Multiple sequence alignment - TraesCS5A01G037400

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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 TraesCS5A01G037400 chr5A 100.000 5596 0 0 1 5596 34659063 34653468 0.000000e+00 10334.0
1 TraesCS5A01G037400 chr5D 96.311 3253 99 12 1549 4798 44190307 44187073 0.000000e+00 5323.0
2 TraesCS5A01G037400 chr5D 90.031 652 50 8 853 1497 44191062 44190419 0.000000e+00 830.0
3 TraesCS5A01G037400 chr5D 83.092 414 39 8 459 852 44191508 44191106 1.150000e-91 348.0
4 TraesCS5A01G037400 chr5D 77.703 296 26 12 265 560 44191867 44191612 1.620000e-30 145.0
5 TraesCS5A01G037400 chr5D 89.583 96 7 2 1565 1659 44190390 44190297 9.850000e-23 119.0
6 TraesCS5A01G037400 chr7D 96.370 799 29 0 4798 5596 170085940 170085142 0.000000e+00 1315.0
7 TraesCS5A01G037400 chr7D 95.995 799 32 0 4798 5596 221803575 221802777 0.000000e+00 1299.0
8 TraesCS5A01G037400 chr7D 95.119 799 39 0 4798 5596 193103299 193102501 0.000000e+00 1260.0
9 TraesCS5A01G037400 chr3D 95.647 804 35 0 4792 5595 521465211 521466014 0.000000e+00 1291.0
10 TraesCS5A01G037400 chr3D 95.244 799 38 0 4798 5596 515268161 515268959 0.000000e+00 1266.0
11 TraesCS5A01G037400 chr2D 95.870 799 32 1 4798 5596 271418599 271419396 0.000000e+00 1291.0
12 TraesCS5A01G037400 chr2D 95.119 799 39 0 4798 5596 417473968 417474766 0.000000e+00 1260.0
13 TraesCS5A01G037400 chr1D 95.244 799 38 0 4798 5596 354976154 354976952 0.000000e+00 1266.0
14 TraesCS5A01G037400 chr6D 95.119 799 39 0 4798 5596 363717859 363718657 0.000000e+00 1260.0
15 TraesCS5A01G037400 chr5B 88.568 971 87 14 2471 3423 43689846 43690810 0.000000e+00 1157.0
16 TraesCS5A01G037400 chr5B 88.629 897 67 13 3842 4714 43690921 43691806 0.000000e+00 1059.0
17 TraesCS5A01G037400 chr5B 82.665 998 98 42 886 1830 43688293 43689268 0.000000e+00 815.0
18 TraesCS5A01G037400 chr5B 91.916 569 13 10 149 699 43836096 43835543 0.000000e+00 765.0
19 TraesCS5A01G037400 chr5B 88.285 478 36 13 1965 2431 43689378 43689846 6.330000e-154 555.0
20 TraesCS5A01G037400 chr5B 83.901 323 29 10 441 750 43808128 43807816 2.550000e-73 287.0
21 TraesCS5A01G037400 chr5B 80.826 339 31 18 440 755 43826703 43826376 9.370000e-58 235.0
22 TraesCS5A01G037400 chr5B 82.564 195 26 6 83 269 43803399 43803205 1.250000e-36 165.0
23 TraesCS5A01G037400 chr5B 82.564 195 26 6 83 269 43815015 43814821 1.250000e-36 165.0
24 TraesCS5A01G037400 chr5B 80.556 108 12 3 3592 3691 461523383 461523277 2.160000e-09 75.0
25 TraesCS5A01G037400 chr5B 94.118 34 2 0 2674 2707 457540168 457540135 1.000000e-02 52.8
26 TraesCS5A01G037400 chr5B 94.118 34 2 0 2674 2707 457541561 457541528 1.000000e-02 52.8
27 TraesCS5A01G037400 chrUn 84.906 159 17 3 441 599 385067543 385067392 2.700000e-33 154.0
28 TraesCS5A01G037400 chr2B 100.000 29 0 0 2676 2704 61934526 61934498 3.000000e-03 54.7
29 TraesCS5A01G037400 chr7B 100.000 28 0 0 2674 2701 669296334 669296361 1.000000e-02 52.8
30 TraesCS5A01G037400 chr4B 100.000 28 0 0 2674 2701 609599963 609599990 1.000000e-02 52.8
31 TraesCS5A01G037400 chr3A 100.000 28 0 0 2674 2701 452757290 452757317 1.000000e-02 52.8
32 TraesCS5A01G037400 chr1B 100.000 28 0 0 2674 2701 49125135 49125162 1.000000e-02 52.8


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 TraesCS5A01G037400 chr5A 34653468 34659063 5595 True 10334.0 10334 100.00000 1 5596 1 chr5A.!!$R1 5595
1 TraesCS5A01G037400 chr5D 44187073 44191867 4794 True 1353.0 5323 87.34400 265 4798 5 chr5D.!!$R1 4533
2 TraesCS5A01G037400 chr7D 170085142 170085940 798 True 1315.0 1315 96.37000 4798 5596 1 chr7D.!!$R1 798
3 TraesCS5A01G037400 chr7D 221802777 221803575 798 True 1299.0 1299 95.99500 4798 5596 1 chr7D.!!$R3 798
4 TraesCS5A01G037400 chr7D 193102501 193103299 798 True 1260.0 1260 95.11900 4798 5596 1 chr7D.!!$R2 798
5 TraesCS5A01G037400 chr3D 521465211 521466014 803 False 1291.0 1291 95.64700 4792 5595 1 chr3D.!!$F2 803
6 TraesCS5A01G037400 chr3D 515268161 515268959 798 False 1266.0 1266 95.24400 4798 5596 1 chr3D.!!$F1 798
7 TraesCS5A01G037400 chr2D 271418599 271419396 797 False 1291.0 1291 95.87000 4798 5596 1 chr2D.!!$F1 798
8 TraesCS5A01G037400 chr2D 417473968 417474766 798 False 1260.0 1260 95.11900 4798 5596 1 chr2D.!!$F2 798
9 TraesCS5A01G037400 chr1D 354976154 354976952 798 False 1266.0 1266 95.24400 4798 5596 1 chr1D.!!$F1 798
10 TraesCS5A01G037400 chr6D 363717859 363718657 798 False 1260.0 1260 95.11900 4798 5596 1 chr6D.!!$F1 798
11 TraesCS5A01G037400 chr5B 43688293 43691806 3513 False 896.5 1157 87.03675 886 4714 4 chr5B.!!$F1 3828
12 TraesCS5A01G037400 chr5B 43835543 43836096 553 True 765.0 765 91.91600 149 699 1 chr5B.!!$R5 550

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
111 112 0.103572 AGCAAGCAAGCAACAACTGG 59.896 50.000 3.19 0.00 36.85 4.00 F
143 144 0.399075 GAAACTCCCTCGGTCCCAAA 59.601 55.000 0.00 0.00 0.00 3.28 F
1490 1786 0.034476 TTGAGTCCTCTGCAGTGCTG 59.966 55.000 17.60 16.40 0.00 4.41 F
1574 1877 0.105658 TTCTATCTCCCCCGGTCTGG 60.106 60.000 0.00 0.00 37.55 3.86 F
1584 1887 0.462047 CCCGGTCTGGTGAAGCATAC 60.462 60.000 0.00 0.00 35.15 2.39 F
2278 2733 1.207089 TGGAGGTATATATGCGGCTGC 59.793 52.381 11.65 11.65 43.20 5.25 F
2293 2748 1.731433 GCTGCGTACTCGGGTCCATA 61.731 60.000 0.00 0.00 37.56 2.74 F
3657 4131 2.159627 GCAACCAGACACCATAAACTCG 59.840 50.000 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 1771 0.034616 AGAACAGCACTGCAGAGGAC 59.965 55.000 23.35 6.32 0.00 3.85 R
1601 1904 1.021202 TTCCACAACCAAAGCTGTCG 58.979 50.000 0.00 0.00 0.00 4.35 R
3459 3933 0.832559 GAGGCCGGGGCTAATACTCT 60.833 60.000 24.48 0.00 38.98 3.24 R
3526 4000 5.587043 TGACTCTTTTACACGGTTGATTTGT 59.413 36.000 0.00 0.00 0.00 2.83 R
3619 4093 1.921982 TGCAACCAATGGTAGCACAT 58.078 45.000 4.88 0.00 33.12 3.21 R
3657 4131 0.520404 CACAGCATGAGGAAGTGCAC 59.480 55.000 9.40 9.40 43.63 4.57 R
4416 4934 3.926616 ACAGACTAATGTTTCTCCACCG 58.073 45.455 0.00 0.00 0.00 4.94 R
4705 5235 0.376152 CCGTGCAGATGCTCAATGAC 59.624 55.000 6.35 0.00 42.66 3.06 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 9.748708 AAAAGAATTCGAAATTTGACAATGAGA 57.251 25.926 0.00 0.00 0.00 3.27
40 41 8.733857 AAGAATTCGAAATTTGACAATGAGAC 57.266 30.769 0.00 0.00 0.00 3.36
41 42 7.017645 AGAATTCGAAATTTGACAATGAGACG 58.982 34.615 0.00 0.00 0.00 4.18
42 43 5.666969 TTCGAAATTTGACAATGAGACGT 57.333 34.783 0.00 0.00 0.00 4.34
43 44 5.666969 TCGAAATTTGACAATGAGACGTT 57.333 34.783 0.00 0.00 0.00 3.99
44 45 6.772770 TCGAAATTTGACAATGAGACGTTA 57.227 33.333 0.00 0.00 0.00 3.18
45 46 7.359262 TCGAAATTTGACAATGAGACGTTAT 57.641 32.000 0.00 0.00 0.00 1.89
46 47 7.233689 TCGAAATTTGACAATGAGACGTTATG 58.766 34.615 0.00 0.00 0.00 1.90
47 48 6.022251 CGAAATTTGACAATGAGACGTTATGC 60.022 38.462 0.00 0.00 0.00 3.14
48 49 6.500684 AATTTGACAATGAGACGTTATGCT 57.499 33.333 0.00 0.00 0.00 3.79
49 50 5.530519 TTTGACAATGAGACGTTATGCTC 57.469 39.130 0.00 0.00 0.00 4.26
50 51 4.186856 TGACAATGAGACGTTATGCTCA 57.813 40.909 7.09 7.09 44.43 4.26
55 56 3.371102 TGAGACGTTATGCTCATAGCC 57.629 47.619 0.83 0.00 41.51 3.93
56 57 2.287608 TGAGACGTTATGCTCATAGCCG 60.288 50.000 0.83 8.49 41.51 5.52
57 58 1.681793 AGACGTTATGCTCATAGCCGT 59.318 47.619 12.98 12.98 41.51 5.68
58 59 1.787155 GACGTTATGCTCATAGCCGTG 59.213 52.381 16.07 0.82 41.51 4.94
59 60 1.407618 ACGTTATGCTCATAGCCGTGA 59.592 47.619 12.59 0.00 41.51 4.35
60 61 2.054363 CGTTATGCTCATAGCCGTGAG 58.946 52.381 10.71 10.71 46.59 3.51
61 62 2.287608 CGTTATGCTCATAGCCGTGAGA 60.288 50.000 17.47 5.65 46.77 3.27
62 63 3.312828 GTTATGCTCATAGCCGTGAGAG 58.687 50.000 17.47 3.07 46.77 3.20
63 64 1.697284 ATGCTCATAGCCGTGAGAGA 58.303 50.000 17.47 5.62 46.77 3.10
64 65 0.741326 TGCTCATAGCCGTGAGAGAC 59.259 55.000 17.47 3.47 46.77 3.36
65 66 0.317436 GCTCATAGCCGTGAGAGACG 60.317 60.000 17.47 0.00 46.77 4.18
72 73 2.409651 CGTGAGAGACGGGCTAGC 59.590 66.667 6.04 6.04 44.85 3.42
73 74 2.115911 CGTGAGAGACGGGCTAGCT 61.116 63.158 15.72 0.00 44.85 3.32
74 75 1.658686 CGTGAGAGACGGGCTAGCTT 61.659 60.000 15.72 0.00 44.85 3.74
75 76 0.533032 GTGAGAGACGGGCTAGCTTT 59.467 55.000 15.72 0.00 0.00 3.51
76 77 1.749634 GTGAGAGACGGGCTAGCTTTA 59.250 52.381 15.72 0.00 0.00 1.85
77 78 1.749634 TGAGAGACGGGCTAGCTTTAC 59.250 52.381 15.72 4.67 0.00 2.01
78 79 2.025898 GAGAGACGGGCTAGCTTTACT 58.974 52.381 15.72 9.46 0.00 2.24
79 80 2.427812 GAGAGACGGGCTAGCTTTACTT 59.572 50.000 15.72 0.00 0.00 2.24
80 81 2.166664 AGAGACGGGCTAGCTTTACTTG 59.833 50.000 15.72 0.00 0.00 3.16
81 82 1.900486 AGACGGGCTAGCTTTACTTGT 59.100 47.619 15.72 2.91 0.00 3.16
82 83 3.094572 AGACGGGCTAGCTTTACTTGTA 58.905 45.455 15.72 0.00 0.00 2.41
83 84 3.119209 AGACGGGCTAGCTTTACTTGTAC 60.119 47.826 15.72 0.00 0.00 2.90
84 85 2.830321 ACGGGCTAGCTTTACTTGTACT 59.170 45.455 15.72 0.00 0.00 2.73
85 86 3.119209 ACGGGCTAGCTTTACTTGTACTC 60.119 47.826 15.72 0.00 0.00 2.59
86 87 3.737355 CGGGCTAGCTTTACTTGTACTCC 60.737 52.174 15.72 1.09 0.00 3.85
87 88 3.431905 GGGCTAGCTTTACTTGTACTCCC 60.432 52.174 15.72 0.00 0.00 4.30
88 89 3.197116 GGCTAGCTTTACTTGTACTCCCA 59.803 47.826 15.72 0.00 0.00 4.37
89 90 4.141688 GGCTAGCTTTACTTGTACTCCCAT 60.142 45.833 15.72 0.00 0.00 4.00
90 91 5.429130 GCTAGCTTTACTTGTACTCCCATT 58.571 41.667 7.70 0.00 0.00 3.16
91 92 6.407752 GGCTAGCTTTACTTGTACTCCCATTA 60.408 42.308 15.72 0.00 0.00 1.90
92 93 7.046033 GCTAGCTTTACTTGTACTCCCATTAA 58.954 38.462 7.70 0.00 0.00 1.40
93 94 7.224949 GCTAGCTTTACTTGTACTCCCATTAAG 59.775 40.741 7.70 0.00 0.00 1.85
94 95 5.880887 AGCTTTACTTGTACTCCCATTAAGC 59.119 40.000 0.00 0.00 0.00 3.09
95 96 5.646360 GCTTTACTTGTACTCCCATTAAGCA 59.354 40.000 0.00 0.00 0.00 3.91
96 97 6.150474 GCTTTACTTGTACTCCCATTAAGCAA 59.850 38.462 0.00 0.00 0.00 3.91
97 98 7.626452 GCTTTACTTGTACTCCCATTAAGCAAG 60.626 40.741 0.00 0.00 38.14 4.01
98 99 4.010349 ACTTGTACTCCCATTAAGCAAGC 58.990 43.478 0.00 0.00 36.34 4.01
99 100 3.712016 TGTACTCCCATTAAGCAAGCA 57.288 42.857 0.00 0.00 0.00 3.91
100 101 4.027674 TGTACTCCCATTAAGCAAGCAA 57.972 40.909 0.00 0.00 0.00 3.91
101 102 4.009675 TGTACTCCCATTAAGCAAGCAAG 58.990 43.478 0.00 0.00 0.00 4.01
102 103 1.821136 ACTCCCATTAAGCAAGCAAGC 59.179 47.619 0.00 0.00 0.00 4.01
103 104 1.820519 CTCCCATTAAGCAAGCAAGCA 59.179 47.619 3.19 0.00 36.85 3.91
104 105 2.231964 CTCCCATTAAGCAAGCAAGCAA 59.768 45.455 3.19 0.00 36.85 3.91
105 106 2.029110 TCCCATTAAGCAAGCAAGCAAC 60.029 45.455 3.19 0.00 36.85 4.17
106 107 2.288948 CCCATTAAGCAAGCAAGCAACA 60.289 45.455 3.19 0.00 36.85 3.33
107 108 3.391965 CCATTAAGCAAGCAAGCAACAA 58.608 40.909 3.19 0.00 36.85 2.83
108 109 3.184986 CCATTAAGCAAGCAAGCAACAAC 59.815 43.478 3.19 0.00 36.85 3.32
109 110 3.799281 TTAAGCAAGCAAGCAACAACT 57.201 38.095 3.19 0.00 36.85 3.16
110 111 1.930567 AAGCAAGCAAGCAACAACTG 58.069 45.000 3.19 0.00 36.85 3.16
111 112 0.103572 AGCAAGCAAGCAACAACTGG 59.896 50.000 3.19 0.00 36.85 4.00
112 113 1.493134 GCAAGCAAGCAACAACTGGC 61.493 55.000 0.00 0.00 36.81 4.85
113 114 0.877213 CAAGCAAGCAACAACTGGCC 60.877 55.000 0.00 0.00 37.30 5.36
114 115 1.329171 AAGCAAGCAACAACTGGCCA 61.329 50.000 4.71 4.71 37.30 5.36
115 116 1.143620 GCAAGCAACAACTGGCCAA 59.856 52.632 7.01 0.00 29.63 4.52
116 117 0.461693 GCAAGCAACAACTGGCCAAA 60.462 50.000 7.01 0.00 29.63 3.28
117 118 1.811176 GCAAGCAACAACTGGCCAAAT 60.811 47.619 7.01 0.00 29.63 2.32
118 119 2.563702 CAAGCAACAACTGGCCAAATT 58.436 42.857 7.01 0.50 0.00 1.82
119 120 3.726607 CAAGCAACAACTGGCCAAATTA 58.273 40.909 7.01 0.00 0.00 1.40
120 121 4.125703 CAAGCAACAACTGGCCAAATTAA 58.874 39.130 7.01 0.00 0.00 1.40
121 122 3.993920 AGCAACAACTGGCCAAATTAAG 58.006 40.909 7.01 0.00 0.00 1.85
122 123 3.066380 GCAACAACTGGCCAAATTAAGG 58.934 45.455 7.01 0.00 0.00 2.69
123 124 3.244044 GCAACAACTGGCCAAATTAAGGA 60.244 43.478 7.01 0.00 0.00 3.36
124 125 4.559153 CAACAACTGGCCAAATTAAGGAG 58.441 43.478 7.01 0.00 0.00 3.69
125 126 4.112634 ACAACTGGCCAAATTAAGGAGA 57.887 40.909 7.01 0.00 0.00 3.71
126 127 4.479158 ACAACTGGCCAAATTAAGGAGAA 58.521 39.130 7.01 0.00 0.00 2.87
127 128 4.898861 ACAACTGGCCAAATTAAGGAGAAA 59.101 37.500 7.01 0.00 0.00 2.52
128 129 5.221441 ACAACTGGCCAAATTAAGGAGAAAC 60.221 40.000 7.01 0.00 0.00 2.78
129 130 4.740902 ACTGGCCAAATTAAGGAGAAACT 58.259 39.130 7.01 0.00 0.00 2.66
130 131 4.767409 ACTGGCCAAATTAAGGAGAAACTC 59.233 41.667 7.01 0.00 0.00 3.01
139 140 1.898885 GGAGAAACTCCCTCGGTCC 59.101 63.158 6.54 0.00 44.36 4.46
140 141 1.615165 GGAGAAACTCCCTCGGTCCC 61.615 65.000 6.54 0.00 44.36 4.46
141 142 0.903454 GAGAAACTCCCTCGGTCCCA 60.903 60.000 0.00 0.00 0.00 4.37
142 143 0.473117 AGAAACTCCCTCGGTCCCAA 60.473 55.000 0.00 0.00 0.00 4.12
143 144 0.399075 GAAACTCCCTCGGTCCCAAA 59.601 55.000 0.00 0.00 0.00 3.28
144 145 0.848053 AAACTCCCTCGGTCCCAAAA 59.152 50.000 0.00 0.00 0.00 2.44
145 146 1.073098 AACTCCCTCGGTCCCAAAAT 58.927 50.000 0.00 0.00 0.00 1.82
146 147 0.618981 ACTCCCTCGGTCCCAAAATC 59.381 55.000 0.00 0.00 0.00 2.17
147 148 0.912486 CTCCCTCGGTCCCAAAATCT 59.088 55.000 0.00 0.00 0.00 2.40
251 252 7.365840 TGTGTAATTACATATTGTCAACGCA 57.634 32.000 20.72 7.21 38.63 5.24
278 279 2.493675 TGCTCAGTACCAGCTGAAGTAG 59.506 50.000 17.39 5.88 43.92 2.57
334 335 3.876198 GCACATACCTTGCCCGCG 61.876 66.667 0.00 0.00 33.58 6.46
382 388 4.162690 CCTAGGCCCGGAGTGCAC 62.163 72.222 9.40 9.40 0.00 4.57
383 389 4.514577 CTAGGCCCGGAGTGCACG 62.515 72.222 12.01 0.00 0.00 5.34
545 657 3.730761 GCCAACAGCCAGCGTGAG 61.731 66.667 0.00 0.00 34.35 3.51
546 658 2.031012 CCAACAGCCAGCGTGAGA 59.969 61.111 0.00 0.00 0.00 3.27
547 659 2.320587 CCAACAGCCAGCGTGAGAC 61.321 63.158 0.00 0.00 0.00 3.36
699 908 3.730761 GCACCGGAGCAACAGCAG 61.731 66.667 19.70 0.00 0.00 4.24
717 926 3.698463 CCGTGGTGTCGACGTTGC 61.698 66.667 11.62 0.93 34.97 4.17
737 953 2.179427 CAGTCCTCATCACCTACCACA 58.821 52.381 0.00 0.00 0.00 4.17
761 977 4.803426 GCAGCCTCAGGTCGTCGG 62.803 72.222 0.00 0.00 0.00 4.79
844 1073 2.568003 AGCGAGGTCGATGACTCAA 58.432 52.632 2.94 0.00 43.02 3.02
858 1130 1.265365 GACTCAACAGTTGCTTGGAGC 59.735 52.381 8.58 0.00 35.60 4.70
863 1135 1.228367 CAGTTGCTTGGAGCCACCT 60.228 57.895 1.08 0.00 41.51 4.00
1093 1378 3.003173 AGCCGCCTAGCCTGTTCA 61.003 61.111 0.00 0.00 0.00 3.18
1094 1379 2.046314 GCCGCCTAGCCTGTTCAA 60.046 61.111 0.00 0.00 0.00 2.69
1095 1380 1.674322 GCCGCCTAGCCTGTTCAAA 60.674 57.895 0.00 0.00 0.00 2.69
1098 1383 1.648467 CGCCTAGCCTGTTCAAAGCC 61.648 60.000 0.00 0.00 0.00 4.35
1099 1384 1.648467 GCCTAGCCTGTTCAAAGCCG 61.648 60.000 0.00 0.00 0.00 5.52
1101 1386 1.648467 CTAGCCTGTTCAAAGCCGGC 61.648 60.000 21.89 21.89 40.99 6.13
1102 1387 4.056125 GCCTGTTCAAAGCCGGCC 62.056 66.667 26.15 7.06 34.75 6.13
1103 1388 3.737172 CCTGTTCAAAGCCGGCCG 61.737 66.667 26.15 21.04 0.00 6.13
1104 1389 4.404654 CTGTTCAAAGCCGGCCGC 62.405 66.667 26.15 16.01 37.98 6.53
1164 1449 3.274455 CTCCTCGCACTGTCGCTGT 62.274 63.158 0.00 0.00 0.00 4.40
1222 1507 1.321474 CAGCCAATGCCGGTATGATT 58.679 50.000 5.55 0.00 38.69 2.57
1223 1508 1.001048 CAGCCAATGCCGGTATGATTG 60.001 52.381 5.55 8.08 38.69 2.67
1224 1509 1.133823 AGCCAATGCCGGTATGATTGA 60.134 47.619 5.55 0.00 38.69 2.57
1227 1512 3.858129 GCCAATGCCGGTATGATTGAATG 60.858 47.826 5.55 0.00 30.03 2.67
1230 1515 2.997980 TGCCGGTATGATTGAATGTGT 58.002 42.857 1.90 0.00 0.00 3.72
1232 1517 3.874543 TGCCGGTATGATTGAATGTGTAC 59.125 43.478 1.90 0.00 0.00 2.90
1235 1526 5.283294 CCGGTATGATTGAATGTGTACGTA 58.717 41.667 0.00 0.00 0.00 3.57
1243 1534 0.986992 AATGTGTACGTACGCGCTTC 59.013 50.000 28.51 12.32 42.83 3.86
1246 1537 0.632241 GTGTACGTACGCGCTTCTTC 59.368 55.000 22.24 0.00 42.83 2.87
1250 1541 0.728466 ACGTACGCGCTTCTTCTGTC 60.728 55.000 16.72 0.00 42.83 3.51
1263 1554 5.523916 GCTTCTTCTGTCTTTTGTCAGTACA 59.476 40.000 0.00 0.00 37.01 2.90
1265 1556 7.254932 GCTTCTTCTGTCTTTTGTCAGTACAAT 60.255 37.037 0.00 0.00 44.85 2.71
1266 1557 8.506168 TTCTTCTGTCTTTTGTCAGTACAATT 57.494 30.769 0.00 0.00 44.85 2.32
1466 1760 2.860735 CGAGGTTAGAAAGATTGCTCCG 59.139 50.000 0.00 0.00 0.00 4.63
1475 1771 2.322355 AGATTGCTCCGTCCATTGAG 57.678 50.000 0.00 0.00 0.00 3.02
1478 1774 0.036388 TTGCTCCGTCCATTGAGTCC 60.036 55.000 0.00 0.00 0.00 3.85
1489 1785 0.982704 ATTGAGTCCTCTGCAGTGCT 59.017 50.000 17.60 4.58 0.00 4.40
1490 1786 0.034476 TTGAGTCCTCTGCAGTGCTG 59.966 55.000 17.60 16.40 0.00 4.41
1503 1799 2.603173 GCAGTGCTGTTCTGTTAAGTGC 60.603 50.000 8.18 0.00 35.60 4.40
1504 1800 1.867233 AGTGCTGTTCTGTTAAGTGCG 59.133 47.619 0.00 0.00 0.00 5.34
1506 1802 1.864711 TGCTGTTCTGTTAAGTGCGAC 59.135 47.619 0.00 0.00 0.00 5.19
1515 1811 3.165890 TGTTAAGTGCGACGAGATTACG 58.834 45.455 0.00 0.00 39.31 3.18
1547 1850 0.607217 CAGCAGTGCAATGACCCTCA 60.607 55.000 20.00 0.00 0.00 3.86
1548 1851 0.322277 AGCAGTGCAATGACCCTCAG 60.322 55.000 20.00 0.00 0.00 3.35
1563 1866 7.546250 TGACCCTCAGGAATTATTCTATCTC 57.454 40.000 4.87 0.00 36.73 2.75
1574 1877 0.105658 TTCTATCTCCCCCGGTCTGG 60.106 60.000 0.00 0.00 37.55 3.86
1584 1887 0.462047 CCCGGTCTGGTGAAGCATAC 60.462 60.000 0.00 0.00 35.15 2.39
1601 1904 5.363939 AGCATACTCTGAATTTCAGGCTAC 58.636 41.667 22.86 10.42 44.39 3.58
1617 1920 2.949714 CTACGACAGCTTTGGTTGTG 57.050 50.000 5.94 0.00 37.03 3.33
1654 2057 5.045359 TCTGAACAACCAGATCAATGGAGAT 60.045 40.000 7.95 0.00 43.57 2.75
1658 2061 6.521151 ACAACCAGATCAATGGAGATTTTC 57.479 37.500 7.95 0.00 43.57 2.29
1744 2155 4.507710 TCCCTGAGATTTTCATTCTCACG 58.492 43.478 0.00 0.00 43.49 4.35
1745 2156 4.222810 TCCCTGAGATTTTCATTCTCACGA 59.777 41.667 0.00 0.00 43.49 4.35
1833 2259 3.015327 CTGAAAGAGGAGCTCAATTGGG 58.985 50.000 17.19 2.47 34.07 4.12
1848 2274 5.128205 TCAATTGGGTCATTCATAGAGCAG 58.872 41.667 5.42 0.00 35.30 4.24
1849 2275 4.785346 ATTGGGTCATTCATAGAGCAGT 57.215 40.909 0.00 0.00 35.30 4.40
1901 2346 6.829229 TCGGTCTTTAACTTCAGATAGACA 57.171 37.500 0.00 0.00 35.02 3.41
2116 2570 5.934935 TCCTACTGTTTTCGGTCAAATTC 57.065 39.130 0.00 0.00 40.29 2.17
2249 2704 1.558233 CGGAGTTCCCCTACTTGACT 58.442 55.000 0.00 0.00 0.00 3.41
2278 2733 1.207089 TGGAGGTATATATGCGGCTGC 59.793 52.381 11.65 11.65 43.20 5.25
2291 2746 3.755628 GCTGCGTACTCGGGTCCA 61.756 66.667 0.00 0.00 37.56 4.02
2292 2747 3.077519 GCTGCGTACTCGGGTCCAT 62.078 63.158 0.00 0.00 37.56 3.41
2293 2748 1.731433 GCTGCGTACTCGGGTCCATA 61.731 60.000 0.00 0.00 37.56 2.74
2336 2792 8.897872 TTTTCTTCCTTTAATCTTCTGTACGT 57.102 30.769 0.00 0.00 0.00 3.57
2440 2896 7.826690 AGATTGCGGTAACAATTCTGTTATTT 58.173 30.769 1.38 0.00 46.91 1.40
2494 2950 4.934797 AATTCTCCACTCTTCAATCCCA 57.065 40.909 0.00 0.00 0.00 4.37
2495 2951 4.934797 ATTCTCCACTCTTCAATCCCAA 57.065 40.909 0.00 0.00 0.00 4.12
2537 2997 9.480053 CTTCATGAAAAGGTCAATTATGTGTTT 57.520 29.630 9.88 0.00 40.50 2.83
2711 3171 2.695666 GAGGAAGAGGACGATGATTCCA 59.304 50.000 5.18 0.00 41.56 3.53
2741 3201 5.473846 TCTGACGATGAATATGAGGAGGTAC 59.526 44.000 0.00 0.00 0.00 3.34
2769 3236 2.203394 CACAGCTGGGCAACTGGT 60.203 61.111 19.93 0.00 38.25 4.00
2854 3322 8.930760 GGTATATATGCTGTTGATGAAGAAGAC 58.069 37.037 0.62 0.00 0.00 3.01
3013 3481 4.030216 TCCATCAGCTTATGTACCACTCA 58.970 43.478 7.11 0.00 0.00 3.41
3014 3482 4.122776 CCATCAGCTTATGTACCACTCAC 58.877 47.826 7.11 0.00 0.00 3.51
3028 3496 2.670414 CCACTCACTCTGAATCGCTTTC 59.330 50.000 0.00 0.00 34.72 2.62
3054 3522 6.986904 AGCCACTATGCTCTTAACTTTTAC 57.013 37.500 0.00 0.00 36.75 2.01
3434 3908 3.526931 TCTGTGTAAGCTCATGCCTAC 57.473 47.619 0.00 0.00 40.80 3.18
3619 4093 6.374053 CACATCCAAACCAGTTGTATGTATCA 59.626 38.462 0.00 0.00 42.94 2.15
3657 4131 2.159627 GCAACCAGACACCATAAACTCG 59.840 50.000 0.00 0.00 0.00 4.18
3797 4271 9.061435 CCCTCCATCTCATTAAAATAGAAGAAC 57.939 37.037 0.00 0.00 0.00 3.01
4063 4570 5.066375 GCACTCTGCACCAAACATAATATCA 59.934 40.000 0.00 0.00 44.26 2.15
4488 5018 5.301551 TGTGGTTCTGAATATTTTGCACTGT 59.698 36.000 0.00 0.00 0.00 3.55
4628 5158 6.967199 AGAGATGTGACGTTTTGTTCTTTTTC 59.033 34.615 0.00 0.00 0.00 2.29
4664 5194 3.426695 CCAGCAACACAAATAGCAGTAGC 60.427 47.826 0.00 0.00 42.56 3.58
4666 5196 2.487762 GCAACACAAATAGCAGTAGCCA 59.512 45.455 0.00 0.00 43.56 4.75
4667 5197 3.129287 GCAACACAAATAGCAGTAGCCAT 59.871 43.478 0.00 0.00 43.56 4.40
4668 5198 4.731773 GCAACACAAATAGCAGTAGCCATC 60.732 45.833 0.00 0.00 43.56 3.51
4685 5215 4.394300 AGCCATCTTGATGAAGTTCTTTCG 59.606 41.667 11.76 0.00 38.71 3.46
4705 5235 7.381948 TCTTTCGAATTCACATTGTGATTTTGG 59.618 33.333 26.43 20.37 42.40 3.28
4714 5244 5.119588 CACATTGTGATTTTGGTCATTGAGC 59.880 40.000 11.45 8.91 35.23 4.26
4715 5245 4.933505 TTGTGATTTTGGTCATTGAGCA 57.066 36.364 14.28 14.28 38.32 4.26
4717 5247 5.063180 TGTGATTTTGGTCATTGAGCATC 57.937 39.130 18.46 13.63 39.81 3.91
4724 5254 0.376152 GTCATTGAGCATCTGCACGG 59.624 55.000 4.79 0.00 45.16 4.94
4726 5256 0.376152 CATTGAGCATCTGCACGGAC 59.624 55.000 4.79 0.00 45.16 4.79
4727 5257 1.086067 ATTGAGCATCTGCACGGACG 61.086 55.000 4.79 0.00 45.16 4.79
4729 5259 2.125912 AGCATCTGCACGGACGAC 60.126 61.111 4.79 0.00 45.16 4.34
4739 5269 2.229543 TGCACGGACGACATAAACTAGT 59.770 45.455 0.00 0.00 0.00 2.57
4772 5302 3.900966 ATTGGGTTCGAGGTACTTACC 57.099 47.619 0.00 0.00 46.82 2.85
4790 5320 2.551270 ACCAGAGGATTAGAGGTGCAA 58.449 47.619 0.00 0.00 0.00 4.08
4907 5437 4.735132 GTGCTGCGCTCCACGGTA 62.735 66.667 9.73 0.00 43.93 4.02
4990 5520 6.743575 AGAAATAGTCAAATTTCAGGTCCG 57.256 37.500 10.86 0.00 44.70 4.79
5008 5538 3.771160 CCCGACGGACCCCAAGAG 61.771 72.222 17.49 0.00 0.00 2.85
5031 5561 2.103771 ACAGCATCTATCGGAGCACAAT 59.896 45.455 0.00 0.00 0.00 2.71
5073 5603 0.530744 ACTACGAGAATTCCTGCGCA 59.469 50.000 10.98 10.98 0.00 6.09
5300 5830 0.323360 GGCTGGCAAACCTGGTGATA 60.323 55.000 0.00 0.00 35.49 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.748708 TCTCATTGTCAAATTTCGAATTCTTTT 57.251 25.926 0.00 0.00 0.00 2.27
14 15 9.185192 GTCTCATTGTCAAATTTCGAATTCTTT 57.815 29.630 0.00 0.00 0.00 2.52
15 16 7.535258 CGTCTCATTGTCAAATTTCGAATTCTT 59.465 33.333 0.00 0.00 0.00 2.52
16 17 7.017645 CGTCTCATTGTCAAATTTCGAATTCT 58.982 34.615 0.00 0.00 0.00 2.40
17 18 6.797033 ACGTCTCATTGTCAAATTTCGAATTC 59.203 34.615 0.00 0.00 0.00 2.17
18 19 6.668323 ACGTCTCATTGTCAAATTTCGAATT 58.332 32.000 0.00 0.00 0.00 2.17
19 20 6.241207 ACGTCTCATTGTCAAATTTCGAAT 57.759 33.333 0.00 0.00 0.00 3.34
20 21 5.666969 ACGTCTCATTGTCAAATTTCGAA 57.333 34.783 0.00 0.00 0.00 3.71
21 22 5.666969 AACGTCTCATTGTCAAATTTCGA 57.333 34.783 0.00 0.00 0.00 3.71
22 23 6.022251 GCATAACGTCTCATTGTCAAATTTCG 60.022 38.462 0.00 0.00 0.00 3.46
23 24 7.023575 AGCATAACGTCTCATTGTCAAATTTC 58.976 34.615 0.00 0.00 0.00 2.17
24 25 6.913170 AGCATAACGTCTCATTGTCAAATTT 58.087 32.000 0.00 0.00 0.00 1.82
25 26 6.149308 TGAGCATAACGTCTCATTGTCAAATT 59.851 34.615 0.83 0.00 34.69 1.82
26 27 5.643348 TGAGCATAACGTCTCATTGTCAAAT 59.357 36.000 0.83 0.00 34.69 2.32
27 28 4.994217 TGAGCATAACGTCTCATTGTCAAA 59.006 37.500 0.83 0.00 34.69 2.69
28 29 4.565022 TGAGCATAACGTCTCATTGTCAA 58.435 39.130 0.83 0.00 34.69 3.18
29 30 4.186856 TGAGCATAACGTCTCATTGTCA 57.813 40.909 0.83 0.00 34.69 3.58
30 31 5.107683 GCTATGAGCATAACGTCTCATTGTC 60.108 44.000 19.04 11.41 42.67 3.18
31 32 4.747108 GCTATGAGCATAACGTCTCATTGT 59.253 41.667 19.04 3.15 42.67 2.71
32 33 4.151335 GGCTATGAGCATAACGTCTCATTG 59.849 45.833 19.04 17.70 44.75 2.82
33 34 4.310769 GGCTATGAGCATAACGTCTCATT 58.689 43.478 19.04 7.23 44.75 2.57
34 35 3.612717 CGGCTATGAGCATAACGTCTCAT 60.613 47.826 18.19 18.19 44.75 2.90
35 36 2.287608 CGGCTATGAGCATAACGTCTCA 60.288 50.000 7.09 7.09 44.75 3.27
36 37 2.287668 ACGGCTATGAGCATAACGTCTC 60.288 50.000 11.61 0.00 44.75 3.36
37 38 1.681793 ACGGCTATGAGCATAACGTCT 59.318 47.619 11.61 0.00 44.75 4.18
38 39 1.787155 CACGGCTATGAGCATAACGTC 59.213 52.381 13.47 0.00 44.75 4.34
39 40 1.407618 TCACGGCTATGAGCATAACGT 59.592 47.619 11.61 11.61 44.75 3.99
40 41 2.054363 CTCACGGCTATGAGCATAACG 58.946 52.381 5.06 10.68 44.75 3.18
41 42 3.004839 TCTCTCACGGCTATGAGCATAAC 59.995 47.826 11.56 0.00 44.75 1.89
42 43 3.004839 GTCTCTCACGGCTATGAGCATAA 59.995 47.826 11.56 0.00 44.75 1.90
43 44 2.554462 GTCTCTCACGGCTATGAGCATA 59.446 50.000 11.56 0.00 44.75 3.14
44 45 1.339610 GTCTCTCACGGCTATGAGCAT 59.660 52.381 11.56 0.00 44.75 3.79
45 46 0.741326 GTCTCTCACGGCTATGAGCA 59.259 55.000 11.56 0.74 44.75 4.26
46 47 0.317436 CGTCTCTCACGGCTATGAGC 60.317 60.000 11.56 0.00 44.94 4.26
47 48 3.835686 CGTCTCTCACGGCTATGAG 57.164 57.895 10.47 10.47 45.46 2.90
56 57 0.533032 AAAGCTAGCCCGTCTCTCAC 59.467 55.000 12.13 0.00 0.00 3.51
57 58 1.749634 GTAAAGCTAGCCCGTCTCTCA 59.250 52.381 12.13 0.00 0.00 3.27
58 59 2.025898 AGTAAAGCTAGCCCGTCTCTC 58.974 52.381 12.13 0.00 0.00 3.20
59 60 2.146920 AGTAAAGCTAGCCCGTCTCT 57.853 50.000 12.13 0.00 0.00 3.10
60 61 2.094130 ACAAGTAAAGCTAGCCCGTCTC 60.094 50.000 12.13 0.00 0.00 3.36
61 62 1.900486 ACAAGTAAAGCTAGCCCGTCT 59.100 47.619 12.13 2.63 0.00 4.18
62 63 2.381725 ACAAGTAAAGCTAGCCCGTC 57.618 50.000 12.13 0.06 0.00 4.79
63 64 2.830321 AGTACAAGTAAAGCTAGCCCGT 59.170 45.455 12.13 0.00 0.00 5.28
64 65 3.445857 GAGTACAAGTAAAGCTAGCCCG 58.554 50.000 12.13 0.00 0.00 6.13
65 66 3.431905 GGGAGTACAAGTAAAGCTAGCCC 60.432 52.174 12.13 0.00 0.00 5.19
66 67 3.197116 TGGGAGTACAAGTAAAGCTAGCC 59.803 47.826 12.13 0.00 0.00 3.93
67 68 4.467198 TGGGAGTACAAGTAAAGCTAGC 57.533 45.455 6.62 6.62 0.00 3.42
68 69 7.224949 GCTTAATGGGAGTACAAGTAAAGCTAG 59.775 40.741 0.00 0.00 0.00 3.42
69 70 7.046033 GCTTAATGGGAGTACAAGTAAAGCTA 58.954 38.462 0.00 0.00 0.00 3.32
70 71 5.880887 GCTTAATGGGAGTACAAGTAAAGCT 59.119 40.000 0.00 0.00 0.00 3.74
71 72 5.646360 TGCTTAATGGGAGTACAAGTAAAGC 59.354 40.000 0.00 2.40 0.00 3.51
72 73 7.626452 GCTTGCTTAATGGGAGTACAAGTAAAG 60.626 40.741 0.00 0.00 36.34 1.85
73 74 6.150474 GCTTGCTTAATGGGAGTACAAGTAAA 59.850 38.462 0.00 0.00 36.34 2.01
74 75 5.646360 GCTTGCTTAATGGGAGTACAAGTAA 59.354 40.000 0.00 0.00 36.34 2.24
75 76 5.183228 GCTTGCTTAATGGGAGTACAAGTA 58.817 41.667 0.00 0.00 36.34 2.24
76 77 4.010349 GCTTGCTTAATGGGAGTACAAGT 58.990 43.478 0.00 0.00 36.34 3.16
77 78 4.009675 TGCTTGCTTAATGGGAGTACAAG 58.990 43.478 0.00 0.00 36.87 3.16
78 79 4.027674 TGCTTGCTTAATGGGAGTACAA 57.972 40.909 0.00 0.00 0.00 2.41
79 80 3.712016 TGCTTGCTTAATGGGAGTACA 57.288 42.857 0.00 0.00 0.00 2.90
80 81 3.181496 GCTTGCTTGCTTAATGGGAGTAC 60.181 47.826 0.00 0.00 0.00 2.73
81 82 3.016736 GCTTGCTTGCTTAATGGGAGTA 58.983 45.455 0.00 0.00 0.00 2.59
82 83 1.821136 GCTTGCTTGCTTAATGGGAGT 59.179 47.619 0.00 0.00 0.00 3.85
83 84 1.820519 TGCTTGCTTGCTTAATGGGAG 59.179 47.619 3.47 0.00 0.00 4.30
84 85 1.921982 TGCTTGCTTGCTTAATGGGA 58.078 45.000 3.47 0.00 0.00 4.37
85 86 2.288948 TGTTGCTTGCTTGCTTAATGGG 60.289 45.455 3.47 0.00 0.00 4.00
86 87 3.029320 TGTTGCTTGCTTGCTTAATGG 57.971 42.857 3.47 0.00 0.00 3.16
87 88 4.053295 AGTTGTTGCTTGCTTGCTTAATG 58.947 39.130 3.47 0.00 0.00 1.90
88 89 4.053295 CAGTTGTTGCTTGCTTGCTTAAT 58.947 39.130 3.47 0.00 0.00 1.40
89 90 3.446799 CAGTTGTTGCTTGCTTGCTTAA 58.553 40.909 3.47 0.00 0.00 1.85
90 91 2.223782 CCAGTTGTTGCTTGCTTGCTTA 60.224 45.455 3.47 0.00 0.00 3.09
91 92 1.472026 CCAGTTGTTGCTTGCTTGCTT 60.472 47.619 3.47 0.00 0.00 3.91
92 93 0.103572 CCAGTTGTTGCTTGCTTGCT 59.896 50.000 3.47 0.00 0.00 3.91
93 94 1.493134 GCCAGTTGTTGCTTGCTTGC 61.493 55.000 0.00 0.00 0.00 4.01
94 95 0.877213 GGCCAGTTGTTGCTTGCTTG 60.877 55.000 0.00 0.00 0.00 4.01
95 96 1.329171 TGGCCAGTTGTTGCTTGCTT 61.329 50.000 0.00 0.00 0.00 3.91
96 97 1.329171 TTGGCCAGTTGTTGCTTGCT 61.329 50.000 5.11 0.00 0.00 3.91
97 98 0.461693 TTTGGCCAGTTGTTGCTTGC 60.462 50.000 5.11 0.00 0.00 4.01
98 99 2.243602 ATTTGGCCAGTTGTTGCTTG 57.756 45.000 5.11 0.00 0.00 4.01
99 100 4.379652 CTTAATTTGGCCAGTTGTTGCTT 58.620 39.130 5.11 0.00 0.00 3.91
100 101 3.244181 CCTTAATTTGGCCAGTTGTTGCT 60.244 43.478 5.11 0.00 0.00 3.91
101 102 3.066380 CCTTAATTTGGCCAGTTGTTGC 58.934 45.455 5.11 0.00 0.00 4.17
102 103 4.280677 TCTCCTTAATTTGGCCAGTTGTTG 59.719 41.667 5.11 0.00 0.00 3.33
103 104 4.479158 TCTCCTTAATTTGGCCAGTTGTT 58.521 39.130 5.11 2.31 0.00 2.83
104 105 4.112634 TCTCCTTAATTTGGCCAGTTGT 57.887 40.909 5.11 0.00 0.00 3.32
105 106 5.011023 AGTTTCTCCTTAATTTGGCCAGTTG 59.989 40.000 5.11 0.00 0.00 3.16
106 107 5.147767 AGTTTCTCCTTAATTTGGCCAGTT 58.852 37.500 5.11 8.17 0.00 3.16
107 108 4.740902 AGTTTCTCCTTAATTTGGCCAGT 58.259 39.130 5.11 0.00 0.00 4.00
108 109 4.158579 GGAGTTTCTCCTTAATTTGGCCAG 59.841 45.833 5.11 0.00 46.41 4.85
109 110 4.086457 GGAGTTTCTCCTTAATTTGGCCA 58.914 43.478 0.00 0.00 46.41 5.36
110 111 4.720649 GGAGTTTCTCCTTAATTTGGCC 57.279 45.455 8.38 0.00 46.41 5.36
122 123 0.903454 TGGGACCGAGGGAGTTTCTC 60.903 60.000 0.00 0.00 0.00 2.87
123 124 0.473117 TTGGGACCGAGGGAGTTTCT 60.473 55.000 0.00 0.00 0.00 2.52
124 125 0.399075 TTTGGGACCGAGGGAGTTTC 59.601 55.000 0.00 0.00 0.00 2.78
125 126 0.848053 TTTTGGGACCGAGGGAGTTT 59.152 50.000 0.00 0.00 0.00 2.66
126 127 1.004394 GATTTTGGGACCGAGGGAGTT 59.996 52.381 0.00 0.00 0.00 3.01
127 128 0.618981 GATTTTGGGACCGAGGGAGT 59.381 55.000 0.00 0.00 0.00 3.85
128 129 0.912486 AGATTTTGGGACCGAGGGAG 59.088 55.000 0.00 0.00 0.00 4.30
129 130 2.116238 CTAGATTTTGGGACCGAGGGA 58.884 52.381 0.00 0.00 0.00 4.20
130 131 1.475213 GCTAGATTTTGGGACCGAGGG 60.475 57.143 0.00 0.00 0.00 4.30
131 132 1.209504 TGCTAGATTTTGGGACCGAGG 59.790 52.381 0.00 0.00 0.00 4.63
132 133 2.168521 TCTGCTAGATTTTGGGACCGAG 59.831 50.000 0.00 0.00 0.00 4.63
133 134 2.093658 GTCTGCTAGATTTTGGGACCGA 60.094 50.000 0.00 0.00 0.00 4.69
134 135 2.093447 AGTCTGCTAGATTTTGGGACCG 60.093 50.000 0.00 0.00 0.00 4.79
135 136 3.636153 AGTCTGCTAGATTTTGGGACC 57.364 47.619 0.00 0.00 0.00 4.46
136 137 5.104900 TCCTTAGTCTGCTAGATTTTGGGAC 60.105 44.000 0.00 0.00 0.00 4.46
137 138 5.030147 TCCTTAGTCTGCTAGATTTTGGGA 58.970 41.667 0.00 0.00 0.00 4.37
138 139 5.359194 TCCTTAGTCTGCTAGATTTTGGG 57.641 43.478 0.00 0.00 0.00 4.12
139 140 6.317391 CCTTTCCTTAGTCTGCTAGATTTTGG 59.683 42.308 0.00 0.00 0.00 3.28
140 141 7.065204 GTCCTTTCCTTAGTCTGCTAGATTTTG 59.935 40.741 0.00 0.00 0.00 2.44
141 142 7.106890 GTCCTTTCCTTAGTCTGCTAGATTTT 58.893 38.462 0.00 0.00 0.00 1.82
142 143 6.213600 TGTCCTTTCCTTAGTCTGCTAGATTT 59.786 38.462 0.00 0.00 0.00 2.17
143 144 5.721960 TGTCCTTTCCTTAGTCTGCTAGATT 59.278 40.000 0.00 0.00 0.00 2.40
144 145 5.273208 TGTCCTTTCCTTAGTCTGCTAGAT 58.727 41.667 0.00 0.00 0.00 1.98
145 146 4.673968 TGTCCTTTCCTTAGTCTGCTAGA 58.326 43.478 0.00 0.00 0.00 2.43
146 147 4.679372 GCTGTCCTTTCCTTAGTCTGCTAG 60.679 50.000 0.00 0.00 0.00 3.42
147 148 3.195825 GCTGTCCTTTCCTTAGTCTGCTA 59.804 47.826 0.00 0.00 0.00 3.49
251 252 1.064906 AGCTGGTACTGAGCATGCAAT 60.065 47.619 21.98 0.00 39.05 3.56
278 279 2.342179 GCTCAGTAGCCTCACAGAAAC 58.658 52.381 0.00 0.00 43.40 2.78
298 299 1.748122 ATTGCTGCCGCTGGAAGAG 60.748 57.895 9.87 0.00 34.07 2.85
387 393 1.105167 TAGACTATCACGCCGTGGGG 61.105 60.000 18.32 10.06 33.87 4.96
388 394 0.311165 CTAGACTATCACGCCGTGGG 59.689 60.000 18.32 10.41 33.87 4.61
389 395 0.317938 GCTAGACTATCACGCCGTGG 60.318 60.000 18.32 3.76 33.87 4.94
530 642 2.320587 GGTCTCACGCTGGCTGTTG 61.321 63.158 0.00 0.00 0.00 3.33
699 908 3.698463 CAACGTCGACACCACGGC 61.698 66.667 17.16 0.00 41.73 5.68
710 919 1.071605 GTGATGAGGACTGCAACGTC 58.928 55.000 0.00 0.00 0.00 4.34
713 922 2.622436 GTAGGTGATGAGGACTGCAAC 58.378 52.381 0.00 0.00 0.00 4.17
717 926 2.167281 CTGTGGTAGGTGATGAGGACTG 59.833 54.545 0.00 0.00 0.00 3.51
737 953 1.307343 ACCTGAGGCTGCCATACCT 60.307 57.895 22.65 0.00 39.65 3.08
761 977 2.456119 CGCCTTCATCAGTGACCGC 61.456 63.158 0.00 0.00 33.11 5.68
763 979 0.460987 CTCCGCCTTCATCAGTGACC 60.461 60.000 0.00 0.00 33.11 4.02
768 984 1.333636 ACCTCCTCCGCCTTCATCAG 61.334 60.000 0.00 0.00 0.00 2.90
836 1065 3.144506 CTCCAAGCAACTGTTGAGTCAT 58.855 45.455 23.81 1.93 0.00 3.06
839 1068 1.312815 GCTCCAAGCAACTGTTGAGT 58.687 50.000 23.81 7.32 41.89 3.41
844 1073 1.529244 GGTGGCTCCAAGCAACTGT 60.529 57.895 6.43 0.00 44.57 3.55
974 1256 0.324943 CCATGGAACGGAGGTGACTT 59.675 55.000 5.56 0.00 44.43 3.01
1045 1327 1.686110 GGGAGCGGGAGAAGAAGGA 60.686 63.158 0.00 0.00 0.00 3.36
1121 1406 3.519973 CTCTGACCGCTGCCACACA 62.520 63.158 0.00 0.00 0.00 3.72
1126 1411 4.479993 ATGGCTCTGACCGCTGCC 62.480 66.667 0.00 0.00 45.10 4.85
1129 1414 1.954362 GAGTGATGGCTCTGACCGCT 61.954 60.000 0.00 0.00 32.99 5.52
1134 1419 1.670949 GCGAGGAGTGATGGCTCTGA 61.671 60.000 0.00 0.00 35.89 3.27
1209 1494 3.554934 ACACATTCAATCATACCGGCAT 58.445 40.909 0.00 0.00 0.00 4.40
1222 1507 0.109643 AGCGCGTACGTACACATTCA 60.110 50.000 24.50 0.00 42.83 2.57
1223 1508 0.986992 AAGCGCGTACGTACACATTC 59.013 50.000 24.50 8.97 42.83 2.67
1224 1509 0.986992 GAAGCGCGTACGTACACATT 59.013 50.000 24.50 12.67 42.83 2.71
1227 1512 0.632241 GAAGAAGCGCGTACGTACAC 59.368 55.000 24.50 14.72 42.83 2.90
1230 1515 0.518636 ACAGAAGAAGCGCGTACGTA 59.481 50.000 17.90 0.00 42.83 3.57
1232 1517 0.454620 AGACAGAAGAAGCGCGTACG 60.455 55.000 11.84 11.84 44.07 3.67
1235 1526 1.261619 CAAAAGACAGAAGAAGCGCGT 59.738 47.619 8.43 0.00 0.00 6.01
1340 1634 2.973180 GATGGTAACGGCCGCCTCTC 62.973 65.000 28.58 15.13 42.51 3.20
1466 1760 1.277557 ACTGCAGAGGACTCAATGGAC 59.722 52.381 23.35 0.00 0.00 4.02
1475 1771 0.034616 AGAACAGCACTGCAGAGGAC 59.965 55.000 23.35 6.32 0.00 3.85
1478 1774 1.590932 AACAGAACAGCACTGCAGAG 58.409 50.000 23.35 14.77 38.74 3.35
1489 1785 2.033675 TCTCGTCGCACTTAACAGAACA 59.966 45.455 0.00 0.00 0.00 3.18
1490 1786 2.658285 TCTCGTCGCACTTAACAGAAC 58.342 47.619 0.00 0.00 0.00 3.01
1503 1799 2.095532 ACTTCTGACCGTAATCTCGTCG 59.904 50.000 0.00 0.00 0.00 5.12
1504 1800 3.119919 ACACTTCTGACCGTAATCTCGTC 60.120 47.826 0.00 0.00 0.00 4.20
1506 1802 3.489180 ACACTTCTGACCGTAATCTCG 57.511 47.619 0.00 0.00 0.00 4.04
1515 1811 1.869767 CACTGCTGAACACTTCTGACC 59.130 52.381 0.00 0.00 0.00 4.02
1547 1850 4.104831 CCGGGGGAGATAGAATAATTCCT 58.895 47.826 0.00 0.00 30.49 3.36
1548 1851 3.844804 ACCGGGGGAGATAGAATAATTCC 59.155 47.826 6.32 0.00 0.00 3.01
1563 1866 4.410400 GCTTCACCAGACCGGGGG 62.410 72.222 6.32 7.01 39.52 5.40
1584 1887 5.727646 GCTGTCGTAGCCTGAAATTCAGAG 61.728 50.000 23.32 14.26 44.03 3.35
1601 1904 1.021202 TTCCACAACCAAAGCTGTCG 58.979 50.000 0.00 0.00 0.00 4.35
1617 1920 7.987458 TCTGGTTGTTCAGAGATATGTAATTCC 59.013 37.037 0.00 0.00 38.70 3.01
1654 2057 1.814429 TGTCAGTCTCCTGGGGAAAA 58.186 50.000 0.00 0.00 39.31 2.29
1658 2061 1.209019 CTGAATGTCAGTCTCCTGGGG 59.791 57.143 1.49 0.00 39.58 4.96
1833 2259 4.662468 TCCTCACTGCTCTATGAATGAC 57.338 45.455 0.00 0.00 0.00 3.06
1848 2274 2.973945 AGCGTGATAAGGTTTCCTCAC 58.026 47.619 0.00 0.00 30.89 3.51
1849 2275 3.695830 AAGCGTGATAAGGTTTCCTCA 57.304 42.857 0.00 0.00 30.89 3.86
1901 2346 9.447157 GAAGGCTATTATTCATAGAGCAATCTT 57.553 33.333 0.00 0.00 37.65 2.40
1936 2381 2.919602 ACACTGAGGTGGGGAAATACAT 59.080 45.455 1.29 0.00 46.85 2.29
2045 2490 7.595819 ATGGGATTGTTCTCAAGTACAAAAA 57.404 32.000 6.34 0.00 38.48 1.94
2046 2491 8.698973 TTATGGGATTGTTCTCAAGTACAAAA 57.301 30.769 6.34 0.00 38.48 2.44
2156 2611 2.479389 CGTTGCATTGTTGTTCACCTGT 60.479 45.455 0.00 0.00 0.00 4.00
2249 2704 5.163652 CGCATATATACCTCCATTCTCGTCA 60.164 44.000 0.00 0.00 0.00 4.35
2278 2733 3.554324 CACAAATTATGGACCCGAGTACG 59.446 47.826 0.00 0.00 39.43 3.67
2293 2748 8.130469 GGAAGAAAAATGACAATTGCACAAATT 58.870 29.630 5.05 4.07 39.13 1.82
2336 2792 6.737720 AATATCTGAGAGTAGATTGCCACA 57.262 37.500 0.00 0.00 38.35 4.17
2385 2841 3.450457 GCCCATAATGTTTTCCATGACCA 59.550 43.478 0.00 0.00 32.82 4.02
2537 2997 1.135141 GCACAAGCCACAAGACACAAA 60.135 47.619 0.00 0.00 33.58 2.83
2659 3119 6.064846 TCTTCTTCTTGTGCAAATGAAGTC 57.935 37.500 24.41 0.00 37.67 3.01
2711 3171 5.923114 CCTCATATTCATCGTCAGAATCGTT 59.077 40.000 0.00 0.00 37.02 3.85
2741 3201 2.416431 GCCCAGCTGTGCAGAATTTTAG 60.416 50.000 16.84 0.00 0.00 1.85
2751 3211 3.677648 CCAGTTGCCCAGCTGTGC 61.678 66.667 14.85 14.85 37.87 4.57
3028 3496 7.617041 AAAAGTTAAGAGCATAGTGGCTAAG 57.383 36.000 0.00 0.00 45.99 2.18
3054 3522 2.417586 TGATTTGCTCGCATTCTGACAG 59.582 45.455 0.00 0.00 0.00 3.51
3244 3718 1.220749 CCGAAATTCCGGGAGCTGA 59.779 57.895 0.00 0.00 45.43 4.26
3279 3753 4.351192 CACTTCCCTTTTTGTCGTCTTTG 58.649 43.478 0.00 0.00 0.00 2.77
3459 3933 0.832559 GAGGCCGGGGCTAATACTCT 60.833 60.000 24.48 0.00 38.98 3.24
3525 3999 6.094325 TGACTCTTTTACACGGTTGATTTGTT 59.906 34.615 0.00 0.00 0.00 2.83
3526 4000 5.587043 TGACTCTTTTACACGGTTGATTTGT 59.413 36.000 0.00 0.00 0.00 2.83
3619 4093 1.921982 TGCAACCAATGGTAGCACAT 58.078 45.000 4.88 0.00 33.12 3.21
3657 4131 0.520404 CACAGCATGAGGAAGTGCAC 59.480 55.000 9.40 9.40 43.63 4.57
4416 4934 3.926616 ACAGACTAATGTTTCTCCACCG 58.073 45.455 0.00 0.00 0.00 4.94
4488 5018 1.749634 GCTGAACTCCGAACTAGCCTA 59.250 52.381 0.00 0.00 0.00 3.93
4628 5158 7.156876 TGTGTTGCTGGATTAAATTTCCTAG 57.843 36.000 0.00 0.00 34.17 3.02
4664 5194 6.486253 TTCGAAAGAACTTCATCAAGATGG 57.514 37.500 9.96 0.00 46.92 3.51
4685 5215 7.894376 ATGACCAAAATCACAATGTGAATTC 57.106 32.000 20.64 7.00 45.96 2.17
4705 5235 0.376152 CCGTGCAGATGCTCAATGAC 59.624 55.000 6.35 0.00 42.66 3.06
4714 5244 1.921243 TTATGTCGTCCGTGCAGATG 58.079 50.000 0.00 0.00 0.00 2.90
4715 5245 2.094182 AGTTTATGTCGTCCGTGCAGAT 60.094 45.455 0.00 0.00 0.00 2.90
4717 5247 1.710013 AGTTTATGTCGTCCGTGCAG 58.290 50.000 0.00 0.00 0.00 4.41
4724 5254 4.559251 CAGAGTGCACTAGTTTATGTCGTC 59.441 45.833 21.73 2.27 0.00 4.20
4726 5256 4.559251 GTCAGAGTGCACTAGTTTATGTCG 59.441 45.833 21.73 1.44 0.00 4.35
4727 5257 4.865365 GGTCAGAGTGCACTAGTTTATGTC 59.135 45.833 21.73 3.90 0.00 3.06
4729 5259 4.820897 TGGTCAGAGTGCACTAGTTTATG 58.179 43.478 21.73 11.68 0.00 1.90
4739 5269 3.344703 CCCAATTGGTCAGAGTGCA 57.655 52.632 22.91 0.00 0.00 4.57
4772 5302 3.902881 AGTTGCACCTCTAATCCTCTG 57.097 47.619 0.00 0.00 0.00 3.35
4790 5320 4.519730 GCTATGTCCGGATCACTAAGTAGT 59.480 45.833 7.81 0.00 36.90 2.73
4907 5437 1.115467 GGATCACATCGTCCCTGTCT 58.885 55.000 0.00 0.00 0.00 3.41
5008 5538 0.676184 TGCTCCGATAGATGCTGTCC 59.324 55.000 0.00 0.00 39.76 4.02
5031 5561 0.736053 GCGTCAACTGTTGGGTTCAA 59.264 50.000 19.55 0.00 0.00 2.69
5073 5603 4.020307 CCAGGCAAATATGTCCCAGTTTTT 60.020 41.667 0.00 0.00 0.00 1.94
5300 5830 5.316987 CAGGATTTGTCCTTCTTTGGTACT 58.683 41.667 0.00 0.00 38.22 2.73


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

AutoCloner maintained by Alex Coulton.