Multiple sequence alignment - TraesCS4A01G432600

Loading Multiple Alignment...

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 TraesCS4A01G432600 chr4A 100.000 3158 0 0 1 3158 703433769 703430612 0.000000e+00 5832.0
1 TraesCS4A01G432600 chr4A 76.980 404 84 9 1584 1981 703410148 703409748 4.100000e-54 222.0
2 TraesCS4A01G432600 chr7D 91.575 1638 96 14 831 2431 27962034 27960402 0.000000e+00 2222.0
3 TraesCS4A01G432600 chr7D 93.933 445 21 3 2665 3103 27844582 27844138 0.000000e+00 667.0
4 TraesCS4A01G432600 chr7D 93.933 445 21 3 2665 3103 27850411 27849967 0.000000e+00 667.0
5 TraesCS4A01G432600 chr7D 93.933 445 21 3 2665 3103 27856234 27855790 0.000000e+00 667.0
6 TraesCS4A01G432600 chr7D 90.659 364 27 4 221 580 27962586 27962226 7.920000e-131 477.0
7 TraesCS4A01G432600 chr7D 81.455 426 68 9 1583 2003 28008432 28008013 3.900000e-89 339.0
8 TraesCS4A01G432600 chr7D 92.361 144 7 4 95 237 522504694 522504834 5.340000e-48 202.0
9 TraesCS4A01G432600 chr7D 76.190 357 63 16 989 1337 28070569 28070227 5.420000e-38 169.0
10 TraesCS4A01G432600 chr7D 98.529 68 1 0 1 68 27965851 27965784 1.540000e-23 121.0
11 TraesCS4A01G432600 chr7D 90.909 66 5 1 2422 2486 27845018 27844953 1.560000e-13 87.9
12 TraesCS4A01G432600 chr7D 90.909 66 5 1 2422 2486 27850847 27850782 1.560000e-13 87.9
13 TraesCS4A01G432600 chr7D 90.909 66 5 1 2422 2486 27856670 27856605 1.560000e-13 87.9
14 TraesCS4A01G432600 chr7A 88.784 1703 114 28 831 2484 28256510 28254836 0.000000e+00 2015.0
15 TraesCS4A01G432600 chr7A 93.483 445 23 3 2665 3103 28045496 28045052 0.000000e+00 656.0
16 TraesCS4A01G432600 chr7A 86.345 498 48 10 2665 3156 28254370 28253887 2.790000e-145 525.0
17 TraesCS4A01G432600 chr7A 74.783 1150 214 42 988 2088 28415376 28414254 6.210000e-122 448.0
18 TraesCS4A01G432600 chr7A 87.097 155 17 1 491 642 28263738 28263584 4.190000e-39 172.0
19 TraesCS4A01G432600 chrUn 93.933 445 21 3 2665 3103 356925267 356925711 0.000000e+00 667.0
20 TraesCS4A01G432600 chrUn 93.933 445 21 3 2665 3103 423932891 423932447 0.000000e+00 667.0
21 TraesCS4A01G432600 chr3B 92.958 142 8 2 89 229 655849414 655849554 4.130000e-49 206.0
22 TraesCS4A01G432600 chr2D 94.118 136 6 2 95 229 575354474 575354340 4.130000e-49 206.0
23 TraesCS4A01G432600 chr2D 92.308 143 7 4 96 237 247099676 247099537 1.920000e-47 200.0
24 TraesCS4A01G432600 chr1A 94.118 136 6 2 95 229 66898397 66898531 4.130000e-49 206.0
25 TraesCS4A01G432600 chr1A 91.391 151 10 3 80 229 393948439 393948587 1.480000e-48 204.0
26 TraesCS4A01G432600 chr4D 91.391 151 10 3 80 229 22433748 22433600 1.480000e-48 204.0
27 TraesCS4A01G432600 chr4B 93.333 135 7 2 96 229 113961281 113961148 6.910000e-47 198.0
28 TraesCS4A01G432600 chr5D 90.728 151 8 6 80 229 420206031 420206176 2.480000e-46 196.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G432600 chr4A 703430612 703433769 3157 True 5832.00 5832 100.000000 1 3158 1 chr4A.!!$R2 3157
1 TraesCS4A01G432600 chr7D 27960402 27965851 5449 True 940.00 2222 93.587667 1 2431 3 chr7D.!!$R6 2430
2 TraesCS4A01G432600 chr7D 27844138 27845018 880 True 377.45 667 92.421000 2422 3103 2 chr7D.!!$R3 681
3 TraesCS4A01G432600 chr7D 27849967 27850847 880 True 377.45 667 92.421000 2422 3103 2 chr7D.!!$R4 681
4 TraesCS4A01G432600 chr7D 27855790 27856670 880 True 377.45 667 92.421000 2422 3103 2 chr7D.!!$R5 681
5 TraesCS4A01G432600 chr7A 28253887 28256510 2623 True 1270.00 2015 87.564500 831 3156 2 chr7A.!!$R4 2325
6 TraesCS4A01G432600 chr7A 28414254 28415376 1122 True 448.00 448 74.783000 988 2088 1 chr7A.!!$R3 1100

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
551 3642 0.098728 CCATTCGATTCAACACCGGC 59.901 55.0 0.0 0.0 0.0 6.13 F
584 3675 0.108585 ATTGTTCTCAGTGCCACGGT 59.891 50.0 0.0 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 4659 0.446616 GCCGGTTCCGAATTGAGTTC 59.553 55.0 13.08 0.0 0.0 3.01 R
2580 6148 0.382158 GATCGTCTGTCCATCGCTGA 59.618 55.0 0.00 0.0 0.0 4.26 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
39 40 4.629200 GGCAGTCTAAGTGTCTTCATTCTG 59.371 45.833 0.00 0.00 0.00 3.02
68 69 2.243810 GGCTGGTGGGTTTGTTATCAA 58.756 47.619 0.00 0.00 0.00 2.57
69 70 2.029380 GGCTGGTGGGTTTGTTATCAAC 60.029 50.000 0.00 0.00 32.93 3.18
70 71 2.029380 GCTGGTGGGTTTGTTATCAACC 60.029 50.000 0.00 0.00 32.93 3.77
71 72 3.496331 CTGGTGGGTTTGTTATCAACCT 58.504 45.455 2.01 0.00 32.93 3.50
72 73 3.895041 CTGGTGGGTTTGTTATCAACCTT 59.105 43.478 2.01 0.00 32.93 3.50
73 74 5.063017 TGGTGGGTTTGTTATCAACCTTA 57.937 39.130 2.01 0.00 32.93 2.69
74 75 4.828387 TGGTGGGTTTGTTATCAACCTTAC 59.172 41.667 2.01 2.55 32.93 2.34
75 76 5.074804 GGTGGGTTTGTTATCAACCTTACT 58.925 41.667 2.01 0.00 32.93 2.24
76 77 5.537295 GGTGGGTTTGTTATCAACCTTACTT 59.463 40.000 2.01 0.00 32.93 2.24
77 78 6.294342 GGTGGGTTTGTTATCAACCTTACTTC 60.294 42.308 2.01 0.00 32.93 3.01
78 79 5.470777 TGGGTTTGTTATCAACCTTACTTCG 59.529 40.000 2.01 0.00 32.93 3.79
79 80 5.106436 GGGTTTGTTATCAACCTTACTTCGG 60.106 44.000 2.01 0.00 32.93 4.30
80 81 5.471116 GGTTTGTTATCAACCTTACTTCGGT 59.529 40.000 0.00 0.00 35.97 4.69
81 82 6.016860 GGTTTGTTATCAACCTTACTTCGGTT 60.017 38.462 0.00 0.00 45.26 4.44
90 91 5.416271 ACCTTACTTCGGTTGATACATGT 57.584 39.130 2.69 2.69 0.00 3.21
91 92 6.534475 ACCTTACTTCGGTTGATACATGTA 57.466 37.500 8.27 8.27 0.00 2.29
92 93 7.120923 ACCTTACTTCGGTTGATACATGTAT 57.879 36.000 18.31 18.31 0.00 2.29
93 94 7.208080 ACCTTACTTCGGTTGATACATGTATC 58.792 38.462 30.80 30.80 41.67 2.24
94 95 6.645415 CCTTACTTCGGTTGATACATGTATCC 59.355 42.308 32.93 22.06 40.84 2.59
95 96 5.871396 ACTTCGGTTGATACATGTATCCT 57.129 39.130 32.93 9.99 40.84 3.24
96 97 6.971726 ACTTCGGTTGATACATGTATCCTA 57.028 37.500 32.93 22.26 40.84 2.94
97 98 6.746120 ACTTCGGTTGATACATGTATCCTAC 58.254 40.000 32.93 28.79 40.84 3.18
98 99 6.550108 ACTTCGGTTGATACATGTATCCTACT 59.450 38.462 32.93 16.91 40.84 2.57
99 100 6.971726 TCGGTTGATACATGTATCCTACTT 57.028 37.500 32.93 7.88 40.84 2.24
100 101 6.978338 TCGGTTGATACATGTATCCTACTTC 58.022 40.000 32.93 20.36 40.84 3.01
101 102 6.015688 TCGGTTGATACATGTATCCTACTTCC 60.016 42.308 32.93 24.20 40.84 3.46
102 103 6.015350 CGGTTGATACATGTATCCTACTTCCT 60.015 42.308 32.93 5.78 40.84 3.36
103 104 7.379750 GGTTGATACATGTATCCTACTTCCTC 58.620 42.308 32.93 17.98 40.84 3.71
104 105 7.233757 GGTTGATACATGTATCCTACTTCCTCT 59.766 40.741 32.93 5.10 40.84 3.69
105 106 7.767250 TGATACATGTATCCTACTTCCTCTG 57.233 40.000 32.93 0.00 40.84 3.35
106 107 7.298374 TGATACATGTATCCTACTTCCTCTGT 58.702 38.462 32.93 4.07 40.84 3.41
107 108 7.785028 TGATACATGTATCCTACTTCCTCTGTT 59.215 37.037 32.93 3.71 40.84 3.16
108 109 6.472686 ACATGTATCCTACTTCCTCTGTTC 57.527 41.667 0.00 0.00 0.00 3.18
109 110 5.364157 ACATGTATCCTACTTCCTCTGTTCC 59.636 44.000 0.00 0.00 0.00 3.62
113 114 7.363031 TGTATCCTACTTCCTCTGTTCCTAAT 58.637 38.462 0.00 0.00 0.00 1.73
199 3126 9.962783 ACACTCTAAAAACGTCTATATACATCC 57.037 33.333 0.00 0.00 0.00 3.51
209 3136 6.432162 ACGTCTATATACATCCGTATGTGGTT 59.568 38.462 3.56 0.00 45.99 3.67
210 3137 7.607607 ACGTCTATATACATCCGTATGTGGTTA 59.392 37.037 3.56 0.00 45.99 2.85
211 3138 8.121086 CGTCTATATACATCCGTATGTGGTTAG 58.879 40.741 3.56 2.56 45.99 2.34
212 3139 8.954350 GTCTATATACATCCGTATGTGGTTAGT 58.046 37.037 3.56 0.00 45.99 2.24
214 3141 3.814005 ACATCCGTATGTGGTTAGTCC 57.186 47.619 0.00 0.00 44.79 3.85
215 3142 3.101437 ACATCCGTATGTGGTTAGTCCA 58.899 45.455 0.00 0.00 44.79 4.02
218 3145 7.419750 ATACATCCGTATGTGGTTAGTCCATTT 60.420 37.037 3.56 0.00 45.99 2.32
242 3329 9.911788 TTTGAATTCTCTATCATAAGAAAGCCT 57.088 29.630 7.05 0.00 35.29 4.58
243 3330 9.911788 TTGAATTCTCTATCATAAGAAAGCCTT 57.088 29.630 7.05 0.00 35.29 4.35
244 3331 9.911788 TGAATTCTCTATCATAAGAAAGCCTTT 57.088 29.630 7.05 0.00 35.29 3.11
293 3380 7.118496 TGCAAAATCTTTTCTCTTAAACCCA 57.882 32.000 0.00 0.00 0.00 4.51
310 3397 3.979911 ACCCAGAACATCATGGCAAATA 58.020 40.909 0.00 0.00 35.10 1.40
311 3398 4.352009 ACCCAGAACATCATGGCAAATAA 58.648 39.130 0.00 0.00 35.10 1.40
325 3412 9.598517 TCATGGCAAATAAGTTCAAATTATTCC 57.401 29.630 3.40 2.91 32.90 3.01
327 3414 7.831753 TGGCAAATAAGTTCAAATTATTCCGA 58.168 30.769 3.40 0.00 32.90 4.55
371 3461 4.069304 TGGCAACTAGTAGAACGCAAAAT 58.931 39.130 3.59 0.00 37.61 1.82
401 3491 2.142356 AAATCCGGAACATCATGGCA 57.858 45.000 9.01 0.00 0.00 4.92
488 3578 0.823356 CAACCACCAACTCCCCTGTG 60.823 60.000 0.00 0.00 0.00 3.66
499 3590 1.694169 CCCCTGTGCCTGGGATACT 60.694 63.158 15.72 0.00 45.28 2.12
505 3596 2.203266 GCCTGGGATACTGCTGGC 60.203 66.667 0.00 0.00 36.15 4.85
539 3630 1.375396 CTGGGTCGTTGCCATTCGA 60.375 57.895 0.00 0.00 0.00 3.71
551 3642 0.098728 CCATTCGATTCAACACCGGC 59.901 55.000 0.00 0.00 0.00 6.13
553 3644 0.672401 ATTCGATTCAACACCGGCGT 60.672 50.000 6.01 0.00 0.00 5.68
556 3647 2.359478 ATTCAACACCGGCGTCCC 60.359 61.111 6.01 0.00 0.00 4.46
570 3661 0.320421 CGTCCCCACGTCTCATTGTT 60.320 55.000 0.00 0.00 41.42 2.83
576 3667 2.289072 CCCACGTCTCATTGTTCTCAGT 60.289 50.000 0.00 0.00 0.00 3.41
580 3671 2.771089 GTCTCATTGTTCTCAGTGCCA 58.229 47.619 0.00 0.00 32.48 4.92
581 3672 2.481952 GTCTCATTGTTCTCAGTGCCAC 59.518 50.000 0.00 0.00 32.48 5.01
582 3673 1.462283 CTCATTGTTCTCAGTGCCACG 59.538 52.381 0.00 0.00 32.48 4.94
583 3674 0.518636 CATTGTTCTCAGTGCCACGG 59.481 55.000 0.00 0.00 0.00 4.94
584 3675 0.108585 ATTGTTCTCAGTGCCACGGT 59.891 50.000 0.00 0.00 0.00 4.83
585 3676 0.813610 TTGTTCTCAGTGCCACGGTG 60.814 55.000 0.00 0.00 0.00 4.94
586 3677 2.280797 TTCTCAGTGCCACGGTGC 60.281 61.111 1.68 0.00 0.00 5.01
587 3678 4.662961 TCTCAGTGCCACGGTGCG 62.663 66.667 1.68 0.00 0.00 5.34
626 3717 2.661594 GTGCTTTGTGGAAAATCGTCC 58.338 47.619 0.00 0.00 38.27 4.79
643 3737 4.487948 TCGTCCGATAACTCGTTTTTCAT 58.512 39.130 0.00 0.00 43.49 2.57
645 3739 4.331962 GTCCGATAACTCGTTTTTCATGC 58.668 43.478 0.00 0.00 43.49 4.06
648 3742 4.260212 CCGATAACTCGTTTTTCATGCGAT 60.260 41.667 0.00 0.00 43.49 4.58
650 3744 5.167803 CGATAACTCGTTTTTCATGCGATTG 59.832 40.000 0.00 0.00 40.07 2.67
652 3746 4.070581 ACTCGTTTTTCATGCGATTGAG 57.929 40.909 0.00 0.00 34.04 3.02
665 3759 3.755905 TGCGATTGAGGAATAGCAAAACA 59.244 39.130 0.00 0.00 44.33 2.83
670 3764 6.483307 CGATTGAGGAATAGCAAAACAGGATA 59.517 38.462 0.00 0.00 0.00 2.59
678 3772 8.424133 GGAATAGCAAAACAGGATATGGAAATT 58.576 33.333 0.00 0.00 0.00 1.82
718 3812 8.766994 ACCATATAACCATGCAAATAGAGTTT 57.233 30.769 0.00 0.00 0.00 2.66
758 3852 7.042335 TGTTGTTTCACGGAAATAATTTTGGT 58.958 30.769 10.17 0.00 35.71 3.67
767 3861 5.414454 CGGAAATAATTTTGGTGAGACTCCA 59.586 40.000 0.00 0.00 0.00 3.86
769 3863 7.090808 GGAAATAATTTTGGTGAGACTCCAAC 58.909 38.462 0.00 0.00 43.45 3.77
787 3881 6.016276 ACTCCAACGAAACAAAATCTGCTAAT 60.016 34.615 0.00 0.00 0.00 1.73
810 3904 0.251165 TTGCAGCCCAAGTAAGGACC 60.251 55.000 0.00 0.00 0.00 4.46
811 3905 1.378646 GCAGCCCAAGTAAGGACCC 60.379 63.158 0.00 0.00 0.00 4.46
812 3906 1.853250 GCAGCCCAAGTAAGGACCCT 61.853 60.000 0.00 0.00 0.00 4.34
813 3907 0.698818 CAGCCCAAGTAAGGACCCTT 59.301 55.000 6.54 6.54 39.83 3.95
814 3908 1.075536 CAGCCCAAGTAAGGACCCTTT 59.924 52.381 6.62 0.00 37.47 3.11
815 3909 1.354705 AGCCCAAGTAAGGACCCTTTC 59.645 52.381 6.62 1.95 37.47 2.62
816 3910 1.354705 GCCCAAGTAAGGACCCTTTCT 59.645 52.381 6.62 4.40 37.47 2.52
817 3911 2.225041 GCCCAAGTAAGGACCCTTTCTT 60.225 50.000 12.92 12.92 41.91 2.52
818 3912 3.754172 GCCCAAGTAAGGACCCTTTCTTT 60.754 47.826 15.22 3.18 40.16 2.52
819 3913 4.480115 CCCAAGTAAGGACCCTTTCTTTT 58.520 43.478 15.22 0.00 40.16 2.27
820 3914 4.899457 CCCAAGTAAGGACCCTTTCTTTTT 59.101 41.667 15.22 0.00 40.16 1.94
864 3958 4.815308 TCTTTGGTTTGTTTGCATTGGATG 59.185 37.500 0.00 0.00 0.00 3.51
897 3992 2.002586 CAGCACATCGGTTGAAGTAGG 58.997 52.381 0.00 0.00 0.00 3.18
968 4063 5.399858 CGAAAGAACGATCTACAAAGGAGA 58.600 41.667 0.00 0.00 33.77 3.71
969 4064 6.037098 CGAAAGAACGATCTACAAAGGAGAT 58.963 40.000 0.00 0.00 36.33 2.75
972 4087 7.883391 AAGAACGATCTACAAAGGAGATCTA 57.117 36.000 15.24 0.00 44.83 1.98
1131 4246 1.340248 GAGTTCACACGAGTCAGGGAA 59.660 52.381 0.00 0.00 0.00 3.97
1140 4255 1.004918 AGTCAGGGAAAAGACGGCG 60.005 57.895 4.80 4.80 39.67 6.46
1167 4282 2.032681 GCCGTCTTGTCAAGCCCT 59.967 61.111 7.78 0.00 0.00 5.19
1172 4287 1.600413 CGTCTTGTCAAGCCCTTTTGC 60.600 52.381 7.78 0.00 0.00 3.68
1209 4331 1.523938 GCGTATCAGGTGCTTCCCC 60.524 63.158 0.00 0.00 36.75 4.81
1218 4340 3.565214 TGCTTCCCCAACGGCAGA 61.565 61.111 0.00 0.00 0.00 4.26
1219 4341 3.056328 GCTTCCCCAACGGCAGAC 61.056 66.667 0.00 0.00 0.00 3.51
1240 4362 2.104792 CTCAAAGATTCGGAGGGCCATA 59.895 50.000 6.18 0.00 0.00 2.74
1245 4367 2.183679 GATTCGGAGGGCCATATCTCT 58.816 52.381 6.18 0.00 0.00 3.10
1320 4442 4.820897 ACAAGATGAGCATACTCGACAAA 58.179 39.130 0.00 0.00 46.69 2.83
1395 4517 1.281925 ATGGTTACTGGGGCTGGAGG 61.282 60.000 0.00 0.00 0.00 4.30
1412 4534 3.882888 TGGAGGAAGTTCATGAAACACAC 59.117 43.478 10.35 0.00 40.56 3.82
1428 4556 2.037772 ACACACAGATCTTGACAGGGAC 59.962 50.000 10.61 0.00 0.00 4.46
1473 4601 2.502080 GTCCTCTGCGACGTCACG 60.502 66.667 17.16 4.07 0.00 4.35
1562 4699 1.735973 CGTCCGAGCCTCATCATGA 59.264 57.895 0.00 0.00 0.00 3.07
1566 4703 1.137675 TCCGAGCCTCATCATGACTTG 59.862 52.381 0.00 0.00 0.00 3.16
1572 4709 2.290916 GCCTCATCATGACTTGCATCTG 59.709 50.000 0.00 0.00 34.15 2.90
1602 4765 1.472728 GCGGACGTAATGATCCACCTT 60.473 52.381 0.00 0.00 34.35 3.50
1655 4818 2.203714 GCTAGAGGCCCGATCCCT 60.204 66.667 0.00 0.00 34.77 4.20
1656 4819 2.578714 GCTAGAGGCCCGATCCCTG 61.579 68.421 0.00 0.00 31.41 4.45
1665 4828 2.158579 GGCCCGATCCCTGGTATTTAAA 60.159 50.000 0.00 0.00 0.00 1.52
1668 4831 4.332828 CCCGATCCCTGGTATTTAAATCC 58.667 47.826 3.39 6.82 0.00 3.01
1725 4888 2.174349 GAACTACGCGTCGACGGT 59.826 61.111 36.13 30.88 40.23 4.83
2047 5210 0.390998 GGAGCAGCTCAAGACACTCC 60.391 60.000 24.09 0.00 37.17 3.85
2174 5337 1.074889 GTGAAGGGTTTAGAAGGCCCA 59.925 52.381 0.00 0.00 44.69 5.36
2228 5391 8.213679 TCTCTGTAGGAAAAGGGAAATATCATG 58.786 37.037 0.00 0.00 0.00 3.07
2308 5476 6.973642 TCCCTTCTTATGATTTCATGGTCTT 58.026 36.000 3.30 0.00 37.15 3.01
2312 5480 7.066284 CCTTCTTATGATTTCATGGTCTTTCGT 59.934 37.037 3.30 0.00 37.15 3.85
2350 5547 8.047310 CCCATTACTCTAGTTCCTTGTATTTGT 58.953 37.037 0.00 0.00 0.00 2.83
2357 5554 9.219603 CTCTAGTTCCTTGTATTTGTGATTTGA 57.780 33.333 0.00 0.00 0.00 2.69
2377 5574 1.066257 CTGTTTGCTGCGCTTTGGT 59.934 52.632 9.73 0.00 0.00 3.67
2399 5596 4.543590 TGGTTGTCATTTGTGTTTTGGT 57.456 36.364 0.00 0.00 0.00 3.67
2402 5599 2.803451 TGTCATTTGTGTTTTGGTCGC 58.197 42.857 0.00 0.00 0.00 5.19
2405 5602 1.857837 CATTTGTGTTTTGGTCGCACC 59.142 47.619 0.00 0.00 39.22 5.01
2422 5619 0.251165 ACCGTGTTGCCCTGCTTTAT 60.251 50.000 0.00 0.00 0.00 1.40
2423 5620 1.003812 ACCGTGTTGCCCTGCTTTATA 59.996 47.619 0.00 0.00 0.00 0.98
2424 5621 2.297701 CCGTGTTGCCCTGCTTTATAT 58.702 47.619 0.00 0.00 0.00 0.86
2425 5622 3.118186 ACCGTGTTGCCCTGCTTTATATA 60.118 43.478 0.00 0.00 0.00 0.86
2428 5625 5.703592 CCGTGTTGCCCTGCTTTATATATAA 59.296 40.000 0.81 0.81 0.00 0.98
2456 5653 9.740239 ATATATAACACGAGACAAAATACACGT 57.260 29.630 0.00 0.00 34.23 4.49
2492 5845 9.250246 CAAGGTACCAAGGAATCCTTTTTATTA 57.750 33.333 12.63 0.00 41.69 0.98
2516 5972 4.841813 TCAGTTATAAAGACAGTGTCCCCA 59.158 41.667 19.71 5.25 32.18 4.96
2517 5973 5.046591 TCAGTTATAAAGACAGTGTCCCCAG 60.047 44.000 19.71 1.34 32.18 4.45
2519 5975 0.690762 TAAAGACAGTGTCCCCAGCC 59.309 55.000 19.71 0.00 32.18 4.85
2520 5976 2.069165 AAAGACAGTGTCCCCAGCCC 62.069 60.000 19.71 0.00 32.18 5.19
2521 5977 2.930562 GACAGTGTCCCCAGCCCT 60.931 66.667 12.54 0.00 0.00 5.19
2524 5980 1.306141 CAGTGTCCCCAGCCCTCTA 60.306 63.158 0.00 0.00 0.00 2.43
2525 5981 1.306226 AGTGTCCCCAGCCCTCTAC 60.306 63.158 0.00 0.00 0.00 2.59
2526 5982 2.040606 TGTCCCCAGCCCTCTACC 59.959 66.667 0.00 0.00 0.00 3.18
2554 6028 1.333931 CGACATAAGCCTAGTCTCGCA 59.666 52.381 0.00 0.00 0.00 5.10
2579 6147 2.967397 TGGACGTGACGATCCACC 59.033 61.111 19.95 11.94 40.17 4.61
2580 6148 1.605451 TGGACGTGACGATCCACCT 60.605 57.895 19.95 0.00 40.17 4.00
2583 6151 0.179161 GACGTGACGATCCACCTCAG 60.179 60.000 13.70 0.00 33.67 3.35
2586 6154 1.677633 TGACGATCCACCTCAGCGA 60.678 57.895 0.00 0.00 0.00 4.93
2589 6157 1.300465 CGATCCACCTCAGCGATGG 60.300 63.158 0.00 0.00 34.58 3.51
2593 6161 1.153489 CCACCTCAGCGATGGACAG 60.153 63.158 0.00 0.00 35.33 3.51
2594 6162 1.607801 CCACCTCAGCGATGGACAGA 61.608 60.000 0.00 0.00 35.33 3.41
2595 6163 0.459237 CACCTCAGCGATGGACAGAC 60.459 60.000 0.00 0.00 0.00 3.51
2596 6164 1.226802 CCTCAGCGATGGACAGACG 60.227 63.158 0.00 0.00 0.00 4.18
2597 6165 1.657751 CCTCAGCGATGGACAGACGA 61.658 60.000 0.00 0.00 0.00 4.20
2598 6166 0.383590 CTCAGCGATGGACAGACGAT 59.616 55.000 0.00 0.00 0.00 3.73
2599 6167 0.382158 TCAGCGATGGACAGACGATC 59.618 55.000 0.00 0.00 0.00 3.69
2602 6170 2.860051 CGATGGACAGACGATCGTG 58.140 57.895 28.12 15.07 46.63 4.35
2603 6171 0.592500 CGATGGACAGACGATCGTGG 60.593 60.000 28.12 19.46 46.63 4.94
2604 6172 0.249073 GATGGACAGACGATCGTGGG 60.249 60.000 28.12 19.08 0.00 4.61
2605 6173 0.970937 ATGGACAGACGATCGTGGGT 60.971 55.000 28.12 22.29 0.00 4.51
2606 6174 1.153823 GGACAGACGATCGTGGGTG 60.154 63.158 28.12 20.94 0.00 4.61
2607 6175 1.585006 GACAGACGATCGTGGGTGT 59.415 57.895 28.12 23.93 0.00 4.16
2608 6176 0.038526 GACAGACGATCGTGGGTGTT 60.039 55.000 28.12 10.34 0.00 3.32
2609 6177 0.319555 ACAGACGATCGTGGGTGTTG 60.320 55.000 28.12 15.09 0.00 3.33
2610 6178 1.374252 AGACGATCGTGGGTGTTGC 60.374 57.895 28.12 8.43 0.00 4.17
2611 6179 2.726691 GACGATCGTGGGTGTTGCG 61.727 63.158 28.12 0.00 0.00 4.85
2612 6180 3.487202 CGATCGTGGGTGTTGCGG 61.487 66.667 7.03 0.00 0.00 5.69
2613 6181 3.799755 GATCGTGGGTGTTGCGGC 61.800 66.667 0.00 0.00 0.00 6.53
2631 6199 3.781307 CCGGTCGCCCATCCTCAA 61.781 66.667 0.00 0.00 0.00 3.02
2632 6200 2.267642 CGGTCGCCCATCCTCAAA 59.732 61.111 0.00 0.00 0.00 2.69
2633 6201 1.815421 CGGTCGCCCATCCTCAAAG 60.815 63.158 0.00 0.00 0.00 2.77
2634 6202 2.115291 GGTCGCCCATCCTCAAAGC 61.115 63.158 0.00 0.00 0.00 3.51
2635 6203 1.377202 GTCGCCCATCCTCAAAGCA 60.377 57.895 0.00 0.00 0.00 3.91
2636 6204 1.078214 TCGCCCATCCTCAAAGCAG 60.078 57.895 0.00 0.00 0.00 4.24
2637 6205 1.078214 CGCCCATCCTCAAAGCAGA 60.078 57.895 0.00 0.00 0.00 4.26
2638 6206 0.465097 CGCCCATCCTCAAAGCAGAT 60.465 55.000 0.00 0.00 0.00 2.90
2639 6207 1.316651 GCCCATCCTCAAAGCAGATC 58.683 55.000 0.00 0.00 0.00 2.75
2640 6208 1.133853 GCCCATCCTCAAAGCAGATCT 60.134 52.381 0.00 0.00 0.00 2.75
2641 6209 2.848691 CCCATCCTCAAAGCAGATCTC 58.151 52.381 0.00 0.00 0.00 2.75
2642 6210 2.172082 CCCATCCTCAAAGCAGATCTCA 59.828 50.000 0.00 0.00 0.00 3.27
2643 6211 3.204526 CCATCCTCAAAGCAGATCTCAC 58.795 50.000 0.00 0.00 0.00 3.51
2644 6212 3.204526 CATCCTCAAAGCAGATCTCACC 58.795 50.000 0.00 0.00 0.00 4.02
2645 6213 1.556911 TCCTCAAAGCAGATCTCACCC 59.443 52.381 0.00 0.00 0.00 4.61
2646 6214 1.558756 CCTCAAAGCAGATCTCACCCT 59.441 52.381 0.00 0.00 0.00 4.34
2647 6215 2.419851 CCTCAAAGCAGATCTCACCCTC 60.420 54.545 0.00 0.00 0.00 4.30
2648 6216 1.205655 TCAAAGCAGATCTCACCCTCG 59.794 52.381 0.00 0.00 0.00 4.63
2649 6217 0.107945 AAAGCAGATCTCACCCTCGC 60.108 55.000 0.00 0.00 0.00 5.03
2650 6218 1.965754 AAGCAGATCTCACCCTCGCC 61.966 60.000 0.00 0.00 0.00 5.54
2651 6219 2.430610 GCAGATCTCACCCTCGCCT 61.431 63.158 0.00 0.00 0.00 5.52
2652 6220 1.739049 CAGATCTCACCCTCGCCTC 59.261 63.158 0.00 0.00 0.00 4.70
2653 6221 1.039785 CAGATCTCACCCTCGCCTCA 61.040 60.000 0.00 0.00 0.00 3.86
2654 6222 0.324738 AGATCTCACCCTCGCCTCAA 60.325 55.000 0.00 0.00 0.00 3.02
2655 6223 0.537188 GATCTCACCCTCGCCTCAAA 59.463 55.000 0.00 0.00 0.00 2.69
2656 6224 0.250513 ATCTCACCCTCGCCTCAAAC 59.749 55.000 0.00 0.00 0.00 2.93
2657 6225 1.118965 TCTCACCCTCGCCTCAAACA 61.119 55.000 0.00 0.00 0.00 2.83
2658 6226 0.250295 CTCACCCTCGCCTCAAACAA 60.250 55.000 0.00 0.00 0.00 2.83
2659 6227 0.534203 TCACCCTCGCCTCAAACAAC 60.534 55.000 0.00 0.00 0.00 3.32
2660 6228 1.597027 ACCCTCGCCTCAAACAACG 60.597 57.895 0.00 0.00 0.00 4.10
2661 6229 2.556287 CCTCGCCTCAAACAACGC 59.444 61.111 0.00 0.00 0.00 4.84
2662 6230 2.556287 CTCGCCTCAAACAACGCC 59.444 61.111 0.00 0.00 0.00 5.68
2663 6231 2.203084 TCGCCTCAAACAACGCCA 60.203 55.556 0.00 0.00 0.00 5.69
2693 6261 1.018752 CGTGAATGACATGGACGCCA 61.019 55.000 0.00 1.01 38.19 5.69
2727 6295 3.866066 GCACTGCTCCAGTTCATCTACAA 60.866 47.826 0.00 0.00 42.59 2.41
2729 6297 3.324846 ACTGCTCCAGTTCATCTACAACA 59.675 43.478 0.00 0.00 42.59 3.33
2737 6305 4.150627 CAGTTCATCTACAACAAGTCACCG 59.849 45.833 0.00 0.00 0.00 4.94
2905 6611 0.684535 TCCTCATGAAGAACACGCCA 59.315 50.000 0.00 0.00 0.00 5.69
2970 6680 5.221263 ACCAGCTAGTATGTTACTCCAATCG 60.221 44.000 0.00 0.00 40.14 3.34
3051 6761 3.751479 ACAGGGCTTTGCTTTTTAAGG 57.249 42.857 0.00 0.00 0.00 2.69
3055 6765 5.221441 ACAGGGCTTTGCTTTTTAAGGTAAG 60.221 40.000 0.00 0.00 0.00 2.34
3073 6785 5.102313 GGTAAGCAATTGAACAATAGCACC 58.898 41.667 10.34 0.00 0.00 5.01
3104 6816 4.487714 TCTGTTGACTGAACTGAAGGTT 57.512 40.909 0.00 0.00 39.00 3.50
3114 6826 7.027778 ACTGAACTGAAGGTTTAATTGTGAC 57.972 36.000 0.00 0.00 38.41 3.67
3116 6828 6.126409 TGAACTGAAGGTTTAATTGTGACCT 58.874 36.000 4.05 4.05 45.42 3.85
3149 6861 8.954950 TTTAGCTATCTCCATCTTCTTCAAAG 57.045 34.615 0.00 0.00 0.00 2.77
3156 6868 4.899502 TCCATCTTCTTCAAAGTCCACTC 58.100 43.478 0.00 0.00 0.00 3.51
3157 6869 4.006319 CCATCTTCTTCAAAGTCCACTCC 58.994 47.826 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.228367 CCCACCAGCCCATATGCTC 60.228 63.158 0.00 0.00 40.32 4.26
68 69 5.416271 ACATGTATCAACCGAAGTAAGGT 57.584 39.130 0.00 0.00 45.29 3.50
69 70 6.645415 GGATACATGTATCAACCGAAGTAAGG 59.355 42.308 35.28 0.00 42.76 2.69
70 71 7.434492 AGGATACATGTATCAACCGAAGTAAG 58.566 38.462 35.28 0.00 42.76 2.34
71 72 7.356089 AGGATACATGTATCAACCGAAGTAA 57.644 36.000 35.28 3.14 42.76 2.24
72 73 6.971726 AGGATACATGTATCAACCGAAGTA 57.028 37.500 35.28 3.57 42.76 2.24
73 74 5.871396 AGGATACATGTATCAACCGAAGT 57.129 39.130 35.28 14.30 42.76 3.01
74 75 6.982852 AGTAGGATACATGTATCAACCGAAG 58.017 40.000 35.28 0.00 46.26 3.79
75 76 6.971726 AGTAGGATACATGTATCAACCGAA 57.028 37.500 35.28 17.28 46.26 4.30
76 77 6.015688 GGAAGTAGGATACATGTATCAACCGA 60.016 42.308 35.28 19.69 46.26 4.69
77 78 6.015350 AGGAAGTAGGATACATGTATCAACCG 60.015 42.308 35.28 0.00 46.26 4.44
78 79 7.233757 AGAGGAAGTAGGATACATGTATCAACC 59.766 40.741 35.28 27.11 46.26 3.77
79 80 8.085296 CAGAGGAAGTAGGATACATGTATCAAC 58.915 40.741 35.28 30.93 46.26 3.18
80 81 7.785028 ACAGAGGAAGTAGGATACATGTATCAA 59.215 37.037 35.28 24.53 46.26 2.57
81 82 7.298374 ACAGAGGAAGTAGGATACATGTATCA 58.702 38.462 35.28 20.55 46.26 2.15
82 83 7.768807 ACAGAGGAAGTAGGATACATGTATC 57.231 40.000 30.03 30.03 46.26 2.24
83 84 7.233757 GGAACAGAGGAAGTAGGATACATGTAT 59.766 40.741 18.31 18.31 46.26 2.29
84 85 6.550108 GGAACAGAGGAAGTAGGATACATGTA 59.450 42.308 8.27 8.27 46.26 2.29
85 86 5.364157 GGAACAGAGGAAGTAGGATACATGT 59.636 44.000 2.69 2.69 46.26 3.21
86 87 5.600484 AGGAACAGAGGAAGTAGGATACATG 59.400 44.000 0.00 0.00 46.26 3.21
87 88 5.782925 AGGAACAGAGGAAGTAGGATACAT 58.217 41.667 0.00 0.00 46.26 2.29
88 89 5.208294 AGGAACAGAGGAAGTAGGATACA 57.792 43.478 0.00 0.00 46.26 2.29
89 90 7.842887 ATTAGGAACAGAGGAAGTAGGATAC 57.157 40.000 0.00 0.00 43.47 2.24
91 92 9.453830 AATAATTAGGAACAGAGGAAGTAGGAT 57.546 33.333 0.00 0.00 0.00 3.24
92 93 8.855804 AATAATTAGGAACAGAGGAAGTAGGA 57.144 34.615 0.00 0.00 0.00 2.94
93 94 9.331282 CAAATAATTAGGAACAGAGGAAGTAGG 57.669 37.037 0.00 0.00 0.00 3.18
94 95 9.892130 ACAAATAATTAGGAACAGAGGAAGTAG 57.108 33.333 0.00 0.00 0.00 2.57
96 97 9.588096 AAACAAATAATTAGGAACAGAGGAAGT 57.412 29.630 0.00 0.00 0.00 3.01
145 146 5.483811 TCACTCATTTTGCTCCGTATGTAA 58.516 37.500 0.00 0.00 0.00 2.41
184 3110 5.942236 ACCACATACGGATGTATATAGACGT 59.058 40.000 14.23 0.00 44.82 4.34
185 3111 6.432607 ACCACATACGGATGTATATAGACG 57.567 41.667 14.23 0.00 44.82 4.18
218 3145 9.911788 AAAGGCTTTCTTATGATAGAGAATTCA 57.088 29.630 6.68 0.00 34.78 2.57
277 3364 7.510549 TGATGTTCTGGGTTTAAGAGAAAAG 57.489 36.000 0.00 0.00 0.00 2.27
293 3380 6.839124 TGAACTTATTTGCCATGATGTTCT 57.161 33.333 0.00 0.00 35.16 3.01
311 3398 9.543783 GTCCTAGTTATCGGAATAATTTGAACT 57.456 33.333 0.00 0.00 30.28 3.01
325 3412 9.197694 CCAGATAAGAAAATGTCCTAGTTATCG 57.802 37.037 0.00 0.00 32.88 2.92
327 3414 8.494433 TGCCAGATAAGAAAATGTCCTAGTTAT 58.506 33.333 0.00 0.00 0.00 1.89
343 3430 4.740695 GCGTTCTACTAGTTGCCAGATAAG 59.259 45.833 0.00 0.00 0.00 1.73
371 3461 7.165485 TGATGTTCCGGATTTAAGAGAAAAGA 58.835 34.615 4.15 0.00 0.00 2.52
444 3534 4.065281 GGGTCCGTGTCGAGGTGG 62.065 72.222 0.00 0.00 0.00 4.61
449 3539 1.808531 ATTGTTCGGGTCCGTGTCGA 61.809 55.000 9.36 0.00 40.74 4.20
452 3542 0.107081 TTGATTGTTCGGGTCCGTGT 59.893 50.000 9.36 0.00 40.74 4.49
488 3578 2.203266 GCCAGCAGTATCCCAGGC 60.203 66.667 0.00 0.00 34.71 4.85
515 3606 2.124695 GCAACGACCCAGATCCCC 60.125 66.667 0.00 0.00 0.00 4.81
519 3610 0.744414 CGAATGGCAACGACCCAGAT 60.744 55.000 11.00 0.00 42.51 2.90
539 3630 2.359478 GGGACGCCGGTGTTGAAT 60.359 61.111 23.85 0.00 0.00 2.57
551 3642 0.320421 AACAATGAGACGTGGGGACG 60.320 55.000 0.00 0.00 39.31 4.79
553 3644 1.275291 GAGAACAATGAGACGTGGGGA 59.725 52.381 0.00 0.00 0.00 4.81
556 3647 2.733552 CACTGAGAACAATGAGACGTGG 59.266 50.000 0.00 0.00 0.00 4.94
565 3656 0.108585 ACCGTGGCACTGAGAACAAT 59.891 50.000 16.24 0.00 0.00 2.71
570 3661 4.662961 CGCACCGTGGCACTGAGA 62.663 66.667 16.24 0.00 0.00 3.27
598 3689 2.336088 CACAAAGCACGCCAAGGG 59.664 61.111 0.00 0.00 0.00 3.95
599 3690 1.733402 TTCCACAAAGCACGCCAAGG 61.733 55.000 0.00 0.00 0.00 3.61
600 3691 0.102120 TTTCCACAAAGCACGCCAAG 59.898 50.000 0.00 0.00 0.00 3.61
601 3692 0.532573 TTTTCCACAAAGCACGCCAA 59.467 45.000 0.00 0.00 0.00 4.52
602 3693 0.749649 ATTTTCCACAAAGCACGCCA 59.250 45.000 0.00 0.00 0.00 5.69
603 3694 1.418373 GATTTTCCACAAAGCACGCC 58.582 50.000 0.00 0.00 0.00 5.68
604 3695 1.052287 CGATTTTCCACAAAGCACGC 58.948 50.000 0.00 0.00 0.00 5.34
605 3696 2.307049 GACGATTTTCCACAAAGCACG 58.693 47.619 0.00 0.00 0.00 5.34
606 3697 2.661594 GGACGATTTTCCACAAAGCAC 58.338 47.619 0.00 0.00 35.49 4.40
607 3698 1.265635 CGGACGATTTTCCACAAAGCA 59.734 47.619 0.00 0.00 35.04 3.91
608 3699 1.533731 TCGGACGATTTTCCACAAAGC 59.466 47.619 0.00 0.00 35.04 3.51
609 3700 5.121768 AGTTATCGGACGATTTTCCACAAAG 59.878 40.000 12.79 0.00 35.04 2.77
610 3701 4.998672 AGTTATCGGACGATTTTCCACAAA 59.001 37.500 12.79 0.00 35.04 2.83
611 3702 4.571919 AGTTATCGGACGATTTTCCACAA 58.428 39.130 12.79 0.00 35.04 3.33
612 3703 4.178540 GAGTTATCGGACGATTTTCCACA 58.821 43.478 12.79 0.00 35.04 4.17
643 3737 3.755905 TGTTTTGCTATTCCTCAATCGCA 59.244 39.130 0.00 0.00 38.56 5.10
645 3739 4.635765 TCCTGTTTTGCTATTCCTCAATCG 59.364 41.667 0.00 0.00 0.00 3.34
648 3742 6.547141 CCATATCCTGTTTTGCTATTCCTCAA 59.453 38.462 0.00 0.00 0.00 3.02
650 3744 6.299141 TCCATATCCTGTTTTGCTATTCCTC 58.701 40.000 0.00 0.00 0.00 3.71
652 3746 6.959639 TTCCATATCCTGTTTTGCTATTCC 57.040 37.500 0.00 0.00 0.00 3.01
723 3817 6.928979 TCCGTGAAACAACATTTTCTCTTA 57.071 33.333 0.00 0.00 36.58 2.10
733 3827 7.010552 CACCAAAATTATTTCCGTGAAACAACA 59.989 33.333 9.94 0.00 34.23 3.33
742 3836 5.414765 GGAGTCTCACCAAAATTATTTCCGT 59.585 40.000 1.47 0.00 0.00 4.69
758 3852 5.007626 CAGATTTTGTTTCGTTGGAGTCTCA 59.992 40.000 1.47 0.00 0.00 3.27
767 3861 6.325919 TCCATTAGCAGATTTTGTTTCGTT 57.674 33.333 0.00 0.00 0.00 3.85
769 3863 6.237648 GCAATCCATTAGCAGATTTTGTTTCG 60.238 38.462 0.00 0.00 30.29 3.46
787 3881 1.616725 CCTTACTTGGGCTGCAATCCA 60.617 52.381 0.50 3.78 0.00 3.41
822 3916 8.997734 ACCAAAGATAATCCTTACTGATTCTCT 58.002 33.333 0.00 0.00 38.87 3.10
823 3917 9.620259 AACCAAAGATAATCCTTACTGATTCTC 57.380 33.333 0.00 0.00 36.41 2.87
824 3918 9.981460 AAACCAAAGATAATCCTTACTGATTCT 57.019 29.630 0.00 0.00 36.41 2.40
826 3920 9.533831 ACAAACCAAAGATAATCCTTACTGATT 57.466 29.630 0.00 0.00 38.47 2.57
827 3921 9.533831 AACAAACCAAAGATAATCCTTACTGAT 57.466 29.630 0.00 0.00 0.00 2.90
828 3922 8.934023 AACAAACCAAAGATAATCCTTACTGA 57.066 30.769 0.00 0.00 0.00 3.41
829 3923 9.410556 CAAACAAACCAAAGATAATCCTTACTG 57.589 33.333 0.00 0.00 0.00 2.74
838 3932 6.586344 TCCAATGCAAACAAACCAAAGATAA 58.414 32.000 0.00 0.00 0.00 1.75
840 3934 5.033589 TCCAATGCAAACAAACCAAAGAT 57.966 34.783 0.00 0.00 0.00 2.40
897 3992 0.718220 GCGCGCGTGTCTTTATATGC 60.718 55.000 32.35 5.38 0.00 3.14
968 4063 2.070650 GCCCGGGGTTGACCTAGAT 61.071 63.158 25.28 0.00 40.03 1.98
969 4064 2.686106 GCCCGGGGTTGACCTAGA 60.686 66.667 25.28 0.00 40.03 2.43
1056 4171 2.671963 GTGCGGAGGGTGGAAACC 60.672 66.667 0.00 0.00 0.00 3.27
1209 4331 2.159787 CGAATCTTTGAGTCTGCCGTTG 60.160 50.000 0.00 0.00 0.00 4.10
1218 4340 0.253327 GGCCCTCCGAATCTTTGAGT 59.747 55.000 0.00 0.00 0.00 3.41
1219 4341 0.253044 TGGCCCTCCGAATCTTTGAG 59.747 55.000 0.00 0.00 34.14 3.02
1240 4362 0.337773 TGCTGGAGGTGGAGAGAGAT 59.662 55.000 0.00 0.00 0.00 2.75
1245 4367 2.117423 TCGTGCTGGAGGTGGAGA 59.883 61.111 0.00 0.00 0.00 3.71
1320 4442 3.461773 CACGACGGCTCCCAGGAT 61.462 66.667 0.00 0.00 0.00 3.24
1395 4517 6.551385 AGATCTGTGTGTTTCATGAACTTC 57.449 37.500 7.89 2.76 39.08 3.01
1412 4534 3.692257 ACTTGTCCCTGTCAAGATCTG 57.308 47.619 11.72 0.00 43.17 2.90
1428 4556 2.927014 GCAGTCGTCCTTGAGGTACTTG 60.927 54.545 0.00 0.00 41.55 3.16
1455 4583 2.126424 GTGACGTCGCAGAGGACC 60.126 66.667 23.67 0.00 46.48 4.46
1513 4650 1.706287 GAATTGAGTTCCTCCGCGGC 61.706 60.000 23.51 5.81 0.00 6.53
1522 4659 0.446616 GCCGGTTCCGAATTGAGTTC 59.553 55.000 13.08 0.00 0.00 3.01
1547 4684 1.579698 CAAGTCATGATGAGGCTCGG 58.420 55.000 10.42 0.00 0.00 4.63
1556 4693 1.306148 CGCCAGATGCAAGTCATGAT 58.694 50.000 0.00 0.00 41.33 2.45
1562 4699 2.042831 GCTTCCGCCAGATGCAAGT 61.043 57.895 0.00 0.00 43.45 3.16
1566 4703 3.885521 GCTGCTTCCGCCAGATGC 61.886 66.667 0.00 3.13 44.08 3.91
1590 4753 0.744414 CGTCGCCAAGGTGGATCATT 60.744 55.000 0.00 0.00 40.96 2.57
1612 4775 2.279120 GTGCGCTCCGATCCTCTG 60.279 66.667 9.73 0.00 0.00 3.35
1641 4804 2.037304 ATACCAGGGATCGGGCCTCT 62.037 60.000 0.84 0.00 0.00 3.69
1655 4818 4.553156 GCGCGATTTCGGATTTAAATACCA 60.553 41.667 12.10 0.00 40.23 3.25
1656 4819 3.904234 GCGCGATTTCGGATTTAAATACC 59.096 43.478 12.10 5.86 40.23 2.73
1665 4828 3.330853 GCGAGCGCGATTTCGGAT 61.331 61.111 15.92 0.00 40.82 4.18
1694 4857 2.987149 CGTAGTTCAGCAATGTTCTCGT 59.013 45.455 0.00 0.00 0.00 4.18
1932 5095 4.082523 GGGCAGCAGTACCGCTCA 62.083 66.667 0.00 0.00 41.38 4.26
2047 5210 4.463879 CAGCAGGACAGAGGGGCG 62.464 72.222 0.00 0.00 0.00 6.13
2118 5281 2.167281 CTGATCCCACACGAGTCTGATT 59.833 50.000 0.00 0.00 0.00 2.57
2200 5363 9.447279 TGATATTTCCCTTTTCCTACAGAGATA 57.553 33.333 0.00 0.00 0.00 1.98
2228 5391 2.203070 CATGTGCCTCCCGTAGCC 60.203 66.667 0.00 0.00 0.00 3.93
2308 5476 7.001099 AGTAATGGGAAAAGAGTAGAACGAA 57.999 36.000 0.00 0.00 0.00 3.85
2312 5480 8.896722 ACTAGAGTAATGGGAAAAGAGTAGAA 57.103 34.615 0.00 0.00 0.00 2.10
2350 5547 3.206034 CGCAGCAAACAGATCAAATCA 57.794 42.857 0.00 0.00 0.00 2.57
2377 5574 4.899502 ACCAAAACACAAATGACAACCAA 58.100 34.783 0.00 0.00 0.00 3.67
2402 5599 1.169661 TAAAGCAGGGCAACACGGTG 61.170 55.000 6.58 6.58 39.74 4.94
2405 5602 6.795098 TTATATATAAAGCAGGGCAACACG 57.205 37.500 2.56 0.00 39.74 4.49
2456 5653 4.283978 TCCTTGGTACCTTGTATTGTTCGA 59.716 41.667 14.36 0.00 0.00 3.71
2492 5845 5.487488 TGGGGACACTGTCTTTATAACTGAT 59.513 40.000 9.08 0.00 33.40 2.90
2493 5846 4.841813 TGGGGACACTGTCTTTATAACTGA 59.158 41.667 9.08 0.00 33.40 3.41
2499 5852 1.282157 GGCTGGGGACACTGTCTTTAT 59.718 52.381 9.08 0.00 35.60 1.40
2500 5853 0.690762 GGCTGGGGACACTGTCTTTA 59.309 55.000 9.08 0.00 35.60 1.85
2512 5968 2.122813 ATCGGTAGAGGGCTGGGG 60.123 66.667 0.00 0.00 0.00 4.96
2519 5975 3.592814 TCGCGGCATCGGTAGAGG 61.593 66.667 6.13 0.00 36.79 3.69
2520 5976 2.353607 GTCGCGGCATCGGTAGAG 60.354 66.667 5.47 0.00 36.79 2.43
2521 5977 1.167781 TATGTCGCGGCATCGGTAGA 61.168 55.000 31.94 8.75 36.79 2.59
2524 5980 1.591594 CTTATGTCGCGGCATCGGT 60.592 57.895 31.94 10.10 36.79 4.69
2525 5981 2.943345 GCTTATGTCGCGGCATCGG 61.943 63.158 31.94 23.33 36.79 4.18
2526 5982 2.546321 GCTTATGTCGCGGCATCG 59.454 61.111 31.94 22.55 39.81 3.84
2554 6028 1.888215 TCGTCACGTCCACTACTTCT 58.112 50.000 0.00 0.00 0.00 2.85
2579 6147 0.383590 ATCGTCTGTCCATCGCTGAG 59.616 55.000 0.00 0.00 0.00 3.35
2580 6148 0.382158 GATCGTCTGTCCATCGCTGA 59.618 55.000 0.00 0.00 0.00 4.26
2583 6151 1.064296 ACGATCGTCTGTCCATCGC 59.936 57.895 16.60 0.00 42.59 4.58
2586 6154 0.970937 ACCCACGATCGTCTGTCCAT 60.971 55.000 19.84 0.00 0.00 3.41
2589 6157 0.038526 AACACCCACGATCGTCTGTC 60.039 55.000 19.84 0.00 0.00 3.51
2593 6161 2.726691 CGCAACACCCACGATCGTC 61.727 63.158 19.84 3.34 0.00 4.20
2594 6162 2.736995 CGCAACACCCACGATCGT 60.737 61.111 16.60 16.60 0.00 3.73
2595 6163 3.487202 CCGCAACACCCACGATCG 61.487 66.667 14.88 14.88 0.00 3.69
2596 6164 3.799755 GCCGCAACACCCACGATC 61.800 66.667 0.00 0.00 0.00 3.69
2617 6185 1.372087 CTGCTTTGAGGATGGGCGAC 61.372 60.000 0.00 0.00 0.00 5.19
2618 6186 1.078214 CTGCTTTGAGGATGGGCGA 60.078 57.895 0.00 0.00 0.00 5.54
2619 6187 0.465097 ATCTGCTTTGAGGATGGGCG 60.465 55.000 0.00 0.00 0.00 6.13
2620 6188 1.133853 AGATCTGCTTTGAGGATGGGC 60.134 52.381 0.00 0.00 0.00 5.36
2621 6189 2.172082 TGAGATCTGCTTTGAGGATGGG 59.828 50.000 0.00 0.00 0.00 4.00
2622 6190 3.204526 GTGAGATCTGCTTTGAGGATGG 58.795 50.000 0.00 0.00 0.00 3.51
2623 6191 3.204526 GGTGAGATCTGCTTTGAGGATG 58.795 50.000 0.00 0.00 0.00 3.51
2624 6192 2.172293 GGGTGAGATCTGCTTTGAGGAT 59.828 50.000 0.00 0.00 0.00 3.24
2625 6193 1.556911 GGGTGAGATCTGCTTTGAGGA 59.443 52.381 0.00 0.00 0.00 3.71
2626 6194 1.558756 AGGGTGAGATCTGCTTTGAGG 59.441 52.381 0.00 0.00 0.00 3.86
2627 6195 2.738000 CGAGGGTGAGATCTGCTTTGAG 60.738 54.545 0.00 0.00 0.00 3.02
2628 6196 1.205655 CGAGGGTGAGATCTGCTTTGA 59.794 52.381 0.00 0.00 0.00 2.69
2629 6197 1.649664 CGAGGGTGAGATCTGCTTTG 58.350 55.000 0.00 0.00 0.00 2.77
2630 6198 0.107945 GCGAGGGTGAGATCTGCTTT 60.108 55.000 0.00 0.00 0.00 3.51
2631 6199 1.519719 GCGAGGGTGAGATCTGCTT 59.480 57.895 0.00 0.00 0.00 3.91
2632 6200 2.430610 GGCGAGGGTGAGATCTGCT 61.431 63.158 0.00 0.00 0.00 4.24
2633 6201 2.107953 GGCGAGGGTGAGATCTGC 59.892 66.667 0.00 0.00 0.00 4.26
2634 6202 1.039785 TGAGGCGAGGGTGAGATCTG 61.040 60.000 0.00 0.00 0.00 2.90
2635 6203 0.324738 TTGAGGCGAGGGTGAGATCT 60.325 55.000 0.00 0.00 0.00 2.75
2636 6204 0.537188 TTTGAGGCGAGGGTGAGATC 59.463 55.000 0.00 0.00 0.00 2.75
2637 6205 0.250513 GTTTGAGGCGAGGGTGAGAT 59.749 55.000 0.00 0.00 0.00 2.75
2638 6206 1.118965 TGTTTGAGGCGAGGGTGAGA 61.119 55.000 0.00 0.00 0.00 3.27
2639 6207 0.250295 TTGTTTGAGGCGAGGGTGAG 60.250 55.000 0.00 0.00 0.00 3.51
2640 6208 0.534203 GTTGTTTGAGGCGAGGGTGA 60.534 55.000 0.00 0.00 0.00 4.02
2641 6209 1.841663 CGTTGTTTGAGGCGAGGGTG 61.842 60.000 0.00 0.00 0.00 4.61
2642 6210 1.597027 CGTTGTTTGAGGCGAGGGT 60.597 57.895 0.00 0.00 0.00 4.34
2643 6211 2.966309 GCGTTGTTTGAGGCGAGGG 61.966 63.158 0.00 0.00 0.00 4.30
2644 6212 2.556287 GCGTTGTTTGAGGCGAGG 59.444 61.111 0.00 0.00 0.00 4.63
2645 6213 1.577328 ATGGCGTTGTTTGAGGCGAG 61.577 55.000 0.00 0.00 0.00 5.03
2646 6214 0.320858 TATGGCGTTGTTTGAGGCGA 60.321 50.000 0.00 0.00 0.00 5.54
2647 6215 0.179200 GTATGGCGTTGTTTGAGGCG 60.179 55.000 0.00 0.00 0.00 5.52
2648 6216 1.130561 GAGTATGGCGTTGTTTGAGGC 59.869 52.381 0.00 0.00 0.00 4.70
2649 6217 1.737793 GGAGTATGGCGTTGTTTGAGG 59.262 52.381 0.00 0.00 0.00 3.86
2650 6218 2.416547 CAGGAGTATGGCGTTGTTTGAG 59.583 50.000 0.00 0.00 0.00 3.02
2651 6219 2.422597 CAGGAGTATGGCGTTGTTTGA 58.577 47.619 0.00 0.00 0.00 2.69
2652 6220 1.135689 GCAGGAGTATGGCGTTGTTTG 60.136 52.381 0.00 0.00 0.00 2.93
2653 6221 1.165270 GCAGGAGTATGGCGTTGTTT 58.835 50.000 0.00 0.00 0.00 2.83
2654 6222 0.324943 AGCAGGAGTATGGCGTTGTT 59.675 50.000 0.00 0.00 0.00 2.83
2655 6223 0.108138 GAGCAGGAGTATGGCGTTGT 60.108 55.000 0.00 0.00 0.00 3.32
2656 6224 1.148157 CGAGCAGGAGTATGGCGTTG 61.148 60.000 0.00 0.00 0.00 4.10
2657 6225 1.141881 CGAGCAGGAGTATGGCGTT 59.858 57.895 0.00 0.00 0.00 4.84
2658 6226 2.052690 ACGAGCAGGAGTATGGCGT 61.053 57.895 0.00 0.00 0.00 5.68
2659 6227 1.589993 CACGAGCAGGAGTATGGCG 60.590 63.158 0.00 0.00 0.00 5.69
2660 6228 0.175760 TTCACGAGCAGGAGTATGGC 59.824 55.000 0.00 0.00 0.00 4.40
2661 6229 2.101415 TCATTCACGAGCAGGAGTATGG 59.899 50.000 0.00 0.00 0.00 2.74
2662 6230 3.119291 GTCATTCACGAGCAGGAGTATG 58.881 50.000 0.00 0.00 0.00 2.39
2663 6231 2.760650 TGTCATTCACGAGCAGGAGTAT 59.239 45.455 0.00 0.00 0.00 2.12
2693 6261 1.064060 GAGCAGTGCTTTGAACACGTT 59.936 47.619 20.80 0.00 42.94 3.99
2793 6361 0.671781 CTCCAGCTCAAACCTGTCGG 60.672 60.000 0.00 0.00 0.00 4.79
2794 6362 0.318441 TCTCCAGCTCAAACCTGTCG 59.682 55.000 0.00 0.00 0.00 4.35
2873 6441 2.661866 GAGGAACTGCGTGCACGT 60.662 61.111 36.80 20.14 41.55 4.49
2905 6611 2.238521 CTAGTTGGTTGCCCATGTGTT 58.761 47.619 0.00 0.00 41.49 3.32
3018 6728 4.429854 AAGCCCTGTTATCTGATCTTCC 57.570 45.455 0.00 0.00 0.00 3.46
3051 6761 4.793216 CGGTGCTATTGTTCAATTGCTTAC 59.207 41.667 23.55 17.14 33.22 2.34
3055 6765 3.216147 ACGGTGCTATTGTTCAATTGC 57.784 42.857 19.21 19.21 0.00 3.56
3073 6785 2.351418 TCAGTCAACAGAACTGCAAACG 59.649 45.455 1.46 0.00 43.09 3.60
3104 6816 9.138596 AGCTAAAGGTTAAAAGGTCACAATTAA 57.861 29.630 0.00 0.00 0.00 1.40
3114 6826 8.214364 AGATGGAGATAGCTAAAGGTTAAAAGG 58.786 37.037 0.00 0.00 0.00 3.11
3116 6828 9.614792 GAAGATGGAGATAGCTAAAGGTTAAAA 57.385 33.333 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.