Multiple sequence alignment - TraesCS4D01G133400

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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 TraesCS4D01G133400 chr4D 100.000 2690 0 0 1 2690 119825307 119827996 0.000000e+00 4968
1 TraesCS4D01G133400 chr4D 94.054 185 10 1 1 185 351667449 351667266 2.040000e-71 279
2 TraesCS4D01G133400 chr4D 98.026 152 3 0 1 152 156516643 156516794 5.710000e-67 265
3 TraesCS4D01G133400 chr4B 93.308 1554 54 14 186 1715 182673685 182675212 0.000000e+00 2248
4 TraesCS4D01G133400 chr4B 87.818 550 63 3 2140 2685 182675838 182676387 2.260000e-180 641
5 TraesCS4D01G133400 chr4B 92.553 94 7 0 1765 1858 182675327 182675420 4.670000e-28 135
6 TraesCS4D01G133400 chr4A 92.842 1453 54 22 471 1898 450793425 450794852 0.000000e+00 2061
7 TraesCS4D01G133400 chr4A 88.918 379 35 6 2006 2384 450795330 450795701 6.790000e-126 460
8 TraesCS4D01G133400 chr4A 93.688 301 14 1 186 481 450792947 450793247 1.900000e-121 446
9 TraesCS4D01G133400 chr4A 89.177 231 24 1 2460 2690 450809711 450809940 1.220000e-73 287
10 TraesCS4D01G133400 chr4A 74.370 476 97 23 2133 2598 714427042 714426582 2.130000e-41 180
11 TraesCS4D01G133400 chr3D 95.833 192 7 1 1 192 508076646 508076456 2.600000e-80 309
12 TraesCS4D01G133400 chr3D 93.333 195 13 0 1 195 547628987 547628793 3.390000e-74 289
13 TraesCS4D01G133400 chr2D 95.135 185 9 0 1 185 492105492 492105308 2.620000e-75 292
14 TraesCS4D01G133400 chr1D 95.135 185 9 0 1 185 41437439 41437623 2.620000e-75 292
15 TraesCS4D01G133400 chr1D 100.000 69 0 0 1 69 460759667 460759599 7.820000e-26 128
16 TraesCS4D01G133400 chr5D 91.710 193 12 3 1 191 546785146 546784956 5.710000e-67 265
17 TraesCS4D01G133400 chr5D 79.599 299 22 21 1431 1701 254519334 254519047 7.650000e-41 178
18 TraesCS4D01G133400 chr5D 100.000 69 0 0 1 69 7472015 7471947 7.820000e-26 128
19 TraesCS4D01G133400 chr5B 74.214 477 98 23 2133 2598 532767978 532767516 2.750000e-40 176
20 TraesCS4D01G133400 chr5B 74.138 464 97 19 2133 2585 149382197 149382648 1.280000e-38 171
21 TraesCS4D01G133400 chr5B 78.618 304 25 22 1428 1701 288330017 288330310 5.960000e-37 165
22 TraesCS4D01G133400 chr5A 79.402 301 22 20 1431 1701 337820298 337820008 2.750000e-40 176
23 TraesCS4D01G133400 chr2A 73.810 462 100 20 2133 2585 644222315 644222764 2.140000e-36 163
24 TraesCS4D01G133400 chr2B 76.897 290 57 9 2314 2598 518772184 518771900 3.590000e-34 156
25 TraesCS4D01G133400 chr7B 74.352 386 86 12 2208 2584 234915002 234915383 4.640000e-33 152
26 TraesCS4D01G133400 chr7A 76.027 292 61 8 2300 2585 275974573 275974861 2.790000e-30 143


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 TraesCS4D01G133400 chr4D 119825307 119827996 2689 False 4968 4968 100.000000 1 2690 1 chr4D.!!$F1 2689
1 TraesCS4D01G133400 chr4B 182673685 182676387 2702 False 1008 2248 91.226333 186 2685 3 chr4B.!!$F1 2499
2 TraesCS4D01G133400 chr4A 450792947 450795701 2754 False 989 2061 91.816000 186 2384 3 chr4A.!!$F2 2198

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
98 99 0.036306 TCTTCCCTTTTCCAGCGGTC 59.964 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 2235 0.178973 TTCCTCCACCTCGACAGACA 60.179 55.0 0.0 0.0 0.0 3.41 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
23 24 5.314923 ACTCAAATTAATGCATGCGAACT 57.685 34.783 14.09 0.00 0.00 3.01
24 25 5.097529 ACTCAAATTAATGCATGCGAACTG 58.902 37.500 14.09 8.39 0.00 3.16
25 26 5.106197 ACTCAAATTAATGCATGCGAACTGA 60.106 36.000 14.09 11.70 0.00 3.41
26 27 5.094812 TCAAATTAATGCATGCGAACTGAC 58.905 37.500 14.09 0.00 0.00 3.51
27 28 2.804421 TTAATGCATGCGAACTGACG 57.196 45.000 14.09 0.00 0.00 4.35
28 29 1.720805 TAATGCATGCGAACTGACGT 58.279 45.000 14.09 0.00 35.59 4.34
29 30 0.166597 AATGCATGCGAACTGACGTG 59.833 50.000 14.09 0.00 35.59 4.49
30 31 1.638388 ATGCATGCGAACTGACGTGG 61.638 55.000 14.09 0.00 35.59 4.94
31 32 2.476051 CATGCGAACTGACGTGGC 59.524 61.111 0.00 0.00 35.59 5.01
32 33 2.030412 ATGCGAACTGACGTGGCA 59.970 55.556 0.00 0.00 37.66 4.92
33 34 2.029288 ATGCGAACTGACGTGGCAG 61.029 57.895 0.00 0.00 41.63 4.85
34 35 2.355837 GCGAACTGACGTGGCAGA 60.356 61.111 10.26 0.00 39.20 4.26
35 36 2.375766 GCGAACTGACGTGGCAGAG 61.376 63.158 10.26 1.69 39.20 3.35
36 37 2.375766 CGAACTGACGTGGCAGAGC 61.376 63.158 10.26 0.00 39.20 4.09
37 38 1.300931 GAACTGACGTGGCAGAGCA 60.301 57.895 10.26 0.00 39.20 4.26
38 39 0.671781 GAACTGACGTGGCAGAGCAT 60.672 55.000 10.26 0.00 39.20 3.79
39 40 0.671781 AACTGACGTGGCAGAGCATC 60.672 55.000 10.26 0.00 39.20 3.91
53 54 1.789464 GAGCATCTTCCTAATCACGCG 59.211 52.381 3.53 3.53 0.00 6.01
54 55 0.861837 GCATCTTCCTAATCACGCGG 59.138 55.000 12.47 0.00 0.00 6.46
55 56 1.502231 CATCTTCCTAATCACGCGGG 58.498 55.000 12.47 6.51 0.00 6.13
56 57 0.393077 ATCTTCCTAATCACGCGGGG 59.607 55.000 9.32 0.00 0.00 5.73
57 58 1.227556 CTTCCTAATCACGCGGGGG 60.228 63.158 9.32 0.50 0.00 5.40
58 59 1.682451 CTTCCTAATCACGCGGGGGA 61.682 60.000 9.32 6.97 0.00 4.81
59 60 1.963464 TTCCTAATCACGCGGGGGAC 61.963 60.000 9.32 0.00 0.00 4.46
60 61 2.727392 CCTAATCACGCGGGGGACA 61.727 63.158 9.32 0.00 0.00 4.02
61 62 1.227263 CTAATCACGCGGGGGACAG 60.227 63.158 9.32 3.45 0.00 3.51
69 70 2.997315 CGGGGGACAGCAGAGTGA 60.997 66.667 0.00 0.00 0.00 3.41
70 71 2.985456 GGGGGACAGCAGAGTGAG 59.015 66.667 0.00 0.00 0.00 3.51
71 72 2.664081 GGGGGACAGCAGAGTGAGG 61.664 68.421 0.00 0.00 0.00 3.86
72 73 2.664081 GGGGACAGCAGAGTGAGGG 61.664 68.421 0.00 0.00 0.00 4.30
73 74 1.610673 GGGACAGCAGAGTGAGGGA 60.611 63.158 0.00 0.00 0.00 4.20
74 75 1.594310 GGACAGCAGAGTGAGGGAC 59.406 63.158 0.00 0.00 0.00 4.46
75 76 1.594310 GACAGCAGAGTGAGGGACC 59.406 63.158 0.00 0.00 0.00 4.46
76 77 2.219325 GACAGCAGAGTGAGGGACCG 62.219 65.000 0.00 0.00 0.00 4.79
77 78 2.681778 AGCAGAGTGAGGGACCGG 60.682 66.667 0.00 0.00 0.00 5.28
78 79 2.997897 GCAGAGTGAGGGACCGGT 60.998 66.667 6.92 6.92 0.00 5.28
79 80 2.584391 GCAGAGTGAGGGACCGGTT 61.584 63.158 9.42 0.00 0.00 4.44
80 81 1.592223 CAGAGTGAGGGACCGGTTC 59.408 63.158 9.42 6.37 0.00 3.62
81 82 0.900647 CAGAGTGAGGGACCGGTTCT 60.901 60.000 13.96 12.05 0.00 3.01
82 83 0.178929 AGAGTGAGGGACCGGTTCTT 60.179 55.000 13.96 4.49 0.00 2.52
83 84 0.246910 GAGTGAGGGACCGGTTCTTC 59.753 60.000 18.01 18.01 0.00 2.87
84 85 1.192803 AGTGAGGGACCGGTTCTTCC 61.193 60.000 21.55 11.93 0.00 3.46
89 90 3.739703 GGACCGGTTCTTCCCTTTT 57.260 52.632 9.42 0.00 0.00 2.27
90 91 1.531423 GGACCGGTTCTTCCCTTTTC 58.469 55.000 9.42 0.00 0.00 2.29
91 92 1.531423 GACCGGTTCTTCCCTTTTCC 58.469 55.000 9.42 0.00 0.00 3.13
92 93 0.848053 ACCGGTTCTTCCCTTTTCCA 59.152 50.000 0.00 0.00 0.00 3.53
93 94 1.202891 ACCGGTTCTTCCCTTTTCCAG 60.203 52.381 0.00 0.00 0.00 3.86
94 95 0.881796 CGGTTCTTCCCTTTTCCAGC 59.118 55.000 0.00 0.00 0.00 4.85
95 96 0.881796 GGTTCTTCCCTTTTCCAGCG 59.118 55.000 0.00 0.00 0.00 5.18
96 97 0.881796 GTTCTTCCCTTTTCCAGCGG 59.118 55.000 0.00 0.00 0.00 5.52
97 98 0.476771 TTCTTCCCTTTTCCAGCGGT 59.523 50.000 0.00 0.00 0.00 5.68
98 99 0.036306 TCTTCCCTTTTCCAGCGGTC 59.964 55.000 0.00 0.00 0.00 4.79
99 100 1.298859 CTTCCCTTTTCCAGCGGTCG 61.299 60.000 0.00 0.00 0.00 4.79
100 101 2.741486 TTCCCTTTTCCAGCGGTCGG 62.741 60.000 0.00 0.00 0.00 4.79
101 102 2.345991 CCTTTTCCAGCGGTCGGA 59.654 61.111 2.27 2.27 0.00 4.55
102 103 2.033194 CCTTTTCCAGCGGTCGGAC 61.033 63.158 0.00 0.00 30.29 4.79
103 104 1.301401 CTTTTCCAGCGGTCGGACA 60.301 57.895 10.76 0.00 30.29 4.02
104 105 1.291877 CTTTTCCAGCGGTCGGACAG 61.292 60.000 10.76 7.23 30.29 3.51
105 106 3.876589 TTTCCAGCGGTCGGACAGC 62.877 63.158 22.98 22.98 39.63 4.40
122 123 4.988598 CACGCGCAGTGGTCCCTT 62.989 66.667 19.93 0.00 46.77 3.95
123 124 4.681978 ACGCGCAGTGGTCCCTTC 62.682 66.667 5.73 0.00 45.78 3.46
125 126 4.329545 GCGCAGTGGTCCCTTCCA 62.330 66.667 0.30 0.00 34.85 3.53
126 127 2.671070 CGCAGTGGTCCCTTCCAT 59.329 61.111 0.00 0.00 39.81 3.41
127 128 1.904771 CGCAGTGGTCCCTTCCATA 59.095 57.895 0.00 0.00 39.81 2.74
128 129 0.469917 CGCAGTGGTCCCTTCCATAT 59.530 55.000 0.00 0.00 39.81 1.78
129 130 1.134098 CGCAGTGGTCCCTTCCATATT 60.134 52.381 0.00 0.00 39.81 1.28
130 131 2.104111 CGCAGTGGTCCCTTCCATATTA 59.896 50.000 0.00 0.00 39.81 0.98
131 132 3.744660 GCAGTGGTCCCTTCCATATTAG 58.255 50.000 0.00 0.00 39.81 1.73
132 133 3.391296 GCAGTGGTCCCTTCCATATTAGA 59.609 47.826 0.00 0.00 39.81 2.10
133 134 4.141482 GCAGTGGTCCCTTCCATATTAGAA 60.141 45.833 0.00 0.00 39.81 2.10
134 135 5.631481 GCAGTGGTCCCTTCCATATTAGAAA 60.631 44.000 0.00 0.00 39.81 2.52
135 136 6.058183 CAGTGGTCCCTTCCATATTAGAAAG 58.942 44.000 0.00 0.00 39.81 2.62
136 137 5.132816 AGTGGTCCCTTCCATATTAGAAAGG 59.867 44.000 0.00 0.00 39.81 3.11
137 138 5.043762 TGGTCCCTTCCATATTAGAAAGGT 58.956 41.667 0.00 0.00 31.96 3.50
138 139 5.104109 TGGTCCCTTCCATATTAGAAAGGTG 60.104 44.000 0.00 0.00 31.96 4.00
139 140 4.822350 GTCCCTTCCATATTAGAAAGGTGC 59.178 45.833 0.00 0.00 0.00 5.01
140 141 3.815401 CCCTTCCATATTAGAAAGGTGCG 59.185 47.826 0.00 0.00 0.00 5.34
141 142 3.251004 CCTTCCATATTAGAAAGGTGCGC 59.749 47.826 0.00 0.00 0.00 6.09
142 143 3.838244 TCCATATTAGAAAGGTGCGCT 57.162 42.857 9.73 0.00 0.00 5.92
143 144 3.728845 TCCATATTAGAAAGGTGCGCTC 58.271 45.455 9.73 4.47 0.00 5.03
144 145 2.476619 CCATATTAGAAAGGTGCGCTCG 59.523 50.000 9.73 0.00 0.00 5.03
145 146 2.218953 TATTAGAAAGGTGCGCTCGG 57.781 50.000 9.73 0.00 0.00 4.63
146 147 1.090052 ATTAGAAAGGTGCGCTCGGC 61.090 55.000 9.73 0.00 43.96 5.54
147 148 2.167398 TTAGAAAGGTGCGCTCGGCT 62.167 55.000 9.73 3.24 44.05 5.52
148 149 1.317431 TAGAAAGGTGCGCTCGGCTA 61.317 55.000 9.73 2.25 44.05 3.93
149 150 2.125512 AAAGGTGCGCTCGGCTAG 60.126 61.111 9.73 0.00 44.05 3.42
150 151 2.558554 GAAAGGTGCGCTCGGCTAGA 62.559 60.000 9.73 0.00 44.05 2.43
151 152 2.837371 AAAGGTGCGCTCGGCTAGAC 62.837 60.000 9.73 0.00 44.05 2.59
152 153 4.129737 GGTGCGCTCGGCTAGACA 62.130 66.667 9.73 0.00 44.05 3.41
153 154 2.580867 GTGCGCTCGGCTAGACAG 60.581 66.667 9.73 0.00 44.05 3.51
163 164 4.135153 CTAGACAGCTGGGCGCGT 62.135 66.667 19.93 0.00 45.59 6.01
164 165 4.435436 TAGACAGCTGGGCGCGTG 62.435 66.667 19.93 0.00 45.59 5.34
245 246 4.005650 TGCTTTCCAGTGCTCTGATTAAG 58.994 43.478 17.19 15.59 43.76 1.85
285 286 3.428534 GGAACGTTAAAAGCAGCCAAATG 59.571 43.478 0.00 0.00 0.00 2.32
421 427 5.578336 GCTGAAAAGAAAGGCATATGGTTTC 59.422 40.000 4.56 0.00 0.00 2.78
450 456 3.904717 TGAGTGGGAAGAGTAGGAGATC 58.095 50.000 0.00 0.00 0.00 2.75
527 721 0.601311 AGTCGTGACTGCCAGCTTTC 60.601 55.000 0.86 0.00 40.75 2.62
538 732 3.025978 TGCCAGCTTTCATTTATCCTGG 58.974 45.455 0.00 0.00 42.04 4.45
555 749 0.108774 TGGTTGTGCCGTGTATCCAA 59.891 50.000 0.00 0.00 41.21 3.53
556 750 0.802494 GGTTGTGCCGTGTATCCAAG 59.198 55.000 0.00 0.00 0.00 3.61
571 765 7.151308 GTGTATCCAAGATCGATTGAGATTCT 58.849 38.462 0.00 0.00 31.55 2.40
575 769 4.989797 CCAAGATCGATTGAGATTCTCCAG 59.010 45.833 11.12 0.71 31.55 3.86
636 830 2.580867 GAGCTGGTCTGCGCGTAG 60.581 66.667 18.85 18.85 38.13 3.51
694 888 2.721603 CGACGTAGCTTGTATCTGCATC 59.278 50.000 0.00 0.00 0.00 3.91
800 997 0.745845 ATGGTCTCATCGCACAAGGC 60.746 55.000 0.00 0.00 39.90 4.35
876 1073 3.695060 ACGTACAGAGCAATAGCACTAGT 59.305 43.478 0.00 0.00 45.49 2.57
877 1074 4.880120 ACGTACAGAGCAATAGCACTAGTA 59.120 41.667 0.00 0.00 45.49 1.82
879 1076 4.314740 ACAGAGCAATAGCACTAGTAGC 57.685 45.455 0.00 1.88 45.49 3.58
880 1077 3.957497 ACAGAGCAATAGCACTAGTAGCT 59.043 43.478 19.21 19.21 45.49 3.32
881 1078 4.202101 ACAGAGCAATAGCACTAGTAGCTG 60.202 45.833 22.32 12.43 45.49 4.24
882 1079 3.957497 AGAGCAATAGCACTAGTAGCTGT 59.043 43.478 22.32 16.20 45.49 4.40
883 1080 5.009110 CAGAGCAATAGCACTAGTAGCTGTA 59.991 44.000 22.32 9.83 45.49 2.74
884 1081 5.009210 AGAGCAATAGCACTAGTAGCTGTAC 59.991 44.000 22.32 14.57 45.49 2.90
885 1082 4.890581 AGCAATAGCACTAGTAGCTGTACT 59.109 41.667 22.32 15.93 45.49 2.73
886 1083 5.009210 AGCAATAGCACTAGTAGCTGTACTC 59.991 44.000 22.32 12.31 45.49 2.59
887 1084 5.764131 CAATAGCACTAGTAGCTGTACTCC 58.236 45.833 22.32 0.00 43.33 3.85
916 1114 4.765339 ACTGGCGCACACATATATAGAGTA 59.235 41.667 10.83 0.00 0.00 2.59
918 1116 4.106197 GGCGCACACATATATAGAGTAGC 58.894 47.826 10.83 0.00 0.00 3.58
967 1165 1.677052 CGAAGAGTAGCCAGTAGACCC 59.323 57.143 0.00 0.00 0.00 4.46
1202 1406 2.348998 CCTCCAAGCTCTTGCGGT 59.651 61.111 4.17 0.00 45.42 5.68
1203 1407 2.037136 CCTCCAAGCTCTTGCGGTG 61.037 63.158 4.17 0.00 45.42 4.94
1204 1408 2.669569 TCCAAGCTCTTGCGGTGC 60.670 61.111 4.17 0.00 45.42 5.01
1205 1409 3.741476 CCAAGCTCTTGCGGTGCC 61.741 66.667 4.17 0.00 45.42 5.01
1399 1621 1.251753 GCGTGTATACTCGTCGTCGC 61.252 60.000 23.66 14.31 35.55 5.19
1452 1674 3.793144 GCTTGCCGGAAGACGCTG 61.793 66.667 5.05 0.00 42.52 5.18
1544 1766 1.445716 GAGGATCCGACGACGACCAT 61.446 60.000 9.28 0.00 42.66 3.55
1662 1893 0.825840 AGCTCATCGCCTCCTACCTC 60.826 60.000 0.00 0.00 40.39 3.85
1722 1953 4.833380 AGCTCCTTAATTACTCCTCGCATA 59.167 41.667 0.00 0.00 0.00 3.14
1723 1954 5.482175 AGCTCCTTAATTACTCCTCGCATAT 59.518 40.000 0.00 0.00 0.00 1.78
1724 1955 6.014156 AGCTCCTTAATTACTCCTCGCATATT 60.014 38.462 0.00 0.00 0.00 1.28
1725 1956 7.178628 AGCTCCTTAATTACTCCTCGCATATTA 59.821 37.037 0.00 0.00 0.00 0.98
1726 1957 7.489757 GCTCCTTAATTACTCCTCGCATATTAG 59.510 40.741 0.00 0.00 0.00 1.73
1728 1959 8.867097 TCCTTAATTACTCCTCGCATATTAGTT 58.133 33.333 0.00 0.00 0.00 2.24
1731 1962 9.616634 TTAATTACTCCTCGCATATTAGTTACG 57.383 33.333 0.00 0.00 0.00 3.18
1732 1963 6.624352 TTACTCCTCGCATATTAGTTACGT 57.376 37.500 0.00 0.00 0.00 3.57
1733 1964 7.728847 TTACTCCTCGCATATTAGTTACGTA 57.271 36.000 0.00 0.00 0.00 3.57
1736 1967 6.931281 ACTCCTCGCATATTAGTTACGTACTA 59.069 38.462 0.00 0.00 38.33 1.82
1737 1968 7.605691 ACTCCTCGCATATTAGTTACGTACTAT 59.394 37.037 0.00 0.00 39.07 2.12
1739 1970 8.873830 TCCTCGCATATTAGTTACGTACTATAC 58.126 37.037 0.00 0.00 39.07 1.47
1740 1971 8.877779 CCTCGCATATTAGTTACGTACTATACT 58.122 37.037 0.00 0.00 39.07 2.12
1859 2185 7.636326 TCAAAACGACCAACTAAGAAGATTTC 58.364 34.615 0.00 0.00 0.00 2.17
1872 2198 5.864628 AGAAGATTTCCTTTAACACGAGC 57.135 39.130 0.00 0.00 34.68 5.03
1884 2210 4.227134 ACGAGCTAGGGGCATGCG 62.227 66.667 12.44 0.00 44.79 4.73
1890 2216 1.526686 CTAGGGGCATGCGCAATGA 60.527 57.895 32.47 15.14 41.24 2.57
1898 2228 2.030540 GGCATGCGCAATGATGTTATCT 60.031 45.455 17.11 0.00 41.24 1.98
1899 2229 3.551454 GGCATGCGCAATGATGTTATCTT 60.551 43.478 17.11 0.00 41.24 2.40
1900 2230 4.320421 GGCATGCGCAATGATGTTATCTTA 60.320 41.667 17.11 0.00 41.24 2.10
1902 2232 4.472691 TGCGCAATGATGTTATCTTAGC 57.527 40.909 8.16 0.00 0.00 3.09
1903 2233 3.876320 TGCGCAATGATGTTATCTTAGCA 59.124 39.130 8.16 0.00 0.00 3.49
1904 2234 4.024641 TGCGCAATGATGTTATCTTAGCAG 60.025 41.667 8.16 0.00 0.00 4.24
1905 2235 4.024556 GCGCAATGATGTTATCTTAGCAGT 60.025 41.667 0.30 0.00 0.00 4.40
1906 2236 5.438117 CGCAATGATGTTATCTTAGCAGTG 58.562 41.667 0.00 0.00 0.00 3.66
1913 2264 4.733850 TGTTATCTTAGCAGTGTCTGTCG 58.266 43.478 0.00 0.00 33.43 4.35
1940 2291 5.009110 GTGGAGGAAAGAGAAACCAAAAGAG 59.991 44.000 0.00 0.00 0.00 2.85
1943 2294 6.016693 GGAGGAAAGAGAAACCAAAAGAGAAG 60.017 42.308 0.00 0.00 0.00 2.85
1971 2596 2.596923 TGGCGAACATGGCAAGCA 60.597 55.556 0.00 0.00 41.96 3.91
1974 2599 0.390209 GGCGAACATGGCAAGCAAAT 60.390 50.000 0.00 0.00 0.00 2.32
2002 2627 6.582677 TTTATGACAAGTTTACATGGTGGG 57.417 37.500 0.00 0.00 0.00 4.61
2003 2628 3.866703 TGACAAGTTTACATGGTGGGA 57.133 42.857 0.00 0.00 0.00 4.37
2004 2629 3.750371 TGACAAGTTTACATGGTGGGAG 58.250 45.455 0.00 0.00 0.00 4.30
2008 2708 3.652057 AGTTTACATGGTGGGAGATGG 57.348 47.619 0.00 0.00 0.00 3.51
2015 2715 3.117512 ACATGGTGGGAGATGGTAAATCC 60.118 47.826 0.00 0.00 0.00 3.01
2033 2733 5.722021 AATCCTGCCTTTTTGTCGTATTT 57.278 34.783 0.00 0.00 0.00 1.40
2034 2734 5.722021 ATCCTGCCTTTTTGTCGTATTTT 57.278 34.783 0.00 0.00 0.00 1.82
2097 2797 1.304381 CACCCACCCTCCCACAATG 60.304 63.158 0.00 0.00 0.00 2.82
2105 2805 2.831526 ACCCTCCCACAATGTAAATTGC 59.168 45.455 5.48 0.00 35.04 3.56
2143 2863 0.608640 AAAAGACATCGACCGAGCCT 59.391 50.000 0.00 0.00 0.00 4.58
2147 2867 2.105128 CATCGACCGAGCCTGACC 59.895 66.667 0.00 0.00 0.00 4.02
2159 2902 3.125316 CGAGCCTGACCTTGAATTAACAC 59.875 47.826 0.00 0.00 0.00 3.32
2160 2903 3.074412 AGCCTGACCTTGAATTAACACG 58.926 45.455 0.00 0.00 0.00 4.49
2222 2966 4.733523 GCAAAGAGAAGGAAAAACAAGCGA 60.734 41.667 0.00 0.00 0.00 4.93
2273 3018 0.246635 AAGCCTCACACGCTACGAAT 59.753 50.000 0.00 0.00 34.84 3.34
2301 3046 1.072266 TAAACACTGGGGCATGGAGT 58.928 50.000 0.00 0.00 0.00 3.85
2362 3107 0.674895 ACAAGAACATGCCGGCTCTC 60.675 55.000 29.70 17.63 0.00 3.20
2384 3129 1.822371 GGAGAGAGGAAGACTGACACC 59.178 57.143 0.00 0.00 0.00 4.16
2387 3132 0.972883 AGAGGAAGACTGACACCAGC 59.027 55.000 0.00 0.00 44.16 4.85
2419 3164 1.005394 ACCAAGCAACTACGGACCG 60.005 57.895 13.61 13.61 0.00 4.79
2420 3165 1.290955 CCAAGCAACTACGGACCGA 59.709 57.895 23.38 3.17 0.00 4.69
2470 3217 0.768221 AGAAGGCCACAACCTCCTCA 60.768 55.000 5.01 0.00 39.93 3.86
2474 3221 0.890683 GGCCACAACCTCCTCATTTG 59.109 55.000 0.00 0.00 0.00 2.32
2477 3224 2.885554 GCCACAACCTCCTCATTTGGAT 60.886 50.000 0.00 0.00 35.30 3.41
2502 3249 3.957535 GGCCGCATCATCGCAAGG 61.958 66.667 0.00 0.00 38.47 3.61
2514 3261 3.914426 ATCGCAAGGTGGATAAGTTCT 57.086 42.857 0.00 0.00 38.47 3.01
2535 3282 7.834068 TTCTCACAAGAACTATAGTGAATGC 57.166 36.000 6.06 0.00 40.14 3.56
2538 3285 3.871594 ACAAGAACTATAGTGAATGCCGC 59.128 43.478 6.06 0.00 0.00 6.53
2563 3310 1.061812 AGATGGCCACATAGAGAGGGT 60.062 52.381 8.16 0.00 37.47 4.34
2566 3313 0.755686 GGCCACATAGAGAGGGTCAG 59.244 60.000 0.00 0.00 0.00 3.51
2571 3318 0.249238 CATAGAGAGGGTCAGCGCAC 60.249 60.000 11.47 0.00 0.00 5.34
2587 3334 2.063979 CACCCCCTATGAGCCGTCA 61.064 63.158 0.00 0.00 37.02 4.35
2588 3335 1.762460 ACCCCCTATGAGCCGTCAG 60.762 63.158 0.00 0.00 35.66 3.51
2620 3367 6.380846 TCCTCTAAAACATTAGCAATTGCCAT 59.619 34.615 26.45 16.04 43.38 4.40
2631 3378 2.594365 AATTGCCATCCCCTCCCAGC 62.594 60.000 0.00 0.00 0.00 4.85
2640 3387 4.452733 CCTCCCAGCGACCGTTCC 62.453 72.222 0.00 0.00 0.00 3.62
2649 3396 1.520666 CGACCGTTCCCTGGCTATT 59.479 57.895 0.00 0.00 0.00 1.73
2658 3405 1.709994 CCCTGGCTATTGGGGTCCTC 61.710 65.000 0.00 0.00 39.76 3.71
2661 3408 0.988145 TGGCTATTGGGGTCCTCCAG 60.988 60.000 0.00 0.00 38.17 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.574055 CAGTTCGCATGCATTAATTTGAGTT 59.426 36.000 19.57 0.00 0.00 3.01
1 2 5.097529 CAGTTCGCATGCATTAATTTGAGT 58.902 37.500 19.57 0.00 0.00 3.41
2 3 5.228635 GTCAGTTCGCATGCATTAATTTGAG 59.771 40.000 19.57 0.00 0.00 3.02
3 4 5.094812 GTCAGTTCGCATGCATTAATTTGA 58.905 37.500 19.57 12.68 0.00 2.69
4 5 4.028268 CGTCAGTTCGCATGCATTAATTTG 60.028 41.667 19.57 10.85 0.00 2.32
5 6 4.097714 CGTCAGTTCGCATGCATTAATTT 58.902 39.130 19.57 0.00 0.00 1.82
6 7 3.126858 ACGTCAGTTCGCATGCATTAATT 59.873 39.130 19.57 2.60 0.00 1.40
7 8 2.677836 ACGTCAGTTCGCATGCATTAAT 59.322 40.909 19.57 0.00 0.00 1.40
8 9 2.073056 ACGTCAGTTCGCATGCATTAA 58.927 42.857 19.57 5.74 0.00 1.40
9 10 1.393196 CACGTCAGTTCGCATGCATTA 59.607 47.619 19.57 0.00 0.00 1.90
10 11 0.166597 CACGTCAGTTCGCATGCATT 59.833 50.000 19.57 0.00 0.00 3.56
11 12 1.638388 CCACGTCAGTTCGCATGCAT 61.638 55.000 19.57 0.00 0.00 3.96
12 13 2.316867 CCACGTCAGTTCGCATGCA 61.317 57.895 19.57 1.73 0.00 3.96
13 14 2.476051 CCACGTCAGTTCGCATGC 59.524 61.111 7.91 7.91 0.00 4.06
14 15 2.231745 CTGCCACGTCAGTTCGCATG 62.232 60.000 0.00 0.00 33.96 4.06
15 16 2.029288 CTGCCACGTCAGTTCGCAT 61.029 57.895 0.00 0.00 33.96 4.73
16 17 2.661537 CTGCCACGTCAGTTCGCA 60.662 61.111 0.00 0.00 33.52 5.10
17 18 2.355837 TCTGCCACGTCAGTTCGC 60.356 61.111 4.38 0.00 35.63 4.70
18 19 2.375766 GCTCTGCCACGTCAGTTCG 61.376 63.158 4.38 0.00 35.63 3.95
19 20 0.671781 ATGCTCTGCCACGTCAGTTC 60.672 55.000 4.38 0.00 35.63 3.01
20 21 0.671781 GATGCTCTGCCACGTCAGTT 60.672 55.000 4.38 0.00 35.63 3.16
21 22 1.079543 GATGCTCTGCCACGTCAGT 60.080 57.895 4.38 0.00 35.63 3.41
22 23 0.390866 AAGATGCTCTGCCACGTCAG 60.391 55.000 0.00 0.00 35.46 3.51
23 24 0.390340 GAAGATGCTCTGCCACGTCA 60.390 55.000 0.00 0.00 0.00 4.35
24 25 1.086634 GGAAGATGCTCTGCCACGTC 61.087 60.000 5.55 0.00 42.14 4.34
25 26 1.078848 GGAAGATGCTCTGCCACGT 60.079 57.895 5.55 0.00 42.14 4.49
26 27 0.461548 TAGGAAGATGCTCTGCCACG 59.538 55.000 11.48 0.00 45.22 4.94
27 28 2.698855 TTAGGAAGATGCTCTGCCAC 57.301 50.000 11.48 0.00 45.22 5.01
28 29 2.773661 TGATTAGGAAGATGCTCTGCCA 59.226 45.455 11.48 0.00 45.22 4.92
29 30 3.137533 GTGATTAGGAAGATGCTCTGCC 58.862 50.000 2.72 2.72 42.96 4.85
30 31 2.799412 CGTGATTAGGAAGATGCTCTGC 59.201 50.000 0.00 0.00 0.00 4.26
31 32 2.799412 GCGTGATTAGGAAGATGCTCTG 59.201 50.000 0.00 0.00 0.00 3.35
32 33 2.544694 CGCGTGATTAGGAAGATGCTCT 60.545 50.000 0.00 0.00 0.00 4.09
33 34 1.789464 CGCGTGATTAGGAAGATGCTC 59.211 52.381 0.00 0.00 0.00 4.26
34 35 1.539065 CCGCGTGATTAGGAAGATGCT 60.539 52.381 4.92 0.00 0.00 3.79
35 36 0.861837 CCGCGTGATTAGGAAGATGC 59.138 55.000 4.92 0.00 0.00 3.91
36 37 1.502231 CCCGCGTGATTAGGAAGATG 58.498 55.000 4.92 0.00 0.00 2.90
37 38 0.393077 CCCCGCGTGATTAGGAAGAT 59.607 55.000 4.92 0.00 0.00 2.40
38 39 1.682451 CCCCCGCGTGATTAGGAAGA 61.682 60.000 4.92 0.00 0.00 2.87
39 40 1.227556 CCCCCGCGTGATTAGGAAG 60.228 63.158 4.92 0.00 0.00 3.46
40 41 1.686455 TCCCCCGCGTGATTAGGAA 60.686 57.895 4.92 0.00 0.00 3.36
41 42 2.042741 TCCCCCGCGTGATTAGGA 60.043 61.111 4.92 0.00 0.00 2.94
42 43 2.108362 GTCCCCCGCGTGATTAGG 59.892 66.667 4.92 0.00 0.00 2.69
43 44 1.227263 CTGTCCCCCGCGTGATTAG 60.227 63.158 4.92 0.00 0.00 1.73
44 45 2.897207 CTGTCCCCCGCGTGATTA 59.103 61.111 4.92 0.00 0.00 1.75
45 46 4.778143 GCTGTCCCCCGCGTGATT 62.778 66.667 4.92 0.00 0.00 2.57
51 52 4.767255 CACTCTGCTGTCCCCCGC 62.767 72.222 0.00 0.00 0.00 6.13
52 53 2.997315 TCACTCTGCTGTCCCCCG 60.997 66.667 0.00 0.00 0.00 5.73
53 54 2.664081 CCTCACTCTGCTGTCCCCC 61.664 68.421 0.00 0.00 0.00 5.40
54 55 2.664081 CCCTCACTCTGCTGTCCCC 61.664 68.421 0.00 0.00 0.00 4.81
55 56 1.610673 TCCCTCACTCTGCTGTCCC 60.611 63.158 0.00 0.00 0.00 4.46
56 57 1.594310 GTCCCTCACTCTGCTGTCC 59.406 63.158 0.00 0.00 0.00 4.02
57 58 1.594310 GGTCCCTCACTCTGCTGTC 59.406 63.158 0.00 0.00 0.00 3.51
58 59 2.279069 CGGTCCCTCACTCTGCTGT 61.279 63.158 0.00 0.00 0.00 4.40
59 60 2.575993 CGGTCCCTCACTCTGCTG 59.424 66.667 0.00 0.00 0.00 4.41
60 61 2.681778 CCGGTCCCTCACTCTGCT 60.682 66.667 0.00 0.00 0.00 4.24
61 62 2.508586 GAACCGGTCCCTCACTCTGC 62.509 65.000 8.04 0.00 0.00 4.26
62 63 0.900647 AGAACCGGTCCCTCACTCTG 60.901 60.000 8.04 0.00 0.00 3.35
63 64 0.178929 AAGAACCGGTCCCTCACTCT 60.179 55.000 8.04 1.26 0.00 3.24
64 65 0.246910 GAAGAACCGGTCCCTCACTC 59.753 60.000 8.04 0.00 0.00 3.51
65 66 1.192803 GGAAGAACCGGTCCCTCACT 61.193 60.000 8.04 0.00 0.00 3.41
66 67 1.295746 GGAAGAACCGGTCCCTCAC 59.704 63.158 8.04 6.56 0.00 3.51
67 68 3.801620 GGAAGAACCGGTCCCTCA 58.198 61.111 8.04 0.00 0.00 3.86
71 72 1.531423 GAAAAGGGAAGAACCGGTCC 58.469 55.000 8.04 4.06 40.11 4.46
72 73 1.202842 TGGAAAAGGGAAGAACCGGTC 60.203 52.381 8.04 0.95 40.11 4.79
73 74 0.848053 TGGAAAAGGGAAGAACCGGT 59.152 50.000 0.00 0.00 40.11 5.28
74 75 1.534729 CTGGAAAAGGGAAGAACCGG 58.465 55.000 0.00 0.00 40.11 5.28
75 76 0.881796 GCTGGAAAAGGGAAGAACCG 59.118 55.000 0.00 0.00 40.11 4.44
76 77 0.881796 CGCTGGAAAAGGGAAGAACC 59.118 55.000 0.00 0.00 41.34 3.62
77 78 0.881796 CCGCTGGAAAAGGGAAGAAC 59.118 55.000 0.00 0.00 41.34 3.01
78 79 0.476771 ACCGCTGGAAAAGGGAAGAA 59.523 50.000 1.50 0.00 41.34 2.52
79 80 0.036306 GACCGCTGGAAAAGGGAAGA 59.964 55.000 1.50 0.00 41.34 2.87
80 81 1.298859 CGACCGCTGGAAAAGGGAAG 61.299 60.000 1.50 0.00 41.34 3.46
81 82 1.302192 CGACCGCTGGAAAAGGGAA 60.302 57.895 1.50 0.00 41.34 3.97
82 83 2.345991 CGACCGCTGGAAAAGGGA 59.654 61.111 1.50 0.00 41.34 4.20
83 84 2.746277 CCGACCGCTGGAAAAGGG 60.746 66.667 1.50 0.00 38.56 3.95
84 85 2.033194 GTCCGACCGCTGGAAAAGG 61.033 63.158 1.50 0.42 37.23 3.11
85 86 1.291877 CTGTCCGACCGCTGGAAAAG 61.292 60.000 1.50 0.00 37.23 2.27
86 87 1.301401 CTGTCCGACCGCTGGAAAA 60.301 57.895 1.50 0.00 37.23 2.29
87 88 2.342279 CTGTCCGACCGCTGGAAA 59.658 61.111 1.50 0.00 37.23 3.13
88 89 4.373116 GCTGTCCGACCGCTGGAA 62.373 66.667 7.62 0.00 37.23 3.53
105 106 4.988598 AAGGGACCACTGCGCGTG 62.989 66.667 20.50 20.50 43.41 5.34
106 107 4.681978 GAAGGGACCACTGCGCGT 62.682 66.667 8.43 0.01 0.00 6.01
108 109 2.252072 TATGGAAGGGACCACTGCGC 62.252 60.000 0.00 0.00 43.03 6.09
109 110 0.469917 ATATGGAAGGGACCACTGCG 59.530 55.000 0.00 0.00 43.03 5.18
110 111 2.736670 AATATGGAAGGGACCACTGC 57.263 50.000 0.00 0.00 43.03 4.40
111 112 5.630415 TTCTAATATGGAAGGGACCACTG 57.370 43.478 0.00 0.00 43.03 3.66
112 113 5.132816 CCTTTCTAATATGGAAGGGACCACT 59.867 44.000 11.82 0.00 43.03 4.00
113 114 5.104067 ACCTTTCTAATATGGAAGGGACCAC 60.104 44.000 19.56 0.00 43.03 4.16
114 115 5.043762 ACCTTTCTAATATGGAAGGGACCA 58.956 41.667 19.56 0.00 40.82 4.02
115 116 5.377478 CACCTTTCTAATATGGAAGGGACC 58.623 45.833 19.56 0.00 40.82 4.46
116 117 4.822350 GCACCTTTCTAATATGGAAGGGAC 59.178 45.833 19.56 11.31 40.82 4.46
117 118 4.444306 CGCACCTTTCTAATATGGAAGGGA 60.444 45.833 19.56 0.00 40.82 4.20
118 119 3.815401 CGCACCTTTCTAATATGGAAGGG 59.185 47.826 14.25 14.25 42.97 3.95
119 120 3.251004 GCGCACCTTTCTAATATGGAAGG 59.749 47.826 0.30 0.37 0.00 3.46
120 121 4.130118 AGCGCACCTTTCTAATATGGAAG 58.870 43.478 11.47 0.00 0.00 3.46
121 122 4.127171 GAGCGCACCTTTCTAATATGGAA 58.873 43.478 11.47 0.00 0.00 3.53
122 123 3.728845 GAGCGCACCTTTCTAATATGGA 58.271 45.455 11.47 0.00 0.00 3.41
123 124 2.476619 CGAGCGCACCTTTCTAATATGG 59.523 50.000 11.47 0.00 0.00 2.74
124 125 2.476619 CCGAGCGCACCTTTCTAATATG 59.523 50.000 11.47 0.00 0.00 1.78
125 126 2.755650 CCGAGCGCACCTTTCTAATAT 58.244 47.619 11.47 0.00 0.00 1.28
126 127 1.805120 GCCGAGCGCACCTTTCTAATA 60.805 52.381 11.47 0.00 37.47 0.98
127 128 1.090052 GCCGAGCGCACCTTTCTAAT 61.090 55.000 11.47 0.00 37.47 1.73
128 129 1.740296 GCCGAGCGCACCTTTCTAA 60.740 57.895 11.47 0.00 37.47 2.10
129 130 1.317431 TAGCCGAGCGCACCTTTCTA 61.317 55.000 11.47 0.00 41.38 2.10
130 131 2.564553 CTAGCCGAGCGCACCTTTCT 62.565 60.000 11.47 0.86 41.38 2.52
131 132 2.125673 TAGCCGAGCGCACCTTTC 60.126 61.111 11.47 0.00 41.38 2.62
132 133 2.125512 CTAGCCGAGCGCACCTTT 60.126 61.111 11.47 0.00 41.38 3.11
133 134 3.068691 TCTAGCCGAGCGCACCTT 61.069 61.111 11.47 0.00 41.38 3.50
134 135 3.827898 GTCTAGCCGAGCGCACCT 61.828 66.667 11.47 1.93 41.38 4.00
135 136 4.129737 TGTCTAGCCGAGCGCACC 62.130 66.667 11.47 0.00 41.38 5.01
136 137 2.580867 CTGTCTAGCCGAGCGCAC 60.581 66.667 11.47 0.96 41.38 5.34
137 138 4.498520 GCTGTCTAGCCGAGCGCA 62.499 66.667 11.47 0.00 44.33 6.09
146 147 4.135153 ACGCGCCCAGCTGTCTAG 62.135 66.667 13.81 2.17 45.59 2.43
147 148 4.435436 CACGCGCCCAGCTGTCTA 62.435 66.667 13.81 0.00 45.59 2.59
170 171 2.023414 TTATGGGACGTGGCTAGCGG 62.023 60.000 9.00 2.96 0.00 5.52
171 172 0.179094 TTTATGGGACGTGGCTAGCG 60.179 55.000 9.00 0.00 0.00 4.26
172 173 2.256117 ATTTATGGGACGTGGCTAGC 57.744 50.000 6.04 6.04 0.00 3.42
173 174 5.007332 GTGTTTATTTATGGGACGTGGCTAG 59.993 44.000 0.00 0.00 0.00 3.42
174 175 4.877251 GTGTTTATTTATGGGACGTGGCTA 59.123 41.667 0.00 0.00 0.00 3.93
175 176 3.692593 GTGTTTATTTATGGGACGTGGCT 59.307 43.478 0.00 0.00 0.00 4.75
176 177 3.486209 CGTGTTTATTTATGGGACGTGGC 60.486 47.826 0.00 0.00 0.00 5.01
177 178 3.486209 GCGTGTTTATTTATGGGACGTGG 60.486 47.826 0.00 0.00 0.00 4.94
178 179 3.676540 GCGTGTTTATTTATGGGACGTG 58.323 45.455 0.00 0.00 0.00 4.49
179 180 2.349275 CGCGTGTTTATTTATGGGACGT 59.651 45.455 0.00 0.00 0.00 4.34
180 181 2.604011 TCGCGTGTTTATTTATGGGACG 59.396 45.455 5.77 0.00 0.00 4.79
181 182 3.866910 TCTCGCGTGTTTATTTATGGGAC 59.133 43.478 5.77 0.00 0.00 4.46
182 183 3.866910 GTCTCGCGTGTTTATTTATGGGA 59.133 43.478 5.77 0.00 0.00 4.37
183 184 3.001939 GGTCTCGCGTGTTTATTTATGGG 59.998 47.826 5.77 0.00 0.00 4.00
184 185 3.869246 AGGTCTCGCGTGTTTATTTATGG 59.131 43.478 5.77 0.00 0.00 2.74
245 246 6.852664 ACGTTCCAACATTCCTAATCATTTC 58.147 36.000 0.00 0.00 0.00 2.17
421 427 2.158608 ACTCTTCCCACTCAAACCCTTG 60.159 50.000 0.00 0.00 0.00 3.61
450 456 2.361610 ATGAGCAAGTTGGGGGCG 60.362 61.111 4.75 0.00 0.00 6.13
527 721 2.091541 ACGGCACAACCAGGATAAATG 58.908 47.619 0.00 0.00 39.03 2.32
555 749 4.648762 ACACTGGAGAATCTCAATCGATCT 59.351 41.667 12.79 0.00 33.73 2.75
556 750 4.942852 ACACTGGAGAATCTCAATCGATC 58.057 43.478 12.79 0.00 33.73 3.69
571 765 3.552132 TGCAACTTTACTGACACTGGA 57.448 42.857 0.00 0.00 0.00 3.86
575 769 6.086222 CCAATACATGCAACTTTACTGACAC 58.914 40.000 0.00 0.00 0.00 3.67
694 888 2.941720 GGGTAGTACACTACTGGAGACG 59.058 54.545 16.84 0.00 46.06 4.18
775 972 0.178767 TGCGATGAGACCATTCCAGG 59.821 55.000 0.00 0.00 32.09 4.45
800 997 7.310664 TGATTTGAAACGACCTACTACTACTG 58.689 38.462 0.00 0.00 0.00 2.74
876 1073 4.142790 GCCAGTATGTAGGAGTACAGCTA 58.857 47.826 0.00 0.00 42.53 3.32
877 1074 2.959707 GCCAGTATGTAGGAGTACAGCT 59.040 50.000 0.00 0.00 42.53 4.24
879 1076 2.287668 GCGCCAGTATGTAGGAGTACAG 60.288 54.545 0.00 0.00 42.53 2.74
880 1077 1.679680 GCGCCAGTATGTAGGAGTACA 59.320 52.381 0.00 0.00 43.43 2.90
881 1078 1.679680 TGCGCCAGTATGTAGGAGTAC 59.320 52.381 4.18 0.00 0.00 2.73
882 1079 1.679680 GTGCGCCAGTATGTAGGAGTA 59.320 52.381 4.18 0.00 0.00 2.59
883 1080 0.460311 GTGCGCCAGTATGTAGGAGT 59.540 55.000 4.18 0.00 0.00 3.85
884 1081 0.459899 TGTGCGCCAGTATGTAGGAG 59.540 55.000 4.18 0.00 0.00 3.69
885 1082 0.174845 GTGTGCGCCAGTATGTAGGA 59.825 55.000 4.18 0.00 0.00 2.94
886 1083 0.108377 TGTGTGCGCCAGTATGTAGG 60.108 55.000 4.18 0.00 0.00 3.18
887 1084 1.939974 ATGTGTGCGCCAGTATGTAG 58.060 50.000 4.18 0.00 0.00 2.74
916 1114 1.630126 AACCGGCATGGAGATCAGCT 61.630 55.000 0.00 0.00 42.00 4.24
918 1116 1.138859 TGTAACCGGCATGGAGATCAG 59.861 52.381 0.00 0.00 42.00 2.90
1556 1778 1.772182 GTCGTTGACCAGAGACACAG 58.228 55.000 0.00 0.00 34.09 3.66
1662 1893 1.519455 GTTGATGGAGGAGACGGCG 60.519 63.158 4.80 4.80 0.00 6.46
1733 1964 9.420551 GGCGATAAATTAAGCAGTAAGTATAGT 57.579 33.333 6.26 0.00 0.00 2.12
1736 1967 9.420551 GTAGGCGATAAATTAAGCAGTAAGTAT 57.579 33.333 6.26 0.00 0.00 2.12
1737 1968 7.869429 GGTAGGCGATAAATTAAGCAGTAAGTA 59.131 37.037 6.26 0.00 0.00 2.24
1739 1970 6.929606 AGGTAGGCGATAAATTAAGCAGTAAG 59.070 38.462 6.26 0.00 0.00 2.34
1740 1971 6.823497 AGGTAGGCGATAAATTAAGCAGTAA 58.177 36.000 6.26 0.00 0.00 2.24
1741 1972 6.415206 AGGTAGGCGATAAATTAAGCAGTA 57.585 37.500 6.26 0.00 0.00 2.74
1742 1973 5.291905 AGGTAGGCGATAAATTAAGCAGT 57.708 39.130 6.26 0.00 0.00 4.40
1745 1976 6.146347 CAGAGAAGGTAGGCGATAAATTAAGC 59.854 42.308 0.00 0.00 0.00 3.09
1746 1977 7.210873 ACAGAGAAGGTAGGCGATAAATTAAG 58.789 38.462 0.00 0.00 0.00 1.85
1758 2027 3.748568 GCTTTGTTGACAGAGAAGGTAGG 59.251 47.826 5.92 0.00 30.38 3.18
1859 2185 1.742750 GCCCCTAGCTCGTGTTAAAGG 60.743 57.143 0.00 0.00 38.99 3.11
1872 2198 0.892358 ATCATTGCGCATGCCCCTAG 60.892 55.000 12.75 0.00 41.78 3.02
1884 2210 6.259608 AGACACTGCTAAGATAACATCATTGC 59.740 38.462 0.00 0.00 0.00 3.56
1885 2211 7.279536 ACAGACACTGCTAAGATAACATCATTG 59.720 37.037 0.00 0.00 34.37 2.82
1890 2216 5.125578 TCGACAGACACTGCTAAGATAACAT 59.874 40.000 0.00 0.00 34.37 2.71
1898 2228 1.269723 CACCTCGACAGACACTGCTAA 59.730 52.381 0.00 0.00 34.37 3.09
1899 2229 0.881796 CACCTCGACAGACACTGCTA 59.118 55.000 0.00 0.00 34.37 3.49
1900 2230 1.662608 CACCTCGACAGACACTGCT 59.337 57.895 0.00 0.00 34.37 4.24
1902 2232 0.242286 CTCCACCTCGACAGACACTG 59.758 60.000 0.00 0.00 37.52 3.66
1903 2233 0.896019 CCTCCACCTCGACAGACACT 60.896 60.000 0.00 0.00 0.00 3.55
1904 2234 0.894184 TCCTCCACCTCGACAGACAC 60.894 60.000 0.00 0.00 0.00 3.67
1905 2235 0.178973 TTCCTCCACCTCGACAGACA 60.179 55.000 0.00 0.00 0.00 3.41
1906 2236 0.966920 TTTCCTCCACCTCGACAGAC 59.033 55.000 0.00 0.00 0.00 3.51
1913 2264 2.372172 TGGTTTCTCTTTCCTCCACCTC 59.628 50.000 0.00 0.00 0.00 3.85
1943 2294 3.300009 CATGTTCGCCAAAAGACAAGTC 58.700 45.455 0.00 0.00 0.00 3.01
1994 2619 3.139025 AGGATTTACCATCTCCCACCATG 59.861 47.826 0.00 0.00 42.04 3.66
1995 2620 3.139025 CAGGATTTACCATCTCCCACCAT 59.861 47.826 0.00 0.00 42.04 3.55
1997 2622 2.749800 GCAGGATTTACCATCTCCCACC 60.750 54.545 0.00 0.00 42.04 4.61
1998 2623 2.576615 GCAGGATTTACCATCTCCCAC 58.423 52.381 0.00 0.00 42.04 4.61
2000 2625 1.777272 AGGCAGGATTTACCATCTCCC 59.223 52.381 0.00 0.00 42.04 4.30
2001 2626 3.584733 AAGGCAGGATTTACCATCTCC 57.415 47.619 0.00 0.00 42.04 3.71
2002 2627 5.185828 ACAAAAAGGCAGGATTTACCATCTC 59.814 40.000 0.00 0.00 42.04 2.75
2003 2628 5.086621 ACAAAAAGGCAGGATTTACCATCT 58.913 37.500 0.00 0.00 42.04 2.90
2004 2629 5.405935 ACAAAAAGGCAGGATTTACCATC 57.594 39.130 0.00 0.00 42.04 3.51
2008 2708 4.499037 ACGACAAAAAGGCAGGATTTAC 57.501 40.909 0.00 0.00 0.00 2.01
2034 2734 9.357652 CATGACAACTTTTGAGAAGAAGAAAAA 57.642 29.630 0.00 0.00 0.00 1.94
2046 2746 8.735315 TCTTTAGAAACACATGACAACTTTTGA 58.265 29.630 0.00 0.00 0.00 2.69
2047 2747 8.909708 TCTTTAGAAACACATGACAACTTTTG 57.090 30.769 0.00 0.00 0.00 2.44
2053 2753 7.437862 GGCAATTTCTTTAGAAACACATGACAA 59.562 33.333 7.05 0.00 45.55 3.18
2123 2843 1.822990 AGGCTCGGTCGATGTCTTTTA 59.177 47.619 0.00 0.00 0.00 1.52
2143 2863 2.156098 GGCCGTGTTAATTCAAGGTCA 58.844 47.619 0.00 0.00 40.31 4.02
2147 2867 4.165779 GTTGATGGCCGTGTTAATTCAAG 58.834 43.478 0.00 0.00 0.00 3.02
2222 2966 8.840321 GTTGTTGTCCAGCACATTATATCTTAT 58.160 33.333 0.00 0.00 33.90 1.73
2235 2979 3.181491 GCTTAGTTTGTTGTTGTCCAGCA 60.181 43.478 0.00 0.00 31.82 4.41
2273 3018 5.186256 TGCCCCAGTGTTTATCTTCATTA 57.814 39.130 0.00 0.00 0.00 1.90
2301 3046 1.874345 GAGGACCTTGGCGTCTTCGA 61.874 60.000 0.00 0.00 39.71 3.71
2312 3057 3.891196 TCGTTCACGGAGGAGGACCTT 62.891 57.143 0.00 0.00 41.71 3.50
2362 3107 2.491693 GTGTCAGTCTTCCTCTCTCCTG 59.508 54.545 0.00 0.00 0.00 3.86
2470 3217 1.668419 CGGCCTCTTTCGATCCAAAT 58.332 50.000 0.00 0.00 0.00 2.32
2474 3221 1.224722 GATGCGGCCTCTTTCGATCC 61.225 60.000 0.00 0.00 0.00 3.36
2477 3224 0.530650 GATGATGCGGCCTCTTTCGA 60.531 55.000 0.00 0.00 0.00 3.71
2484 3231 2.898840 CTTGCGATGATGCGGCCT 60.899 61.111 0.00 0.00 37.81 5.19
2485 3232 3.957535 CCTTGCGATGATGCGGCC 61.958 66.667 0.00 0.00 37.81 6.13
2492 3239 3.197766 AGAACTTATCCACCTTGCGATGA 59.802 43.478 0.00 0.00 0.00 2.92
2514 3261 5.109210 CGGCATTCACTATAGTTCTTGTGA 58.891 41.667 1.56 0.00 37.62 3.58
2531 3278 2.774799 GCCATCTTTCGGCGGCATT 61.775 57.895 10.53 0.00 44.25 3.56
2538 3285 2.103094 TCTCTATGTGGCCATCTTTCGG 59.897 50.000 9.72 0.00 32.29 4.30
2555 3302 3.386237 GGTGCGCTGACCCTCTCT 61.386 66.667 9.73 0.00 0.00 3.10
2563 3310 2.364973 TCATAGGGGGTGCGCTGA 60.365 61.111 9.73 0.00 0.00 4.26
2566 3313 4.937431 GGCTCATAGGGGGTGCGC 62.937 72.222 0.00 0.00 0.00 6.09
2571 3318 1.457643 TCTGACGGCTCATAGGGGG 60.458 63.158 0.00 0.00 0.00 5.40
2573 3320 2.045280 CCTCTGACGGCTCATAGGG 58.955 63.158 0.00 0.00 37.20 3.53
2591 3338 6.934048 ATTGCTAATGTTTTAGAGGAGAGC 57.066 37.500 0.00 0.00 37.59 4.09
2606 3353 2.601905 GAGGGGATGGCAATTGCTAAT 58.398 47.619 28.42 21.60 41.70 1.73
2609 3356 1.075748 GGAGGGGATGGCAATTGCT 60.076 57.895 28.42 11.27 41.70 3.91
2631 3378 0.810031 CAATAGCCAGGGAACGGTCG 60.810 60.000 0.00 0.00 0.00 4.79
2633 3380 1.607612 CCAATAGCCAGGGAACGGT 59.392 57.895 0.00 0.00 0.00 4.83
2640 3387 1.709994 GGAGGACCCCAATAGCCAGG 61.710 65.000 0.00 0.00 0.00 4.45
2661 3408 0.880718 GACGCCTCCGGATTCAATCC 60.881 60.000 3.57 6.32 46.22 3.01


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

AutoCloner maintained by Alex Coulton.