0.00 0.00 4.30
7094 7322 6.127591 TGTTGGGATTTCGTGGTTTTATATGG 60.128 38.462 0.00 0.00 0.00 2.74
7107 7335 4.568152 AGAAACAACTGTTGGGATTTCG 57.432 40.909 23.15 0.00 38.44 3.46
7145 7374 8.918202 TTGAACCACTTTCATACTAGTTTGAT 57.082 30.769 15.53 0.67 43.99 2.57
7162 7391 2.806244 AGCATGTCGTTACTTGAACCAC 59.194 45.455 0.00 0.00 34.21 4.16
7173 7402 2.095919 GCGAGGTTTTAAGCATGTCGTT 60.096 45.455 0.00 0.00 0.00 3.85
7178 7407 2.253603 GCAAGCGAGGTTTTAAGCATG 58.746 47.619 0.00 0.00 0.00 4.06
7194 7439 4.903054 TCCTATATGATCTGCAAGGCAAG 58.097 43.478 0.00 0.00 38.41 4.01
7254 7499 2.890945 ACCTGGCATCCACAGTTTTTAC 59.109 45.455 0.00 0.00 34.16 2.01
7298 7543 2.224079 ACTGTCGTGTGCATCATGTTTC 59.776 45.455 0.00 0.00 34.87 2.78
7313 7558 0.798776 AGTTACGGACCGTACTGTCG 59.201 55.000 26.03 8.88 42.13 4.35
7321 7566 3.577667 TGTTATGTTCAGTTACGGACCG 58.422 45.455 13.61 13.61 0.00 4.79
7323 7568 6.535274 AACTTGTTATGTTCAGTTACGGAC 57.465 37.500 0.00 0.00 0.00 4.79
7327 7572 8.283291 CCTCTCAAACTTGTTATGTTCAGTTAC 58.717 37.037 0.00 0.00 0.00 2.50
7365 7610 8.924691 GCAAGCAATTTTCTGTTATGTTATGAA 58.075 29.630 0.00 0.00 0.00 2.57
7382 7627 5.476599 TGTGGTTCTATGTTAGCAAGCAATT 59.523 36.000 0.00 0.00 30.88 2.32
7385 7630 4.002982 CTGTGGTTCTATGTTAGCAAGCA 58.997 43.478 0.00 0.00 0.00 3.91
7386 7631 3.181506 GCTGTGGTTCTATGTTAGCAAGC 60.182 47.826 0.00 0.00 0.00 4.01
7412 7657 4.142816 GGTGATGACTGATGCAGTGTTAAC 60.143 45.833 4.60 0.00 45.44 2.01
7415 7660 2.224597 TGGTGATGACTGATGCAGTGTT 60.225 45.455 4.60 0.00 45.44 3.32
7439 7685 9.840427 AGTTATGTTATGCATTTTGTTCAGTAC 57.160 29.630 3.54 0.00 38.94 2.73
7444 7690 9.190858 TGTTCAGTTATGTTATGCATTTTGTTC 57.809 29.630 3.54 0.00 38.94 3.18
7486 7732 9.793252 GCTTCAATGTTCAGTTATGTTATGAAT 57.207 29.630 0.00 0.00 35.56 2.57
7487 7733 8.791675 TGCTTCAATGTTCAGTTATGTTATGAA 58.208 29.630 0.00 0.00 0.00 2.57
7507 7753 5.163269 ACTGATCCAGTTATGCTATGCTTCA 60.163 40.000 0.00 0.00 42.59 3.02
7522 7768 0.539051 GTGGGGTGAGACTGATCCAG 59.461 60.000 0.00 0.00 37.52 3.86
7524 7770 0.909610 TGGTGGGGTGAGACTGATCC 60.910 60.000 0.00 0.00 0.00 3.36
7525 7771 0.984230 TTGGTGGGGTGAGACTGATC 59.016 55.000 0.00 0.00 0.00 2.92
7526 7772 0.693049 GTTGGTGGGGTGAGACTGAT 59.307 55.000 0.00 0.00 0.00 2.90
7527 7773 1.415672 GGTTGGTGGGGTGAGACTGA 61.416 60.000 0.00 0.00 0.00 3.41
7528 7774 1.073199 GGTTGGTGGGGTGAGACTG 59.927 63.158 0.00 0.00 0.00 3.51
7530 7776 1.073199 CTGGTTGGTGGGGTGAGAC 59.927 63.158 0.00 0.00 0.00 3.36
7533 7779 3.182263 CCCTGGTTGGTGGGGTGA 61.182 66.667 0.00 0.00 39.76 4.02
7538 7784 0.609131 GTGATGTCCCTGGTTGGTGG 60.609 60.000 0.00 0.00 0.00 4.61
7539 7785 0.110295 TGTGATGTCCCTGGTTGGTG 59.890 55.000 0.00 0.00 0.00 4.17
7540 7786 0.401738 CTGTGATGTCCCTGGTTGGT 59.598 55.000 0.00 0.00 0.00 3.67
7542 7788 1.813513 GTCTGTGATGTCCCTGGTTG 58.186 55.000 0.00 0.00 0.00 3.77
7543 7789 0.321671 CGTCTGTGATGTCCCTGGTT 59.678 55.000 0.00 0.00 0.00 3.67
7545 7791 1.448540 GCGTCTGTGATGTCCCTGG 60.449 63.158 0.00 0.00 0.00 4.45
7546 7792 0.738762 CAGCGTCTGTGATGTCCCTG 60.739 60.000 0.00 0.00 0.00 4.45
7559 7814 2.240279 AGGTAGATGGGTATCAGCGTC 58.760 52.381 0.00 0.00 36.78 5.19
7562 7817 6.211584 TGAAATCTAGGTAGATGGGTATCAGC 59.788 42.308 0.14 0.00 41.96 4.26
7568 7823 4.656112 CAGGTGAAATCTAGGTAGATGGGT 59.344 45.833 0.14 0.00 41.96 4.51
7573 7828 3.380637 GCGTCAGGTGAAATCTAGGTAGA 59.619 47.826 0.00 0.00 36.65 2.59
7590 7845 2.181777 GACAGGATCAGCGCGTCA 59.818 61.111 8.43 0.00 0.00 4.35
7596 7851 2.617308 CAACATCATGGACAGGATCAGC 59.383 50.000 0.00 0.00 28.16 4.26
7640 7895 3.808466 AGAAGATCATCGTGCTGCTTA 57.192 42.857 0.00 0.00 0.00 3.09
7654 7909 0.459237 CGTGAGCGCCTGAAGAAGAT 60.459 55.000 2.29 0.00 0.00 2.40
7718 7973 2.062777 TTGGGCAACAAGCTGGCAA 61.063 52.632 0.00 0.00 43.45 4.52
7731 7986 0.251354 TGTCTGATGAGCTCTTGGGC 59.749 55.000 16.19 6.11 0.00 5.36
7737 7992 1.830477 AGGGAACTGTCTGATGAGCTC 59.170 52.381 6.82 6.82 41.13 4.09
7764 8019 1.139947 GCGGCTAGTGGAGAGTGAC 59.860 63.158 0.00 0.00 0.00 3.67
7794 8049 3.200593 CTGGCGCTGCATGTCCTC 61.201 66.667 7.64 0.00 0.00 3.71
7815 8070 1.522355 CGTGCTCCGGCTCATTGAT 60.522 57.895 0.00 0.00 39.59 2.57
7818 8073 1.522355 CATCGTGCTCCGGCTCATT 60.522 57.895 0.00 0.00 39.59 2.57
7845 8100 4.899239 GCGCGCCTGACTGCCTAT 62.899 66.667 23.24 0.00 0.00 2.57
7875 8130 4.666253 GAGTTGGCAGGGCAGGCA 62.666 66.667 1.34 1.34 42.83 4.75


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

AutoCloner maintained by Alex Coulton.