Multiple sequence alignment - TraesCS6B01G460200

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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 TraesCS6B01G460200 chr6B 100.000 4739 0 0 1 4739 714047773 714052511 0.000000e+00 8752.0
1 TraesCS6B01G460200 chr6B 99.897 969 1 0 3771 4739 714058373 714059341 0.000000e+00 1784.0
2 TraesCS6B01G460200 chr6B 98.968 969 9 1 3771 4739 296378584 296377617 0.000000e+00 1733.0
3 TraesCS6B01G460200 chr6B 76.604 1278 244 39 2391 3631 715078591 715079850 0.000000e+00 652.0
4 TraesCS6B01G460200 chr6B 74.878 1234 263 32 2391 3592 714265148 714263930 7.030000e-143 518.0
5 TraesCS6B01G460200 chr6B 75.000 616 123 24 1222 1824 715077000 715077597 6.090000e-64 255.0
6 TraesCS6B01G460200 chr6D 89.092 3172 214 45 665 3771 467927205 467930309 0.000000e+00 3819.0
7 TraesCS6B01G460200 chr6D 74.841 1411 303 34 2393 3780 468089167 468087786 4.080000e-165 592.0
8 TraesCS6B01G460200 chr6D 75.816 521 91 23 1264 1774 468016800 468016305 1.030000e-56 231.0
9 TraesCS6B01G460200 chr3B 99.174 969 7 1 3771 4739 178205804 178206771 0.000000e+00 1744.0
10 TraesCS6B01G460200 chr3B 99.174 969 7 1 3771 4739 724765254 724766221 0.000000e+00 1744.0
11 TraesCS6B01G460200 chr3B 99.174 968 7 1 3772 4739 178199009 178199975 0.000000e+00 1742.0
12 TraesCS6B01G460200 chr3B 99.070 968 8 1 3772 4739 724758387 724759353 0.000000e+00 1736.0
13 TraesCS6B01G460200 chr3B 96.491 114 4 0 1 114 603442453 603442340 6.260000e-44 189.0
14 TraesCS6B01G460200 chr3B 85.135 74 8 3 2717 2789 826965697 826965768 6.580000e-09 73.1
15 TraesCS6B01G460200 chr3A 99.071 969 8 1 3771 4739 24085741 24086708 0.000000e+00 1738.0
16 TraesCS6B01G460200 chr3A 90.000 120 8 2 119 238 143227305 143227190 8.210000e-33 152.0
17 TraesCS6B01G460200 chr3A 88.235 119 9 4 117 235 542226634 542226521 2.300000e-28 137.0
18 TraesCS6B01G460200 chr4A 98.969 970 9 1 3771 4739 162674917 162673948 0.000000e+00 1735.0
19 TraesCS6B01G460200 chr4A 90.090 111 10 1 118 227 549138495 549138385 4.940000e-30 143.0
20 TraesCS6B01G460200 chr4A 90.000 110 9 1 122 231 603760449 603760342 1.780000e-29 141.0
21 TraesCS6B01G460200 chr7A 98.968 969 9 1 3771 4739 260781223 260782190 0.000000e+00 1733.0
22 TraesCS6B01G460200 chr6A 91.840 1201 72 9 2140 3318 614004805 614006001 0.000000e+00 1652.0
23 TraesCS6B01G460200 chr6A 89.843 1083 94 10 1061 2140 614003441 614004510 0.000000e+00 1376.0
24 TraesCS6B01G460200 chr6A 94.601 426 18 4 235 659 614002200 614002621 0.000000e+00 654.0
25 TraesCS6B01G460200 chr6A 92.118 406 32 0 3366 3771 614005999 614006404 1.480000e-159 573.0
26 TraesCS6B01G460200 chr6A 74.974 975 204 30 2388 3345 614129258 614128307 3.410000e-111 412.0
27 TraesCS6B01G460200 chr6A 89.952 209 11 4 664 868 614003041 614003243 1.310000e-65 261.0
28 TraesCS6B01G460200 chr6A 75.624 521 92 23 1264 1774 614098160 614097665 4.770000e-55 226.0
29 TraesCS6B01G460200 chr6A 95.690 116 5 0 1 116 539166336 539166221 2.250000e-43 187.0
30 TraesCS6B01G460200 chr5B 85.100 349 41 8 238 583 40774590 40774250 3.510000e-91 346.0
31 TraesCS6B01G460200 chr4B 95.690 116 5 0 1 116 602778445 602778560 2.250000e-43 187.0
32 TraesCS6B01G460200 chr4B 95.652 115 5 0 1 115 72644937 72645051 8.100000e-43 185.0
33 TraesCS6B01G460200 chr4B 95.652 115 5 0 1 115 81937459 81937573 8.100000e-43 185.0
34 TraesCS6B01G460200 chr2A 95.652 115 5 0 1 115 104986824 104986938 8.100000e-43 185.0
35 TraesCS6B01G460200 chrUn 95.614 114 5 0 1 114 282653787 282653674 2.910000e-42 183.0
36 TraesCS6B01G460200 chrUn 77.972 286 47 11 1264 1544 477256377 477256103 1.060000e-36 165.0
37 TraesCS6B01G460200 chrUn 74.754 305 51 18 1360 1657 79468122 79467837 3.880000e-21 113.0
38 TraesCS6B01G460200 chr2D 95.614 114 5 0 1 114 119370976 119371089 2.910000e-42 183.0
39 TraesCS6B01G460200 chr2D 95.614 114 5 0 1 114 351377092 351377205 2.910000e-42 183.0
40 TraesCS6B01G460200 chr2D 90.265 113 8 2 119 231 397569296 397569405 1.370000e-30 145.0
41 TraesCS6B01G460200 chr3D 91.743 109 5 2 119 227 551893818 551893714 1.060000e-31 148.0
42 TraesCS6B01G460200 chr2B 88.189 127 9 3 119 240 797738970 797738845 3.820000e-31 147.0
43 TraesCS6B01G460200 chr7D 88.889 117 11 1 119 235 14255673 14255559 4.940000e-30 143.0
44 TraesCS6B01G460200 chr1B 87.805 123 10 3 118 240 625933233 625933350 6.390000e-29 139.0
45 TraesCS6B01G460200 chr1D 83.529 85 12 2 2715 2798 21802713 21802630 1.410000e-10 78.7


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 TraesCS6B01G460200 chr6B 714047773 714052511 4738 False 8752.0 8752 100.0000 1 4739 1 chr6B.!!$F1 4738
1 TraesCS6B01G460200 chr6B 714058373 714059341 968 False 1784.0 1784 99.8970 3771 4739 1 chr6B.!!$F2 968
2 TraesCS6B01G460200 chr6B 296377617 296378584 967 True 1733.0 1733 98.9680 3771 4739 1 chr6B.!!$R1 968
3 TraesCS6B01G460200 chr6B 714263930 714265148 1218 True 518.0 518 74.8780 2391 3592 1 chr6B.!!$R2 1201
4 TraesCS6B01G460200 chr6B 715077000 715079850 2850 False 453.5 652 75.8020 1222 3631 2 chr6B.!!$F3 2409
5 TraesCS6B01G460200 chr6D 467927205 467930309 3104 False 3819.0 3819 89.0920 665 3771 1 chr6D.!!$F1 3106
6 TraesCS6B01G460200 chr6D 468087786 468089167 1381 True 592.0 592 74.8410 2393 3780 1 chr6D.!!$R2 1387
7 TraesCS6B01G460200 chr3B 178205804 178206771 967 False 1744.0 1744 99.1740 3771 4739 1 chr3B.!!$F2 968
8 TraesCS6B01G460200 chr3B 724765254 724766221 967 False 1744.0 1744 99.1740 3771 4739 1 chr3B.!!$F4 968
9 TraesCS6B01G460200 chr3B 178199009 178199975 966 False 1742.0 1742 99.1740 3772 4739 1 chr3B.!!$F1 967
10 TraesCS6B01G460200 chr3B 724758387 724759353 966 False 1736.0 1736 99.0700 3772 4739 1 chr3B.!!$F3 967
11 TraesCS6B01G460200 chr3A 24085741 24086708 967 False 1738.0 1738 99.0710 3771 4739 1 chr3A.!!$F1 968
12 TraesCS6B01G460200 chr4A 162673948 162674917 969 True 1735.0 1735 98.9690 3771 4739 1 chr4A.!!$R1 968
13 TraesCS6B01G460200 chr7A 260781223 260782190 967 False 1733.0 1733 98.9680 3771 4739 1 chr7A.!!$F1 968
14 TraesCS6B01G460200 chr6A 614002200 614006404 4204 False 903.2 1652 91.6708 235 3771 5 chr6A.!!$F1 3536
15 TraesCS6B01G460200 chr6A 614128307 614129258 951 True 412.0 412 74.9740 2388 3345 1 chr6A.!!$R3 957

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
335 336 0.036732 AGCTCGAGAAAATGCCACCA 59.963 50.0 18.75 0.00 0.00 4.17 F
960 1411 0.038526 CAGACCACCACCAGTACGTC 60.039 60.0 0.00 0.00 0.00 4.34 F
2192 3350 0.095417 GCGTTCTGGTCGAGCAAATC 59.905 55.0 19.16 10.09 0.00 2.17 F
2270 3434 0.308993 GAGTTGTGTTGCTGCTGGAC 59.691 55.0 0.00 0.00 0.00 4.02 F
2275 3439 0.520404 GTGTTGCTGCTGGACATGAG 59.480 55.0 0.00 0.00 0.00 2.90 F
2641 3827 0.531753 AAAACACGCCCAATTGTGCC 60.532 50.0 7.35 0.00 39.71 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2270 3434 0.248498 CAATCTTGCGGCAGCTCATG 60.248 55.000 10.92 0.0 45.42 3.07 R
2641 3827 0.739462 TCCTAGCATCACGCAAACCG 60.739 55.000 0.00 0.0 46.13 4.44 R
3278 4490 0.531974 TTCCAGCGAGTGTTGGTGTC 60.532 55.000 0.00 0.0 45.90 3.67 R
3505 4717 1.003464 TGGCAGTCTTATGAGCAAGCA 59.997 47.619 0.00 0.0 0.00 3.91 R
3506 4718 1.742761 TGGCAGTCTTATGAGCAAGC 58.257 50.000 0.00 0.0 0.00 4.01 R
3751 4963 2.029369 GTGTCGGCGGTTGTACCA 59.971 61.111 7.21 0.0 38.47 3.25 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
24 25 4.135153 CGGAGGGAGCGTCCACAG 62.135 72.222 6.41 0.00 38.64 3.66
25 26 4.459089 GGAGGGAGCGTCCACAGC 62.459 72.222 6.41 0.00 38.64 4.40
26 27 4.803426 GAGGGAGCGTCCACAGCG 62.803 72.222 6.41 0.00 38.64 5.18
40 41 4.578898 AGCGCGACACGTGGTGAA 62.579 61.111 21.57 0.00 46.01 3.18
41 42 3.411351 GCGCGACACGTGGTGAAT 61.411 61.111 21.57 0.00 46.11 2.57
42 43 2.469847 CGCGACACGTGGTGAATG 59.530 61.111 21.57 3.66 36.96 2.67
43 44 2.860293 GCGACACGTGGTGAATGG 59.140 61.111 21.57 0.24 36.96 3.16
44 45 2.860293 CGACACGTGGTGAATGGC 59.140 61.111 21.57 0.00 36.96 4.40
45 46 1.667830 CGACACGTGGTGAATGGCT 60.668 57.895 21.57 0.00 36.96 4.75
46 47 1.868997 GACACGTGGTGAATGGCTG 59.131 57.895 21.57 0.00 36.96 4.85
47 48 0.884704 GACACGTGGTGAATGGCTGT 60.885 55.000 21.57 0.00 36.96 4.40
48 49 1.165907 ACACGTGGTGAATGGCTGTG 61.166 55.000 21.57 0.00 36.96 3.66
49 50 0.884259 CACGTGGTGAATGGCTGTGA 60.884 55.000 7.95 0.00 35.23 3.58
50 51 0.603707 ACGTGGTGAATGGCTGTGAG 60.604 55.000 0.00 0.00 0.00 3.51
51 52 1.878775 GTGGTGAATGGCTGTGAGC 59.121 57.895 0.00 0.00 41.46 4.26
52 53 1.672030 TGGTGAATGGCTGTGAGCG 60.672 57.895 0.00 0.00 43.62 5.03
53 54 2.482374 GTGAATGGCTGTGAGCGC 59.518 61.111 0.00 0.00 43.62 5.92
54 55 3.120385 TGAATGGCTGTGAGCGCG 61.120 61.111 0.00 0.00 43.62 6.86
55 56 4.527157 GAATGGCTGTGAGCGCGC 62.527 66.667 26.66 26.66 43.62 6.86
61 62 4.081030 CTGTGAGCGCGCCAAGTG 62.081 66.667 30.33 12.20 0.00 3.16
72 73 4.201951 CCAAGTGGCGCTAATCGT 57.798 55.556 7.64 0.00 41.07 3.73
73 74 2.466867 CCAAGTGGCGCTAATCGTT 58.533 52.632 7.64 0.00 41.07 3.85
74 75 0.096976 CCAAGTGGCGCTAATCGTTG 59.903 55.000 7.64 3.42 41.07 4.10
75 76 0.521242 CAAGTGGCGCTAATCGTTGC 60.521 55.000 7.64 0.00 41.07 4.17
81 82 4.110493 GCTAATCGTTGCGAGGCT 57.890 55.556 0.00 0.00 39.91 4.58
82 83 1.927931 GCTAATCGTTGCGAGGCTC 59.072 57.895 3.87 3.87 39.91 4.70
83 84 1.491505 GCTAATCGTTGCGAGGCTCC 61.492 60.000 9.32 2.37 39.91 4.70
84 85 0.876342 CTAATCGTTGCGAGGCTCCC 60.876 60.000 9.32 0.00 39.91 4.30
85 86 2.622903 TAATCGTTGCGAGGCTCCCG 62.623 60.000 9.32 6.56 39.91 5.14
87 88 4.735132 CGTTGCGAGGCTCCCGAA 62.735 66.667 9.32 0.00 0.00 4.30
88 89 2.815647 GTTGCGAGGCTCCCGAAG 60.816 66.667 9.32 0.00 0.00 3.79
101 102 4.470876 CGAAGGAGCGCTCGTTAA 57.529 55.556 36.96 0.00 37.75 2.01
102 103 2.959275 CGAAGGAGCGCTCGTTAAT 58.041 52.632 36.96 21.62 37.75 1.40
103 104 1.278238 CGAAGGAGCGCTCGTTAATT 58.722 50.000 36.96 21.28 37.75 1.40
104 105 2.456989 CGAAGGAGCGCTCGTTAATTA 58.543 47.619 36.96 0.00 37.75 1.40
105 106 2.468040 CGAAGGAGCGCTCGTTAATTAG 59.532 50.000 36.96 23.67 37.75 1.73
106 107 3.445857 GAAGGAGCGCTCGTTAATTAGT 58.554 45.455 36.96 19.55 37.75 2.24
107 108 3.521947 AGGAGCGCTCGTTAATTAGTT 57.478 42.857 29.81 3.47 0.00 2.24
108 109 3.187700 AGGAGCGCTCGTTAATTAGTTG 58.812 45.455 29.81 0.00 0.00 3.16
109 110 2.285660 GGAGCGCTCGTTAATTAGTTGC 60.286 50.000 29.81 8.45 0.00 4.17
110 111 2.603560 GAGCGCTCGTTAATTAGTTGCT 59.396 45.455 23.61 7.90 31.95 3.91
111 112 2.603560 AGCGCTCGTTAATTAGTTGCTC 59.396 45.455 2.64 0.00 0.00 4.26
112 113 2.285660 GCGCTCGTTAATTAGTTGCTCC 60.286 50.000 0.00 0.00 0.00 4.70
113 114 2.284417 CGCTCGTTAATTAGTTGCTCCC 59.716 50.000 0.00 0.00 0.00 4.30
114 115 2.284417 GCTCGTTAATTAGTTGCTCCCG 59.716 50.000 0.00 0.00 0.00 5.14
115 116 3.518590 CTCGTTAATTAGTTGCTCCCGT 58.481 45.455 0.00 0.00 0.00 5.28
116 117 3.514645 TCGTTAATTAGTTGCTCCCGTC 58.485 45.455 0.00 0.00 0.00 4.79
117 118 2.280708 CGTTAATTAGTTGCTCCCGTCG 59.719 50.000 0.00 0.00 0.00 5.12
118 119 2.589798 TAATTAGTTGCTCCCGTCGG 57.410 50.000 3.60 3.60 0.00 4.79
119 120 0.899720 AATTAGTTGCTCCCGTCGGA 59.100 50.000 14.39 0.00 36.45 4.55
120 121 1.120530 ATTAGTTGCTCCCGTCGGAT 58.879 50.000 14.39 0.00 37.60 4.18
121 122 0.174845 TTAGTTGCTCCCGTCGGATG 59.825 55.000 14.39 5.96 37.60 3.51
122 123 2.292794 TAGTTGCTCCCGTCGGATGC 62.293 60.000 14.39 16.41 37.60 3.91
123 124 3.700970 TTGCTCCCGTCGGATGCA 61.701 61.111 21.45 21.45 39.23 3.96
124 125 3.950794 TTGCTCCCGTCGGATGCAC 62.951 63.158 23.88 6.70 40.08 4.57
125 126 4.451150 GCTCCCGTCGGATGCACA 62.451 66.667 14.39 0.00 37.60 4.57
126 127 2.264480 CTCCCGTCGGATGCACAA 59.736 61.111 14.39 0.00 37.60 3.33
127 128 1.375396 CTCCCGTCGGATGCACAAA 60.375 57.895 14.39 0.00 37.60 2.83
128 129 0.953471 CTCCCGTCGGATGCACAAAA 60.953 55.000 14.39 0.00 37.60 2.44
129 130 0.535328 TCCCGTCGGATGCACAAAAA 60.535 50.000 14.39 0.00 31.13 1.94
130 131 0.525761 CCCGTCGGATGCACAAAAAT 59.474 50.000 14.39 0.00 0.00 1.82
131 132 1.067915 CCCGTCGGATGCACAAAAATT 60.068 47.619 14.39 0.00 0.00 1.82
132 133 2.609244 CCCGTCGGATGCACAAAAATTT 60.609 45.455 14.39 0.00 0.00 1.82
133 134 3.366476 CCCGTCGGATGCACAAAAATTTA 60.366 43.478 14.39 0.00 0.00 1.40
134 135 3.851403 CCGTCGGATGCACAAAAATTTAG 59.149 43.478 4.91 0.00 0.00 1.85
135 136 4.472286 CGTCGGATGCACAAAAATTTAGT 58.528 39.130 0.00 0.00 0.00 2.24
136 137 5.391097 CCGTCGGATGCACAAAAATTTAGTA 60.391 40.000 4.91 0.00 0.00 1.82
137 138 5.506832 CGTCGGATGCACAAAAATTTAGTAC 59.493 40.000 0.00 0.00 0.00 2.73
138 139 5.798434 GTCGGATGCACAAAAATTTAGTACC 59.202 40.000 0.00 0.00 0.00 3.34
139 140 5.473846 TCGGATGCACAAAAATTTAGTACCA 59.526 36.000 0.00 0.00 0.00 3.25
140 141 5.571357 CGGATGCACAAAAATTTAGTACCAC 59.429 40.000 0.00 0.00 0.00 4.16
141 142 5.867174 GGATGCACAAAAATTTAGTACCACC 59.133 40.000 0.00 0.00 0.00 4.61
142 143 6.295067 GGATGCACAAAAATTTAGTACCACCT 60.295 38.462 0.00 0.00 0.00 4.00
143 144 6.079424 TGCACAAAAATTTAGTACCACCTC 57.921 37.500 0.00 0.00 0.00 3.85
144 145 5.151389 GCACAAAAATTTAGTACCACCTCG 58.849 41.667 0.00 0.00 0.00 4.63
145 146 5.049267 GCACAAAAATTTAGTACCACCTCGA 60.049 40.000 0.00 0.00 0.00 4.04
146 147 6.513720 GCACAAAAATTTAGTACCACCTCGAA 60.514 38.462 0.00 0.00 0.00 3.71
147 148 7.590279 CACAAAAATTTAGTACCACCTCGAAT 58.410 34.615 0.00 0.00 0.00 3.34
148 149 8.723311 CACAAAAATTTAGTACCACCTCGAATA 58.277 33.333 0.00 0.00 0.00 1.75
149 150 8.943002 ACAAAAATTTAGTACCACCTCGAATAG 58.057 33.333 0.00 0.00 0.00 1.73
150 151 9.158233 CAAAAATTTAGTACCACCTCGAATAGA 57.842 33.333 0.00 0.00 0.00 1.98
151 152 9.729281 AAAAATTTAGTACCACCTCGAATAGAA 57.271 29.630 0.00 0.00 0.00 2.10
152 153 9.729281 AAAATTTAGTACCACCTCGAATAGAAA 57.271 29.630 0.00 0.00 0.00 2.52
153 154 9.729281 AAATTTAGTACCACCTCGAATAGAAAA 57.271 29.630 0.00 0.00 0.00 2.29
154 155 9.729281 AATTTAGTACCACCTCGAATAGAAAAA 57.271 29.630 0.00 0.00 0.00 1.94
185 186 8.952713 ATTTTCGACGGTGAACGGATGAAAATA 61.953 37.037 21.52 5.75 46.84 1.40
191 192 7.836358 CGGTGAACGGATGAAAATATTTATG 57.164 36.000 0.01 0.00 39.42 1.90
192 193 7.635423 CGGTGAACGGATGAAAATATTTATGA 58.365 34.615 0.01 0.00 39.42 2.15
193 194 8.126074 CGGTGAACGGATGAAAATATTTATGAA 58.874 33.333 0.01 0.00 39.42 2.57
194 195 9.796120 GGTGAACGGATGAAAATATTTATGAAA 57.204 29.630 0.01 0.00 0.00 2.69
198 199 9.814899 AACGGATGAAAATATTTATGAAATGCA 57.185 25.926 0.01 0.00 32.38 3.96
199 200 9.248291 ACGGATGAAAATATTTATGAAATGCAC 57.752 29.630 0.01 0.00 32.38 4.57
200 201 8.702438 CGGATGAAAATATTTATGAAATGCACC 58.298 33.333 0.01 0.00 32.38 5.01
201 202 9.768662 GGATGAAAATATTTATGAAATGCACCT 57.231 29.630 0.01 0.00 32.38 4.00
204 205 8.881743 TGAAAATATTTATGAAATGCACCTTGC 58.118 29.630 0.01 0.00 45.29 4.01
205 206 9.101655 GAAAATATTTATGAAATGCACCTTGCT 57.898 29.630 0.01 0.00 45.31 3.91
206 207 9.452287 AAAATATTTATGAAATGCACCTTGCTT 57.548 25.926 0.01 0.00 45.31 3.91
207 208 9.452287 AAATATTTATGAAATGCACCTTGCTTT 57.548 25.926 0.00 0.00 45.31 3.51
212 213 9.585099 TTTATGAAATGCACCTTGCTTTATTAG 57.415 29.630 0.00 0.00 45.31 1.73
213 214 6.588719 TGAAATGCACCTTGCTTTATTAGT 57.411 33.333 0.00 0.00 45.31 2.24
214 215 7.695480 TGAAATGCACCTTGCTTTATTAGTA 57.305 32.000 0.00 0.00 45.31 1.82
215 216 8.292444 TGAAATGCACCTTGCTTTATTAGTAT 57.708 30.769 0.00 0.00 45.31 2.12
216 217 9.402320 TGAAATGCACCTTGCTTTATTAGTATA 57.598 29.630 0.00 0.00 45.31 1.47
217 218 9.884465 GAAATGCACCTTGCTTTATTAGTATAG 57.116 33.333 0.00 0.00 45.31 1.31
218 219 7.986085 ATGCACCTTGCTTTATTAGTATAGG 57.014 36.000 0.00 0.00 45.31 2.57
219 220 6.895782 TGCACCTTGCTTTATTAGTATAGGT 58.104 36.000 0.00 0.00 45.31 3.08
220 221 8.025270 TGCACCTTGCTTTATTAGTATAGGTA 57.975 34.615 0.00 0.00 45.31 3.08
221 222 8.656806 TGCACCTTGCTTTATTAGTATAGGTAT 58.343 33.333 0.00 0.00 45.31 2.73
275 276 2.026822 AGCCCCTATTCGCTCATTATGG 60.027 50.000 0.00 0.00 0.00 2.74
289 290 5.106197 GCTCATTATGGTGTCATTTGTGTGA 60.106 40.000 0.00 0.00 34.96 3.58
290 291 6.570186 GCTCATTATGGTGTCATTTGTGTGAA 60.570 38.462 0.00 0.00 34.96 3.18
321 322 4.693283 TCATGTTTACCCATTAGAGCTCG 58.307 43.478 8.37 0.00 0.00 5.03
335 336 0.036732 AGCTCGAGAAAATGCCACCA 59.963 50.000 18.75 0.00 0.00 4.17
371 372 2.111756 CTGACTTTTTGACGCTGTTGC 58.888 47.619 0.00 0.00 0.00 4.17
375 376 3.888934 ACTTTTTGACGCTGTTGCATAG 58.111 40.909 0.00 0.00 39.64 2.23
376 377 2.330231 TTTTGACGCTGTTGCATAGC 57.670 45.000 12.16 12.16 39.64 2.97
400 401 7.503566 AGCGTACCTCCAACACTTATAAGTATA 59.496 37.037 17.62 1.92 37.08 1.47
401 402 8.137437 GCGTACCTCCAACACTTATAAGTATAA 58.863 37.037 17.62 2.27 37.08 0.98
511 512 3.360867 TGGACAGTCAAACCATTTGTGT 58.639 40.909 2.17 0.17 41.36 3.72
529 530 9.135843 CATTTGTGTTACTAAACGATCTCACTA 57.864 33.333 0.00 0.00 38.53 2.74
545 546 9.907576 CGATCTCACTATTTTAGTTTGTCAATC 57.092 33.333 0.00 0.00 36.76 2.67
579 581 5.990408 ACATTTGCTTATGATAGCTTACGC 58.010 37.500 0.00 0.00 41.76 4.42
601 603 6.142817 CGCTGTAAAGAAACTATTGCACTTT 58.857 36.000 0.00 0.00 35.47 2.66
659 661 6.710744 CCCTATAATGTTCAACCAGATGTACC 59.289 42.308 0.00 0.00 0.00 3.34
660 662 6.423905 CCTATAATGTTCAACCAGATGTACCG 59.576 42.308 0.00 0.00 0.00 4.02
662 664 1.972075 TGTTCAACCAGATGTACCGGA 59.028 47.619 9.46 0.00 0.00 5.14
749 1170 1.374758 GCTCTACTGCCAGCGTGTT 60.375 57.895 0.00 0.00 0.00 3.32
767 1188 2.279120 CGCCGGAGATGCTCTCAC 60.279 66.667 5.05 4.51 45.12 3.51
799 1220 0.175073 GAAAGGGATAGCGTGTCCGT 59.825 55.000 0.07 0.00 36.58 4.69
815 1236 0.244721 CCGTCAGAGATGCTCACACA 59.755 55.000 0.00 0.00 32.06 3.72
816 1237 1.344458 CGTCAGAGATGCTCACACAC 58.656 55.000 0.00 0.00 32.06 3.82
817 1238 1.344458 GTCAGAGATGCTCACACACG 58.656 55.000 0.00 0.00 32.06 4.49
818 1239 0.961753 TCAGAGATGCTCACACACGT 59.038 50.000 0.00 0.00 32.06 4.49
819 1240 2.095212 GTCAGAGATGCTCACACACGTA 60.095 50.000 0.00 0.00 32.06 3.57
820 1241 2.095212 TCAGAGATGCTCACACACGTAC 60.095 50.000 0.00 0.00 32.06 3.67
868 1289 0.970937 TCCGCCGGAGATTCTCTTGT 60.971 55.000 5.05 0.00 0.00 3.16
872 1323 1.195115 CCGGAGATTCTCTTGTCCCA 58.805 55.000 13.22 0.00 0.00 4.37
874 1325 2.622436 CGGAGATTCTCTTGTCCCAAC 58.378 52.381 13.22 0.00 0.00 3.77
876 1327 2.305927 GGAGATTCTCTTGTCCCAACCA 59.694 50.000 13.22 0.00 0.00 3.67
879 1330 5.003096 AGATTCTCTTGTCCCAACCAAAT 57.997 39.130 0.00 0.00 0.00 2.32
880 1331 6.139679 AGATTCTCTTGTCCCAACCAAATA 57.860 37.500 0.00 0.00 0.00 1.40
882 1333 6.830838 AGATTCTCTTGTCCCAACCAAATATC 59.169 38.462 0.00 0.00 0.00 1.63
892 1343 5.103558 TCCCAACCAAATATCCATCTCACAT 60.104 40.000 0.00 0.00 0.00 3.21
896 1347 5.391256 ACCAAATATCCATCTCACATGCAT 58.609 37.500 0.00 0.00 0.00 3.96
898 1349 6.657966 ACCAAATATCCATCTCACATGCATAG 59.342 38.462 0.00 0.00 0.00 2.23
909 1360 2.888447 ATGCATAGCTCCTCGGCCC 61.888 63.158 0.00 0.00 0.00 5.80
933 1384 1.566211 CACACTCTCCTCCACTCCAT 58.434 55.000 0.00 0.00 0.00 3.41
941 1392 1.354368 TCCTCCACTCCATTTTCCACC 59.646 52.381 0.00 0.00 0.00 4.61
943 1394 2.440409 CTCCACTCCATTTTCCACCAG 58.560 52.381 0.00 0.00 0.00 4.00
944 1395 2.040278 CTCCACTCCATTTTCCACCAGA 59.960 50.000 0.00 0.00 0.00 3.86
945 1396 2.162681 CCACTCCATTTTCCACCAGAC 58.837 52.381 0.00 0.00 0.00 3.51
946 1397 2.162681 CACTCCATTTTCCACCAGACC 58.837 52.381 0.00 0.00 0.00 3.85
947 1398 1.780309 ACTCCATTTTCCACCAGACCA 59.220 47.619 0.00 0.00 0.00 4.02
948 1399 2.162681 CTCCATTTTCCACCAGACCAC 58.837 52.381 0.00 0.00 0.00 4.16
949 1400 1.203001 TCCATTTTCCACCAGACCACC 60.203 52.381 0.00 0.00 0.00 4.61
950 1401 1.480312 CCATTTTCCACCAGACCACCA 60.480 52.381 0.00 0.00 0.00 4.17
960 1411 0.038526 CAGACCACCACCAGTACGTC 60.039 60.000 0.00 0.00 0.00 4.34
962 1413 1.518056 GACCACCACCAGTACGTCGA 61.518 60.000 0.00 0.00 0.00 4.20
989 1442 5.722172 AATTGATCCTCTCTCATTCCCAA 57.278 39.130 0.00 0.00 0.00 4.12
1005 1458 0.393077 CCAAGTCCCAACTCGACAGT 59.607 55.000 0.00 0.00 33.48 3.55
1029 1489 3.640000 GATCAATGGCGTCGGGCG 61.640 66.667 0.00 0.00 44.92 6.13
1076 1536 1.459455 CGCCCATTGTGGTCCAAACA 61.459 55.000 0.00 0.00 36.44 2.83
1142 1602 1.556911 TCAGGCACTTTCCAGGATCTC 59.443 52.381 0.00 0.00 34.60 2.75
1169 1629 1.213013 CCTCGACGGACAAGACCAG 59.787 63.158 0.00 0.00 33.16 4.00
1176 1636 1.572085 CGGACAAGACCAGCAAGCAG 61.572 60.000 0.00 0.00 0.00 4.24
1250 1710 1.925847 GCATTTCTCAGAGAGTCGCTG 59.074 52.381 16.98 16.98 32.70 5.18
1335 1798 3.136443 TCAAGACTTCCTGAAGAAAGCCA 59.864 43.478 13.58 0.00 40.79 4.75
1348 1811 3.537206 AAGCCAGCCTCGTCCACAC 62.537 63.158 0.00 0.00 0.00 3.82
1357 1820 3.345808 CGTCCACACCAAGGCACG 61.346 66.667 0.00 0.00 0.00 5.34
1360 1823 2.669569 CCACACCAAGGCACGGAG 60.670 66.667 0.00 0.00 0.00 4.63
1553 2016 3.538591 CTTGCATGAGGCTATCAAGTCA 58.461 45.455 0.00 0.00 42.53 3.41
1577 2040 1.608590 CCCGTTGGGCACAATGATATC 59.391 52.381 22.67 0.00 44.58 1.63
1602 2065 2.235898 GAGTTGCTCATGAAGGAGGACT 59.764 50.000 0.00 0.00 34.80 3.85
1616 2079 3.426568 GACTCGCAGTTGGCCAGC 61.427 66.667 12.39 12.39 40.31 4.85
1619 2082 2.203337 TCGCAGTTGGCCAGCTTT 60.203 55.556 20.89 0.00 40.31 3.51
1622 2085 1.905354 GCAGTTGGCCAGCTTTCCT 60.905 57.895 20.89 0.00 36.11 3.36
1666 2129 1.992519 CTGGCCATCTTGGAGGGGAG 61.993 65.000 5.51 0.00 40.96 4.30
1667 2130 1.694169 GGCCATCTTGGAGGGGAGA 60.694 63.158 0.00 0.00 40.96 3.71
1675 2138 2.372172 TCTTGGAGGGGAGAAGTTTCAC 59.628 50.000 0.00 0.00 0.00 3.18
1688 2151 2.018544 TTTCACCGCGGAAACACTG 58.981 52.632 35.90 19.13 32.12 3.66
1742 2205 2.288702 TGGACCAAATGGACAAAATGCG 60.289 45.455 6.42 0.00 38.94 4.73
1760 2223 2.986306 GCTGCATGCTGCCGTTCTT 61.986 57.895 32.46 0.00 44.23 2.52
1779 2242 1.083489 TCGAGGCAAAGGTAAATGCG 58.917 50.000 0.00 0.00 43.47 4.73
1780 2243 0.802494 CGAGGCAAAGGTAAATGCGT 59.198 50.000 0.00 0.00 43.47 5.24
1800 2267 3.186613 CGTGCCTTCCTCTTCAACTTTAC 59.813 47.826 0.00 0.00 0.00 2.01
1877 2344 7.092716 ACAGTTGAAAATACATTTGCCTCATC 58.907 34.615 0.00 0.00 0.00 2.92
1882 2349 6.209192 TGAAAATACATTTGCCTCATCAGTGT 59.791 34.615 0.00 0.00 0.00 3.55
1906 2373 5.637006 TTTACATTTTGGATTCAGGACCG 57.363 39.130 0.00 0.00 0.00 4.79
1910 2377 5.074115 ACATTTTGGATTCAGGACCGTTAA 58.926 37.500 0.00 0.00 0.00 2.01
1911 2378 5.048294 ACATTTTGGATTCAGGACCGTTAAC 60.048 40.000 0.00 0.00 0.00 2.01
1916 2383 4.081531 TGGATTCAGGACCGTTAACGTATT 60.082 41.667 25.15 10.19 37.74 1.89
1922 2389 6.219473 TCAGGACCGTTAACGTATTTGTTTA 58.781 36.000 25.15 1.29 37.74 2.01
1934 2405 6.708676 ACGTATTTGTTTAAAGGCTATACGC 58.291 36.000 17.41 0.00 35.10 4.42
1951 2517 5.961396 ATACGCCGAGTTCTATGTTCTAT 57.039 39.130 0.00 0.00 0.00 1.98
2047 2614 2.776312 TATCCGATTCTGTGTCGAGC 57.224 50.000 0.00 0.00 41.40 5.03
2119 2688 5.188948 TGAATACACCTAGCTTGTACACCAT 59.811 40.000 0.00 0.00 32.30 3.55
2120 2689 5.693769 ATACACCTAGCTTGTACACCATT 57.306 39.130 0.00 0.00 32.30 3.16
2180 3338 2.099062 GCTTCCATGCGCGTTCTG 59.901 61.111 8.43 2.62 0.00 3.02
2192 3350 0.095417 GCGTTCTGGTCGAGCAAATC 59.905 55.000 19.16 10.09 0.00 2.17
2213 3377 2.223829 CCAGAGCGGATAATCGTGTCTT 60.224 50.000 0.00 0.00 36.56 3.01
2229 3393 3.311322 GTGTCTTGTGTTTCCGTTCATGA 59.689 43.478 0.00 0.00 0.00 3.07
2245 3409 4.341366 TCATGATCGGAGTTGTGCATAT 57.659 40.909 0.00 0.00 0.00 1.78
2270 3434 0.308993 GAGTTGTGTTGCTGCTGGAC 59.691 55.000 0.00 0.00 0.00 4.02
2275 3439 0.520404 GTGTTGCTGCTGGACATGAG 59.480 55.000 0.00 0.00 0.00 2.90
2279 3443 3.499050 CTGCTGGACATGAGCTGC 58.501 61.111 0.00 0.00 37.35 5.25
2287 3451 1.077930 ACATGAGCTGCCGCAAGAT 60.078 52.632 0.00 0.00 43.02 2.40
2310 3475 4.858935 TGCGTCTTCAATCTTTGGAAAAG 58.141 39.130 0.00 0.00 0.00 2.27
2313 3478 4.913924 CGTCTTCAATCTTTGGAAAAGCTG 59.086 41.667 0.00 0.00 0.00 4.24
2328 3493 5.065346 GGAAAAGCTGACATCTAGTTTAGCC 59.935 44.000 0.00 0.00 39.88 3.93
2336 3501 7.094592 GCTGACATCTAGTTTAGCCTTCTTTTT 60.095 37.037 0.00 0.00 35.77 1.94
2487 3655 1.312371 TTTGCCGCCATAGCTGTTCC 61.312 55.000 0.00 0.00 36.60 3.62
2617 3803 4.083271 GCAACAAGGGTAGTCAGTGAATTC 60.083 45.833 0.00 0.00 0.00 2.17
2626 3812 7.040409 AGGGTAGTCAGTGAATTCATTGAAAAC 60.040 37.037 28.77 26.18 42.82 2.43
2641 3827 0.531753 AAAACACGCCCAATTGTGCC 60.532 50.000 7.35 0.00 39.71 5.01
2666 3852 2.016318 TGCGTGATGCTAGGAAAATGG 58.984 47.619 0.00 0.00 46.63 3.16
2914 4109 7.203255 AGCGTATCAAAATATTCCTAAAGGC 57.797 36.000 0.00 0.00 34.44 4.35
2985 4194 4.256920 AGCTTGTAGGTGAGCATAAACAG 58.743 43.478 0.00 0.00 41.31 3.16
2995 4204 5.105997 GGTGAGCATAAACAGCTGAGATTTT 60.106 40.000 23.35 12.86 43.58 1.82
3053 4262 5.477510 CACAGTGAAGCAAGAATACTCTCT 58.522 41.667 0.00 0.00 0.00 3.10
3094 4303 1.665137 AAAAGGGGTATCCGTCACCT 58.335 50.000 0.00 0.00 40.89 4.00
3095 4304 0.909623 AAAGGGGTATCCGTCACCTG 59.090 55.000 0.00 0.00 38.87 4.00
3096 4305 1.623542 AAGGGGTATCCGTCACCTGC 61.624 60.000 0.00 0.00 38.87 4.85
3111 4320 2.749621 CACCTGCAGGATTACCTTGAAC 59.250 50.000 39.19 0.00 45.36 3.18
3115 4327 4.082571 CCTGCAGGATTACCTTGAACAAAG 60.083 45.833 29.88 0.00 45.36 2.77
3188 4400 1.059264 GACGCGACACAAAGTCTATGC 59.941 52.381 15.93 0.00 45.32 3.14
3278 4490 3.555795 CCGATGATCACACTAATGGAGGG 60.556 52.174 0.00 0.00 33.21 4.30
3403 4615 2.153034 TCACCCATACGACATCCTCA 57.847 50.000 0.00 0.00 0.00 3.86
3437 4649 2.284417 GCACTTACGCATTGCCTACTAC 59.716 50.000 2.41 0.00 0.00 2.73
3467 4679 3.066203 CGGTTTCAGTTACAAGCTTGGTT 59.934 43.478 29.18 12.81 0.00 3.67
3482 4694 1.300388 GGTTGCTGCCTTTGCACTG 60.300 57.895 0.00 0.00 44.23 3.66
3505 4717 5.253330 TGGCTACCTATACCATACTAGCTCT 59.747 44.000 0.00 0.00 0.00 4.09
3506 4718 5.591067 GGCTACCTATACCATACTAGCTCTG 59.409 48.000 0.00 0.00 0.00 3.35
3527 4739 2.290093 GCTTGCTCATAAGACTGCCATC 59.710 50.000 0.00 0.00 0.00 3.51
3545 4757 4.331168 GCCATCGGATTATGTATCTTGAGC 59.669 45.833 0.00 0.00 33.53 4.26
3616 4828 1.207488 ATGGTAGCACCCCTCTGCAA 61.207 55.000 0.00 0.00 39.86 4.08
3632 4844 5.028549 TCTGCAAGAGAAATGGGATAGTC 57.971 43.478 0.00 0.00 38.67 2.59
3638 4850 4.889780 AGAGAAATGGGATAGTCTGGACT 58.110 43.478 8.36 8.36 45.02 3.85
3751 4963 4.700213 CCATAGTCGAAAAGTGGAACCATT 59.300 41.667 0.00 0.00 37.80 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.078426 ACGCTCCCTCCGGATTTTG 60.078 57.895 3.57 0.00 37.60 2.44
2 3 2.732619 GGACGCTCCCTCCGGATTT 61.733 63.158 3.57 0.00 37.60 2.17
3 4 3.155167 GGACGCTCCCTCCGGATT 61.155 66.667 3.57 0.00 37.60 3.01
7 8 4.135153 CTGTGGACGCTCCCTCCG 62.135 72.222 2.23 0.00 35.03 4.63
8 9 4.459089 GCTGTGGACGCTCCCTCC 62.459 72.222 2.23 0.00 35.03 4.30
9 10 4.803426 CGCTGTGGACGCTCCCTC 62.803 72.222 2.23 0.00 35.03 4.30
23 24 3.858868 ATTCACCACGTGTCGCGCT 62.859 57.895 15.65 0.00 46.11 5.92
24 25 3.411351 ATTCACCACGTGTCGCGC 61.411 61.111 15.65 0.00 46.11 6.86
26 27 2.860293 CCATTCACCACGTGTCGC 59.140 61.111 15.65 0.00 34.79 5.19
27 28 1.667830 AGCCATTCACCACGTGTCG 60.668 57.895 15.65 4.88 34.79 4.35
28 29 0.884704 ACAGCCATTCACCACGTGTC 60.885 55.000 15.65 0.00 34.79 3.67
29 30 1.148273 ACAGCCATTCACCACGTGT 59.852 52.632 15.65 0.00 34.79 4.49
30 31 0.884259 TCACAGCCATTCACCACGTG 60.884 55.000 9.08 9.08 34.45 4.49
31 32 0.603707 CTCACAGCCATTCACCACGT 60.604 55.000 0.00 0.00 0.00 4.49
32 33 1.915614 GCTCACAGCCATTCACCACG 61.916 60.000 0.00 0.00 34.48 4.94
33 34 1.878775 GCTCACAGCCATTCACCAC 59.121 57.895 0.00 0.00 34.48 4.16
34 35 1.672030 CGCTCACAGCCATTCACCA 60.672 57.895 0.00 0.00 38.18 4.17
35 36 3.044059 GCGCTCACAGCCATTCACC 62.044 63.158 0.00 0.00 38.18 4.02
36 37 2.482374 GCGCTCACAGCCATTCAC 59.518 61.111 0.00 0.00 38.18 3.18
37 38 3.120385 CGCGCTCACAGCCATTCA 61.120 61.111 5.56 0.00 38.18 2.57
38 39 4.527157 GCGCGCTCACAGCCATTC 62.527 66.667 26.67 0.00 38.18 2.67
44 45 4.081030 CACTTGGCGCGCTCACAG 62.081 66.667 32.29 23.79 0.00 3.66
55 56 0.096976 CAACGATTAGCGCCACTTGG 59.903 55.000 2.29 0.00 46.04 3.61
56 57 0.521242 GCAACGATTAGCGCCACTTG 60.521 55.000 2.29 0.00 46.04 3.16
57 58 1.794222 GCAACGATTAGCGCCACTT 59.206 52.632 2.29 0.00 46.04 3.16
58 59 3.486263 GCAACGATTAGCGCCACT 58.514 55.556 2.29 0.00 46.04 4.00
64 65 1.491505 GGAGCCTCGCAACGATTAGC 61.492 60.000 0.00 0.00 34.61 3.09
65 66 0.876342 GGGAGCCTCGCAACGATTAG 60.876 60.000 3.57 0.00 34.61 1.73
66 67 1.143183 GGGAGCCTCGCAACGATTA 59.857 57.895 3.57 0.00 34.61 1.75
67 68 2.125106 GGGAGCCTCGCAACGATT 60.125 61.111 3.57 0.00 34.61 3.34
68 69 4.514577 CGGGAGCCTCGCAACGAT 62.515 66.667 9.61 0.00 34.61 3.73
70 71 4.735132 TTCGGGAGCCTCGCAACG 62.735 66.667 9.61 0.36 0.00 4.10
71 72 2.815647 CTTCGGGAGCCTCGCAAC 60.816 66.667 9.61 0.00 0.00 4.17
72 73 4.082523 CCTTCGGGAGCCTCGCAA 62.083 66.667 9.61 2.18 37.25 4.85
82 83 2.552585 TTAACGAGCGCTCCTTCGGG 62.553 60.000 30.66 17.99 0.00 5.14
83 84 0.527817 ATTAACGAGCGCTCCTTCGG 60.528 55.000 30.66 18.71 0.00 4.30
84 85 1.278238 AATTAACGAGCGCTCCTTCG 58.722 50.000 30.66 22.24 0.00 3.79
85 86 3.445857 ACTAATTAACGAGCGCTCCTTC 58.554 45.455 30.66 8.16 0.00 3.46
86 87 3.521947 ACTAATTAACGAGCGCTCCTT 57.478 42.857 30.66 26.03 0.00 3.36
87 88 3.187700 CAACTAATTAACGAGCGCTCCT 58.812 45.455 30.66 20.33 0.00 3.69
88 89 2.285660 GCAACTAATTAACGAGCGCTCC 60.286 50.000 30.66 13.79 0.00 4.70
89 90 2.603560 AGCAACTAATTAACGAGCGCTC 59.396 45.455 27.64 27.64 0.00 5.03
90 91 2.603560 GAGCAACTAATTAACGAGCGCT 59.396 45.455 11.27 11.27 0.00 5.92
91 92 2.285660 GGAGCAACTAATTAACGAGCGC 60.286 50.000 0.00 0.00 0.00 5.92
92 93 2.284417 GGGAGCAACTAATTAACGAGCG 59.716 50.000 0.00 0.00 0.00 5.03
93 94 2.284417 CGGGAGCAACTAATTAACGAGC 59.716 50.000 0.00 0.00 0.00 5.03
94 95 3.518590 ACGGGAGCAACTAATTAACGAG 58.481 45.455 0.00 0.00 0.00 4.18
95 96 3.514645 GACGGGAGCAACTAATTAACGA 58.485 45.455 0.00 0.00 0.00 3.85
96 97 2.280708 CGACGGGAGCAACTAATTAACG 59.719 50.000 0.00 0.00 0.00 3.18
97 98 2.606272 CCGACGGGAGCAACTAATTAAC 59.394 50.000 5.81 0.00 34.06 2.01
98 99 2.496871 TCCGACGGGAGCAACTAATTAA 59.503 45.455 15.25 0.00 37.43 1.40
99 100 2.101783 TCCGACGGGAGCAACTAATTA 58.898 47.619 15.25 0.00 37.43 1.40
100 101 0.899720 TCCGACGGGAGCAACTAATT 59.100 50.000 15.25 0.00 37.43 1.40
101 102 2.587080 TCCGACGGGAGCAACTAAT 58.413 52.632 15.25 0.00 37.43 1.73
102 103 4.100479 TCCGACGGGAGCAACTAA 57.900 55.556 15.25 0.00 37.43 2.24
111 112 0.525761 ATTTTTGTGCATCCGACGGG 59.474 50.000 15.25 0.00 0.00 5.28
112 113 2.346099 AATTTTTGTGCATCCGACGG 57.654 45.000 7.84 7.84 0.00 4.79
113 114 4.472286 ACTAAATTTTTGTGCATCCGACG 58.528 39.130 0.00 0.00 0.00 5.12
114 115 5.798434 GGTACTAAATTTTTGTGCATCCGAC 59.202 40.000 12.13 0.16 0.00 4.79
115 116 5.473846 TGGTACTAAATTTTTGTGCATCCGA 59.526 36.000 12.13 0.00 0.00 4.55
116 117 5.571357 GTGGTACTAAATTTTTGTGCATCCG 59.429 40.000 12.13 0.00 0.00 4.18
117 118 5.867174 GGTGGTACTAAATTTTTGTGCATCC 59.133 40.000 12.13 9.80 0.00 3.51
118 119 6.687604 AGGTGGTACTAAATTTTTGTGCATC 58.312 36.000 12.13 5.88 0.00 3.91
119 120 6.569610 CGAGGTGGTACTAAATTTTTGTGCAT 60.570 38.462 12.13 0.00 0.00 3.96
120 121 5.278071 CGAGGTGGTACTAAATTTTTGTGCA 60.278 40.000 12.13 0.00 0.00 4.57
121 122 5.049267 TCGAGGTGGTACTAAATTTTTGTGC 60.049 40.000 0.00 5.15 0.00 4.57
122 123 6.548441 TCGAGGTGGTACTAAATTTTTGTG 57.452 37.500 0.00 0.00 0.00 3.33
123 124 7.754851 ATTCGAGGTGGTACTAAATTTTTGT 57.245 32.000 0.00 2.00 0.00 2.83
124 125 9.158233 TCTATTCGAGGTGGTACTAAATTTTTG 57.842 33.333 0.00 0.00 0.00 2.44
125 126 9.729281 TTCTATTCGAGGTGGTACTAAATTTTT 57.271 29.630 0.00 0.00 0.00 1.94
126 127 9.729281 TTTCTATTCGAGGTGGTACTAAATTTT 57.271 29.630 0.00 0.00 0.00 1.82
127 128 9.729281 TTTTCTATTCGAGGTGGTACTAAATTT 57.271 29.630 0.00 0.00 0.00 1.82
128 129 9.729281 TTTTTCTATTCGAGGTGGTACTAAATT 57.271 29.630 0.00 0.00 0.00 1.82
153 154 5.049543 TCCGTTCACCGTCGAAAATATTTTT 60.050 36.000 14.45 0.00 33.66 1.94
154 155 4.451774 TCCGTTCACCGTCGAAAATATTTT 59.548 37.500 13.24 13.24 33.66 1.82
155 156 3.995705 TCCGTTCACCGTCGAAAATATTT 59.004 39.130 0.00 0.00 33.66 1.40
156 157 3.587923 TCCGTTCACCGTCGAAAATATT 58.412 40.909 0.00 0.00 33.66 1.28
157 158 3.235157 TCCGTTCACCGTCGAAAATAT 57.765 42.857 0.00 0.00 33.66 1.28
158 159 2.721274 TCCGTTCACCGTCGAAAATA 57.279 45.000 0.00 0.00 33.66 1.40
159 160 1.730064 CATCCGTTCACCGTCGAAAAT 59.270 47.619 0.00 0.00 33.66 1.82
160 161 1.141645 CATCCGTTCACCGTCGAAAA 58.858 50.000 0.00 0.00 33.66 2.29
161 162 0.314618 TCATCCGTTCACCGTCGAAA 59.685 50.000 0.00 0.00 33.66 3.46
162 163 0.314618 TTCATCCGTTCACCGTCGAA 59.685 50.000 0.00 0.00 33.66 3.71
163 164 0.314618 TTTCATCCGTTCACCGTCGA 59.685 50.000 0.00 0.00 33.66 4.20
164 165 1.141645 TTTTCATCCGTTCACCGTCG 58.858 50.000 0.00 0.00 33.66 5.12
165 166 5.479716 AATATTTTCATCCGTTCACCGTC 57.520 39.130 0.00 0.00 33.66 4.79
166 167 5.890424 AAATATTTTCATCCGTTCACCGT 57.110 34.783 0.00 0.00 33.66 4.83
167 168 7.635423 TCATAAATATTTTCATCCGTTCACCG 58.365 34.615 5.91 0.00 0.00 4.94
168 169 9.796120 TTTCATAAATATTTTCATCCGTTCACC 57.204 29.630 5.91 0.00 0.00 4.02
172 173 9.814899 TGCATTTCATAAATATTTTCATCCGTT 57.185 25.926 5.91 0.00 0.00 4.44
173 174 9.248291 GTGCATTTCATAAATATTTTCATCCGT 57.752 29.630 5.91 0.00 0.00 4.69
174 175 8.702438 GGTGCATTTCATAAATATTTTCATCCG 58.298 33.333 5.91 0.00 0.00 4.18
175 176 9.768662 AGGTGCATTTCATAAATATTTTCATCC 57.231 29.630 5.91 0.00 0.00 3.51
178 179 8.881743 GCAAGGTGCATTTCATAAATATTTTCA 58.118 29.630 5.91 0.00 44.26 2.69
223 224 9.835389 ACACGATCCTTATCTATACTCTATACC 57.165 37.037 0.00 0.00 0.00 2.73
226 227 9.742144 ACAACACGATCCTTATCTATACTCTAT 57.258 33.333 0.00 0.00 0.00 1.98
228 229 9.570468 TTACAACACGATCCTTATCTATACTCT 57.430 33.333 0.00 0.00 0.00 3.24
229 230 9.828852 CTTACAACACGATCCTTATCTATACTC 57.171 37.037 0.00 0.00 0.00 2.59
230 231 8.298140 GCTTACAACACGATCCTTATCTATACT 58.702 37.037 0.00 0.00 0.00 2.12
231 232 7.541437 GGCTTACAACACGATCCTTATCTATAC 59.459 40.741 0.00 0.00 0.00 1.47
232 233 7.309621 GGGCTTACAACACGATCCTTATCTATA 60.310 40.741 0.00 0.00 0.00 1.31
233 234 6.456501 GGCTTACAACACGATCCTTATCTAT 58.543 40.000 0.00 0.00 0.00 1.98
236 237 3.808174 GGGCTTACAACACGATCCTTATC 59.192 47.826 0.00 0.00 0.00 1.75
248 249 2.210961 GAGCGAATAGGGGCTTACAAC 58.789 52.381 0.00 0.00 40.16 3.32
321 322 1.821136 CCCTTCTGGTGGCATTTTCTC 59.179 52.381 0.00 0.00 0.00 2.87
335 336 4.984146 AGTCAGCTTTAGTTTCCCTTCT 57.016 40.909 0.00 0.00 0.00 2.85
371 372 2.961526 AGTGTTGGAGGTACGCTATG 57.038 50.000 0.00 0.00 34.77 2.23
375 376 4.752146 ACTTATAAGTGTTGGAGGTACGC 58.248 43.478 17.35 0.00 37.98 4.42
376 377 9.674824 CTTATACTTATAAGTGTTGGAGGTACG 57.325 37.037 25.27 0.00 39.99 3.67
552 553 9.929722 CGTAAGCTATCATAAGCAAATGTAAAA 57.070 29.630 0.00 0.00 45.30 1.52
577 579 5.283060 AGTGCAATAGTTTCTTTACAGCG 57.717 39.130 0.00 0.00 0.00 5.18
579 581 9.599322 CACTAAAGTGCAATAGTTTCTTTACAG 57.401 33.333 5.58 0.53 39.39 2.74
659 661 0.524862 ATCTGCTTTGCTTTGCTCCG 59.475 50.000 0.00 0.00 0.00 4.63
660 662 1.992170 CATCTGCTTTGCTTTGCTCC 58.008 50.000 0.00 0.00 0.00 4.70
662 664 3.509388 GCATCTGCTTTGCTTTGCT 57.491 47.368 0.00 0.00 37.14 3.91
767 1188 2.351276 CTTTCCCTCCCACCACCG 59.649 66.667 0.00 0.00 0.00 4.94
799 1220 0.961753 ACGTGTGTGAGCATCTCTGA 59.038 50.000 0.00 0.00 34.92 3.27
818 1239 4.700448 TTCCCTCCGGCCACCGTA 62.700 66.667 2.24 0.00 46.80 4.02
831 1252 1.152383 GACACGCTATCGCCTTTCCC 61.152 60.000 0.00 0.00 39.84 3.97
868 1289 4.229353 TGTGAGATGGATATTTGGTTGGGA 59.771 41.667 0.00 0.00 0.00 4.37
872 1323 5.202765 TGCATGTGAGATGGATATTTGGTT 58.797 37.500 0.00 0.00 0.00 3.67
874 1325 5.977489 ATGCATGTGAGATGGATATTTGG 57.023 39.130 0.00 0.00 0.00 3.28
876 1327 6.482524 AGCTATGCATGTGAGATGGATATTT 58.517 36.000 10.16 0.00 33.08 1.40
879 1330 4.081254 GGAGCTATGCATGTGAGATGGATA 60.081 45.833 10.16 3.91 32.38 2.59
880 1331 3.307550 GGAGCTATGCATGTGAGATGGAT 60.308 47.826 10.16 1.72 34.47 3.41
882 1333 2.038689 AGGAGCTATGCATGTGAGATGG 59.961 50.000 10.16 0.00 0.00 3.51
892 1343 3.550431 GGGCCGAGGAGCTATGCA 61.550 66.667 0.00 0.00 0.00 3.96
909 1360 1.915266 TGGAGGAGAGTGTGGCCAG 60.915 63.158 5.11 0.00 0.00 4.85
915 1366 2.334006 AATGGAGTGGAGGAGAGTGT 57.666 50.000 0.00 0.00 0.00 3.55
922 1373 1.075374 TGGTGGAAAATGGAGTGGAGG 59.925 52.381 0.00 0.00 0.00 4.30
933 1384 0.106419 GGTGGTGGTCTGGTGGAAAA 60.106 55.000 0.00 0.00 0.00 2.29
941 1392 0.038526 GACGTACTGGTGGTGGTCTG 60.039 60.000 0.00 0.00 33.16 3.51
943 1394 1.080974 CGACGTACTGGTGGTGGTC 60.081 63.158 0.00 0.00 32.83 4.02
944 1395 1.529010 TCGACGTACTGGTGGTGGT 60.529 57.895 0.00 0.00 0.00 4.16
945 1396 1.080974 GTCGACGTACTGGTGGTGG 60.081 63.158 0.00 0.00 0.00 4.61
946 1397 1.080974 GGTCGACGTACTGGTGGTG 60.081 63.158 9.92 0.00 0.00 4.17
947 1398 2.270986 GGGTCGACGTACTGGTGGT 61.271 63.158 9.92 0.00 0.00 4.16
948 1399 1.808531 TTGGGTCGACGTACTGGTGG 61.809 60.000 9.92 0.00 0.00 4.61
949 1400 0.032403 TTTGGGTCGACGTACTGGTG 59.968 55.000 9.92 0.00 0.00 4.17
950 1401 0.971386 ATTTGGGTCGACGTACTGGT 59.029 50.000 9.92 0.00 0.00 4.00
960 1411 3.118629 TGAGAGAGGATCAATTTGGGTCG 60.119 47.826 0.00 0.00 37.82 4.79
962 1413 5.444176 GAATGAGAGAGGATCAATTTGGGT 58.556 41.667 0.00 0.00 37.82 4.51
989 1442 1.367840 GCACTGTCGAGTTGGGACT 59.632 57.895 0.00 0.00 39.32 3.85
1005 1458 2.823593 CGCCATTGATCACCGGCA 60.824 61.111 26.40 1.20 45.14 5.69
1041 1501 4.154347 CGAGCTGGGACTGGGAGC 62.154 72.222 0.00 0.00 0.00 4.70
1212 1672 3.338126 CTTCCTCGTCGTCACCGGG 62.338 68.421 6.32 0.00 33.95 5.73
1335 1798 2.743718 CTTGGTGTGGACGAGGCT 59.256 61.111 0.00 0.00 0.00 4.58
1357 1820 0.392336 CTGCACATAGAGGAGGCTCC 59.608 60.000 26.42 26.42 36.58 4.70
1360 1823 1.208052 TGTTCTGCACATAGAGGAGGC 59.792 52.381 0.00 0.00 0.00 4.70
1369 1832 2.079158 CTCCGTCATTGTTCTGCACAT 58.921 47.619 0.00 0.00 34.43 3.21
1435 1898 2.533535 GCAAGATCAATGAGACGAGACG 59.466 50.000 0.00 0.00 0.00 4.18
1441 1904 3.118482 TCCTCTGGCAAGATCAATGAGAC 60.118 47.826 0.00 0.00 0.00 3.36
1577 2040 0.994995 CCTTCATGAGCAACTCGACG 59.005 55.000 0.00 0.00 32.35 5.12
1616 2079 2.348666 CGACGTGCCATCTTTAGGAAAG 59.651 50.000 0.00 0.00 39.88 2.62
1619 2082 0.459585 GCGACGTGCCATCTTTAGGA 60.460 55.000 0.00 0.00 37.76 2.94
1666 2129 3.449789 GTTTCCGCGGTGAAACTTC 57.550 52.632 26.60 8.41 46.72 3.01
1675 2138 0.999406 CTCATACAGTGTTTCCGCGG 59.001 55.000 22.12 22.12 0.00 6.46
1688 2151 0.811616 CCCCGCTGCTCAACTCATAC 60.812 60.000 0.00 0.00 0.00 2.39
1754 2217 2.074547 TACCTTTGCCTCGAAGAACG 57.925 50.000 0.00 0.00 44.09 3.95
1760 2223 1.083489 CGCATTTACCTTTGCCTCGA 58.917 50.000 0.00 0.00 35.41 4.04
1779 2242 4.134563 TGTAAAGTTGAAGAGGAAGGCAC 58.865 43.478 0.00 0.00 0.00 5.01
1780 2243 4.431416 TGTAAAGTTGAAGAGGAAGGCA 57.569 40.909 0.00 0.00 0.00 4.75
1849 2316 8.028354 TGAGGCAAATGTATTTTCAACTGTATG 58.972 33.333 0.00 0.00 0.00 2.39
1858 2325 6.624423 ACACTGATGAGGCAAATGTATTTTC 58.376 36.000 0.00 0.00 0.00 2.29
1877 2344 7.925483 TCCTGAATCCAAAATGTAAAAACACTG 59.075 33.333 0.00 0.00 0.00 3.66
1882 2349 6.041069 ACGGTCCTGAATCCAAAATGTAAAAA 59.959 34.615 0.00 0.00 0.00 1.94
1910 2377 6.708676 GCGTATAGCCTTTAAACAAATACGT 58.291 36.000 18.78 0.00 41.46 3.57
1981 2548 6.017440 CCGAATCCACTTAAAACTCTGTTTGA 60.017 38.462 0.00 0.00 0.00 2.69
1997 2564 5.644636 TCCAAAACTAACATACCGAATCCAC 59.355 40.000 0.00 0.00 0.00 4.02
1998 2565 5.806818 TCCAAAACTAACATACCGAATCCA 58.193 37.500 0.00 0.00 0.00 3.41
1999 2566 5.878669 ACTCCAAAACTAACATACCGAATCC 59.121 40.000 0.00 0.00 0.00 3.01
2001 2568 7.446013 TGAAACTCCAAAACTAACATACCGAAT 59.554 33.333 0.00 0.00 0.00 3.34
2002 2569 6.766944 TGAAACTCCAAAACTAACATACCGAA 59.233 34.615 0.00 0.00 0.00 4.30
2047 2614 5.517054 GCCTAGACTCTGAATCGTTTACTTG 59.483 44.000 0.00 0.00 0.00 3.16
2104 2671 7.667043 TGTTTTCTAATGGTGTACAAGCTAG 57.333 36.000 0.00 0.00 0.00 3.42
2152 2721 2.551032 CGCATGGAAGCACATATCATGT 59.449 45.455 0.00 0.00 46.22 3.21
2155 3311 0.946528 GCGCATGGAAGCACATATCA 59.053 50.000 0.30 0.00 0.00 2.15
2166 3322 2.434185 GACCAGAACGCGCATGGA 60.434 61.111 25.97 0.00 37.54 3.41
2169 3325 2.507102 CTCGACCAGAACGCGCAT 60.507 61.111 5.73 0.00 0.00 4.73
2180 3338 1.424493 CGCTCTGGATTTGCTCGACC 61.424 60.000 0.00 0.00 0.00 4.79
2192 3350 1.338337 AGACACGATTATCCGCTCTGG 59.662 52.381 0.00 0.00 40.09 3.86
2196 3354 2.094182 ACACAAGACACGATTATCCGCT 60.094 45.455 0.00 0.00 0.00 5.52
2205 3363 1.928503 GAACGGAAACACAAGACACGA 59.071 47.619 0.00 0.00 0.00 4.35
2206 3364 1.661617 TGAACGGAAACACAAGACACG 59.338 47.619 0.00 0.00 0.00 4.49
2229 3393 6.041423 TCATCATATATGCACAACTCCGAT 57.959 37.500 7.92 0.00 0.00 4.18
2245 3409 3.437741 CAGCAGCAACACAACTCATCATA 59.562 43.478 0.00 0.00 0.00 2.15
2270 3434 0.248498 CAATCTTGCGGCAGCTCATG 60.248 55.000 10.92 0.00 45.42 3.07
2287 3451 4.909696 TTTCCAAAGATTGAAGACGCAA 57.090 36.364 0.00 0.00 0.00 4.85
2292 3456 5.593909 TGTCAGCTTTTCCAAAGATTGAAGA 59.406 36.000 0.25 0.00 0.00 2.87
2310 3475 5.017294 AGAAGGCTAAACTAGATGTCAGC 57.983 43.478 0.00 0.00 0.00 4.26
2487 3655 5.411361 TGTGAACGTATTTTCTGATTCCCTG 59.589 40.000 0.00 0.00 0.00 4.45
2617 3803 3.059733 CACAATTGGGCGTGTTTTCAATG 60.060 43.478 10.83 0.00 31.20 2.82
2641 3827 0.739462 TCCTAGCATCACGCAAACCG 60.739 55.000 0.00 0.00 46.13 4.44
2666 3852 4.300803 TCAACTGCAACATGAAGAAATGC 58.699 39.130 0.00 0.75 37.52 3.56
2957 4166 1.731720 CTCACCTACAAGCTTCTGCC 58.268 55.000 0.00 0.00 40.80 4.85
2985 4194 3.437049 AGTTAGACCGCAAAAATCTCAGC 59.563 43.478 0.00 0.00 0.00 4.26
2995 4204 6.276832 ACATAAGTAGAAGTTAGACCGCAA 57.723 37.500 0.00 0.00 0.00 4.85
3053 4262 7.695480 TTTAGCACCAGCATATTGAAGTAAA 57.305 32.000 0.00 0.00 45.49 2.01
3094 4303 3.255642 GCTTTGTTCAAGGTAATCCTGCA 59.744 43.478 0.00 0.00 44.35 4.41
3095 4304 3.255642 TGCTTTGTTCAAGGTAATCCTGC 59.744 43.478 0.00 0.00 44.35 4.85
3096 4305 5.452078 TTGCTTTGTTCAAGGTAATCCTG 57.548 39.130 0.00 0.00 44.35 3.86
3188 4400 1.865865 CGATAAGGACCGACCCAATG 58.134 55.000 0.00 0.00 40.05 2.82
3278 4490 0.531974 TTCCAGCGAGTGTTGGTGTC 60.532 55.000 0.00 0.00 45.90 3.67
3403 4615 1.957877 GTAAGTGCTCTATCCGGCTCT 59.042 52.381 0.00 0.00 34.41 4.09
3437 4649 3.659786 TGTAACTGAAACCGACATGAGG 58.340 45.455 0.00 4.95 0.00 3.86
3482 4694 5.591067 CAGAGCTAGTATGGTATAGGTAGCC 59.409 48.000 0.00 0.00 34.65 3.93
3505 4717 1.003464 TGGCAGTCTTATGAGCAAGCA 59.997 47.619 0.00 0.00 0.00 3.91
3506 4718 1.742761 TGGCAGTCTTATGAGCAAGC 58.257 50.000 0.00 0.00 0.00 4.01
3527 4739 6.266168 AGAGAGCTCAAGATACATAATCCG 57.734 41.667 17.77 0.00 34.90 4.18
3616 4828 4.889780 AGTCCAGACTATCCCATTTCTCT 58.110 43.478 0.00 0.00 40.43 3.10
3623 4835 3.519510 CTCCAAAAGTCCAGACTATCCCA 59.480 47.826 0.00 0.00 41.58 4.37
3632 4844 3.199880 ACTGACACTCCAAAAGTCCAG 57.800 47.619 0.00 0.00 39.68 3.86
3638 4850 9.661563 ACGATAAATAATACTGACACTCCAAAA 57.338 29.630 0.00 0.00 0.00 2.44
3751 4963 2.029369 GTGTCGGCGGTTGTACCA 59.971 61.111 7.21 0.00 38.47 3.25


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

AutoCloner maintained by Alex Coulton.