Multiple sequence alignment - TraesCS3D01G012800

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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 TraesCS3D01G012800 chr3D 100.000 3437 0 0 1 3437 4460032 4463468 0.000000e+00 6348.0
1 TraesCS3D01G012800 chr3D 94.680 1579 80 4 1150 2728 4950938 4949364 0.000000e+00 2447.0
2 TraesCS3D01G012800 chr3D 85.625 640 64 16 2790 3411 4948901 4948272 0.000000e+00 647.0
3 TraesCS3D01G012800 chr3D 98.997 299 3 0 1 299 56335145 56335443 1.400000e-148 536.0
4 TraesCS3D01G012800 chr3D 98.662 299 4 0 1 299 204410060 204409762 6.530000e-147 531.0
5 TraesCS3D01G012800 chr3D 82.995 394 48 13 497 886 4951650 4951272 4.250000e-89 339.0
6 TraesCS3D01G012800 chr3D 92.727 110 8 0 340 449 4952067 4951958 3.550000e-35 159.0
7 TraesCS3D01G012800 chr3D 88.421 95 10 1 810 903 27655817 27655911 2.800000e-21 113.0
8 TraesCS3D01G012800 chr3A 96.429 2660 64 6 806 3437 10257705 10260361 0.000000e+00 4357.0
9 TraesCS3D01G012800 chr3A 90.772 2319 155 28 1150 3428 10245017 10247316 0.000000e+00 3042.0
10 TraesCS3D01G012800 chr3A 93.984 1978 69 21 806 2759 10153195 10155146 0.000000e+00 2948.0
11 TraesCS3D01G012800 chr3A 88.969 1659 135 20 1790 3411 10505089 10503442 0.000000e+00 2006.0
12 TraesCS3D01G012800 chr3A 86.527 1336 167 11 1213 2544 38021574 38020248 0.000000e+00 1458.0
13 TraesCS3D01G012800 chr3A 92.988 656 32 6 340 990 10239445 10240091 0.000000e+00 944.0
14 TraesCS3D01G012800 chr3A 80.071 281 34 13 497 773 10510313 10510051 4.530000e-44 189.0
15 TraesCS3D01G012800 chr3A 89.041 146 15 1 806 950 10244657 10244802 2.730000e-41 180.0
16 TraesCS3D01G012800 chr3A 94.872 78 0 2 577 654 10221436 10221509 6.030000e-23 119.0
17 TraesCS3D01G012800 chr3A 83.333 102 13 2 1116 1216 10240258 10240356 1.310000e-14 91.6
18 TraesCS3D01G012800 chr3A 92.308 52 4 0 1168 1219 10245080 10245131 1.320000e-09 75.0
19 TraesCS3D01G012800 chr3B 87.079 2585 225 49 920 3428 13764198 13766749 0.000000e+00 2822.0
20 TraesCS3D01G012800 chr3B 87.343 1272 156 5 1204 2472 46282160 46283429 0.000000e+00 1452.0
21 TraesCS3D01G012800 chr3B 83.297 461 53 14 535 990 13755664 13756105 1.490000e-108 403.0
22 TraesCS3D01G012800 chr3B 91.176 102 9 0 398 499 13755326 13755427 4.630000e-29 139.0
23 TraesCS3D01G012800 chr3B 95.000 40 0 2 506 545 13761344 13761381 1.030000e-05 62.1
24 TraesCS3D01G012800 chrUn 88.112 2330 201 32 1168 3435 34574610 34576925 0.000000e+00 2699.0
25 TraesCS3D01G012800 chrUn 87.980 1772 147 30 1723 3435 35534453 35536217 0.000000e+00 2032.0
26 TraesCS3D01G012800 chrUn 87.980 1772 147 30 1723 3435 244213687 244211923 0.000000e+00 2032.0
27 TraesCS3D01G012800 chrUn 93.343 1367 82 5 1168 2530 35690568 35689207 0.000000e+00 2012.0
28 TraesCS3D01G012800 chrUn 84.071 452 35 12 563 993 35691290 35690855 5.340000e-108 401.0
29 TraesCS3D01G012800 chrUn 86.217 341 17 11 563 882 34573394 34573725 3.280000e-90 342.0
30 TraesCS3D01G012800 chr2D 99.331 299 2 0 1 299 595423089 595423387 3.020000e-150 542.0
31 TraesCS3D01G012800 chr2D 99.331 299 2 0 1 299 615882364 615882066 3.020000e-150 542.0
32 TraesCS3D01G012800 chr2D 98.671 301 2 1 1 299 548626172 548626472 1.820000e-147 532.0
33 TraesCS3D01G012800 chr2D 98.662 299 4 0 1 299 6809871 6810169 6.530000e-147 531.0
34 TraesCS3D01G012800 chr1D 98.671 301 2 1 1 299 468532123 468531823 1.820000e-147 532.0
35 TraesCS3D01G012800 chr1D 98.662 299 4 0 1 299 438189630 438189332 6.530000e-147 531.0
36 TraesCS3D01G012800 chr7D 98.662 299 4 0 1 299 557729232 557729530 6.530000e-147 531.0


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 TraesCS3D01G012800 chr3D 4460032 4463468 3436 False 6348.00 6348 100.00000 1 3437 1 chr3D.!!$F1 3436
1 TraesCS3D01G012800 chr3D 4948272 4952067 3795 True 898.00 2447 89.00675 340 3411 4 chr3D.!!$R2 3071
2 TraesCS3D01G012800 chr3A 10257705 10260361 2656 False 4357.00 4357 96.42900 806 3437 1 chr3A.!!$F3 2631
3 TraesCS3D01G012800 chr3A 10153195 10155146 1951 False 2948.00 2948 93.98400 806 2759 1 chr3A.!!$F1 1953
4 TraesCS3D01G012800 chr3A 10503442 10505089 1647 True 2006.00 2006 88.96900 1790 3411 1 chr3A.!!$R1 1621
5 TraesCS3D01G012800 chr3A 38020248 38021574 1326 True 1458.00 1458 86.52700 1213 2544 1 chr3A.!!$R3 1331
6 TraesCS3D01G012800 chr3A 10244657 10247316 2659 False 1099.00 3042 90.70700 806 3428 3 chr3A.!!$F5 2622
7 TraesCS3D01G012800 chr3A 10239445 10240356 911 False 517.80 944 88.16050 340 1216 2 chr3A.!!$F4 876
8 TraesCS3D01G012800 chr3B 46282160 46283429 1269 False 1452.00 1452 87.34300 1204 2472 1 chr3B.!!$F1 1268
9 TraesCS3D01G012800 chr3B 13761344 13766749 5405 False 1442.05 2822 91.03950 506 3428 2 chr3B.!!$F3 2922
10 TraesCS3D01G012800 chr3B 13755326 13756105 779 False 271.00 403 87.23650 398 990 2 chr3B.!!$F2 592
11 TraesCS3D01G012800 chrUn 35534453 35536217 1764 False 2032.00 2032 87.98000 1723 3435 1 chrUn.!!$F1 1712
12 TraesCS3D01G012800 chrUn 244211923 244213687 1764 True 2032.00 2032 87.98000 1723 3435 1 chrUn.!!$R1 1712
13 TraesCS3D01G012800 chrUn 34573394 34576925 3531 False 1520.50 2699 87.16450 563 3435 2 chrUn.!!$F2 2872
14 TraesCS3D01G012800 chrUn 35689207 35691290 2083 True 1206.50 2012 88.70700 563 2530 2 chrUn.!!$R2 1967

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
73 74 0.033991 TCTCGGAGAAGGAGAGGTGG 60.034 60.0 4.96 0.0 35.7 4.61 F
1146 4490 0.108138 GCTATCGCCCAATATCGCCT 60.108 55.0 0.00 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1148 4492 0.462759 CAAGGGCCTAGCAGCTGTAC 60.463 60.000 16.64 0.00 0.00 2.90 R
2722 6771 3.235157 GCATTTTGGAGCATGCTGTTA 57.765 42.857 28.27 8.07 42.25 2.41 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
27 28 8.483759 ATGTAGCCGGTAGTGTCGGATAGATA 62.484 46.154 1.90 0.00 46.00 1.98
28 29 9.694522 ATGTAGCCGGTAGTGTCGGATAGATAT 62.695 44.444 1.90 0.00 46.00 1.63
31 32 5.386810 CGGTAGTGTCGGATAGATATACG 57.613 47.826 0.00 0.00 41.30 3.06
32 33 5.105063 CGGTAGTGTCGGATAGATATACGA 58.895 45.833 3.03 3.03 46.01 3.43
41 42 7.741027 TCGGATAGATATACGAGAACTTGTT 57.259 36.000 3.03 0.00 43.57 2.83
42 43 7.582352 TCGGATAGATATACGAGAACTTGTTG 58.418 38.462 3.03 0.00 43.57 3.33
43 44 7.228108 TCGGATAGATATACGAGAACTTGTTGT 59.772 37.037 3.03 0.00 43.57 3.32
44 45 7.861372 CGGATAGATATACGAGAACTTGTTGTT 59.139 37.037 0.00 0.00 42.53 2.83
56 57 6.481954 GAACTTGTTGTTCGACCAATATCT 57.518 37.500 0.00 0.00 44.49 1.98
57 58 6.481954 AACTTGTTGTTCGACCAATATCTC 57.518 37.500 0.00 0.00 32.63 2.75
58 59 4.625742 ACTTGTTGTTCGACCAATATCTCG 59.374 41.667 0.00 0.00 0.00 4.04
59 60 3.517602 TGTTGTTCGACCAATATCTCGG 58.482 45.455 0.00 0.00 0.00 4.63
60 61 3.193903 TGTTGTTCGACCAATATCTCGGA 59.806 43.478 0.00 0.00 0.00 4.55
61 62 3.710326 TGTTCGACCAATATCTCGGAG 57.290 47.619 0.00 0.00 0.00 4.63
62 63 3.284617 TGTTCGACCAATATCTCGGAGA 58.715 45.455 10.62 10.62 0.00 3.71
63 64 3.697542 TGTTCGACCAATATCTCGGAGAA 59.302 43.478 12.40 2.26 34.09 2.87
64 65 4.202020 TGTTCGACCAATATCTCGGAGAAG 60.202 45.833 12.40 2.81 34.09 2.85
65 66 2.885266 TCGACCAATATCTCGGAGAAGG 59.115 50.000 12.40 13.38 34.09 3.46
66 67 2.885266 CGACCAATATCTCGGAGAAGGA 59.115 50.000 12.40 0.97 34.09 3.36
67 68 3.057876 CGACCAATATCTCGGAGAAGGAG 60.058 52.174 12.40 3.16 34.09 3.69
68 69 4.145807 GACCAATATCTCGGAGAAGGAGA 58.854 47.826 12.40 0.00 44.08 3.71
69 70 4.148838 ACCAATATCTCGGAGAAGGAGAG 58.851 47.826 12.40 2.66 43.27 3.20
70 71 3.509575 CCAATATCTCGGAGAAGGAGAGG 59.490 52.174 12.40 6.07 43.27 3.69
71 72 4.148838 CAATATCTCGGAGAAGGAGAGGT 58.851 47.826 12.40 0.00 43.27 3.85
72 73 2.065899 ATCTCGGAGAAGGAGAGGTG 57.934 55.000 12.40 0.00 43.27 4.00
73 74 0.033991 TCTCGGAGAAGGAGAGGTGG 60.034 60.000 4.96 0.00 35.70 4.61
74 75 0.323908 CTCGGAGAAGGAGAGGTGGT 60.324 60.000 0.00 0.00 34.09 4.16
75 76 0.323542 TCGGAGAAGGAGAGGTGGTC 60.324 60.000 0.00 0.00 0.00 4.02
76 77 1.658686 CGGAGAAGGAGAGGTGGTCG 61.659 65.000 0.00 0.00 0.00 4.79
77 78 0.323542 GGAGAAGGAGAGGTGGTCGA 60.324 60.000 0.00 0.00 0.00 4.20
78 79 1.686741 GGAGAAGGAGAGGTGGTCGAT 60.687 57.143 0.00 0.00 0.00 3.59
79 80 2.423088 GGAGAAGGAGAGGTGGTCGATA 60.423 54.545 0.00 0.00 0.00 2.92
80 81 3.492337 GAGAAGGAGAGGTGGTCGATAT 58.508 50.000 0.00 0.00 0.00 1.63
81 82 3.492337 AGAAGGAGAGGTGGTCGATATC 58.508 50.000 0.00 0.00 0.00 1.63
82 83 3.117474 AGAAGGAGAGGTGGTCGATATCA 60.117 47.826 3.12 0.00 0.00 2.15
83 84 2.588620 AGGAGAGGTGGTCGATATCAC 58.411 52.381 3.12 7.65 35.87 3.06
84 85 2.175931 AGGAGAGGTGGTCGATATCACT 59.824 50.000 3.12 0.81 36.90 3.41
85 86 2.959707 GGAGAGGTGGTCGATATCACTT 59.040 50.000 3.12 8.14 36.90 3.16
86 87 3.004944 GGAGAGGTGGTCGATATCACTTC 59.995 52.174 15.52 15.52 41.84 3.01
87 88 3.904717 AGAGGTGGTCGATATCACTTCT 58.095 45.455 18.29 18.29 45.56 2.85
88 89 4.231718 GAGGTGGTCGATATCACTTCTC 57.768 50.000 15.82 11.24 39.21 2.87
89 90 3.886505 GAGGTGGTCGATATCACTTCTCT 59.113 47.826 15.82 6.90 39.21 3.10
90 91 3.886505 AGGTGGTCGATATCACTTCTCTC 59.113 47.826 3.12 0.74 36.90 3.20
91 92 3.886505 GGTGGTCGATATCACTTCTCTCT 59.113 47.826 3.12 0.00 36.90 3.10
92 93 4.261405 GGTGGTCGATATCACTTCTCTCTG 60.261 50.000 3.12 0.00 36.90 3.35
93 94 4.336993 GTGGTCGATATCACTTCTCTCTGT 59.663 45.833 3.12 0.00 33.64 3.41
94 95 5.527951 GTGGTCGATATCACTTCTCTCTGTA 59.472 44.000 3.12 0.00 33.64 2.74
95 96 6.205853 GTGGTCGATATCACTTCTCTCTGTAT 59.794 42.308 3.12 0.00 33.64 2.29
96 97 6.205658 TGGTCGATATCACTTCTCTCTGTATG 59.794 42.308 3.12 0.00 0.00 2.39
97 98 6.083630 GTCGATATCACTTCTCTCTGTATGC 58.916 44.000 3.12 0.00 0.00 3.14
98 99 5.765182 TCGATATCACTTCTCTCTGTATGCA 59.235 40.000 3.12 0.00 0.00 3.96
99 100 6.432472 TCGATATCACTTCTCTCTGTATGCAT 59.568 38.462 3.79 3.79 0.00 3.96
100 101 7.607991 TCGATATCACTTCTCTCTGTATGCATA 59.392 37.037 1.16 1.16 0.00 3.14
101 102 8.404765 CGATATCACTTCTCTCTGTATGCATAT 58.595 37.037 10.16 0.00 0.00 1.78
130 131 9.770097 ATATATGTTCATGACGATCTTCTGTTT 57.230 29.630 0.00 0.00 0.00 2.83
131 132 5.845985 TGTTCATGACGATCTTCTGTTTC 57.154 39.130 0.00 0.00 0.00 2.78
132 133 4.690748 TGTTCATGACGATCTTCTGTTTCC 59.309 41.667 0.00 0.00 0.00 3.13
133 134 4.808414 TCATGACGATCTTCTGTTTCCT 57.192 40.909 0.48 0.00 0.00 3.36
134 135 5.152623 TCATGACGATCTTCTGTTTCCTT 57.847 39.130 0.48 0.00 0.00 3.36
135 136 5.171476 TCATGACGATCTTCTGTTTCCTTC 58.829 41.667 0.48 0.00 0.00 3.46
136 137 4.600692 TGACGATCTTCTGTTTCCTTCA 57.399 40.909 0.48 0.00 0.00 3.02
137 138 5.152623 TGACGATCTTCTGTTTCCTTCAT 57.847 39.130 0.48 0.00 0.00 2.57
138 139 5.551233 TGACGATCTTCTGTTTCCTTCATT 58.449 37.500 0.48 0.00 0.00 2.57
139 140 5.997746 TGACGATCTTCTGTTTCCTTCATTT 59.002 36.000 0.48 0.00 0.00 2.32
140 141 6.073058 TGACGATCTTCTGTTTCCTTCATTTG 60.073 38.462 0.48 0.00 0.00 2.32
141 142 5.997746 ACGATCTTCTGTTTCCTTCATTTGA 59.002 36.000 0.00 0.00 0.00 2.69
142 143 6.656693 ACGATCTTCTGTTTCCTTCATTTGAT 59.343 34.615 0.00 0.00 0.00 2.57
143 144 7.175641 ACGATCTTCTGTTTCCTTCATTTGATT 59.824 33.333 0.00 0.00 0.00 2.57
144 145 8.668353 CGATCTTCTGTTTCCTTCATTTGATTA 58.332 33.333 0.00 0.00 0.00 1.75
145 146 9.780413 GATCTTCTGTTTCCTTCATTTGATTAC 57.220 33.333 0.00 0.00 0.00 1.89
146 147 8.924511 TCTTCTGTTTCCTTCATTTGATTACT 57.075 30.769 0.00 0.00 0.00 2.24
149 150 8.268850 TCTGTTTCCTTCATTTGATTACTAGC 57.731 34.615 0.00 0.00 0.00 3.42
150 151 8.103305 TCTGTTTCCTTCATTTGATTACTAGCT 58.897 33.333 0.00 0.00 0.00 3.32
151 152 9.383519 CTGTTTCCTTCATTTGATTACTAGCTA 57.616 33.333 0.00 0.00 0.00 3.32
152 153 9.383519 TGTTTCCTTCATTTGATTACTAGCTAG 57.616 33.333 19.44 19.44 0.00 3.42
153 154 8.338986 GTTTCCTTCATTTGATTACTAGCTAGC 58.661 37.037 20.91 6.62 0.00 3.42
154 155 6.216569 TCCTTCATTTGATTACTAGCTAGCG 58.783 40.000 20.91 0.00 0.00 4.26
155 156 5.986135 CCTTCATTTGATTACTAGCTAGCGT 59.014 40.000 20.91 5.75 0.00 5.07
156 157 6.074088 CCTTCATTTGATTACTAGCTAGCGTG 60.074 42.308 20.91 8.74 0.00 5.34
157 158 5.902681 TCATTTGATTACTAGCTAGCGTGT 58.097 37.500 20.91 14.25 0.00 4.49
158 159 5.977725 TCATTTGATTACTAGCTAGCGTGTC 59.022 40.000 20.91 13.47 0.00 3.67
159 160 5.578005 TTTGATTACTAGCTAGCGTGTCT 57.422 39.130 20.91 2.54 0.00 3.41
160 161 6.688637 TTTGATTACTAGCTAGCGTGTCTA 57.311 37.500 20.91 8.08 0.00 2.59
161 162 5.670149 TGATTACTAGCTAGCGTGTCTAC 57.330 43.478 20.91 10.72 0.00 2.59
162 163 5.366460 TGATTACTAGCTAGCGTGTCTACT 58.634 41.667 20.91 0.28 0.00 2.57
163 164 5.466058 TGATTACTAGCTAGCGTGTCTACTC 59.534 44.000 20.91 8.54 0.00 2.59
164 165 2.563702 ACTAGCTAGCGTGTCTACTCC 58.436 52.381 20.91 0.00 0.00 3.85
165 166 2.171027 ACTAGCTAGCGTGTCTACTCCT 59.829 50.000 20.91 0.00 0.00 3.69
166 167 1.670791 AGCTAGCGTGTCTACTCCTC 58.329 55.000 9.55 0.00 0.00 3.71
167 168 1.210967 AGCTAGCGTGTCTACTCCTCT 59.789 52.381 9.55 0.00 0.00 3.69
168 169 1.600485 GCTAGCGTGTCTACTCCTCTC 59.400 57.143 0.00 0.00 0.00 3.20
169 170 2.215196 CTAGCGTGTCTACTCCTCTCC 58.785 57.143 0.00 0.00 0.00 3.71
170 171 0.328592 AGCGTGTCTACTCCTCTCCA 59.671 55.000 0.00 0.00 0.00 3.86
171 172 1.064314 AGCGTGTCTACTCCTCTCCAT 60.064 52.381 0.00 0.00 0.00 3.41
172 173 2.172930 AGCGTGTCTACTCCTCTCCATA 59.827 50.000 0.00 0.00 0.00 2.74
173 174 2.291190 GCGTGTCTACTCCTCTCCATAC 59.709 54.545 0.00 0.00 0.00 2.39
174 175 2.544686 CGTGTCTACTCCTCTCCATACG 59.455 54.545 0.00 0.00 0.00 3.06
175 176 3.543665 GTGTCTACTCCTCTCCATACGT 58.456 50.000 0.00 0.00 0.00 3.57
176 177 4.701765 GTGTCTACTCCTCTCCATACGTA 58.298 47.826 0.00 0.00 0.00 3.57
177 178 5.307204 GTGTCTACTCCTCTCCATACGTAT 58.693 45.833 1.14 1.14 0.00 3.06
178 179 6.462500 GTGTCTACTCCTCTCCATACGTATA 58.538 44.000 7.96 0.00 0.00 1.47
179 180 7.104939 GTGTCTACTCCTCTCCATACGTATAT 58.895 42.308 7.96 0.00 0.00 0.86
180 181 8.256605 GTGTCTACTCCTCTCCATACGTATATA 58.743 40.741 7.96 0.00 0.00 0.86
181 182 8.476447 TGTCTACTCCTCTCCATACGTATATAG 58.524 40.741 7.96 8.68 0.00 1.31
182 183 8.477256 GTCTACTCCTCTCCATACGTATATAGT 58.523 40.741 7.96 6.75 0.00 2.12
183 184 9.706529 TCTACTCCTCTCCATACGTATATAGTA 57.293 37.037 7.96 7.44 0.00 1.82
184 185 9.748708 CTACTCCTCTCCATACGTATATAGTAC 57.251 40.741 7.96 0.00 0.00 2.73
185 186 7.264221 ACTCCTCTCCATACGTATATAGTACG 58.736 42.308 7.96 6.11 45.44 3.67
195 196 4.790823 CGTATATAGTACGTAGCGTCGAC 58.209 47.826 5.18 5.18 41.54 4.20
196 197 4.320953 CGTATATAGTACGTAGCGTCGACA 59.679 45.833 17.16 0.00 41.54 4.35
197 198 5.164187 CGTATATAGTACGTAGCGTCGACAA 60.164 44.000 17.16 0.00 41.54 3.18
198 199 5.657470 ATATAGTACGTAGCGTCGACAAA 57.343 39.130 17.16 0.00 41.54 2.83
199 200 2.238245 AGTACGTAGCGTCGACAAAG 57.762 50.000 17.16 5.23 41.54 2.77
200 201 0.632241 GTACGTAGCGTCGACAAAGC 59.368 55.000 17.16 11.10 41.54 3.51
201 202 0.238025 TACGTAGCGTCGACAAAGCA 59.762 50.000 17.16 0.00 41.54 3.91
202 203 1.273455 ACGTAGCGTCGACAAAGCAC 61.273 55.000 17.16 10.42 33.69 4.40
203 204 1.411089 GTAGCGTCGACAAAGCACG 59.589 57.895 17.16 0.75 34.45 5.34
204 205 1.731613 TAGCGTCGACAAAGCACGG 60.732 57.895 17.16 0.00 34.45 4.94
205 206 2.132517 TAGCGTCGACAAAGCACGGA 62.133 55.000 17.16 0.00 34.45 4.69
206 207 3.000080 GCGTCGACAAAGCACGGAG 62.000 63.158 17.16 0.00 34.04 4.63
207 208 1.371267 CGTCGACAAAGCACGGAGA 60.371 57.895 17.16 0.00 0.00 3.71
208 209 0.732880 CGTCGACAAAGCACGGAGAT 60.733 55.000 17.16 0.00 0.00 2.75
209 210 1.466866 CGTCGACAAAGCACGGAGATA 60.467 52.381 17.16 0.00 0.00 1.98
210 211 2.602878 GTCGACAAAGCACGGAGATAA 58.397 47.619 11.55 0.00 0.00 1.75
211 212 2.599082 GTCGACAAAGCACGGAGATAAG 59.401 50.000 11.55 0.00 0.00 1.73
212 213 2.490509 TCGACAAAGCACGGAGATAAGA 59.509 45.455 0.00 0.00 0.00 2.10
213 214 2.854777 CGACAAAGCACGGAGATAAGAG 59.145 50.000 0.00 0.00 0.00 2.85
214 215 3.427638 CGACAAAGCACGGAGATAAGAGA 60.428 47.826 0.00 0.00 0.00 3.10
215 216 4.109050 GACAAAGCACGGAGATAAGAGAG 58.891 47.826 0.00 0.00 0.00 3.20
216 217 3.118956 ACAAAGCACGGAGATAAGAGAGG 60.119 47.826 0.00 0.00 0.00 3.69
217 218 2.738587 AGCACGGAGATAAGAGAGGA 57.261 50.000 0.00 0.00 0.00 3.71
218 219 2.303175 AGCACGGAGATAAGAGAGGAC 58.697 52.381 0.00 0.00 0.00 3.85
219 220 2.025155 GCACGGAGATAAGAGAGGACA 58.975 52.381 0.00 0.00 0.00 4.02
220 221 2.223618 GCACGGAGATAAGAGAGGACAC 60.224 54.545 0.00 0.00 0.00 3.67
221 222 3.283751 CACGGAGATAAGAGAGGACACT 58.716 50.000 0.00 0.00 0.00 3.55
222 223 3.697045 CACGGAGATAAGAGAGGACACTT 59.303 47.826 0.00 0.00 0.00 3.16
223 224 3.949113 ACGGAGATAAGAGAGGACACTTC 59.051 47.826 0.00 0.00 0.00 3.01
224 225 4.204012 CGGAGATAAGAGAGGACACTTCT 58.796 47.826 0.00 0.00 0.00 2.85
225 226 4.274950 CGGAGATAAGAGAGGACACTTCTC 59.725 50.000 0.00 0.00 0.00 2.87
226 227 5.445964 GGAGATAAGAGAGGACACTTCTCT 58.554 45.833 7.43 7.43 43.56 3.10
238 239 8.856103 AGAGGACACTTCTCTCTATTAATTAGC 58.144 37.037 0.00 0.00 36.99 3.09
239 240 8.776061 AGGACACTTCTCTCTATTAATTAGCT 57.224 34.615 0.00 0.00 0.00 3.32
240 241 9.869667 AGGACACTTCTCTCTATTAATTAGCTA 57.130 33.333 0.00 0.00 0.00 3.32
242 243 9.620660 GACACTTCTCTCTATTAATTAGCTAGC 57.379 37.037 6.62 6.62 0.00 3.42
243 244 9.362151 ACACTTCTCTCTATTAATTAGCTAGCT 57.638 33.333 23.12 23.12 0.00 3.32
276 277 7.907841 ATATGAAACACCTAAATTAACCCCC 57.092 36.000 0.00 0.00 0.00 5.40
291 292 3.076350 CCCCCAAAACCCCTAAACC 57.924 57.895 0.00 0.00 0.00 3.27
292 293 0.191314 CCCCCAAAACCCCTAAACCA 59.809 55.000 0.00 0.00 0.00 3.67
293 294 1.344065 CCCCAAAACCCCTAAACCAC 58.656 55.000 0.00 0.00 0.00 4.16
294 295 1.344065 CCCAAAACCCCTAAACCACC 58.656 55.000 0.00 0.00 0.00 4.61
295 296 1.132977 CCCAAAACCCCTAAACCACCT 60.133 52.381 0.00 0.00 0.00 4.00
296 297 2.244695 CCAAAACCCCTAAACCACCTC 58.755 52.381 0.00 0.00 0.00 3.85
297 298 2.244695 CAAAACCCCTAAACCACCTCC 58.755 52.381 0.00 0.00 0.00 4.30
298 299 1.842699 AAACCCCTAAACCACCTCCT 58.157 50.000 0.00 0.00 0.00 3.69
299 300 1.369403 AACCCCTAAACCACCTCCTC 58.631 55.000 0.00 0.00 0.00 3.71
300 301 0.549413 ACCCCTAAACCACCTCCTCC 60.549 60.000 0.00 0.00 0.00 4.30
301 302 0.253207 CCCCTAAACCACCTCCTCCT 60.253 60.000 0.00 0.00 0.00 3.69
302 303 1.205055 CCCTAAACCACCTCCTCCTC 58.795 60.000 0.00 0.00 0.00 3.71
303 304 1.205055 CCTAAACCACCTCCTCCTCC 58.795 60.000 0.00 0.00 0.00 4.30
304 305 1.273896 CCTAAACCACCTCCTCCTCCT 60.274 57.143 0.00 0.00 0.00 3.69
305 306 2.112190 CTAAACCACCTCCTCCTCCTC 58.888 57.143 0.00 0.00 0.00 3.71
306 307 0.547954 AAACCACCTCCTCCTCCTCC 60.548 60.000 0.00 0.00 0.00 4.30
307 308 1.751143 AACCACCTCCTCCTCCTCCA 61.751 60.000 0.00 0.00 0.00 3.86
308 309 1.687493 CCACCTCCTCCTCCTCCAC 60.687 68.421 0.00 0.00 0.00 4.02
309 310 1.687493 CACCTCCTCCTCCTCCACC 60.687 68.421 0.00 0.00 0.00 4.61
310 311 2.177518 ACCTCCTCCTCCTCCACCA 61.178 63.158 0.00 0.00 0.00 4.17
311 312 1.081092 CCTCCTCCTCCTCCACCAA 59.919 63.158 0.00 0.00 0.00 3.67
312 313 0.547712 CCTCCTCCTCCTCCACCAAA 60.548 60.000 0.00 0.00 0.00 3.28
313 314 1.362224 CTCCTCCTCCTCCACCAAAA 58.638 55.000 0.00 0.00 0.00 2.44
314 315 1.705186 CTCCTCCTCCTCCACCAAAAA 59.295 52.381 0.00 0.00 0.00 1.94
335 336 6.391227 AAAAGTTAGGGTTTGTGTCTCATG 57.609 37.500 0.00 0.00 0.00 3.07
336 337 3.412386 AGTTAGGGTTTGTGTCTCATGC 58.588 45.455 0.00 0.00 0.00 4.06
337 338 2.093306 TAGGGTTTGTGTCTCATGCG 57.907 50.000 0.00 0.00 0.00 4.73
338 339 0.606401 AGGGTTTGTGTCTCATGCGG 60.606 55.000 0.00 0.00 0.00 5.69
345 346 2.105128 GTCTCATGCGGACCCTCG 59.895 66.667 7.21 0.00 0.00 4.63
388 389 0.389166 GGTGAGTGAGACTTGGCTCG 60.389 60.000 0.00 0.00 37.73 5.03
622 3376 9.362539 CTCCCAAGATGATATTTTGTCAAAAAG 57.637 33.333 14.47 0.00 38.62 2.27
623 3377 7.818930 TCCCAAGATGATATTTTGTCAAAAAGC 59.181 33.333 14.47 7.85 38.62 3.51
624 3378 7.603404 CCCAAGATGATATTTTGTCAAAAAGCA 59.397 33.333 14.47 12.43 38.62 3.91
625 3379 9.158233 CCAAGATGATATTTTGTCAAAAAGCAT 57.842 29.630 14.47 15.82 38.62 3.79
1146 4490 0.108138 GCTATCGCCCAATATCGCCT 60.108 55.000 0.00 0.00 0.00 5.52
1147 4491 1.645034 CTATCGCCCAATATCGCCTG 58.355 55.000 0.00 0.00 0.00 4.85
1148 4492 0.249120 TATCGCCCAATATCGCCTGG 59.751 55.000 0.00 0.00 0.00 4.45
1359 5018 5.185635 AGTTGGCTTCATTTTGCTTAGCATA 59.814 36.000 8.05 0.00 38.76 3.14
1375 5034 2.016604 GCATATTGTTCCTCGGCACCA 61.017 52.381 0.00 0.00 0.00 4.17
1604 5266 2.597510 AGCGGGTCAGGGCAAAAC 60.598 61.111 0.00 0.00 0.00 2.43
1729 5391 2.952310 GAGTACATGCCAAAAGGATCCC 59.048 50.000 8.55 0.00 0.00 3.85
2025 5687 3.691118 CCGAATGGTTGACATCACAGATT 59.309 43.478 0.00 0.00 39.40 2.40
2219 5883 1.376543 CTAGCACACAAGCAGGATGG 58.623 55.000 0.00 0.00 35.86 3.51
2322 5986 1.314534 TGGAAGGTGCCATGAATGCG 61.315 55.000 0.00 0.00 31.66 4.73
2521 6187 6.862209 TGTAAAGCAAATGACAAGTCTGTTT 58.138 32.000 1.53 0.94 35.30 2.83
2527 6193 6.262944 AGCAAATGACAAGTCTGTTTGTATCA 59.737 34.615 21.16 1.89 41.15 2.15
2610 6276 9.995003 ATTTCAATATTGCAAACCTTCTTGTTA 57.005 25.926 10.76 0.00 0.00 2.41
2732 6781 8.020819 TCATTGTAGTTAAAACTAACAGCATGC 58.979 33.333 10.51 10.51 42.66 4.06
2805 6883 4.647291 ATCACGTGCTTTTAAGTTCTCG 57.353 40.909 11.67 0.00 0.00 4.04
3192 7304 1.768684 TTCCACCTCTGGCCTCACAC 61.769 60.000 3.32 0.00 37.49 3.82
3193 7305 2.348998 CACCTCTGGCCTCACACC 59.651 66.667 3.32 0.00 0.00 4.16
3194 7306 3.314331 ACCTCTGGCCTCACACCG 61.314 66.667 3.32 0.00 0.00 4.94
3274 7398 8.435187 AGATTATGAGCAGGACATGAGATTTTA 58.565 33.333 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.884579 CCGACACTACCGGCTACATAT 59.115 52.381 0.00 0.00 40.54 1.78
1 2 1.134128 TCCGACACTACCGGCTACATA 60.134 52.381 0.00 0.00 46.10 2.29
2 3 0.394762 TCCGACACTACCGGCTACAT 60.395 55.000 0.00 0.00 46.10 2.29
3 4 0.394762 ATCCGACACTACCGGCTACA 60.395 55.000 0.00 0.00 46.10 2.74
4 5 1.534595 CTATCCGACACTACCGGCTAC 59.465 57.143 0.00 0.00 46.10 3.58
5 6 1.417517 TCTATCCGACACTACCGGCTA 59.582 52.381 0.00 0.00 46.10 3.93
6 7 0.182061 TCTATCCGACACTACCGGCT 59.818 55.000 0.00 0.00 46.10 5.52
7 8 1.245732 ATCTATCCGACACTACCGGC 58.754 55.000 0.00 0.00 46.10 6.13
9 10 5.105063 TCGTATATCTATCCGACACTACCG 58.895 45.833 0.00 0.00 0.00 4.02
10 11 6.336566 TCTCGTATATCTATCCGACACTACC 58.663 44.000 0.00 0.00 0.00 3.18
11 12 7.545265 AGTTCTCGTATATCTATCCGACACTAC 59.455 40.741 0.00 0.00 0.00 2.73
12 13 7.609960 AGTTCTCGTATATCTATCCGACACTA 58.390 38.462 0.00 0.00 0.00 2.74
13 14 6.465948 AGTTCTCGTATATCTATCCGACACT 58.534 40.000 0.00 0.00 0.00 3.55
14 15 6.724694 AGTTCTCGTATATCTATCCGACAC 57.275 41.667 0.00 0.00 0.00 3.67
15 16 6.709397 ACAAGTTCTCGTATATCTATCCGACA 59.291 38.462 0.00 0.00 0.00 4.35
16 17 7.131498 ACAAGTTCTCGTATATCTATCCGAC 57.869 40.000 0.00 0.00 0.00 4.79
17 18 7.228108 ACAACAAGTTCTCGTATATCTATCCGA 59.772 37.037 0.00 0.00 0.00 4.55
18 19 7.361127 ACAACAAGTTCTCGTATATCTATCCG 58.639 38.462 0.00 0.00 0.00 4.18
34 35 5.120208 CGAGATATTGGTCGAACAACAAGTT 59.880 40.000 20.01 4.58 44.93 2.66
35 36 4.625742 CGAGATATTGGTCGAACAACAAGT 59.374 41.667 20.01 5.00 38.50 3.16
36 37 4.032900 CCGAGATATTGGTCGAACAACAAG 59.967 45.833 20.01 6.96 38.50 3.16
37 38 3.930229 CCGAGATATTGGTCGAACAACAA 59.070 43.478 20.01 10.43 38.50 2.83
38 39 3.193903 TCCGAGATATTGGTCGAACAACA 59.806 43.478 20.01 7.54 38.50 3.33
39 40 3.777478 TCCGAGATATTGGTCGAACAAC 58.223 45.455 20.01 6.07 38.50 3.32
40 41 3.697542 TCTCCGAGATATTGGTCGAACAA 59.302 43.478 19.88 19.88 38.50 2.83
41 42 3.284617 TCTCCGAGATATTGGTCGAACA 58.715 45.455 0.00 0.00 38.50 3.18
42 43 3.984508 TCTCCGAGATATTGGTCGAAC 57.015 47.619 0.00 0.00 38.50 3.95
43 44 3.318275 CCTTCTCCGAGATATTGGTCGAA 59.682 47.826 0.00 0.00 38.50 3.71
44 45 2.885266 CCTTCTCCGAGATATTGGTCGA 59.115 50.000 0.00 0.00 38.50 4.20
45 46 2.885266 TCCTTCTCCGAGATATTGGTCG 59.115 50.000 0.00 0.00 35.91 4.79
46 47 4.145807 TCTCCTTCTCCGAGATATTGGTC 58.854 47.826 0.00 0.00 31.39 4.02
47 48 4.148838 CTCTCCTTCTCCGAGATATTGGT 58.851 47.826 0.00 0.00 35.85 3.67
48 49 3.509575 CCTCTCCTTCTCCGAGATATTGG 59.490 52.174 0.00 0.60 35.85 3.16
49 50 4.022416 CACCTCTCCTTCTCCGAGATATTG 60.022 50.000 0.00 0.00 35.85 1.90
50 51 4.148838 CACCTCTCCTTCTCCGAGATATT 58.851 47.826 0.00 0.00 35.85 1.28
51 52 3.499563 CCACCTCTCCTTCTCCGAGATAT 60.500 52.174 0.00 0.00 35.85 1.63
52 53 2.158593 CCACCTCTCCTTCTCCGAGATA 60.159 54.545 0.00 0.00 35.85 1.98
53 54 1.410932 CCACCTCTCCTTCTCCGAGAT 60.411 57.143 0.00 0.00 35.85 2.75
54 55 0.033991 CCACCTCTCCTTCTCCGAGA 60.034 60.000 0.00 0.00 35.14 4.04
55 56 0.323908 ACCACCTCTCCTTCTCCGAG 60.324 60.000 0.00 0.00 0.00 4.63
56 57 0.323542 GACCACCTCTCCTTCTCCGA 60.324 60.000 0.00 0.00 0.00 4.55
57 58 1.658686 CGACCACCTCTCCTTCTCCG 61.659 65.000 0.00 0.00 0.00 4.63
58 59 0.323542 TCGACCACCTCTCCTTCTCC 60.324 60.000 0.00 0.00 0.00 3.71
59 60 1.770294 ATCGACCACCTCTCCTTCTC 58.230 55.000 0.00 0.00 0.00 2.87
60 61 3.117474 TGATATCGACCACCTCTCCTTCT 60.117 47.826 0.00 0.00 0.00 2.85
61 62 3.004944 GTGATATCGACCACCTCTCCTTC 59.995 52.174 0.00 0.00 0.00 3.46
62 63 2.959707 GTGATATCGACCACCTCTCCTT 59.040 50.000 0.00 0.00 0.00 3.36
63 64 2.175931 AGTGATATCGACCACCTCTCCT 59.824 50.000 9.84 0.00 34.00 3.69
64 65 2.588620 AGTGATATCGACCACCTCTCC 58.411 52.381 9.84 0.00 34.00 3.71
65 66 3.886505 AGAAGTGATATCGACCACCTCTC 59.113 47.826 9.84 6.02 30.63 3.20
66 67 3.886505 GAGAAGTGATATCGACCACCTCT 59.113 47.826 12.55 12.55 36.94 3.69
67 68 3.886505 AGAGAAGTGATATCGACCACCTC 59.113 47.826 9.84 10.01 34.00 3.85
68 69 3.886505 GAGAGAAGTGATATCGACCACCT 59.113 47.826 9.84 3.06 34.00 4.00
69 70 3.886505 AGAGAGAAGTGATATCGACCACC 59.113 47.826 9.84 0.00 34.00 4.61
70 71 4.336993 ACAGAGAGAAGTGATATCGACCAC 59.663 45.833 0.00 6.38 0.00 4.16
71 72 4.527944 ACAGAGAGAAGTGATATCGACCA 58.472 43.478 0.00 0.00 0.00 4.02
72 73 6.607689 CATACAGAGAGAAGTGATATCGACC 58.392 44.000 0.00 0.00 0.00 4.79
73 74 6.083630 GCATACAGAGAGAAGTGATATCGAC 58.916 44.000 0.00 0.00 0.00 4.20
74 75 5.765182 TGCATACAGAGAGAAGTGATATCGA 59.235 40.000 0.00 0.00 0.00 3.59
75 76 6.006759 TGCATACAGAGAGAAGTGATATCG 57.993 41.667 0.00 0.00 0.00 2.92
104 105 9.770097 AAACAGAAGATCGTCATGAACATATAT 57.230 29.630 11.35 0.00 0.00 0.86
105 106 9.249457 GAAACAGAAGATCGTCATGAACATATA 57.751 33.333 11.35 0.00 0.00 0.86
106 107 7.225538 GGAAACAGAAGATCGTCATGAACATAT 59.774 37.037 11.35 0.00 0.00 1.78
107 108 6.535150 GGAAACAGAAGATCGTCATGAACATA 59.465 38.462 11.35 0.00 0.00 2.29
108 109 5.352569 GGAAACAGAAGATCGTCATGAACAT 59.647 40.000 11.35 0.00 0.00 2.71
109 110 4.690748 GGAAACAGAAGATCGTCATGAACA 59.309 41.667 11.35 0.00 0.00 3.18
110 111 4.932200 AGGAAACAGAAGATCGTCATGAAC 59.068 41.667 11.35 0.06 0.00 3.18
111 112 5.152623 AGGAAACAGAAGATCGTCATGAA 57.847 39.130 11.35 0.00 0.00 2.57
112 113 4.808414 AGGAAACAGAAGATCGTCATGA 57.192 40.909 11.35 0.00 0.00 3.07
113 114 4.931601 TGAAGGAAACAGAAGATCGTCATG 59.068 41.667 11.35 8.56 0.00 3.07
114 115 5.152623 TGAAGGAAACAGAAGATCGTCAT 57.847 39.130 11.35 0.00 0.00 3.06
115 116 4.600692 TGAAGGAAACAGAAGATCGTCA 57.399 40.909 11.35 0.00 0.00 4.35
116 117 6.147821 TCAAATGAAGGAAACAGAAGATCGTC 59.852 38.462 0.00 0.00 0.00 4.20
117 118 5.997746 TCAAATGAAGGAAACAGAAGATCGT 59.002 36.000 0.00 0.00 0.00 3.73
118 119 6.486253 TCAAATGAAGGAAACAGAAGATCG 57.514 37.500 0.00 0.00 0.00 3.69
119 120 9.780413 GTAATCAAATGAAGGAAACAGAAGATC 57.220 33.333 0.00 0.00 0.00 2.75
120 121 9.525826 AGTAATCAAATGAAGGAAACAGAAGAT 57.474 29.630 0.00 0.00 0.00 2.40
121 122 8.924511 AGTAATCAAATGAAGGAAACAGAAGA 57.075 30.769 0.00 0.00 0.00 2.87
123 124 8.730680 GCTAGTAATCAAATGAAGGAAACAGAA 58.269 33.333 0.00 0.00 0.00 3.02
124 125 8.103305 AGCTAGTAATCAAATGAAGGAAACAGA 58.897 33.333 0.00 0.00 0.00 3.41
125 126 8.273780 AGCTAGTAATCAAATGAAGGAAACAG 57.726 34.615 0.00 0.00 0.00 3.16
126 127 9.383519 CTAGCTAGTAATCAAATGAAGGAAACA 57.616 33.333 12.92 0.00 0.00 2.83
127 128 8.338986 GCTAGCTAGTAATCAAATGAAGGAAAC 58.661 37.037 21.62 0.00 0.00 2.78
128 129 7.224753 CGCTAGCTAGTAATCAAATGAAGGAAA 59.775 37.037 21.62 0.00 0.00 3.13
129 130 6.701841 CGCTAGCTAGTAATCAAATGAAGGAA 59.298 38.462 21.62 0.00 0.00 3.36
130 131 6.183360 ACGCTAGCTAGTAATCAAATGAAGGA 60.183 38.462 21.62 0.00 0.00 3.36
131 132 5.986135 ACGCTAGCTAGTAATCAAATGAAGG 59.014 40.000 21.62 0.00 0.00 3.46
132 133 6.477033 ACACGCTAGCTAGTAATCAAATGAAG 59.523 38.462 21.62 0.00 0.00 3.02
133 134 6.338146 ACACGCTAGCTAGTAATCAAATGAA 58.662 36.000 21.62 0.00 0.00 2.57
134 135 5.902681 ACACGCTAGCTAGTAATCAAATGA 58.097 37.500 21.62 0.00 0.00 2.57
135 136 5.980116 AGACACGCTAGCTAGTAATCAAATG 59.020 40.000 21.62 10.66 0.00 2.32
136 137 6.150396 AGACACGCTAGCTAGTAATCAAAT 57.850 37.500 21.62 0.54 0.00 2.32
137 138 5.578005 AGACACGCTAGCTAGTAATCAAA 57.422 39.130 21.62 0.00 0.00 2.69
138 139 5.821470 AGTAGACACGCTAGCTAGTAATCAA 59.179 40.000 21.62 0.70 0.00 2.57
139 140 5.366460 AGTAGACACGCTAGCTAGTAATCA 58.634 41.667 21.62 0.00 0.00 2.57
140 141 5.106987 GGAGTAGACACGCTAGCTAGTAATC 60.107 48.000 21.62 12.75 0.00 1.75
141 142 4.756135 GGAGTAGACACGCTAGCTAGTAAT 59.244 45.833 21.62 4.67 0.00 1.89
142 143 4.125703 GGAGTAGACACGCTAGCTAGTAA 58.874 47.826 21.62 0.53 0.00 2.24
143 144 3.387374 AGGAGTAGACACGCTAGCTAGTA 59.613 47.826 21.62 2.66 0.00 1.82
144 145 2.171027 AGGAGTAGACACGCTAGCTAGT 59.829 50.000 21.62 10.90 0.00 2.57
145 146 2.803956 GAGGAGTAGACACGCTAGCTAG 59.196 54.545 16.84 16.84 0.00 3.42
146 147 2.435069 AGAGGAGTAGACACGCTAGCTA 59.565 50.000 13.93 0.00 0.00 3.32
147 148 1.210967 AGAGGAGTAGACACGCTAGCT 59.789 52.381 13.93 0.00 0.00 3.32
148 149 1.600485 GAGAGGAGTAGACACGCTAGC 59.400 57.143 4.06 4.06 0.00 3.42
149 150 2.215196 GGAGAGGAGTAGACACGCTAG 58.785 57.143 0.00 0.00 0.00 3.42
150 151 1.558294 TGGAGAGGAGTAGACACGCTA 59.442 52.381 0.00 0.00 0.00 4.26
151 152 0.328592 TGGAGAGGAGTAGACACGCT 59.671 55.000 0.00 0.00 0.00 5.07
152 153 1.394618 ATGGAGAGGAGTAGACACGC 58.605 55.000 0.00 0.00 0.00 5.34
153 154 2.544686 CGTATGGAGAGGAGTAGACACG 59.455 54.545 0.00 0.00 0.00 4.49
154 155 3.543665 ACGTATGGAGAGGAGTAGACAC 58.456 50.000 0.00 0.00 0.00 3.67
155 156 3.928005 ACGTATGGAGAGGAGTAGACA 57.072 47.619 0.00 0.00 0.00 3.41
156 157 8.477256 ACTATATACGTATGGAGAGGAGTAGAC 58.523 40.741 18.37 0.00 0.00 2.59
157 158 8.606754 ACTATATACGTATGGAGAGGAGTAGA 57.393 38.462 18.37 0.00 0.00 2.59
158 159 9.748708 GTACTATATACGTATGGAGAGGAGTAG 57.251 40.741 18.37 8.19 0.00 2.57
159 160 8.409371 CGTACTATATACGTATGGAGAGGAGTA 58.591 40.741 18.37 10.74 36.31 2.59
160 161 7.264221 CGTACTATATACGTATGGAGAGGAGT 58.736 42.308 18.37 11.56 36.31 3.85
161 162 7.697352 CGTACTATATACGTATGGAGAGGAG 57.303 44.000 18.37 6.90 36.31 3.69
173 174 4.320953 TGTCGACGCTACGTACTATATACG 59.679 45.833 11.62 5.00 41.37 3.06
174 175 5.747262 TGTCGACGCTACGTACTATATAC 57.253 43.478 11.62 0.00 41.37 1.47
175 176 6.616471 GCTTTGTCGACGCTACGTACTATATA 60.616 42.308 11.62 0.00 41.37 0.86
176 177 5.657470 TTTGTCGACGCTACGTACTATAT 57.343 39.130 11.62 0.00 41.37 0.86
177 178 4.550831 GCTTTGTCGACGCTACGTACTATA 60.551 45.833 11.62 0.00 41.37 1.31
178 179 3.786818 GCTTTGTCGACGCTACGTACTAT 60.787 47.826 11.62 0.00 41.37 2.12
179 180 2.474526 GCTTTGTCGACGCTACGTACTA 60.475 50.000 11.62 0.00 41.37 1.82
180 181 1.727213 GCTTTGTCGACGCTACGTACT 60.727 52.381 11.62 0.00 41.37 2.73
181 182 0.632241 GCTTTGTCGACGCTACGTAC 59.368 55.000 11.62 0.00 41.37 3.67
182 183 0.238025 TGCTTTGTCGACGCTACGTA 59.762 50.000 11.62 0.00 41.37 3.57
183 184 1.008194 TGCTTTGTCGACGCTACGT 60.008 52.632 11.62 0.00 45.10 3.57
184 185 1.411089 GTGCTTTGTCGACGCTACG 59.589 57.895 11.62 0.00 0.00 3.51
185 186 1.411089 CGTGCTTTGTCGACGCTAC 59.589 57.895 11.62 8.34 0.00 3.58
186 187 1.731613 CCGTGCTTTGTCGACGCTA 60.732 57.895 11.62 0.00 0.00 4.26
187 188 3.036084 CCGTGCTTTGTCGACGCT 61.036 61.111 11.62 0.00 0.00 5.07
188 189 3.000080 CTCCGTGCTTTGTCGACGC 62.000 63.158 11.62 9.03 0.00 5.19
189 190 0.732880 ATCTCCGTGCTTTGTCGACG 60.733 55.000 11.62 0.00 0.00 5.12
190 191 2.273370 TATCTCCGTGCTTTGTCGAC 57.727 50.000 9.11 9.11 0.00 4.20
191 192 2.490509 TCTTATCTCCGTGCTTTGTCGA 59.509 45.455 0.00 0.00 0.00 4.20
192 193 2.854777 CTCTTATCTCCGTGCTTTGTCG 59.145 50.000 0.00 0.00 0.00 4.35
193 194 4.109050 CTCTCTTATCTCCGTGCTTTGTC 58.891 47.826 0.00 0.00 0.00 3.18
194 195 3.118956 CCTCTCTTATCTCCGTGCTTTGT 60.119 47.826 0.00 0.00 0.00 2.83
195 196 3.131223 TCCTCTCTTATCTCCGTGCTTTG 59.869 47.826 0.00 0.00 0.00 2.77
196 197 3.131400 GTCCTCTCTTATCTCCGTGCTTT 59.869 47.826 0.00 0.00 0.00 3.51
197 198 2.691011 GTCCTCTCTTATCTCCGTGCTT 59.309 50.000 0.00 0.00 0.00 3.91
198 199 2.303175 GTCCTCTCTTATCTCCGTGCT 58.697 52.381 0.00 0.00 0.00 4.40
199 200 2.025155 TGTCCTCTCTTATCTCCGTGC 58.975 52.381 0.00 0.00 0.00 5.34
200 201 3.283751 AGTGTCCTCTCTTATCTCCGTG 58.716 50.000 0.00 0.00 0.00 4.94
201 202 3.655615 AGTGTCCTCTCTTATCTCCGT 57.344 47.619 0.00 0.00 0.00 4.69
202 203 4.204012 AGAAGTGTCCTCTCTTATCTCCG 58.796 47.826 0.00 0.00 0.00 4.63
203 204 5.445964 AGAGAAGTGTCCTCTCTTATCTCC 58.554 45.833 0.00 0.00 39.76 3.71
212 213 8.856103 GCTAATTAATAGAGAGAAGTGTCCTCT 58.144 37.037 0.00 0.00 43.16 3.69
213 214 8.856103 AGCTAATTAATAGAGAGAAGTGTCCTC 58.144 37.037 0.00 0.00 33.04 3.71
214 215 8.776061 AGCTAATTAATAGAGAGAAGTGTCCT 57.224 34.615 0.00 0.00 33.04 3.85
216 217 9.620660 GCTAGCTAATTAATAGAGAGAAGTGTC 57.379 37.037 7.70 0.00 33.04 3.67
217 218 9.362151 AGCTAGCTAATTAATAGAGAGAAGTGT 57.638 33.333 17.69 0.00 33.04 3.55
250 251 9.596308 GGGGGTTAATTTAGGTGTTTCATATAT 57.404 33.333 0.00 0.00 0.00 0.86
251 252 8.999905 GGGGGTTAATTTAGGTGTTTCATATA 57.000 34.615 0.00 0.00 0.00 0.86
252 253 7.907841 GGGGGTTAATTTAGGTGTTTCATAT 57.092 36.000 0.00 0.00 0.00 1.78
273 274 0.191314 TGGTTTAGGGGTTTTGGGGG 59.809 55.000 0.00 0.00 0.00 5.40
274 275 1.344065 GTGGTTTAGGGGTTTTGGGG 58.656 55.000 0.00 0.00 0.00 4.96
275 276 1.132977 AGGTGGTTTAGGGGTTTTGGG 60.133 52.381 0.00 0.00 0.00 4.12
276 277 2.244695 GAGGTGGTTTAGGGGTTTTGG 58.755 52.381 0.00 0.00 0.00 3.28
277 278 2.158370 AGGAGGTGGTTTAGGGGTTTTG 60.158 50.000 0.00 0.00 0.00 2.44
278 279 2.109480 GAGGAGGTGGTTTAGGGGTTTT 59.891 50.000 0.00 0.00 0.00 2.43
279 280 1.709115 GAGGAGGTGGTTTAGGGGTTT 59.291 52.381 0.00 0.00 0.00 3.27
280 281 1.369403 GAGGAGGTGGTTTAGGGGTT 58.631 55.000 0.00 0.00 0.00 4.11
281 282 0.549413 GGAGGAGGTGGTTTAGGGGT 60.549 60.000 0.00 0.00 0.00 4.95
282 283 0.253207 AGGAGGAGGTGGTTTAGGGG 60.253 60.000 0.00 0.00 0.00 4.79
283 284 1.205055 GAGGAGGAGGTGGTTTAGGG 58.795 60.000 0.00 0.00 0.00 3.53
284 285 1.205055 GGAGGAGGAGGTGGTTTAGG 58.795 60.000 0.00 0.00 0.00 2.69
285 286 2.112190 GAGGAGGAGGAGGTGGTTTAG 58.888 57.143 0.00 0.00 0.00 1.85
286 287 1.273666 GGAGGAGGAGGAGGTGGTTTA 60.274 57.143 0.00 0.00 0.00 2.01
287 288 0.547954 GGAGGAGGAGGAGGTGGTTT 60.548 60.000 0.00 0.00 0.00 3.27
288 289 1.081277 GGAGGAGGAGGAGGTGGTT 59.919 63.158 0.00 0.00 0.00 3.67
289 290 2.177518 TGGAGGAGGAGGAGGTGGT 61.178 63.158 0.00 0.00 0.00 4.16
290 291 1.687493 GTGGAGGAGGAGGAGGTGG 60.687 68.421 0.00 0.00 0.00 4.61
291 292 1.687493 GGTGGAGGAGGAGGAGGTG 60.687 68.421 0.00 0.00 0.00 4.00
292 293 1.751143 TTGGTGGAGGAGGAGGAGGT 61.751 60.000 0.00 0.00 0.00 3.85
293 294 0.547712 TTTGGTGGAGGAGGAGGAGG 60.548 60.000 0.00 0.00 0.00 4.30
294 295 1.362224 TTTTGGTGGAGGAGGAGGAG 58.638 55.000 0.00 0.00 0.00 3.69
295 296 1.827792 TTTTTGGTGGAGGAGGAGGA 58.172 50.000 0.00 0.00 0.00 3.71
311 312 6.682861 GCATGAGACACAAACCCTAACTTTTT 60.683 38.462 0.00 0.00 0.00 1.94
312 313 5.221244 GCATGAGACACAAACCCTAACTTTT 60.221 40.000 0.00 0.00 0.00 2.27
313 314 4.278419 GCATGAGACACAAACCCTAACTTT 59.722 41.667 0.00 0.00 0.00 2.66
314 315 3.821033 GCATGAGACACAAACCCTAACTT 59.179 43.478 0.00 0.00 0.00 2.66
315 316 3.412386 GCATGAGACACAAACCCTAACT 58.588 45.455 0.00 0.00 0.00 2.24
316 317 2.159627 CGCATGAGACACAAACCCTAAC 59.840 50.000 0.00 0.00 0.00 2.34
317 318 2.422597 CGCATGAGACACAAACCCTAA 58.577 47.619 0.00 0.00 0.00 2.69
318 319 1.338674 CCGCATGAGACACAAACCCTA 60.339 52.381 0.00 0.00 0.00 3.53
319 320 0.606401 CCGCATGAGACACAAACCCT 60.606 55.000 0.00 0.00 0.00 4.34
320 321 0.605319 TCCGCATGAGACACAAACCC 60.605 55.000 0.00 0.00 0.00 4.11
321 322 0.517316 GTCCGCATGAGACACAAACC 59.483 55.000 10.51 0.00 34.27 3.27
322 323 0.517316 GGTCCGCATGAGACACAAAC 59.483 55.000 15.65 0.00 35.89 2.93
323 324 0.605319 GGGTCCGCATGAGACACAAA 60.605 55.000 15.65 0.00 37.60 2.83
324 325 1.003839 GGGTCCGCATGAGACACAA 60.004 57.895 15.65 0.00 37.60 3.33
325 326 1.888436 GAGGGTCCGCATGAGACACA 61.888 60.000 17.75 0.00 40.27 3.72
326 327 1.153549 GAGGGTCCGCATGAGACAC 60.154 63.158 15.65 12.93 37.96 3.67
327 328 2.710902 CGAGGGTCCGCATGAGACA 61.711 63.158 15.65 0.00 35.89 3.41
328 329 2.105128 CGAGGGTCCGCATGAGAC 59.895 66.667 0.00 1.88 0.00 3.36
329 330 2.362503 ACGAGGGTCCGCATGAGA 60.363 61.111 0.00 0.00 0.00 3.27
330 331 2.105128 GACGAGGGTCCGCATGAG 59.895 66.667 0.00 0.00 37.19 2.90
331 332 2.362503 AGACGAGGGTCCGCATGA 60.363 61.111 0.00 0.00 44.54 3.07
332 333 2.202797 CAGACGAGGGTCCGCATG 60.203 66.667 0.00 0.00 44.54 4.06
333 334 3.461773 CCAGACGAGGGTCCGCAT 61.462 66.667 0.00 0.00 44.54 4.73
334 335 4.671590 TCCAGACGAGGGTCCGCA 62.672 66.667 0.00 0.00 44.54 5.69
335 336 4.131088 GTCCAGACGAGGGTCCGC 62.131 72.222 0.00 0.00 44.54 5.54
345 346 2.350522 ACTCATTGATTGCGTCCAGAC 58.649 47.619 0.00 0.00 0.00 3.51
361 362 4.021104 CCAAGTCTCACTCACCATAACTCA 60.021 45.833 0.00 0.00 0.00 3.41
388 389 5.235186 GCTATGATATGCCGTCAACCATATC 59.765 44.000 11.67 11.67 45.26 1.63
622 3376 8.084073 AGGTGTTATCATATAAAACATGCATGC 58.916 33.333 26.53 11.82 35.72 4.06
670 3432 8.842280 TGTAGGAAATAGACAAACACGATTTTT 58.158 29.630 0.00 0.00 0.00 1.94
672 3434 7.360946 GCTGTAGGAAATAGACAAACACGATTT 60.361 37.037 0.00 0.00 0.00 2.17
1146 4490 2.367202 GGGCCTAGCAGCTGTACCA 61.367 63.158 16.64 0.00 0.00 3.25
1147 4491 1.627297 AAGGGCCTAGCAGCTGTACC 61.627 60.000 16.64 9.56 0.00 3.34
1148 4492 0.462759 CAAGGGCCTAGCAGCTGTAC 60.463 60.000 16.64 0.00 0.00 2.90
1359 5018 1.923356 AATTGGTGCCGAGGAACAAT 58.077 45.000 2.20 3.47 33.55 2.71
1604 5266 2.813754 TGAACCTCTGCAGAAAATTCCG 59.186 45.455 18.85 3.79 0.00 4.30
2219 5883 3.558829 TGCGAGCTTCATCATCTCAATTC 59.441 43.478 0.00 0.00 0.00 2.17
2322 5986 6.510799 CGAAGTTATGATCAATGTTGCTCTCC 60.511 42.308 0.00 0.00 0.00 3.71
2610 6276 3.641434 AATTCAGTCCAGCTGCTGTAT 57.359 42.857 26.41 12.46 44.66 2.29
2722 6771 3.235157 GCATTTTGGAGCATGCTGTTA 57.765 42.857 28.27 8.07 42.25 2.41
2805 6883 5.382618 AATGAAAAGACACTGGAGATTGC 57.617 39.130 0.00 0.00 0.00 3.56
3064 7175 3.502211 AGCAACTTCCGACTGGTTTTATG 59.498 43.478 0.00 0.00 36.30 1.90
3192 7304 0.544697 ACCTTGGGCCTTATACACGG 59.455 55.000 4.53 0.74 0.00 4.94
3193 7305 3.547054 TTACCTTGGGCCTTATACACG 57.453 47.619 4.53 0.00 0.00 4.49
3194 7306 5.889289 TCATTTTACCTTGGGCCTTATACAC 59.111 40.000 4.53 0.00 0.00 2.90
3274 7398 4.827692 ACATGTCATTTGCTTTGCATCAT 58.172 34.783 0.00 0.00 38.76 2.45


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

AutoCloner maintained by Alex Coulton.