Multiple sequence alignment - TraesCS1B01G445600

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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 TraesCS1B01G445600 chr1B 100.000 4302 0 0 1 4302 665455935 665451634 0.000000e+00 7945.0
1 TraesCS1B01G445600 chr1D 92.406 2752 130 23 666 3366 478256363 478253640 0.000000e+00 3851.0
2 TraesCS1B01G445600 chr1D 84.868 456 41 11 172 610 478256997 478256553 6.610000e-118 435.0
3 TraesCS1B01G445600 chr1D 91.781 146 11 1 3388 3533 478253652 478253508 7.290000e-48 202.0
4 TraesCS1B01G445600 chr1A 91.105 2552 169 25 860 3366 574483865 574481327 0.000000e+00 3402.0
5 TraesCS1B01G445600 chr1A 91.329 173 14 1 3388 3560 574481339 574481168 7.190000e-58 235.0
6 TraesCS1B01G445600 chr1A 89.947 189 7 6 686 867 574484090 574483907 2.590000e-57 233.0
7 TraesCS1B01G445600 chr3A 94.467 741 31 1 3562 4302 12608725 12607995 0.000000e+00 1133.0
8 TraesCS1B01G445600 chr3A 94.332 741 32 1 3562 4302 12593096 12592366 0.000000e+00 1127.0
9 TraesCS1B01G445600 chr3A 95.714 70 3 0 3741 3810 12594425 12594356 3.520000e-21 113.0
10 TraesCS1B01G445600 chr7D 91.812 745 41 6 3564 4302 566252190 566251460 0.000000e+00 1020.0
11 TraesCS1B01G445600 chr7D 91.340 739 50 6 3564 4299 561542257 561542984 0.000000e+00 998.0
12 TraesCS1B01G445600 chr2A 79.344 1554 222 57 1790 3305 769342574 769341082 0.000000e+00 1000.0
13 TraesCS1B01G445600 chr2A 85.294 68 7 3 1570 1635 32880981 32881047 2.780000e-07 67.6
14 TraesCS1B01G445600 chr3D 91.389 720 53 7 3588 4302 160708605 160709320 0.000000e+00 977.0
15 TraesCS1B01G445600 chr3D 96.053 76 3 0 1 76 552735541 552735466 1.620000e-24 124.0
16 TraesCS1B01G445600 chr3D 84.694 98 12 2 1606 1702 582611976 582611881 1.270000e-15 95.3
17 TraesCS1B01G445600 chr4A 90.553 741 42 13 3564 4302 602242573 602243287 0.000000e+00 955.0
18 TraesCS1B01G445600 chr4A 80.473 169 22 8 4063 4228 602243485 602243645 7.560000e-23 119.0
19 TraesCS1B01G445600 chr4A 84.545 110 14 2 1606 1714 618561445 618561552 5.880000e-19 106.0
20 TraesCS1B01G445600 chr7A 90.392 739 40 16 3564 4302 608509120 608508413 0.000000e+00 942.0
21 TraesCS1B01G445600 chr7A 83.740 123 14 4 4107 4228 608508276 608508159 1.260000e-20 111.0
22 TraesCS1B01G445600 chr2D 79.860 1142 163 42 1790 2902 644203823 644202720 0.000000e+00 773.0
23 TraesCS1B01G445600 chr2D 80.912 351 55 4 2925 3275 644192333 644191995 2.550000e-67 267.0
24 TraesCS1B01G445600 chr2D 79.832 119 21 2 1597 1714 114144776 114144892 2.760000e-12 84.2
25 TraesCS1B01G445600 chr5A 92.053 453 34 2 3564 4016 306991360 306990910 1.690000e-178 636.0
26 TraesCS1B01G445600 chr5A 95.536 112 5 0 4191 4302 306963508 306963397 3.420000e-41 180.0
27 TraesCS1B01G445600 chr5A 93.694 111 6 1 4187 4297 306972887 306972778 9.570000e-37 165.0
28 TraesCS1B01G445600 chr6D 93.600 375 24 0 3568 3942 446950051 446950425 1.040000e-155 560.0
29 TraesCS1B01G445600 chr2B 97.674 86 2 0 1 86 748871207 748871122 9.640000e-32 148.0
30 TraesCS1B01G445600 chr2B 94.737 76 4 0 1 76 650493431 650493506 7.560000e-23 119.0
31 TraesCS1B01G445600 chr2B 80.488 123 21 3 1596 1717 741357952 741358072 1.650000e-14 91.6
32 TraesCS1B01G445600 chr6B 98.780 82 1 0 1 82 683497228 683497309 3.470000e-31 147.0
33 TraesCS1B01G445600 chr6B 97.561 82 2 0 1 82 683499180 683499261 1.610000e-29 141.0
34 TraesCS1B01G445600 chr6B 96.053 76 3 0 1 76 6528998 6529073 1.620000e-24 124.0
35 TraesCS1B01G445600 chr3B 97.647 85 2 0 1 85 815846451 815846367 3.470000e-31 147.0
36 TraesCS1B01G445600 chr3B 82.569 109 16 2 1610 1717 445147327 445147221 4.580000e-15 93.5
37 TraesCS1B01G445600 chr5B 98.649 74 1 0 1 74 697285760 697285833 9.710000e-27 132.0
38 TraesCS1B01G445600 chr5B 81.818 110 17 2 1606 1714 220707542 220707649 5.930000e-14 89.8
39 TraesCS1B01G445600 chr4B 94.737 76 4 0 1 76 599605598 599605673 7.560000e-23 119.0
40 TraesCS1B01G445600 chr5D 79.675 123 20 4 1593 1714 416595919 416595801 2.760000e-12 84.2


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 TraesCS1B01G445600 chr1B 665451634 665455935 4301 True 7945.0 7945 100.000000 1 4302 1 chr1B.!!$R1 4301
1 TraesCS1B01G445600 chr1D 478253508 478256997 3489 True 1496.0 3851 89.685000 172 3533 3 chr1D.!!$R1 3361
2 TraesCS1B01G445600 chr1A 574481168 574484090 2922 True 1290.0 3402 90.793667 686 3560 3 chr1A.!!$R1 2874
3 TraesCS1B01G445600 chr3A 12607995 12608725 730 True 1133.0 1133 94.467000 3562 4302 1 chr3A.!!$R1 740
4 TraesCS1B01G445600 chr3A 12592366 12594425 2059 True 620.0 1127 95.023000 3562 4302 2 chr3A.!!$R2 740
5 TraesCS1B01G445600 chr7D 566251460 566252190 730 True 1020.0 1020 91.812000 3564 4302 1 chr7D.!!$R1 738
6 TraesCS1B01G445600 chr7D 561542257 561542984 727 False 998.0 998 91.340000 3564 4299 1 chr7D.!!$F1 735
7 TraesCS1B01G445600 chr2A 769341082 769342574 1492 True 1000.0 1000 79.344000 1790 3305 1 chr2A.!!$R1 1515
8 TraesCS1B01G445600 chr3D 160708605 160709320 715 False 977.0 977 91.389000 3588 4302 1 chr3D.!!$F1 714
9 TraesCS1B01G445600 chr4A 602242573 602243645 1072 False 537.0 955 85.513000 3564 4302 2 chr4A.!!$F2 738
10 TraesCS1B01G445600 chr7A 608508159 608509120 961 True 526.5 942 87.066000 3564 4302 2 chr7A.!!$R1 738
11 TraesCS1B01G445600 chr2D 644202720 644203823 1103 True 773.0 773 79.860000 1790 2902 1 chr2D.!!$R2 1112

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
27 28 0.107066 CCTGCTGGATATGCCACACA 60.107 55.0 2.92 0.00 43.33 3.72 F
371 372 0.178961 GCCCAAGAAACTTCCCCAGT 60.179 55.0 0.00 0.00 37.30 4.00 F
410 411 0.668401 GCGCGTTAACCAGGTGTACT 60.668 55.0 8.43 0.00 0.00 2.73 F
894 1103 0.954449 CTGGTCAGCTGCACCTCTTG 60.954 60.0 25.75 14.83 34.66 3.02 F
2207 2533 0.992072 CCAGTACAAGCATGACGTCG 59.008 55.0 11.62 0.00 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 2304 1.192146 ACCGCTTCTGTAGGGCTTCA 61.192 55.000 0.00 0.0 35.57 3.02 R
2242 2568 0.401105 ATCCAGAGGGTAGCAGCCAT 60.401 55.000 7.06 0.0 38.48 4.40 R
2275 2613 1.306226 GTAGTCCCTGAGGTGCCCT 60.306 63.158 0.00 0.0 36.03 5.19 R
2557 2895 0.036388 GGAACATCCTGCCGAACTCA 60.036 55.000 0.00 0.0 32.53 3.41 R
3810 4153 0.110486 GAGGTGAAGAGGGGTTTGCA 59.890 55.000 0.00 0.0 0.00 4.08 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
17 18 4.437587 GTGGGCTGCCTGCTGGAT 62.438 66.667 19.68 0.00 42.39 3.41
18 19 2.691996 TGGGCTGCCTGCTGGATA 60.692 61.111 19.68 0.17 42.39 2.59
19 20 2.080536 TGGGCTGCCTGCTGGATAT 61.081 57.895 19.68 0.00 42.39 1.63
20 21 1.602888 GGGCTGCCTGCTGGATATG 60.603 63.158 19.68 0.85 42.39 1.78
21 22 2.266627 GGCTGCCTGCTGGATATGC 61.267 63.158 14.77 10.37 42.39 3.14
22 23 2.266627 GCTGCCTGCTGGATATGCC 61.267 63.158 14.77 0.00 38.95 4.40
24 25 1.152902 TGCCTGCTGGATATGCCAC 60.153 57.895 14.77 0.00 43.33 5.01
25 26 1.152902 GCCTGCTGGATATGCCACA 60.153 57.895 14.77 0.00 43.33 4.17
26 27 1.450531 GCCTGCTGGATATGCCACAC 61.451 60.000 14.77 0.00 43.33 3.82
27 28 0.107066 CCTGCTGGATATGCCACACA 60.107 55.000 2.92 0.00 43.33 3.72
28 29 1.306148 CTGCTGGATATGCCACACAG 58.694 55.000 0.00 0.00 43.33 3.66
29 30 0.107066 TGCTGGATATGCCACACAGG 60.107 55.000 0.00 0.00 43.33 4.00
46 47 4.626081 GCCTGTGTGGGCGAGTGT 62.626 66.667 0.00 0.00 42.82 3.55
54 55 3.578456 GGGCGAGTGTCCATTGTG 58.422 61.111 0.00 0.00 40.65 3.33
55 56 2.690778 GGGCGAGTGTCCATTGTGC 61.691 63.158 0.00 0.00 40.65 4.57
56 57 2.690778 GGCGAGTGTCCATTGTGCC 61.691 63.158 0.00 0.00 0.00 5.01
58 59 1.868997 CGAGTGTCCATTGTGCCAC 59.131 57.895 0.00 0.00 0.00 5.01
59 60 0.884259 CGAGTGTCCATTGTGCCACA 60.884 55.000 0.00 0.00 0.00 4.17
60 61 0.593128 GAGTGTCCATTGTGCCACAC 59.407 55.000 0.00 0.00 39.61 3.82
61 62 1.165907 AGTGTCCATTGTGCCACACG 61.166 55.000 0.00 0.00 43.28 4.49
62 63 1.153066 TGTCCATTGTGCCACACGT 60.153 52.632 0.00 0.00 37.14 4.49
63 64 1.282570 GTCCATTGTGCCACACGTG 59.717 57.895 15.48 15.48 37.14 4.49
64 65 1.153066 TCCATTGTGCCACACGTGT 60.153 52.632 17.22 17.22 37.14 4.49
65 66 1.008652 CCATTGTGCCACACGTGTG 60.009 57.895 36.13 36.13 45.23 3.82
75 76 0.438445 CACACGTGTGGCAGTTATCG 59.562 55.000 35.65 10.61 42.10 2.92
76 77 1.289109 ACACGTGTGGCAGTTATCGC 61.289 55.000 22.71 0.00 34.19 4.58
78 79 1.803922 CGTGTGGCAGTTATCGCGA 60.804 57.895 13.09 13.09 36.17 5.87
79 80 1.708027 GTGTGGCAGTTATCGCGAC 59.292 57.895 12.93 0.00 38.44 5.19
81 82 2.171725 GTGGCAGTTATCGCGACCC 61.172 63.158 12.93 5.87 32.56 4.46
82 83 2.185867 GGCAGTTATCGCGACCCA 59.814 61.111 12.93 0.00 0.00 4.51
83 84 1.448893 GGCAGTTATCGCGACCCAA 60.449 57.895 12.93 2.74 0.00 4.12
84 85 1.022451 GGCAGTTATCGCGACCCAAA 61.022 55.000 12.93 0.17 0.00 3.28
85 86 0.800012 GCAGTTATCGCGACCCAAAA 59.200 50.000 12.93 0.00 0.00 2.44
87 88 1.801771 CAGTTATCGCGACCCAAAACA 59.198 47.619 12.93 0.00 0.00 2.83
88 89 2.224549 CAGTTATCGCGACCCAAAACAA 59.775 45.455 12.93 0.00 0.00 2.83
89 90 2.879646 AGTTATCGCGACCCAAAACAAA 59.120 40.909 12.93 0.00 0.00 2.83
90 91 3.315749 AGTTATCGCGACCCAAAACAAAA 59.684 39.130 12.93 0.00 0.00 2.44
91 92 4.022676 AGTTATCGCGACCCAAAACAAAAT 60.023 37.500 12.93 0.00 0.00 1.82
92 93 5.181622 AGTTATCGCGACCCAAAACAAAATA 59.818 36.000 12.93 0.00 0.00 1.40
93 94 4.712122 ATCGCGACCCAAAACAAAATAT 57.288 36.364 12.93 0.00 0.00 1.28
95 96 2.344142 CGCGACCCAAAACAAAATATGC 59.656 45.455 0.00 0.00 0.00 3.14
96 97 3.584834 GCGACCCAAAACAAAATATGCT 58.415 40.909 0.00 0.00 0.00 3.79
98 99 4.091365 GCGACCCAAAACAAAATATGCTTC 59.909 41.667 0.00 0.00 0.00 3.86
99 100 5.226396 CGACCCAAAACAAAATATGCTTCA 58.774 37.500 0.00 0.00 0.00 3.02
100 101 5.345741 CGACCCAAAACAAAATATGCTTCAG 59.654 40.000 0.00 0.00 0.00 3.02
117 118 4.336433 GCTTCAGCACTAAAATCCTATGCA 59.664 41.667 0.00 0.00 41.59 3.96
118 119 5.505324 GCTTCAGCACTAAAATCCTATGCAG 60.505 44.000 0.00 0.00 41.59 4.41
119 120 5.357742 TCAGCACTAAAATCCTATGCAGA 57.642 39.130 0.00 0.00 38.79 4.26
120 121 5.118990 TCAGCACTAAAATCCTATGCAGAC 58.881 41.667 0.00 0.00 38.79 3.51
121 122 4.274459 CAGCACTAAAATCCTATGCAGACC 59.726 45.833 0.00 0.00 38.79 3.85
122 123 3.565902 GCACTAAAATCCTATGCAGACCC 59.434 47.826 0.00 0.00 36.30 4.46
123 124 4.137543 CACTAAAATCCTATGCAGACCCC 58.862 47.826 0.00 0.00 0.00 4.95
143 144 2.706071 CCCCCTTCCCTAGCTCCT 59.294 66.667 0.00 0.00 0.00 3.69
144 145 1.460497 CCCCCTTCCCTAGCTCCTC 60.460 68.421 0.00 0.00 0.00 3.71
146 147 1.460497 CCCTTCCCTAGCTCCTCCC 60.460 68.421 0.00 0.00 0.00 4.30
149 150 3.311511 TTCCCTAGCTCCTCCCGCA 62.312 63.158 0.00 0.00 0.00 5.69
150 151 2.525381 CCCTAGCTCCTCCCGCAT 60.525 66.667 0.00 0.00 0.00 4.73
153 154 3.565910 CTAGCTCCTCCCGCATCGC 62.566 68.421 0.00 0.00 0.00 4.58
224 225 1.307430 GCCCTTCTCCCTTCCTCCT 60.307 63.158 0.00 0.00 0.00 3.69
228 229 1.562783 CTTCTCCCTTCCTCCTTCGT 58.437 55.000 0.00 0.00 0.00 3.85
253 254 4.974438 ACGGGGCCTGACTGGGAA 62.974 66.667 21.81 0.00 36.00 3.97
282 283 1.908299 CAACCAGTTTGGCCCTCCC 60.908 63.158 0.00 0.00 42.67 4.30
285 286 2.036256 CAGTTTGGCCCTCCCCAG 59.964 66.667 0.00 0.00 36.00 4.45
305 306 4.065088 CAGCCAGTTTTAGTAGCACTTGA 58.935 43.478 0.00 0.00 0.00 3.02
358 359 2.030562 AAGTCGACACGGCCCAAG 59.969 61.111 19.50 0.00 28.67 3.61
371 372 0.178961 GCCCAAGAAACTTCCCCAGT 60.179 55.000 0.00 0.00 37.30 4.00
372 373 1.620822 CCCAAGAAACTTCCCCAGTG 58.379 55.000 0.00 0.00 35.12 3.66
391 392 3.045142 CTTGCAAGCCCACACTGG 58.955 61.111 14.65 0.00 37.25 4.00
400 401 2.554272 CCACACTGGCGCGTTAAC 59.446 61.111 8.43 0.00 0.00 2.01
401 402 2.554272 CACACTGGCGCGTTAACC 59.446 61.111 8.43 0.00 0.00 2.85
406 407 2.666862 TGGCGCGTTAACCAGGTG 60.667 61.111 8.43 0.00 0.00 4.00
410 411 0.668401 GCGCGTTAACCAGGTGTACT 60.668 55.000 8.43 0.00 0.00 2.73
441 448 5.244626 ACTTGTAGCCGTTACCTCTTTTCTA 59.755 40.000 0.00 0.00 0.00 2.10
450 457 6.338937 CGTTACCTCTTTTCTATTGGCTAGT 58.661 40.000 0.00 0.00 0.00 2.57
480 498 1.982660 CTGAGGCCGGTGTAGATAGA 58.017 55.000 1.90 0.00 0.00 1.98
522 540 3.983741 ACTCATCTCCGAATTCGAATCC 58.016 45.455 28.76 0.00 43.02 3.01
525 543 5.478679 ACTCATCTCCGAATTCGAATCCTAT 59.521 40.000 28.76 10.17 43.02 2.57
535 553 7.201444 CCGAATTCGAATCCTATCTAATTTCCG 60.201 40.741 28.76 1.37 43.02 4.30
536 554 7.541091 CGAATTCGAATCCTATCTAATTTCCGA 59.459 37.037 23.29 0.00 43.02 4.55
553 571 4.884668 TCCGAGAAACCTTAGTTCATGT 57.115 40.909 0.00 0.00 34.19 3.21
554 572 4.566004 TCCGAGAAACCTTAGTTCATGTG 58.434 43.478 0.00 0.00 34.19 3.21
555 573 4.282449 TCCGAGAAACCTTAGTTCATGTGA 59.718 41.667 0.00 0.00 34.19 3.58
556 574 4.389077 CCGAGAAACCTTAGTTCATGTGAC 59.611 45.833 0.00 0.00 34.19 3.67
565 583 1.417517 AGTTCATGTGACTGAGCCACA 59.582 47.619 3.59 3.59 46.90 4.17
576 594 4.011023 GACTGAGCCACAACTAGAGAGTA 58.989 47.826 0.00 0.00 33.58 2.59
582 600 3.428316 GCCACAACTAGAGAGTAGCTCAC 60.428 52.174 0.00 0.00 46.45 3.51
591 609 3.391382 GTAGCTCACACCGGCCCT 61.391 66.667 0.00 0.00 0.00 5.19
611 629 3.880490 CCTGGCGCACCTTGTAAAATATA 59.120 43.478 10.83 0.00 36.63 0.86
614 632 5.672503 TGGCGCACCTTGTAAAATATACTA 58.327 37.500 10.83 0.00 36.63 1.82
615 633 6.114089 TGGCGCACCTTGTAAAATATACTAA 58.886 36.000 10.83 0.00 36.63 2.24
617 635 6.480981 GGCGCACCTTGTAAAATATACTAAGA 59.519 38.462 10.83 0.00 0.00 2.10
618 636 7.172703 GGCGCACCTTGTAAAATATACTAAGAT 59.827 37.037 10.83 0.00 0.00 2.40
619 637 8.221766 GCGCACCTTGTAAAATATACTAAGATC 58.778 37.037 0.30 0.00 0.00 2.75
620 638 9.256477 CGCACCTTGTAAAATATACTAAGATCA 57.744 33.333 0.00 0.00 0.00 2.92
638 755 6.102897 AGATCATCTGTAATAAACTCCCGG 57.897 41.667 0.00 0.00 0.00 5.73
639 756 5.839063 AGATCATCTGTAATAAACTCCCGGA 59.161 40.000 0.73 0.00 0.00 5.14
643 760 4.346730 TCTGTAATAAACTCCCGGACTCA 58.653 43.478 0.73 0.00 0.00 3.41
651 768 2.779506 ACTCCCGGACTCATTTTTGAC 58.220 47.619 0.73 0.00 0.00 3.18
652 769 2.105821 ACTCCCGGACTCATTTTTGACA 59.894 45.455 0.73 0.00 0.00 3.58
655 772 4.148838 TCCCGGACTCATTTTTGACAATT 58.851 39.130 0.73 0.00 0.00 2.32
657 774 4.685628 CCCGGACTCATTTTTGACAATTTG 59.314 41.667 0.73 0.00 0.00 2.32
661 778 7.336975 CGGACTCATTTTTGACAATTTGTTTC 58.663 34.615 3.08 0.00 0.00 2.78
662 779 7.516627 CGGACTCATTTTTGACAATTTGTTTCC 60.517 37.037 3.08 0.00 0.00 3.13
663 780 7.495606 GGACTCATTTTTGACAATTTGTTTCCT 59.504 33.333 3.08 0.00 0.00 3.36
734 890 4.225267 ACGGATGGGATGGAATAGGATAAC 59.775 45.833 0.00 0.00 0.00 1.89
858 1020 2.910977 ACCTACCTAGTCCAAAACCCAG 59.089 50.000 0.00 0.00 0.00 4.45
894 1103 0.954449 CTGGTCAGCTGCACCTCTTG 60.954 60.000 25.75 14.83 34.66 3.02
953 1167 5.016173 CACATTTGTTTCCCTCCCTTCATA 58.984 41.667 0.00 0.00 0.00 2.15
1085 1302 1.666311 CGACCTGAAGACCGTGAAGAC 60.666 57.143 0.00 0.00 0.00 3.01
1219 1439 1.790818 AGGTACTCCCTTCGATTCCC 58.209 55.000 0.00 0.00 42.73 3.97
1255 1512 6.176183 CAGATTTCTGTGGGAGTGTAGATTT 58.824 40.000 0.00 0.00 39.09 2.17
1330 1588 2.748388 AGAAATGGCGGGAGTACTACT 58.252 47.619 4.77 0.00 0.00 2.57
1345 1603 6.365518 GGAGTACTACTTAAAATATGAGCGCC 59.634 42.308 2.29 0.00 0.00 6.53
1393 1651 6.560253 TGAATTTCTTCTTTTCCTCTTCCG 57.440 37.500 0.00 0.00 32.29 4.30
1400 1658 1.719780 CTTTTCCTCTTCCGTTCGTCG 59.280 52.381 0.00 0.00 39.52 5.12
1456 1714 1.131504 GACGCACACCAAAGTCACAAA 59.868 47.619 0.00 0.00 34.09 2.83
1534 1792 5.163120 ACTCCTACGTCCACCATATTCTCTA 60.163 44.000 0.00 0.00 0.00 2.43
1579 1883 6.408662 GGCTGGACAGTCTAATTTCTCCTATT 60.409 42.308 0.00 0.00 0.00 1.73
1584 1888 7.509659 GGACAGTCTAATTTCTCCTATTAGGGA 59.490 40.741 9.88 3.70 36.61 4.20
1586 1890 9.453830 ACAGTCTAATTTCTCCTATTAGGGAAT 57.546 33.333 9.88 5.70 36.61 3.01
1634 1938 6.736853 GTCCGAAAATACTTGTCGAAGAAATG 59.263 38.462 1.13 0.00 39.69 2.32
1635 1939 6.021596 CCGAAAATACTTGTCGAAGAAATGG 58.978 40.000 1.13 0.00 39.69 3.16
1714 2018 6.192970 ACAAATATTTCTGATCGGAGGGAT 57.807 37.500 4.04 3.75 38.35 3.85
1787 2091 5.621197 AATGTTGAAATTTCGATCACGGA 57.379 34.783 11.31 0.00 40.21 4.69
2032 2349 3.546009 GGCACAGCCCCGTATAGA 58.454 61.111 0.00 0.00 44.06 1.98
2137 2463 1.011904 CAATCGAATGCTCGCCACG 60.012 57.895 0.00 0.00 45.04 4.94
2207 2533 0.992072 CCAGTACAAGCATGACGTCG 59.008 55.000 11.62 0.00 0.00 5.12
2208 2534 1.402325 CCAGTACAAGCATGACGTCGA 60.402 52.381 11.62 0.26 0.00 4.20
2260 2589 1.003442 ATGGCTGCTACCCTCTGGA 59.997 57.895 0.00 0.00 34.81 3.86
2275 2613 3.631087 CCTCTGGATGGAGTTTCCCTCTA 60.631 52.174 1.36 0.00 40.30 2.43
2298 2636 1.682684 ACCTCAGGGACTACGGCAG 60.683 63.158 0.00 0.00 36.02 4.85
2536 2874 2.441532 CTCGTCCCGGGGCTCTTA 60.442 66.667 25.54 4.73 0.00 2.10
2557 2895 0.686441 TCGTCCCGTCATTCCAGGAT 60.686 55.000 0.00 0.00 0.00 3.24
2563 2901 2.555199 CCGTCATTCCAGGATGAGTTC 58.445 52.381 0.00 0.00 39.69 3.01
2633 2971 0.399075 CCTGTTCCACCCGGTTAACT 59.601 55.000 5.42 0.00 0.00 2.24
2662 3000 2.541178 GCGCGCAGTCACTAGTTACTAT 60.541 50.000 29.10 0.00 0.00 2.12
2744 3082 2.430244 AGACGCCGCTACAACACG 60.430 61.111 0.00 0.00 0.00 4.49
2834 3172 3.958147 AACGCATCCGACCAGGCTG 62.958 63.158 7.75 7.75 40.77 4.85
2893 3231 4.057943 AGGGAGGAGTACGGCGGT 62.058 66.667 13.24 1.39 0.00 5.68
3043 3381 0.100146 GCTTCTCGACGTTCGGGTAT 59.900 55.000 7.07 0.00 41.96 2.73
3097 3435 2.363276 ATGCCCAGCACACCCATG 60.363 61.111 0.00 0.00 43.04 3.66
3114 3452 1.874345 ATGTGGTCCGAGTCCGACAC 61.874 60.000 12.71 9.47 38.22 3.67
3157 3495 4.969196 CCACCGTGTGTGCGAGCT 62.969 66.667 0.00 0.00 44.01 4.09
3358 3696 8.839310 ATACTGTTCTCATATAAAGGCATCAC 57.161 34.615 0.00 0.00 0.00 3.06
3359 3697 6.653020 ACTGTTCTCATATAAAGGCATCACA 58.347 36.000 0.00 0.00 0.00 3.58
3360 3698 6.765036 ACTGTTCTCATATAAAGGCATCACAG 59.235 38.462 0.00 0.00 34.28 3.66
3361 3699 6.057533 TGTTCTCATATAAAGGCATCACAGG 58.942 40.000 0.00 0.00 0.00 4.00
3362 3700 5.894298 TCTCATATAAAGGCATCACAGGT 57.106 39.130 0.00 0.00 0.00 4.00
3363 3701 6.252599 TCTCATATAAAGGCATCACAGGTT 57.747 37.500 0.00 0.00 0.00 3.50
3364 3702 6.291377 TCTCATATAAAGGCATCACAGGTTC 58.709 40.000 0.00 0.00 0.00 3.62
3365 3703 6.100279 TCTCATATAAAGGCATCACAGGTTCT 59.900 38.462 0.00 0.00 0.00 3.01
3366 3704 6.662755 TCATATAAAGGCATCACAGGTTCTT 58.337 36.000 0.00 0.00 0.00 2.52
3367 3705 7.118723 TCATATAAAGGCATCACAGGTTCTTT 58.881 34.615 0.00 0.00 0.00 2.52
3368 3706 7.615365 TCATATAAAGGCATCACAGGTTCTTTT 59.385 33.333 0.00 0.00 0.00 2.27
3369 3707 6.670695 ATAAAGGCATCACAGGTTCTTTTT 57.329 33.333 0.00 0.00 0.00 1.94
3370 3708 4.590850 AAGGCATCACAGGTTCTTTTTC 57.409 40.909 0.00 0.00 0.00 2.29
3371 3709 3.837355 AGGCATCACAGGTTCTTTTTCT 58.163 40.909 0.00 0.00 0.00 2.52
3372 3710 4.218312 AGGCATCACAGGTTCTTTTTCTT 58.782 39.130 0.00 0.00 0.00 2.52
3373 3711 4.651045 AGGCATCACAGGTTCTTTTTCTTT 59.349 37.500 0.00 0.00 0.00 2.52
3374 3712 5.129320 AGGCATCACAGGTTCTTTTTCTTTT 59.871 36.000 0.00 0.00 0.00 2.27
3375 3713 5.817296 GGCATCACAGGTTCTTTTTCTTTTT 59.183 36.000 0.00 0.00 0.00 1.94
3409 3747 3.451402 TCACAGGTTCTAGCTAGGTGA 57.549 47.619 20.58 20.04 29.78 4.02
3417 3755 8.005388 ACAGGTTCTAGCTAGGTGATTAATCTA 58.995 37.037 20.58 0.45 0.00 1.98
3426 3764 6.588373 GCTAGGTGATTAATCTAAGCTAGTGC 59.412 42.308 26.59 18.18 40.93 4.40
3456 3794 4.415596 ACAAATAGAATTGTTCCCCAGCA 58.584 39.130 0.00 0.00 40.52 4.41
3472 3810 2.032071 CACGAACACCCTCCACCC 59.968 66.667 0.00 0.00 0.00 4.61
3473 3811 2.446994 ACGAACACCCTCCACCCA 60.447 61.111 0.00 0.00 0.00 4.51
3484 3822 1.553248 CCTCCACCCATACGACAAGAA 59.447 52.381 0.00 0.00 0.00 2.52
3488 3826 3.071892 TCCACCCATACGACAAGAAACTT 59.928 43.478 0.00 0.00 0.00 2.66
3491 3829 4.090930 CACCCATACGACAAGAAACTTACG 59.909 45.833 0.00 0.00 0.00 3.18
3496 3834 7.191551 CCATACGACAAGAAACTTACGATCTA 58.808 38.462 13.43 2.07 0.00 1.98
3533 3871 0.884259 GGCCCAAAAACACCATGCAC 60.884 55.000 0.00 0.00 0.00 4.57
3535 3873 1.873486 GCCCAAAAACACCATGCACTC 60.873 52.381 0.00 0.00 0.00 3.51
3549 3887 0.108898 GCACTCAGTCATCGCAGTCT 60.109 55.000 0.00 0.00 0.00 3.24
3560 3898 4.082190 GTCATCGCAGTCTGCCCTTATATA 60.082 45.833 19.14 0.00 41.12 0.86
3653 3991 3.813443 CTGGCACCTGTAAATAGCAGAT 58.187 45.455 0.00 0.00 36.12 2.90
3705 4045 1.067213 CGGGTTGGGCTAAACATTTGG 60.067 52.381 0.00 0.00 0.00 3.28
3719 4059 1.555477 ATTTGGCCCGGTTCGTCCTA 61.555 55.000 0.00 0.00 0.00 2.94
3729 4069 3.323243 CGGTTCGTCCTAGACAACAAAT 58.677 45.455 0.00 0.00 30.88 2.32
3731 4071 4.566987 GGTTCGTCCTAGACAACAAATCT 58.433 43.478 0.00 0.00 30.88 2.40
3810 4153 1.817941 AGTGGAACGCACGCAAAGT 60.818 52.632 0.00 0.00 45.86 2.66
3959 4305 8.482128 ACATGGGAAAGACAGTAAAAATTTCAA 58.518 29.630 0.00 0.00 32.73 2.69
3962 4308 9.898152 TGGGAAAGACAGTAAAAATTTCAAAAT 57.102 25.926 0.00 0.00 32.73 1.82
4028 4374 9.444600 CCCATGTAACTATACTTGTAAAACACT 57.555 33.333 0.00 0.00 36.13 3.55
4116 4462 8.755028 TCTAGTAATTACACTGCCAGTAAATCA 58.245 33.333 17.65 0.00 35.33 2.57
4162 4508 7.286775 TCCTAGAAATTTACAGTGCAAAAACCT 59.713 33.333 0.00 0.00 0.00 3.50
4287 4633 9.817809 TGACAGTGTAAATCATAGAGAATTACC 57.182 33.333 0.00 0.00 40.39 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.266627 GGCATATCCAGCAGGCAGC 61.267 63.158 0.00 0.00 46.19 5.25
5 6 1.149854 TGGCATATCCAGCAGGCAG 59.850 57.895 0.00 0.00 40.72 4.85
6 7 3.333499 TGGCATATCCAGCAGGCA 58.667 55.556 0.00 0.00 40.72 4.75
30 31 2.357517 GACACTCGCCCACACAGG 60.358 66.667 0.00 0.00 37.03 4.00
31 32 2.357517 GGACACTCGCCCACACAG 60.358 66.667 0.00 0.00 0.00 3.66
32 33 2.050836 AATGGACACTCGCCCACACA 62.051 55.000 0.00 0.00 34.92 3.72
33 34 1.302511 AATGGACACTCGCCCACAC 60.303 57.895 0.00 0.00 34.92 3.82
34 35 1.302431 CAATGGACACTCGCCCACA 60.302 57.895 0.00 0.00 34.92 4.17
35 36 1.302511 ACAATGGACACTCGCCCAC 60.303 57.895 0.00 0.00 34.92 4.61
36 37 1.302431 CACAATGGACACTCGCCCA 60.302 57.895 0.00 0.00 36.79 5.36
37 38 2.690778 GCACAATGGACACTCGCCC 61.691 63.158 0.00 0.00 0.00 6.13
38 39 2.690778 GGCACAATGGACACTCGCC 61.691 63.158 0.00 0.00 0.00 5.54
39 40 1.965930 TGGCACAATGGACACTCGC 60.966 57.895 0.00 0.00 31.92 5.03
40 41 0.884259 TGTGGCACAATGGACACTCG 60.884 55.000 19.74 0.00 44.16 4.18
41 42 0.593128 GTGTGGCACAATGGACACTC 59.407 55.000 23.90 2.29 44.16 3.51
43 44 1.282570 CGTGTGGCACAATGGACAC 59.717 57.895 23.90 7.00 44.16 3.67
44 45 1.153066 ACGTGTGGCACAATGGACA 60.153 52.632 23.90 0.00 44.16 4.02
45 46 1.282570 CACGTGTGGCACAATGGAC 59.717 57.895 23.90 8.57 44.16 4.02
46 47 1.153066 ACACGTGTGGCACAATGGA 60.153 52.632 27.40 4.51 44.16 3.41
56 57 0.438445 CGATAACTGCCACACGTGTG 59.562 55.000 36.13 36.13 45.23 3.82
58 59 1.419922 GCGATAACTGCCACACGTG 59.580 57.895 15.48 15.48 0.00 4.49
59 60 2.092291 CGCGATAACTGCCACACGT 61.092 57.895 0.00 0.00 0.00 4.49
60 61 1.803922 TCGCGATAACTGCCACACG 60.804 57.895 3.71 0.00 0.00 4.49
61 62 1.693083 GGTCGCGATAACTGCCACAC 61.693 60.000 14.06 0.00 0.00 3.82
62 63 1.447140 GGTCGCGATAACTGCCACA 60.447 57.895 14.06 0.00 0.00 4.17
63 64 2.171725 GGGTCGCGATAACTGCCAC 61.172 63.158 14.06 0.00 0.00 5.01
64 65 2.173758 TTGGGTCGCGATAACTGCCA 62.174 55.000 14.06 0.86 0.00 4.92
65 66 1.022451 TTTGGGTCGCGATAACTGCC 61.022 55.000 14.06 7.46 0.00 4.85
66 67 0.800012 TTTTGGGTCGCGATAACTGC 59.200 50.000 14.06 0.00 0.00 4.40
67 68 1.801771 TGTTTTGGGTCGCGATAACTG 59.198 47.619 14.06 0.00 0.00 3.16
70 71 3.984508 TTTTGTTTTGGGTCGCGATAA 57.015 38.095 14.06 5.64 0.00 1.75
72 73 4.420168 CATATTTTGTTTTGGGTCGCGAT 58.580 39.130 14.06 0.00 0.00 4.58
73 74 3.827625 CATATTTTGTTTTGGGTCGCGA 58.172 40.909 3.71 3.71 0.00 5.87
74 75 2.344142 GCATATTTTGTTTTGGGTCGCG 59.656 45.455 0.00 0.00 0.00 5.87
75 76 3.584834 AGCATATTTTGTTTTGGGTCGC 58.415 40.909 0.00 0.00 0.00 5.19
76 77 5.226396 TGAAGCATATTTTGTTTTGGGTCG 58.774 37.500 0.00 0.00 0.00 4.79
78 79 4.996758 GCTGAAGCATATTTTGTTTTGGGT 59.003 37.500 0.00 0.00 41.59 4.51
79 80 5.535043 GCTGAAGCATATTTTGTTTTGGG 57.465 39.130 0.00 0.00 41.59 4.12
95 96 5.819379 TCTGCATAGGATTTTAGTGCTGAAG 59.181 40.000 0.00 0.00 39.62 3.02
96 97 5.586243 GTCTGCATAGGATTTTAGTGCTGAA 59.414 40.000 6.77 0.00 42.55 3.02
98 99 4.274459 GGTCTGCATAGGATTTTAGTGCTG 59.726 45.833 0.00 0.00 36.78 4.41
99 100 4.455606 GGTCTGCATAGGATTTTAGTGCT 58.544 43.478 0.00 0.00 36.78 4.40
100 101 3.565902 GGGTCTGCATAGGATTTTAGTGC 59.434 47.826 0.00 0.00 36.39 4.40
102 103 3.138468 GGGGGTCTGCATAGGATTTTAGT 59.862 47.826 0.00 0.00 0.00 2.24
103 104 3.756117 GGGGGTCTGCATAGGATTTTAG 58.244 50.000 0.00 0.00 0.00 1.85
104 105 3.876309 GGGGGTCTGCATAGGATTTTA 57.124 47.619 0.00 0.00 0.00 1.52
105 106 2.755952 GGGGGTCTGCATAGGATTTT 57.244 50.000 0.00 0.00 0.00 1.82
126 127 1.460497 GAGGAGCTAGGGAAGGGGG 60.460 68.421 0.00 0.00 0.00 5.40
127 128 1.460497 GGAGGAGCTAGGGAAGGGG 60.460 68.421 0.00 0.00 0.00 4.79
128 129 1.460497 GGGAGGAGCTAGGGAAGGG 60.460 68.421 0.00 0.00 0.00 3.95
129 130 1.834822 CGGGAGGAGCTAGGGAAGG 60.835 68.421 0.00 0.00 0.00 3.46
130 131 2.503382 GCGGGAGGAGCTAGGGAAG 61.503 68.421 0.00 0.00 0.00 3.46
131 132 2.444140 GCGGGAGGAGCTAGGGAA 60.444 66.667 0.00 0.00 0.00 3.97
133 134 2.525381 ATGCGGGAGGAGCTAGGG 60.525 66.667 0.00 0.00 35.28 3.53
135 136 2.647875 CGATGCGGGAGGAGCTAG 59.352 66.667 0.00 0.00 33.06 3.42
136 137 3.606662 GCGATGCGGGAGGAGCTA 61.607 66.667 0.00 0.00 33.06 3.32
155 156 4.802051 CCCTGGTCGCCATGTGGG 62.802 72.222 0.54 7.11 40.85 4.61
156 157 4.802051 CCCCTGGTCGCCATGTGG 62.802 72.222 0.00 0.00 38.53 4.17
157 158 4.802051 CCCCCTGGTCGCCATGTG 62.802 72.222 0.00 0.00 30.82 3.21
159 160 2.779742 TTTTCCCCCTGGTCGCCATG 62.780 60.000 0.00 0.00 30.82 3.66
160 161 2.543797 TTTTCCCCCTGGTCGCCAT 61.544 57.895 0.00 0.00 30.82 4.40
162 163 2.675423 GTTTTCCCCCTGGTCGCC 60.675 66.667 0.00 0.00 0.00 5.54
163 164 1.844544 TAGGTTTTCCCCCTGGTCGC 61.845 60.000 0.00 0.00 41.86 5.19
164 165 0.694196 TTAGGTTTTCCCCCTGGTCG 59.306 55.000 0.00 0.00 41.86 4.79
165 166 2.357881 GGATTAGGTTTTCCCCCTGGTC 60.358 54.545 0.00 0.00 41.86 4.02
166 167 1.644337 GGATTAGGTTTTCCCCCTGGT 59.356 52.381 0.00 0.00 41.86 4.00
168 169 2.022238 GCGGATTAGGTTTTCCCCCTG 61.022 57.143 0.00 0.00 41.86 4.45
169 170 0.257905 GCGGATTAGGTTTTCCCCCT 59.742 55.000 0.00 0.00 41.86 4.79
205 206 2.379459 GGAGGAAGGGAGAAGGGCC 61.379 68.421 0.00 0.00 0.00 5.80
207 208 1.208706 GAAGGAGGAAGGGAGAAGGG 58.791 60.000 0.00 0.00 0.00 3.95
217 218 1.302511 GGCAGCAACGAAGGAGGAA 60.303 57.895 0.00 0.00 0.00 3.36
250 251 0.481128 TGGTTGGGGAGGACTTTTCC 59.519 55.000 0.00 0.00 43.22 3.13
251 252 1.145119 ACTGGTTGGGGAGGACTTTTC 59.855 52.381 0.00 0.00 0.00 2.29
252 253 1.231963 ACTGGTTGGGGAGGACTTTT 58.768 50.000 0.00 0.00 0.00 2.27
253 254 1.231963 AACTGGTTGGGGAGGACTTT 58.768 50.000 0.00 0.00 0.00 2.66
266 267 3.590574 GGGGAGGGCCAAACTGGT 61.591 66.667 6.18 0.00 40.46 4.00
282 283 3.059352 AGTGCTACTAAAACTGGCTGG 57.941 47.619 0.00 0.00 0.00 4.85
285 286 3.188667 GGTCAAGTGCTACTAAAACTGGC 59.811 47.826 0.00 0.00 0.00 4.85
325 326 4.162592 TTGCAGTGGTGGAGCAAG 57.837 55.556 0.00 0.00 42.71 4.01
327 328 1.227943 GACTTGCAGTGGTGGAGCA 60.228 57.895 0.00 0.00 36.32 4.26
358 359 0.961753 CAAGCCACTGGGGAAGTTTC 59.038 55.000 0.00 0.00 36.83 2.78
384 385 2.170260 CTGGTTAACGCGCCAGTGTG 62.170 60.000 18.90 0.00 45.28 3.82
386 387 2.860293 CTGGTTAACGCGCCAGTG 59.140 61.111 18.90 0.00 45.28 3.66
391 392 0.668401 AGTACACCTGGTTAACGCGC 60.668 55.000 5.73 0.00 0.00 6.86
393 394 0.794473 GCAGTACACCTGGTTAACGC 59.206 55.000 0.00 3.38 41.81 4.84
400 401 3.510360 ACAAGTAGTAGCAGTACACCTGG 59.490 47.826 0.00 0.00 41.81 4.45
401 402 4.785511 ACAAGTAGTAGCAGTACACCTG 57.214 45.455 0.00 0.00 44.53 4.00
426 427 6.338937 ACTAGCCAATAGAAAAGAGGTAACG 58.661 40.000 0.00 0.00 37.09 3.18
441 448 1.981256 CCGCCCAATTACTAGCCAAT 58.019 50.000 0.00 0.00 0.00 3.16
450 457 2.124320 GCCTCAGCCGCCCAATTA 60.124 61.111 0.00 0.00 0.00 1.40
471 478 3.719871 ACCACCCACACATCTATCTACA 58.280 45.455 0.00 0.00 0.00 2.74
480 498 1.460255 CTCCCAACCACCCACACAT 59.540 57.895 0.00 0.00 0.00 3.21
522 540 9.819267 AACTAAGGTTTCTCGGAAATTAGATAG 57.181 33.333 17.38 11.72 30.55 2.08
525 543 7.673180 TGAACTAAGGTTTCTCGGAAATTAGA 58.327 34.615 17.38 0.00 35.58 2.10
535 553 6.223852 TCAGTCACATGAACTAAGGTTTCTC 58.776 40.000 0.00 0.00 35.58 2.87
536 554 6.174720 TCAGTCACATGAACTAAGGTTTCT 57.825 37.500 0.00 0.00 35.58 2.52
553 571 2.822561 CTCTCTAGTTGTGGCTCAGTCA 59.177 50.000 0.00 0.00 0.00 3.41
554 572 2.823154 ACTCTCTAGTTGTGGCTCAGTC 59.177 50.000 0.00 0.00 29.00 3.51
555 573 2.883026 ACTCTCTAGTTGTGGCTCAGT 58.117 47.619 0.00 0.00 29.00 3.41
556 574 3.181491 GCTACTCTCTAGTTGTGGCTCAG 60.181 52.174 11.21 0.00 37.15 3.35
565 583 3.011119 CGGTGTGAGCTACTCTCTAGTT 58.989 50.000 0.00 0.00 42.38 2.24
591 609 4.519213 AGTATATTTTACAAGGTGCGCCA 58.481 39.130 20.59 0.00 37.19 5.69
611 629 8.361139 CGGGAGTTTATTACAGATGATCTTAGT 58.639 37.037 0.00 0.00 0.00 2.24
614 632 6.326583 TCCGGGAGTTTATTACAGATGATCTT 59.673 38.462 0.00 0.00 0.00 2.40
615 633 5.839063 TCCGGGAGTTTATTACAGATGATCT 59.161 40.000 0.00 0.00 0.00 2.75
617 635 5.602978 AGTCCGGGAGTTTATTACAGATGAT 59.397 40.000 0.00 0.00 0.00 2.45
618 636 4.960469 AGTCCGGGAGTTTATTACAGATGA 59.040 41.667 0.00 0.00 0.00 2.92
619 637 5.163447 TGAGTCCGGGAGTTTATTACAGATG 60.163 44.000 5.71 0.00 0.00 2.90
620 638 4.960469 TGAGTCCGGGAGTTTATTACAGAT 59.040 41.667 5.71 0.00 0.00 2.90
621 639 4.346730 TGAGTCCGGGAGTTTATTACAGA 58.653 43.478 5.71 0.00 0.00 3.41
638 755 8.330302 CAGGAAACAAATTGTCAAAAATGAGTC 58.670 33.333 0.00 0.00 0.00 3.36
639 756 8.040132 TCAGGAAACAAATTGTCAAAAATGAGT 58.960 29.630 0.00 0.00 0.00 3.41
678 830 0.037232 CGTCTCCCGAGCTCCTTTTT 60.037 55.000 8.47 0.00 39.56 1.94
734 890 3.989698 ATGGACGACTTCGCCTGCG 62.990 63.158 4.92 4.92 44.43 5.18
770 926 2.246739 CCAGGCATGTGCGATACGG 61.247 63.158 0.00 0.00 43.26 4.02
858 1020 4.246458 GACCAGTCAATCACAAGACCTAC 58.754 47.826 0.00 0.00 35.38 3.18
894 1103 1.632422 GCTGTGTGCATATTTGTGGC 58.368 50.000 0.00 0.00 42.31 5.01
953 1167 2.550978 CGGACTTGCGTGGATAGAATT 58.449 47.619 0.00 0.00 0.00 2.17
1072 1289 2.049433 CCGCGTCTTCACGGTCTT 60.049 61.111 4.92 0.00 46.80 3.01
1146 1366 2.203015 ACAACTGCGAGCACCGTT 60.203 55.556 0.00 0.00 41.15 4.44
1191 1411 3.855159 GGGAGTACCTTGCACGAAT 57.145 52.632 0.00 0.00 35.85 3.34
1294 1552 7.857885 CCGCCATTTCTAAATAGATGTCTTTTC 59.142 37.037 0.00 0.00 31.40 2.29
1304 1562 5.855045 AGTACTCCCGCCATTTCTAAATAG 58.145 41.667 0.00 0.00 0.00 1.73
1330 1588 5.771469 CCAATCATGGCGCTCATATTTTAA 58.229 37.500 7.64 0.00 40.58 1.52
1393 1651 1.402968 TGGTATAGGCACTCGACGAAC 59.597 52.381 0.00 0.00 41.75 3.95
1400 1658 7.766278 CACTATAATGGAATGGTATAGGCACTC 59.234 40.741 0.00 0.00 41.75 3.51
1456 1714 1.354031 TGTCCAGTGGCACATGGTAAT 59.646 47.619 25.27 2.33 44.52 1.89
1534 1792 3.826729 GCCTGTTTTCTAGTTTGGGTGAT 59.173 43.478 0.00 0.00 0.00 3.06
1684 1988 6.445267 CGATCAGAAATATTTGTCGGAGAG 57.555 41.667 5.17 0.00 36.95 3.20
1781 2085 5.647658 AGACATTTCATTAGCAAATCCGTGA 59.352 36.000 0.00 0.00 0.00 4.35
1987 2304 1.192146 ACCGCTTCTGTAGGGCTTCA 61.192 55.000 0.00 0.00 35.57 3.02
2242 2568 0.401105 ATCCAGAGGGTAGCAGCCAT 60.401 55.000 7.06 0.00 38.48 4.40
2275 2613 1.306226 GTAGTCCCTGAGGTGCCCT 60.306 63.158 0.00 0.00 36.03 5.19
2557 2895 0.036388 GGAACATCCTGCCGAACTCA 60.036 55.000 0.00 0.00 32.53 3.41
2633 2971 4.771356 GACTGCGCGCCAGACGTA 62.771 66.667 30.77 6.77 44.64 3.57
2653 2991 2.026641 AGGTTGGCGCGATAGTAACTA 58.973 47.619 12.10 0.00 39.35 2.24
2718 3056 2.558554 TAGCGGCGTCTGCTTCTTCC 62.559 60.000 16.44 0.00 43.71 3.46
2809 3147 3.554129 CCTGGTCGGATGCGTTGATATTA 60.554 47.826 6.49 0.00 33.16 0.98
2812 3150 0.104120 CCTGGTCGGATGCGTTGATA 59.896 55.000 6.49 0.00 33.16 2.15
2834 3172 1.067213 GCTCAGAGAAGTGACCAGGAC 60.067 57.143 0.00 0.00 0.00 3.85
3097 3435 2.257676 GTGTCGGACTCGGACCAC 59.742 66.667 9.88 8.26 36.95 4.16
3114 3452 3.353836 CCACCTTTGTGTCGGCCG 61.354 66.667 22.12 22.12 41.09 6.13
3121 3459 1.826054 TTCCGGCACCACCTTTGTG 60.826 57.895 0.00 0.00 42.39 3.33
3157 3495 2.795973 CACGGCTCGACGGACATA 59.204 61.111 0.00 0.00 38.39 2.29
3336 3674 6.204301 CCTGTGATGCCTTTATATGAGAACAG 59.796 42.308 0.00 0.00 0.00 3.16
3340 3678 5.894298 ACCTGTGATGCCTTTATATGAGA 57.106 39.130 0.00 0.00 0.00 3.27
3375 3713 0.958091 CTGTGATGTCCCCGCAAAAA 59.042 50.000 0.00 0.00 0.00 1.94
3376 3714 0.893270 CCTGTGATGTCCCCGCAAAA 60.893 55.000 0.00 0.00 0.00 2.44
3377 3715 1.303236 CCTGTGATGTCCCCGCAAA 60.303 57.895 0.00 0.00 0.00 3.68
3378 3716 2.063015 AACCTGTGATGTCCCCGCAA 62.063 55.000 0.00 0.00 0.00 4.85
3379 3717 2.463589 GAACCTGTGATGTCCCCGCA 62.464 60.000 0.00 0.00 0.00 5.69
3380 3718 1.745489 GAACCTGTGATGTCCCCGC 60.745 63.158 0.00 0.00 0.00 6.13
3381 3719 1.137086 CTAGAACCTGTGATGTCCCCG 59.863 57.143 0.00 0.00 0.00 5.73
3382 3720 1.134371 GCTAGAACCTGTGATGTCCCC 60.134 57.143 0.00 0.00 0.00 4.81
3383 3721 1.834263 AGCTAGAACCTGTGATGTCCC 59.166 52.381 0.00 0.00 0.00 4.46
3384 3722 3.068873 CCTAGCTAGAACCTGTGATGTCC 59.931 52.174 22.70 0.00 0.00 4.02
3385 3723 3.702045 ACCTAGCTAGAACCTGTGATGTC 59.298 47.826 22.70 0.00 0.00 3.06
3386 3724 3.449018 CACCTAGCTAGAACCTGTGATGT 59.551 47.826 22.70 4.32 0.00 3.06
3409 3747 9.050601 GTTTCATCTGCACTAGCTTAGATTAAT 57.949 33.333 0.00 0.00 42.74 1.40
3417 3755 5.972107 ATTTGTTTCATCTGCACTAGCTT 57.028 34.783 0.00 0.00 42.74 3.74
3426 3764 7.761249 GGGGAACAATTCTATTTGTTTCATCTG 59.239 37.037 9.78 0.00 46.84 2.90
3456 3794 0.545787 TATGGGTGGAGGGTGTTCGT 60.546 55.000 0.00 0.00 0.00 3.85
3472 3810 8.610855 TTAGATCGTAAGTTTCTTGTCGTATG 57.389 34.615 0.00 0.00 39.48 2.39
3473 3811 9.630098 TTTTAGATCGTAAGTTTCTTGTCGTAT 57.370 29.630 0.00 0.00 39.48 3.06
3484 3822 5.124936 GGGGCATGTTTTTAGATCGTAAGTT 59.875 40.000 0.00 0.00 39.48 2.66
3488 3826 4.223556 TGGGGCATGTTTTTAGATCGTA 57.776 40.909 0.00 0.00 0.00 3.43
3491 3829 5.118286 CCAATTGGGGCATGTTTTTAGATC 58.882 41.667 17.36 0.00 0.00 2.75
3533 3871 0.805322 GGCAGACTGCGATGACTGAG 60.805 60.000 20.82 0.00 46.21 3.35
3535 3873 1.812922 GGGCAGACTGCGATGACTG 60.813 63.158 20.82 0.00 46.21 3.51
3549 3887 5.162637 AGACAGTCCCAATATATAAGGGCA 58.837 41.667 15.33 5.29 42.52 5.36
3663 4001 5.916320 CCGTTTAGGCGTTCTTTTTGTTATT 59.084 36.000 0.00 0.00 0.00 1.40
3705 4045 1.880819 TTGTCTAGGACGAACCGGGC 61.881 60.000 6.32 0.00 44.74 6.13
3719 4059 7.000472 TGATTTTCTGGAGAGATTTGTTGTCT 59.000 34.615 0.00 0.00 0.00 3.41
3729 4069 1.561542 GCCCCTGATTTTCTGGAGAGA 59.438 52.381 2.33 0.00 37.65 3.10
3731 4071 0.625849 GGCCCCTGATTTTCTGGAGA 59.374 55.000 0.00 0.00 37.65 3.71
3810 4153 0.110486 GAGGTGAAGAGGGGTTTGCA 59.890 55.000 0.00 0.00 0.00 4.08
3968 4314 7.288158 ACTGGAAATTACTAGGATCCTACACTC 59.712 40.741 18.00 8.32 0.00 3.51
4090 4436 8.755028 TGATTTACTGGCAGTGTAATTACTAGA 58.245 33.333 29.65 2.03 31.13 2.43
4093 4439 9.547753 CTATGATTTACTGGCAGTGTAATTACT 57.452 33.333 29.65 16.72 31.13 2.24
4116 4462 8.421784 TCTAGGATTCGCACTGTAATTTTCTAT 58.578 33.333 0.00 0.00 0.00 1.98
4162 4508 7.487484 TGCATCTTTTGTCTACATTTTTCACA 58.513 30.769 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.