Multiple sequence alignment - TraesCS7B01G099200

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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 TraesCS7B01G099200 chr7B 100.000 3083 0 0 1 3083 113540830 113537748 0.000000e+00 5694
1 TraesCS7B01G099200 chr7B 88.862 1634 125 33 513 2107 113803339 113801724 0.000000e+00 1956
2 TraesCS7B01G099200 chr7B 85.317 1832 170 54 493 2263 113529004 113527211 0.000000e+00 1801
3 TraesCS7B01G099200 chr7B 91.658 995 71 6 1275 2263 113571922 113570934 0.000000e+00 1367
4 TraesCS7B01G099200 chr7A 90.108 1951 131 29 179 2098 151861937 151863856 0.000000e+00 2477
5 TraesCS7B01G099200 chr7A 91.007 1390 100 15 739 2114 152084214 152085592 0.000000e+00 1851
6 TraesCS7B01G099200 chr7A 88.146 329 16 9 579 889 151872799 151873122 1.350000e-98 370
7 TraesCS7B01G099200 chr7A 87.129 101 11 1 179 277 151872123 151872223 2.510000e-21 113
8 TraesCS7B01G099200 chr7D 90.954 1824 117 21 1280 3066 151779196 151777384 0.000000e+00 2410
9 TraesCS7B01G099200 chr7D 89.691 1620 126 25 518 2107 151824345 151825953 0.000000e+00 2028
10 TraesCS7B01G099200 chr7D 89.310 1637 134 23 501 2107 151930509 151932134 0.000000e+00 2015
11 TraesCS7B01G099200 chr7D 90.641 1154 59 24 179 1302 151780351 151779217 0.000000e+00 1487
12 TraesCS7B01G099200 chr7D 86.792 1272 129 25 938 2196 151917030 151915785 0.000000e+00 1382
13 TraesCS7B01G099200 chr7D 88.150 1173 99 23 938 2098 151791512 151790368 0.000000e+00 1360
14 TraesCS7B01G099200 chr7D 91.349 971 69 9 1300 2263 151698031 151697069 0.000000e+00 1314
15 TraesCS7B01G099200 chr7D 87.455 279 29 3 938 1213 151699421 151699146 1.780000e-82 316
16 TraesCS7B01G099200 chr6D 76.856 808 140 28 2272 3052 91069790 91070577 2.210000e-111 412
17 TraesCS7B01G099200 chr5B 89.630 135 13 1 2443 2577 578719337 578719204 1.470000e-38 171
18 TraesCS7B01G099200 chr4B 84.375 128 19 1 2458 2585 517562984 517563110 1.160000e-24 124


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 TraesCS7B01G099200 chr7B 113537748 113540830 3082 True 5694.0 5694 100.0000 1 3083 1 chr7B.!!$R2 3082
1 TraesCS7B01G099200 chr7B 113801724 113803339 1615 True 1956.0 1956 88.8620 513 2107 1 chr7B.!!$R4 1594
2 TraesCS7B01G099200 chr7B 113527211 113529004 1793 True 1801.0 1801 85.3170 493 2263 1 chr7B.!!$R1 1770
3 TraesCS7B01G099200 chr7B 113570934 113571922 988 True 1367.0 1367 91.6580 1275 2263 1 chr7B.!!$R3 988
4 TraesCS7B01G099200 chr7A 151861937 151863856 1919 False 2477.0 2477 90.1080 179 2098 1 chr7A.!!$F1 1919
5 TraesCS7B01G099200 chr7A 152084214 152085592 1378 False 1851.0 1851 91.0070 739 2114 1 chr7A.!!$F2 1375
6 TraesCS7B01G099200 chr7A 151872123 151873122 999 False 241.5 370 87.6375 179 889 2 chr7A.!!$F3 710
7 TraesCS7B01G099200 chr7D 151824345 151825953 1608 False 2028.0 2028 89.6910 518 2107 1 chr7D.!!$F1 1589
8 TraesCS7B01G099200 chr7D 151930509 151932134 1625 False 2015.0 2015 89.3100 501 2107 1 chr7D.!!$F2 1606
9 TraesCS7B01G099200 chr7D 151777384 151780351 2967 True 1948.5 2410 90.7975 179 3066 2 chr7D.!!$R4 2887
10 TraesCS7B01G099200 chr7D 151915785 151917030 1245 True 1382.0 1382 86.7920 938 2196 1 chr7D.!!$R2 1258
11 TraesCS7B01G099200 chr7D 151790368 151791512 1144 True 1360.0 1360 88.1500 938 2098 1 chr7D.!!$R1 1160
12 TraesCS7B01G099200 chr7D 151697069 151699421 2352 True 815.0 1314 89.4020 938 2263 2 chr7D.!!$R3 1325
13 TraesCS7B01G099200 chr6D 91069790 91070577 787 False 412.0 412 76.8560 2272 3052 1 chr6D.!!$F1 780

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
129 130 0.046397 AAACTCCCTCCCCCTGCTAT 59.954 55.0 0.00 0.0 0.00 2.97 F
137 138 0.188587 TCCCCCTGCTATCGTCAGAT 59.811 55.0 0.00 0.0 40.76 2.90 F
391 633 0.249073 AGAAGGCATCGAATCGTCCG 60.249 55.0 1.52 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1011 1382 0.255318 CCAGAGGGAGCAGCAAAGAT 59.745 55.0 0.00 0.0 35.59 2.40 R
1124 1500 0.755686 GATCTTGGCCATCTCCTCGT 59.244 55.0 6.09 0.0 0.00 4.18 R
2388 3911 0.107703 GTTGGGCACATCGATCTCCA 60.108 55.0 0.00 0.0 0.00 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.324991 GGGGTTGGCCGTCTCGTT 62.325 66.667 0.00 0.00 34.97 3.85
18 19 2.281276 GGGTTGGCCGTCTCGTTT 60.281 61.111 0.00 0.00 34.97 3.60
19 20 2.613506 GGGTTGGCCGTCTCGTTTG 61.614 63.158 0.00 0.00 34.97 2.93
20 21 2.613506 GGTTGGCCGTCTCGTTTGG 61.614 63.158 0.00 0.00 0.00 3.28
21 22 1.890510 GTTGGCCGTCTCGTTTGGT 60.891 57.895 0.00 0.00 0.00 3.67
22 23 1.153127 TTGGCCGTCTCGTTTGGTT 60.153 52.632 0.00 0.00 0.00 3.67
23 24 0.106335 TTGGCCGTCTCGTTTGGTTA 59.894 50.000 0.00 0.00 0.00 2.85
24 25 0.320073 TGGCCGTCTCGTTTGGTTAG 60.320 55.000 0.00 0.00 0.00 2.34
25 26 1.017701 GGCCGTCTCGTTTGGTTAGG 61.018 60.000 0.00 0.00 0.00 2.69
26 27 1.632948 GCCGTCTCGTTTGGTTAGGC 61.633 60.000 0.00 0.00 36.32 3.93
27 28 0.320073 CCGTCTCGTTTGGTTAGGCA 60.320 55.000 0.00 0.00 0.00 4.75
28 29 1.504359 CGTCTCGTTTGGTTAGGCAA 58.496 50.000 0.00 0.00 0.00 4.52
29 30 1.868498 CGTCTCGTTTGGTTAGGCAAA 59.132 47.619 0.00 0.00 0.00 3.68
30 31 2.349155 CGTCTCGTTTGGTTAGGCAAAC 60.349 50.000 0.00 0.00 37.78 2.93
40 41 2.525368 GTTAGGCAAACCCAATGACCT 58.475 47.619 0.00 0.00 36.11 3.85
41 42 3.692690 GTTAGGCAAACCCAATGACCTA 58.307 45.455 0.00 0.00 36.11 3.08
42 43 4.278310 GTTAGGCAAACCCAATGACCTAT 58.722 43.478 0.00 0.00 36.11 2.57
43 44 3.473113 AGGCAAACCCAATGACCTATT 57.527 42.857 0.00 0.00 36.11 1.73
44 45 3.790126 AGGCAAACCCAATGACCTATTT 58.210 40.909 0.00 0.00 36.11 1.40
45 46 4.167319 AGGCAAACCCAATGACCTATTTT 58.833 39.130 0.00 0.00 36.11 1.82
46 47 4.222810 AGGCAAACCCAATGACCTATTTTC 59.777 41.667 0.00 0.00 36.11 2.29
47 48 4.173256 GCAAACCCAATGACCTATTTTCG 58.827 43.478 0.00 0.00 0.00 3.46
48 49 4.321675 GCAAACCCAATGACCTATTTTCGT 60.322 41.667 0.00 0.00 0.00 3.85
49 50 5.778862 CAAACCCAATGACCTATTTTCGTT 58.221 37.500 0.00 0.00 0.00 3.85
50 51 5.638596 AACCCAATGACCTATTTTCGTTC 57.361 39.130 0.00 0.00 0.00 3.95
51 52 3.687698 ACCCAATGACCTATTTTCGTTCG 59.312 43.478 0.00 0.00 0.00 3.95
52 53 3.687698 CCCAATGACCTATTTTCGTTCGT 59.312 43.478 0.00 0.00 0.00 3.85
53 54 4.871557 CCCAATGACCTATTTTCGTTCGTA 59.128 41.667 0.00 0.00 0.00 3.43
54 55 5.526111 CCCAATGACCTATTTTCGTTCGTAT 59.474 40.000 0.00 0.00 0.00 3.06
55 56 6.702723 CCCAATGACCTATTTTCGTTCGTATA 59.297 38.462 0.00 0.00 0.00 1.47
56 57 7.225145 CCCAATGACCTATTTTCGTTCGTATAA 59.775 37.037 0.00 0.00 0.00 0.98
57 58 8.605746 CCAATGACCTATTTTCGTTCGTATAAA 58.394 33.333 0.00 0.00 0.00 1.40
58 59 9.417284 CAATGACCTATTTTCGTTCGTATAAAC 57.583 33.333 0.00 0.00 0.00 2.01
59 60 8.706492 ATGACCTATTTTCGTTCGTATAAACA 57.294 30.769 0.00 0.00 0.00 2.83
60 61 8.706492 TGACCTATTTTCGTTCGTATAAACAT 57.294 30.769 0.00 0.00 0.00 2.71
61 62 8.810427 TGACCTATTTTCGTTCGTATAAACATC 58.190 33.333 0.00 0.00 0.00 3.06
62 63 7.834529 ACCTATTTTCGTTCGTATAAACATCG 58.165 34.615 0.00 0.00 0.00 3.84
63 64 6.784227 CCTATTTTCGTTCGTATAAACATCGC 59.216 38.462 0.00 0.00 0.00 4.58
64 65 3.804262 TTCGTTCGTATAAACATCGCG 57.196 42.857 0.00 0.00 0.00 5.87
65 66 3.050273 TCGTTCGTATAAACATCGCGA 57.950 42.857 13.09 13.09 0.00 5.87
66 67 2.777845 TCGTTCGTATAAACATCGCGAC 59.222 45.455 12.93 0.00 0.00 5.19
67 68 2.405140 CGTTCGTATAAACATCGCGACG 60.405 50.000 12.93 5.44 0.00 5.12
68 69 2.735643 TCGTATAAACATCGCGACGA 57.264 45.000 12.93 11.56 41.13 4.20
69 70 3.050273 TCGTATAAACATCGCGACGAA 57.950 42.857 12.93 0.00 39.99 3.85
70 71 3.620761 TCGTATAAACATCGCGACGAAT 58.379 40.909 12.93 2.62 39.99 3.34
71 72 3.660813 TCGTATAAACATCGCGACGAATC 59.339 43.478 12.93 0.00 39.99 2.52
72 73 3.419596 CGTATAAACATCGCGACGAATCA 59.580 43.478 12.93 0.00 39.99 2.57
73 74 4.085974 CGTATAAACATCGCGACGAATCAA 60.086 41.667 12.93 0.00 39.99 2.57
74 75 5.387035 CGTATAAACATCGCGACGAATCAAT 60.387 40.000 12.93 2.06 39.99 2.57
75 76 6.183359 CGTATAAACATCGCGACGAATCAATA 60.183 38.462 12.93 1.02 39.99 1.90
76 77 4.850859 AAACATCGCGACGAATCAATAA 57.149 36.364 12.93 0.00 39.99 1.40
77 78 4.850859 AACATCGCGACGAATCAATAAA 57.149 36.364 12.93 0.00 39.99 1.40
78 79 4.437858 ACATCGCGACGAATCAATAAAG 57.562 40.909 12.93 0.00 39.99 1.85
79 80 2.990774 TCGCGACGAATCAATAAAGC 57.009 45.000 3.71 0.00 31.06 3.51
80 81 2.536365 TCGCGACGAATCAATAAAGCT 58.464 42.857 3.71 0.00 31.06 3.74
81 82 2.927477 TCGCGACGAATCAATAAAGCTT 59.073 40.909 3.71 0.00 31.06 3.74
82 83 3.000078 TCGCGACGAATCAATAAAGCTTC 60.000 43.478 3.71 0.00 31.06 3.86
83 84 3.272567 GCGACGAATCAATAAAGCTTCG 58.727 45.455 0.00 0.00 44.41 3.79
84 85 3.272567 CGACGAATCAATAAAGCTTCGC 58.727 45.455 0.00 0.00 43.07 4.70
85 86 3.241963 CGACGAATCAATAAAGCTTCGCA 60.242 43.478 0.00 0.00 43.07 5.10
86 87 4.647964 GACGAATCAATAAAGCTTCGCAA 58.352 39.130 0.00 0.00 43.07 4.85
87 88 4.651994 ACGAATCAATAAAGCTTCGCAAG 58.348 39.130 0.00 0.00 43.07 4.01
103 104 5.749596 TCGCAAGATTGTCTCAAAAGAAA 57.250 34.783 0.00 0.00 45.01 2.52
104 105 6.130298 TCGCAAGATTGTCTCAAAAGAAAA 57.870 33.333 0.00 0.00 45.01 2.29
105 106 6.559810 TCGCAAGATTGTCTCAAAAGAAAAA 58.440 32.000 0.00 0.00 45.01 1.94
106 107 6.692681 TCGCAAGATTGTCTCAAAAGAAAAAG 59.307 34.615 0.00 0.00 45.01 2.27
107 108 6.692681 CGCAAGATTGTCTCAAAAGAAAAAGA 59.307 34.615 0.00 0.00 43.02 2.52
108 109 7.220683 CGCAAGATTGTCTCAAAAGAAAAAGAA 59.779 33.333 0.00 0.00 43.02 2.52
109 110 8.872845 GCAAGATTGTCTCAAAAGAAAAAGAAA 58.127 29.630 0.00 0.00 32.42 2.52
126 127 1.465172 AAAAACTCCCTCCCCCTGC 59.535 57.895 0.00 0.00 0.00 4.85
127 128 1.074296 AAAAACTCCCTCCCCCTGCT 61.074 55.000 0.00 0.00 0.00 4.24
128 129 0.178843 AAAACTCCCTCCCCCTGCTA 60.179 55.000 0.00 0.00 0.00 3.49
129 130 0.046397 AAACTCCCTCCCCCTGCTAT 59.954 55.000 0.00 0.00 0.00 2.97
130 131 0.400670 AACTCCCTCCCCCTGCTATC 60.401 60.000 0.00 0.00 0.00 2.08
131 132 1.910772 CTCCCTCCCCCTGCTATCG 60.911 68.421 0.00 0.00 0.00 2.92
132 133 2.122813 CCCTCCCCCTGCTATCGT 60.123 66.667 0.00 0.00 0.00 3.73
133 134 2.210711 CCCTCCCCCTGCTATCGTC 61.211 68.421 0.00 0.00 0.00 4.20
134 135 1.457643 CCTCCCCCTGCTATCGTCA 60.458 63.158 0.00 0.00 0.00 4.35
135 136 1.467678 CCTCCCCCTGCTATCGTCAG 61.468 65.000 0.00 0.00 0.00 3.51
136 137 0.468214 CTCCCCCTGCTATCGTCAGA 60.468 60.000 0.00 0.00 33.54 3.27
137 138 0.188587 TCCCCCTGCTATCGTCAGAT 59.811 55.000 0.00 0.00 40.76 2.90
138 139 0.319728 CCCCCTGCTATCGTCAGATG 59.680 60.000 0.00 0.00 37.70 2.90
139 140 1.043816 CCCCTGCTATCGTCAGATGT 58.956 55.000 0.00 0.00 37.70 3.06
140 141 2.239400 CCCCTGCTATCGTCAGATGTA 58.761 52.381 0.00 0.00 37.70 2.29
141 142 2.828520 CCCCTGCTATCGTCAGATGTAT 59.171 50.000 0.00 0.00 37.70 2.29
142 143 4.017126 CCCCTGCTATCGTCAGATGTATA 58.983 47.826 0.00 0.00 37.70 1.47
143 144 4.646945 CCCCTGCTATCGTCAGATGTATAT 59.353 45.833 0.00 0.00 37.70 0.86
144 145 5.127845 CCCCTGCTATCGTCAGATGTATATT 59.872 44.000 0.00 0.00 37.70 1.28
145 146 6.269315 CCCTGCTATCGTCAGATGTATATTC 58.731 44.000 0.00 0.00 37.70 1.75
146 147 5.968261 CCTGCTATCGTCAGATGTATATTCG 59.032 44.000 0.00 0.00 37.70 3.34
147 148 6.183360 CCTGCTATCGTCAGATGTATATTCGA 60.183 42.308 0.00 0.00 37.70 3.71
148 149 6.776094 TGCTATCGTCAGATGTATATTCGAG 58.224 40.000 0.00 0.00 37.70 4.04
149 150 6.371825 TGCTATCGTCAGATGTATATTCGAGT 59.628 38.462 0.00 0.00 37.70 4.18
150 151 6.902948 GCTATCGTCAGATGTATATTCGAGTC 59.097 42.308 0.00 0.00 37.70 3.36
151 152 5.608676 TCGTCAGATGTATATTCGAGTCC 57.391 43.478 0.00 0.00 0.00 3.85
152 153 5.306394 TCGTCAGATGTATATTCGAGTCCT 58.694 41.667 0.00 0.00 0.00 3.85
153 154 5.763698 TCGTCAGATGTATATTCGAGTCCTT 59.236 40.000 0.00 0.00 0.00 3.36
154 155 6.932960 TCGTCAGATGTATATTCGAGTCCTTA 59.067 38.462 0.00 0.00 0.00 2.69
155 156 7.443272 TCGTCAGATGTATATTCGAGTCCTTAA 59.557 37.037 0.00 0.00 0.00 1.85
156 157 8.237949 CGTCAGATGTATATTCGAGTCCTTAAT 58.762 37.037 0.00 0.00 0.00 1.40
199 200 5.644636 TGTGTTTTCAGAAGTAAACGGAACT 59.355 36.000 0.00 0.00 37.70 3.01
256 259 4.063998 TCGCTGCTAGATGTGATTGATT 57.936 40.909 0.00 0.00 0.00 2.57
287 529 2.776536 AGCTATGTCATCCTTTCAGCCT 59.223 45.455 0.00 0.00 0.00 4.58
301 543 1.675641 AGCCTCGGAACAATGGTGC 60.676 57.895 0.00 0.00 0.00 5.01
318 560 2.687436 CGCGTACGTGCTGCTTAC 59.313 61.111 16.78 0.00 33.53 2.34
331 573 1.740025 CTGCTTACTGCCTTTGCTACC 59.260 52.381 0.00 0.00 42.00 3.18
332 574 0.727398 GCTTACTGCCTTTGCTACCG 59.273 55.000 0.00 0.00 38.71 4.02
333 575 1.944430 GCTTACTGCCTTTGCTACCGT 60.944 52.381 0.00 0.00 38.71 4.83
354 596 2.736721 TGTCATGCAAAGTAGTTCTCGC 59.263 45.455 0.00 0.00 0.00 5.03
356 598 2.028112 TCATGCAAAGTAGTTCTCGCCT 60.028 45.455 0.00 0.00 0.00 5.52
359 601 2.297880 TGCAAAGTAGTTCTCGCCTGTA 59.702 45.455 0.00 0.00 0.00 2.74
372 614 1.740043 CGCCTGTACAGATGCATGACA 60.740 52.381 24.68 1.93 0.00 3.58
376 618 3.869832 CCTGTACAGATGCATGACAGAAG 59.130 47.826 24.68 7.34 39.94 2.85
384 626 1.338960 TGCATGACAGAAGGCATCGAA 60.339 47.619 0.00 0.00 0.00 3.71
385 627 1.945394 GCATGACAGAAGGCATCGAAT 59.055 47.619 0.00 0.00 0.00 3.34
386 628 2.032204 GCATGACAGAAGGCATCGAATC 60.032 50.000 0.00 0.00 0.00 2.52
387 629 1.926561 TGACAGAAGGCATCGAATCG 58.073 50.000 0.00 0.00 0.00 3.34
388 630 1.204704 TGACAGAAGGCATCGAATCGT 59.795 47.619 1.52 0.00 0.00 3.73
389 631 1.855360 GACAGAAGGCATCGAATCGTC 59.145 52.381 1.52 0.00 0.00 4.20
390 632 1.212616 CAGAAGGCATCGAATCGTCC 58.787 55.000 1.52 3.02 0.00 4.79
391 633 0.249073 AGAAGGCATCGAATCGTCCG 60.249 55.000 1.52 0.00 0.00 4.79
392 634 0.527817 GAAGGCATCGAATCGTCCGT 60.528 55.000 1.52 1.22 0.00 4.69
393 635 0.527817 AAGGCATCGAATCGTCCGTC 60.528 55.000 1.52 0.00 0.00 4.79
394 636 1.226859 GGCATCGAATCGTCCGTCA 60.227 57.895 1.52 0.00 0.00 4.35
402 644 1.930908 AATCGTCCGTCAGTCCGTCC 61.931 60.000 0.00 0.00 0.00 4.79
426 668 2.060383 CGACCTGGCCTCATCTCCA 61.060 63.158 3.32 0.00 0.00 3.86
437 679 0.460109 TCATCTCCACGTTGCCATCG 60.460 55.000 0.00 0.00 0.00 3.84
457 699 3.803082 CCATTGCCACCGTCGCTG 61.803 66.667 0.00 0.00 0.00 5.18
459 701 4.015406 ATTGCCACCGTCGCTGGA 62.015 61.111 10.85 0.00 0.00 3.86
464 708 2.511600 CACCGTCGCTGGATTCCC 60.512 66.667 0.00 0.00 0.00 3.97
465 709 3.000819 ACCGTCGCTGGATTCCCA 61.001 61.111 0.00 0.00 40.95 4.37
474 718 1.924939 TGGATTCCCAGCTGGCTCA 60.925 57.895 28.39 15.99 37.58 4.26
588 882 5.435686 AACACTCCAGCATTAACCTGATA 57.564 39.130 6.55 0.00 32.03 2.15
589 883 4.770795 ACACTCCAGCATTAACCTGATAC 58.229 43.478 6.55 0.00 32.03 2.24
590 884 4.471386 ACACTCCAGCATTAACCTGATACT 59.529 41.667 6.55 0.00 32.03 2.12
670 970 4.831710 TCCTGTGATGAGACAGATGATAGG 59.168 45.833 0.00 0.00 45.39 2.57
684 1004 5.301045 CAGATGATAGGTTGATGGCATGTTT 59.699 40.000 3.81 0.00 0.00 2.83
765 1104 2.434185 CTGGTTCGCTTAGCCGCA 60.434 61.111 0.00 0.00 0.00 5.69
878 1228 3.002791 CAATGCACCAAGTCTACGTCAT 58.997 45.455 0.00 0.00 0.00 3.06
953 1314 1.741993 CCAAAACGTTCTTGTCTGCG 58.258 50.000 0.00 0.00 0.00 5.18
1011 1382 1.688735 CTAAGGTCCATGGCGATCAGA 59.311 52.381 6.96 0.00 0.00 3.27
1335 2815 0.534412 CTGTCCTGCTCGAATCCACT 59.466 55.000 0.00 0.00 0.00 4.00
1740 3220 1.515954 CGAGAACGGTGCCTATGGT 59.484 57.895 0.00 0.00 35.72 3.55
1743 3223 1.207329 GAGAACGGTGCCTATGGTCTT 59.793 52.381 0.00 0.00 0.00 3.01
1746 3226 1.563924 ACGGTGCCTATGGTCTTGTA 58.436 50.000 0.00 0.00 0.00 2.41
1870 3350 2.093106 CCTTCGACACCAGCTACTACT 58.907 52.381 0.00 0.00 0.00 2.57
1999 3479 2.037772 GAGTTCTTCAGGGACTTCAGCA 59.962 50.000 0.00 0.00 34.60 4.41
2101 3581 7.384115 CCAACTAGAGTTCGTTGATTCTTGTAA 59.616 37.037 0.00 0.00 42.24 2.41
2107 3587 8.926710 AGAGTTCGTTGATTCTTGTAATTGTAG 58.073 33.333 0.00 0.00 0.00 2.74
2141 3641 1.132453 CTGCACGAGTTCGAGGATGTA 59.868 52.381 8.72 0.00 43.02 2.29
2232 3735 7.412853 ACATTCTCTAACAATCATTGAATCGC 58.587 34.615 3.79 0.00 0.00 4.58
2256 3759 9.773328 CGCTATCTTTATCTTCAAATTGTCAAA 57.227 29.630 0.00 0.00 0.00 2.69
2315 3819 8.426881 AAACAAACAAATTACAATGGGTACAC 57.573 30.769 0.00 0.00 0.00 2.90
2382 3905 5.745312 TTTCCACAAGAGAGCTCAGATTA 57.255 39.130 17.77 0.00 0.00 1.75
2388 3911 5.931146 CACAAGAGAGCTCAGATTAACTGTT 59.069 40.000 17.77 0.00 45.86 3.16
2396 3919 4.505922 GCTCAGATTAACTGTTGGAGATCG 59.494 45.833 2.69 0.47 45.86 3.69
2427 3952 0.436150 CTAATCATCATGCGTCGCCG 59.564 55.000 15.88 6.06 37.07 6.46
2465 3990 2.202932 CCGCCGGAGAAGGACATG 60.203 66.667 5.05 0.00 0.00 3.21
2591 4117 1.742768 GTCGGCCGGAGATCATCTT 59.257 57.895 27.83 0.00 0.00 2.40
2608 4134 1.205655 TCTTCAAGTCTGCCAGATCCG 59.794 52.381 0.00 0.00 0.00 4.18
2609 4135 0.391661 TTCAAGTCTGCCAGATCCGC 60.392 55.000 0.00 0.00 0.00 5.54
2654 4181 1.142965 GGAGAAGAAGAGGAGCGCC 59.857 63.158 2.29 0.00 0.00 6.53
2655 4182 1.226831 GAGAAGAAGAGGAGCGCCG 60.227 63.158 2.29 0.00 39.96 6.46
2678 4205 2.463620 CCATCATCCGCACACCACG 61.464 63.158 0.00 0.00 0.00 4.94
2688 4220 1.597854 CACACCACGCTCCACACAT 60.598 57.895 0.00 0.00 0.00 3.21
2703 4235 5.555966 TCCACACATATACTCTGCACAAAA 58.444 37.500 0.00 0.00 0.00 2.44
2712 4244 3.527533 ACTCTGCACAAAACTGACGTAA 58.472 40.909 0.00 0.00 0.00 3.18
2766 4304 1.986698 ACCTAACATCGACGAAACCG 58.013 50.000 0.00 0.00 0.00 4.44
2779 4317 1.342796 GAAACCGAAGTCCGACGAGC 61.343 60.000 0.00 0.00 41.76 5.03
2784 4322 1.006571 GAAGTCCGACGAGCCACAA 60.007 57.895 0.00 0.00 0.00 3.33
2786 4324 1.461091 AAGTCCGACGAGCCACAAGA 61.461 55.000 0.00 0.00 0.00 3.02
2789 4327 2.811317 CGACGAGCCACAAGAGCC 60.811 66.667 0.00 0.00 0.00 4.70
2805 4343 2.742372 CCACCTGCTTTCCGACGG 60.742 66.667 7.84 7.84 0.00 4.79
2825 4363 0.527113 TGCCGATTGAAGCACCAATG 59.473 50.000 8.09 2.45 36.93 2.82
2857 4395 6.463614 GGAAGAAGCAGAGCCATCTTATTCTA 60.464 42.308 7.39 0.00 37.03 2.10
2860 4398 5.620738 AGCAGAGCCATCTTATTCTAACA 57.379 39.130 0.00 0.00 31.64 2.41
2866 4404 3.454375 CCATCTTATTCTAACACGGCGT 58.546 45.455 6.77 6.77 0.00 5.68
2884 4422 1.098050 GTTGATCCCACCACTGATGC 58.902 55.000 0.00 0.00 0.00 3.91
2885 4423 0.697658 TTGATCCCACCACTGATGCA 59.302 50.000 0.00 0.00 0.00 3.96
2886 4424 0.697658 TGATCCCACCACTGATGCAA 59.302 50.000 0.00 0.00 0.00 4.08
2887 4425 1.098050 GATCCCACCACTGATGCAAC 58.902 55.000 0.00 0.00 0.00 4.17
2927 4465 8.906238 AAAACTAAACCTACCCTATCTAGTCA 57.094 34.615 0.00 0.00 0.00 3.41
2930 4468 4.894252 AACCTACCCTATCTAGTCACCA 57.106 45.455 0.00 0.00 0.00 4.17
2931 4469 4.456662 ACCTACCCTATCTAGTCACCAG 57.543 50.000 0.00 0.00 0.00 4.00
2941 4479 3.230976 TCTAGTCACCAGAGCAAAGTCA 58.769 45.455 0.00 0.00 0.00 3.41
2952 4490 1.302511 CAAAGTCACCAGGGTCCCG 60.303 63.158 0.99 0.00 0.00 5.14
2954 4492 2.976284 AAAGTCACCAGGGTCCCGGA 62.976 60.000 21.40 7.91 0.00 5.14
3036 4575 1.737355 GAGCAGGCAGAGAGATCGCT 61.737 60.000 0.00 0.00 0.00 4.93
3047 4586 1.134699 AGAGATCGCTTTGGAATCGCA 60.135 47.619 0.00 0.00 0.00 5.10
3052 4591 0.168788 CGCTTTGGAATCGCATGTGT 59.831 50.000 6.09 0.00 0.00 3.72
3066 4605 0.884704 ATGTGTGTGTGAGGCGGTTC 60.885 55.000 0.00 0.00 0.00 3.62
3067 4606 2.110213 TGTGTGTGAGGCGGTTCC 59.890 61.111 0.00 0.00 0.00 3.62
3068 4607 2.110213 GTGTGTGAGGCGGTTCCA 59.890 61.111 0.00 0.00 37.29 3.53
3069 4608 1.525077 GTGTGTGAGGCGGTTCCAA 60.525 57.895 0.00 0.00 37.29 3.53
3070 4609 1.525077 TGTGTGAGGCGGTTCCAAC 60.525 57.895 0.00 0.00 37.29 3.77
3071 4610 2.280524 TGTGAGGCGGTTCCAACG 60.281 61.111 0.00 0.00 37.29 4.10
3072 4611 2.029964 GTGAGGCGGTTCCAACGA 59.970 61.111 0.00 0.00 37.29 3.85
3073 4612 1.595929 GTGAGGCGGTTCCAACGAA 60.596 57.895 0.00 0.00 37.29 3.85
3074 4613 1.301401 TGAGGCGGTTCCAACGAAG 60.301 57.895 0.00 0.00 37.29 3.79
3075 4614 2.668550 AGGCGGTTCCAACGAAGC 60.669 61.111 0.00 0.00 42.02 3.86
3079 4618 3.740513 GGTTCCAACGAAGCGGTT 58.259 55.556 0.00 0.00 36.81 4.44
3080 4619 1.281656 GGTTCCAACGAAGCGGTTG 59.718 57.895 3.70 10.23 45.32 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.837570 AAACGAGACGGCCAACCCC 62.838 63.158 2.24 0.00 0.00 4.95
1 2 2.281276 AAACGAGACGGCCAACCC 60.281 61.111 2.24 0.00 0.00 4.11
2 3 2.613506 CCAAACGAGACGGCCAACC 61.614 63.158 2.24 0.00 0.00 3.77
3 4 1.441732 AACCAAACGAGACGGCCAAC 61.442 55.000 2.24 0.00 0.00 3.77
4 5 0.106335 TAACCAAACGAGACGGCCAA 59.894 50.000 2.24 0.00 0.00 4.52
5 6 0.320073 CTAACCAAACGAGACGGCCA 60.320 55.000 2.24 0.00 0.00 5.36
6 7 1.017701 CCTAACCAAACGAGACGGCC 61.018 60.000 0.00 0.00 0.00 6.13
7 8 1.632948 GCCTAACCAAACGAGACGGC 61.633 60.000 0.00 0.00 0.00 5.68
8 9 0.320073 TGCCTAACCAAACGAGACGG 60.320 55.000 0.00 0.00 0.00 4.79
9 10 1.504359 TTGCCTAACCAAACGAGACG 58.496 50.000 0.00 0.00 0.00 4.18
10 11 3.263602 GTTTGCCTAACCAAACGAGAC 57.736 47.619 0.00 0.00 43.31 3.36
20 21 2.525368 AGGTCATTGGGTTTGCCTAAC 58.475 47.619 0.00 0.00 38.08 2.34
21 22 2.990740 AGGTCATTGGGTTTGCCTAA 57.009 45.000 0.00 0.00 39.61 2.69
22 23 4.601406 AATAGGTCATTGGGTTTGCCTA 57.399 40.909 0.00 0.00 33.74 3.93
23 24 3.473113 AATAGGTCATTGGGTTTGCCT 57.527 42.857 0.00 0.00 34.45 4.75
24 25 4.503910 GAAAATAGGTCATTGGGTTTGCC 58.496 43.478 0.00 0.00 0.00 4.52
25 26 4.173256 CGAAAATAGGTCATTGGGTTTGC 58.827 43.478 0.00 0.00 0.00 3.68
26 27 5.385509 ACGAAAATAGGTCATTGGGTTTG 57.614 39.130 0.00 0.00 0.00 2.93
27 28 5.335348 CGAACGAAAATAGGTCATTGGGTTT 60.335 40.000 0.00 0.00 0.00 3.27
28 29 4.155280 CGAACGAAAATAGGTCATTGGGTT 59.845 41.667 0.00 0.00 0.00 4.11
29 30 3.687698 CGAACGAAAATAGGTCATTGGGT 59.312 43.478 0.00 0.00 0.00 4.51
30 31 3.687698 ACGAACGAAAATAGGTCATTGGG 59.312 43.478 0.14 0.00 0.00 4.12
31 32 4.939509 ACGAACGAAAATAGGTCATTGG 57.060 40.909 0.14 0.00 0.00 3.16
32 33 9.417284 GTTTATACGAACGAAAATAGGTCATTG 57.583 33.333 0.14 0.00 0.00 2.82
33 34 9.153721 TGTTTATACGAACGAAAATAGGTCATT 57.846 29.630 0.14 0.00 32.18 2.57
34 35 8.706492 TGTTTATACGAACGAAAATAGGTCAT 57.294 30.769 0.14 0.00 32.18 3.06
35 36 8.706492 ATGTTTATACGAACGAAAATAGGTCA 57.294 30.769 0.14 0.00 32.18 4.02
36 37 7.994894 CGATGTTTATACGAACGAAAATAGGTC 59.005 37.037 0.14 0.00 32.18 3.85
37 38 7.515684 GCGATGTTTATACGAACGAAAATAGGT 60.516 37.037 0.14 0.00 32.18 3.08
38 39 6.784227 GCGATGTTTATACGAACGAAAATAGG 59.216 38.462 0.14 0.00 32.18 2.57
39 40 6.507322 CGCGATGTTTATACGAACGAAAATAG 59.493 38.462 0.00 0.00 32.18 1.73
40 41 6.196168 TCGCGATGTTTATACGAACGAAAATA 59.804 34.615 3.71 0.00 32.18 1.40
41 42 5.004630 TCGCGATGTTTATACGAACGAAAAT 59.995 36.000 3.71 0.00 32.18 1.82
42 43 4.323070 TCGCGATGTTTATACGAACGAAAA 59.677 37.500 3.71 0.00 32.18 2.29
43 44 3.850837 TCGCGATGTTTATACGAACGAAA 59.149 39.130 3.71 0.00 32.18 3.46
44 45 3.238114 GTCGCGATGTTTATACGAACGAA 59.762 43.478 14.06 0.00 34.12 3.85
45 46 2.777845 GTCGCGATGTTTATACGAACGA 59.222 45.455 14.06 0.00 34.12 3.85
46 47 2.405140 CGTCGCGATGTTTATACGAACG 60.405 50.000 20.17 6.95 34.12 3.95
47 48 2.777845 TCGTCGCGATGTTTATACGAAC 59.222 45.455 26.40 1.89 36.53 3.95
48 49 3.050273 TCGTCGCGATGTTTATACGAA 57.950 42.857 26.40 2.30 36.53 3.85
49 50 2.735643 TCGTCGCGATGTTTATACGA 57.264 45.000 26.40 18.40 37.05 3.43
50 51 3.419596 TGATTCGTCGCGATGTTTATACG 59.580 43.478 26.40 16.37 35.23 3.06
51 52 4.941727 TGATTCGTCGCGATGTTTATAC 57.058 40.909 26.40 13.73 35.23 1.47
52 53 7.626144 TTATTGATTCGTCGCGATGTTTATA 57.374 32.000 26.40 14.88 35.23 0.98
53 54 6.519353 TTATTGATTCGTCGCGATGTTTAT 57.481 33.333 26.40 17.88 35.23 1.40
54 55 5.952698 TTATTGATTCGTCGCGATGTTTA 57.047 34.783 26.40 14.23 35.23 2.01
55 56 4.850859 TTATTGATTCGTCGCGATGTTT 57.149 36.364 26.40 15.61 35.23 2.83
56 57 4.782195 GCTTTATTGATTCGTCGCGATGTT 60.782 41.667 26.40 15.96 35.23 2.71
57 58 3.302480 GCTTTATTGATTCGTCGCGATGT 60.302 43.478 26.40 9.74 35.23 3.06
58 59 3.060272 AGCTTTATTGATTCGTCGCGATG 60.060 43.478 22.29 22.29 35.23 3.84
59 60 3.123804 AGCTTTATTGATTCGTCGCGAT 58.876 40.909 14.06 0.00 35.23 4.58
60 61 2.536365 AGCTTTATTGATTCGTCGCGA 58.464 42.857 3.71 3.71 0.00 5.87
61 62 2.998668 AGCTTTATTGATTCGTCGCG 57.001 45.000 0.00 0.00 0.00 5.87
62 63 3.272567 CGAAGCTTTATTGATTCGTCGC 58.727 45.455 0.00 0.00 46.48 5.19
79 80 5.348418 TCTTTTGAGACAATCTTGCGAAG 57.652 39.130 0.00 0.00 0.00 3.79
80 81 5.749596 TTCTTTTGAGACAATCTTGCGAA 57.250 34.783 0.00 0.00 0.00 4.70
81 82 5.749596 TTTCTTTTGAGACAATCTTGCGA 57.250 34.783 0.00 0.00 0.00 5.10
82 83 6.692681 TCTTTTTCTTTTGAGACAATCTTGCG 59.307 34.615 0.00 0.00 0.00 4.85
83 84 7.992180 TCTTTTTCTTTTGAGACAATCTTGC 57.008 32.000 0.00 0.00 0.00 4.01
108 109 1.074296 AGCAGGGGGAGGGAGTTTTT 61.074 55.000 0.00 0.00 0.00 1.94
109 110 0.178843 TAGCAGGGGGAGGGAGTTTT 60.179 55.000 0.00 0.00 0.00 2.43
110 111 0.046397 ATAGCAGGGGGAGGGAGTTT 59.954 55.000 0.00 0.00 0.00 2.66
111 112 0.400670 GATAGCAGGGGGAGGGAGTT 60.401 60.000 0.00 0.00 0.00 3.01
112 113 1.237458 GATAGCAGGGGGAGGGAGT 59.763 63.158 0.00 0.00 0.00 3.85
113 114 1.910772 CGATAGCAGGGGGAGGGAG 60.911 68.421 0.00 0.00 0.00 4.30
114 115 2.201490 CGATAGCAGGGGGAGGGA 59.799 66.667 0.00 0.00 0.00 4.20
115 116 2.122813 ACGATAGCAGGGGGAGGG 60.123 66.667 0.00 0.00 42.67 4.30
116 117 1.457643 TGACGATAGCAGGGGGAGG 60.458 63.158 0.00 0.00 42.67 4.30
117 118 0.468214 TCTGACGATAGCAGGGGGAG 60.468 60.000 0.00 0.00 39.58 4.30
118 119 0.188587 ATCTGACGATAGCAGGGGGA 59.811 55.000 0.00 0.00 39.58 4.81
119 120 0.319728 CATCTGACGATAGCAGGGGG 59.680 60.000 0.00 0.00 39.58 5.40
120 121 1.043816 ACATCTGACGATAGCAGGGG 58.956 55.000 0.00 0.00 39.58 4.79
121 122 5.843673 ATATACATCTGACGATAGCAGGG 57.156 43.478 0.00 0.00 39.58 4.45
122 123 5.968261 CGAATATACATCTGACGATAGCAGG 59.032 44.000 0.00 0.00 39.58 4.85
123 124 6.776094 TCGAATATACATCTGACGATAGCAG 58.224 40.000 0.00 0.00 40.18 4.24
124 125 6.371825 ACTCGAATATACATCTGACGATAGCA 59.628 38.462 0.00 0.00 42.67 3.49
125 126 6.777101 ACTCGAATATACATCTGACGATAGC 58.223 40.000 0.00 0.00 42.67 2.97
126 127 7.279090 AGGACTCGAATATACATCTGACGATAG 59.721 40.741 0.00 0.00 46.19 2.08
127 128 7.104290 AGGACTCGAATATACATCTGACGATA 58.896 38.462 0.00 0.00 0.00 2.92
128 129 5.941058 AGGACTCGAATATACATCTGACGAT 59.059 40.000 0.00 0.00 0.00 3.73
129 130 5.306394 AGGACTCGAATATACATCTGACGA 58.694 41.667 0.00 0.00 0.00 4.20
130 131 5.614923 AGGACTCGAATATACATCTGACG 57.385 43.478 0.00 0.00 0.00 4.35
159 160 9.577110 CTGAAAACACAGATGCATGTAATAAAT 57.423 29.630 2.46 0.00 39.94 1.40
160 161 8.791675 TCTGAAAACACAGATGCATGTAATAAA 58.208 29.630 2.46 0.00 41.21 1.40
161 162 8.334263 TCTGAAAACACAGATGCATGTAATAA 57.666 30.769 2.46 0.00 41.21 1.40
162 163 7.920160 TCTGAAAACACAGATGCATGTAATA 57.080 32.000 2.46 0.00 41.21 0.98
163 164 6.822667 TCTGAAAACACAGATGCATGTAAT 57.177 33.333 2.46 0.00 41.21 1.89
164 165 6.262944 ACTTCTGAAAACACAGATGCATGTAA 59.737 34.615 2.46 0.00 44.67 2.41
165 166 5.764686 ACTTCTGAAAACACAGATGCATGTA 59.235 36.000 2.46 0.00 44.67 2.29
166 167 4.581824 ACTTCTGAAAACACAGATGCATGT 59.418 37.500 2.46 0.00 44.67 3.21
167 168 5.117355 ACTTCTGAAAACACAGATGCATG 57.883 39.130 2.46 0.00 44.67 4.06
168 169 6.882610 TTACTTCTGAAAACACAGATGCAT 57.117 33.333 0.00 0.00 44.67 3.96
169 170 6.494842 GTTTACTTCTGAAAACACAGATGCA 58.505 36.000 0.00 0.00 44.67 3.96
170 171 5.621228 CGTTTACTTCTGAAAACACAGATGC 59.379 40.000 0.00 0.00 44.67 3.91
171 172 6.018262 TCCGTTTACTTCTGAAAACACAGATG 60.018 38.462 0.00 0.00 44.67 2.90
172 173 6.053005 TCCGTTTACTTCTGAAAACACAGAT 58.947 36.000 0.00 0.00 44.67 2.90
173 174 5.421277 TCCGTTTACTTCTGAAAACACAGA 58.579 37.500 0.00 0.00 43.83 3.41
174 175 5.728351 TCCGTTTACTTCTGAAAACACAG 57.272 39.130 4.80 0.00 35.74 3.66
175 176 5.644636 AGTTCCGTTTACTTCTGAAAACACA 59.355 36.000 4.80 0.00 35.74 3.72
176 177 6.115450 AGTTCCGTTTACTTCTGAAAACAC 57.885 37.500 4.80 0.00 35.74 3.32
177 178 6.746745 AAGTTCCGTTTACTTCTGAAAACA 57.253 33.333 4.80 0.00 35.74 2.83
243 246 6.349944 GCTGTTCCAAGAAATCAATCACATCT 60.350 38.462 0.00 0.00 0.00 2.90
248 251 6.660521 ACATAGCTGTTCCAAGAAATCAATCA 59.339 34.615 0.00 0.00 28.70 2.57
256 259 4.225942 AGGATGACATAGCTGTTCCAAGAA 59.774 41.667 0.00 0.00 35.53 2.52
287 529 2.766875 TACGCGCACCATTGTTCCGA 62.767 55.000 5.73 0.00 0.00 4.55
301 543 1.800315 AGTAAGCAGCACGTACGCG 60.800 57.895 16.72 3.53 44.93 6.01
318 560 0.602638 TGACACGGTAGCAAAGGCAG 60.603 55.000 0.00 0.00 44.61 4.85
331 573 3.181540 CGAGAACTACTTTGCATGACACG 60.182 47.826 0.00 0.00 0.00 4.49
332 574 3.423645 GCGAGAACTACTTTGCATGACAC 60.424 47.826 0.00 0.00 32.87 3.67
333 575 2.736721 GCGAGAACTACTTTGCATGACA 59.263 45.455 0.00 0.00 32.87 3.58
354 596 3.531934 TCTGTCATGCATCTGTACAGG 57.468 47.619 22.48 8.81 38.44 4.00
356 598 3.865446 CCTTCTGTCATGCATCTGTACA 58.135 45.455 0.00 0.00 0.00 2.90
359 601 1.003928 TGCCTTCTGTCATGCATCTGT 59.996 47.619 0.00 0.00 0.00 3.41
372 614 0.249073 CGGACGATTCGATGCCTTCT 60.249 55.000 13.95 0.00 0.00 2.85
376 618 1.209275 CTGACGGACGATTCGATGCC 61.209 60.000 13.95 9.77 0.00 4.40
384 626 2.404995 GGACGGACTGACGGACGAT 61.405 63.158 0.00 0.00 38.39 3.73
385 627 3.052082 GGACGGACTGACGGACGA 61.052 66.667 0.00 0.00 38.39 4.20
386 628 4.456253 CGGACGGACTGACGGACG 62.456 72.222 0.00 0.00 38.39 4.79
387 629 2.912624 AACGGACGGACTGACGGAC 61.913 63.158 0.00 0.00 38.39 4.79
388 630 2.595463 AACGGACGGACTGACGGA 60.595 61.111 0.00 0.00 38.39 4.69
389 631 2.430244 CAACGGACGGACTGACGG 60.430 66.667 0.00 0.00 38.39 4.79
390 632 1.728426 GTCAACGGACGGACTGACG 60.728 63.158 7.68 0.00 40.31 4.35
391 633 4.240049 GTCAACGGACGGACTGAC 57.760 61.111 7.68 7.68 33.68 3.51
402 644 2.432628 GAGGCCAGGTCGTCAACG 60.433 66.667 5.01 0.00 41.45 4.10
413 655 1.296392 CAACGTGGAGATGAGGCCA 59.704 57.895 5.01 0.00 0.00 5.36
457 699 1.153005 CTGAGCCAGCTGGGAATCC 60.153 63.158 33.46 16.68 40.01 3.01
588 882 7.482169 TCAAGAGAATAACCTCACATGTAGT 57.518 36.000 0.00 0.00 35.68 2.73
589 883 7.042187 GCATCAAGAGAATAACCTCACATGTAG 60.042 40.741 0.00 0.00 35.68 2.74
590 884 6.763135 GCATCAAGAGAATAACCTCACATGTA 59.237 38.462 0.00 0.00 35.68 2.29
684 1004 1.118965 ACCAGTGTGTCGTCCATGGA 61.119 55.000 11.44 11.44 0.00 3.41
765 1104 3.743911 TCAATGATCAAACGTACGCAACT 59.256 39.130 16.72 0.00 0.00 3.16
836 1184 2.669569 CAGCGTGACAACCTGGGG 60.670 66.667 0.00 0.00 0.00 4.96
837 1185 1.961277 GTCAGCGTGACAACCTGGG 60.961 63.158 11.62 0.00 46.22 4.45
878 1228 3.332783 TCCCTCTACTTATAGATGGCCGA 59.667 47.826 0.00 0.00 41.00 5.54
953 1314 4.718940 AAGCACAATTTACTATGTGGCC 57.281 40.909 0.00 0.00 45.46 5.36
1011 1382 0.255318 CCAGAGGGAGCAGCAAAGAT 59.745 55.000 0.00 0.00 35.59 2.40
1124 1500 0.755686 GATCTTGGCCATCTCCTCGT 59.244 55.000 6.09 0.00 0.00 4.18
1740 3220 1.277273 TCGAGAGACGGGTCTACAAGA 59.723 52.381 0.48 0.00 40.61 3.02
1999 3479 4.042884 TCTCCCATCTTGATCATGGACTT 58.957 43.478 14.30 0.00 43.32 3.01
2101 3581 6.145048 GTGCAGTTACGACTTACAACTACAAT 59.855 38.462 0.00 0.00 32.54 2.71
2107 3587 3.044986 TCGTGCAGTTACGACTTACAAC 58.955 45.455 0.00 0.00 46.94 3.32
2141 3641 8.097038 ACAACTACAATGAACAGTATCAGACAT 58.903 33.333 0.00 0.00 31.76 3.06
2263 3766 5.888724 TGGACTTGTGGTAATTCTGACAAAA 59.111 36.000 0.00 0.00 0.00 2.44
2269 3772 7.881142 TGTTTAATGGACTTGTGGTAATTCTG 58.119 34.615 0.00 0.00 0.00 3.02
2315 3819 0.591659 TCTCTTCGAGTGACCACGTG 59.408 55.000 9.08 9.08 36.20 4.49
2382 3905 2.350522 GCACATCGATCTCCAACAGTT 58.649 47.619 0.00 0.00 0.00 3.16
2388 3911 0.107703 GTTGGGCACATCGATCTCCA 60.108 55.000 0.00 0.00 0.00 3.86
2396 3919 3.554934 TGATGATTAGGTTGGGCACATC 58.445 45.455 0.00 0.00 34.98 3.06
2459 3984 0.036732 TGTGGAGGTTGCTCATGTCC 59.963 55.000 0.00 0.00 0.00 4.02
2465 3990 1.398692 TTTTGGTGTGGAGGTTGCTC 58.601 50.000 0.00 0.00 0.00 4.26
2526 4051 3.442273 GTCTTTGACCGGCCATTTAATCA 59.558 43.478 0.00 0.00 0.00 2.57
2539 4064 2.409975 TCGGTTTCATCGTCTTTGACC 58.590 47.619 0.00 0.00 0.00 4.02
2591 4117 1.219124 GCGGATCTGGCAGACTTGA 59.781 57.895 21.37 0.00 0.00 3.02
2609 4135 0.109458 TTGGATGAAGACGACGACGG 60.109 55.000 12.58 0.00 44.46 4.79
2654 4181 3.204119 TGCGGATGATGGCTTGCG 61.204 61.111 0.00 0.00 36.36 4.85
2655 4182 2.409055 TGTGCGGATGATGGCTTGC 61.409 57.895 0.00 0.00 0.00 4.01
2678 4205 3.126831 GTGCAGAGTATATGTGTGGAGC 58.873 50.000 0.00 0.00 0.00 4.70
2684 4211 6.537566 GTCAGTTTTGTGCAGAGTATATGTG 58.462 40.000 0.00 0.00 0.00 3.21
2685 4212 5.348724 CGTCAGTTTTGTGCAGAGTATATGT 59.651 40.000 0.00 0.00 0.00 2.29
2688 4220 4.878439 ACGTCAGTTTTGTGCAGAGTATA 58.122 39.130 0.00 0.00 0.00 1.47
2703 4235 1.028330 TCTCGGGCGATTACGTCAGT 61.028 55.000 0.00 0.00 46.58 3.41
2712 4244 3.148279 GGTGTCCTCTCGGGCGAT 61.148 66.667 0.00 0.00 37.90 4.58
2727 4265 1.529244 GTGCTGGCTGGAGTTTGGT 60.529 57.895 0.00 0.00 0.00 3.67
2766 4304 1.006571 TTGTGGCTCGTCGGACTTC 60.007 57.895 6.57 0.00 0.00 3.01
2789 4327 2.030562 ACCGTCGGAAAGCAGGTG 59.969 61.111 20.51 0.00 33.37 4.00
2800 4338 3.081133 CTTCAATCGGCACCGTCG 58.919 61.111 9.23 0.00 40.74 5.12
2825 4363 0.251634 CTCTGCTTCTTCCCCACTCC 59.748 60.000 0.00 0.00 0.00 3.85
2857 4395 1.964373 GTGGGATCAACGCCGTGTT 60.964 57.895 0.00 0.00 43.09 3.32
2860 4398 3.632080 TGGTGGGATCAACGCCGT 61.632 61.111 12.74 0.00 41.36 5.68
2866 4404 0.697658 TGCATCAGTGGTGGGATCAA 59.302 50.000 5.34 0.00 0.00 2.57
2884 4422 1.593196 TTTCTCAGAGGCGTTGGTTG 58.407 50.000 0.00 0.00 0.00 3.77
2885 4423 2.341846 TTTTCTCAGAGGCGTTGGTT 57.658 45.000 0.00 0.00 0.00 3.67
2886 4424 1.947456 GTTTTTCTCAGAGGCGTTGGT 59.053 47.619 0.00 0.00 0.00 3.67
2887 4425 2.222027 AGTTTTTCTCAGAGGCGTTGG 58.778 47.619 0.00 0.00 0.00 3.77
2927 4465 0.109342 CCTGGTGACTTTGCTCTGGT 59.891 55.000 0.00 0.00 0.00 4.00
2930 4468 0.398318 GACCCTGGTGACTTTGCTCT 59.602 55.000 0.00 0.00 0.00 4.09
2931 4469 0.606673 GGACCCTGGTGACTTTGCTC 60.607 60.000 0.00 0.00 0.00 4.26
2941 4479 4.817909 GGGATCCGGGACCCTGGT 62.818 72.222 23.35 4.34 42.88 4.00
3013 4551 1.338973 GATCTCTCTGCCTGCTCTCTG 59.661 57.143 0.00 0.00 0.00 3.35
3020 4558 1.288350 CAAAGCGATCTCTCTGCCTG 58.712 55.000 0.00 0.00 0.00 4.85
3036 4575 1.952990 ACACACACATGCGATTCCAAA 59.047 42.857 0.00 0.00 0.00 3.28
3047 4586 0.884704 GAACCGCCTCACACACACAT 60.885 55.000 0.00 0.00 0.00 3.21
3052 4591 1.525077 GTTGGAACCGCCTCACACA 60.525 57.895 0.00 0.00 37.63 3.72


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

AutoCloner maintained by Alex Coulton.