Multiple sequence alignment - TraesCS3A01G501200

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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 TraesCS3A01G501200 chr3A 100.000 2237 0 0 1 2237 725460567 725462803 0.000000e+00 4132
1 TraesCS3A01G501200 chr3A 84.908 1418 123 32 248 1609 725555803 725557185 0.000000e+00 1349
2 TraesCS3A01G501200 chr3A 84.908 1418 123 32 248 1609 725598351 725599733 0.000000e+00 1349
3 TraesCS3A01G501200 chr3A 88.924 641 38 14 1605 2237 41411474 41412089 0.000000e+00 760
4 TraesCS3A01G501200 chr3A 78.556 457 74 16 282 722 725476558 725477006 1.690000e-71 279
5 TraesCS3A01G501200 chr3B 84.577 1394 126 45 256 1609 798231579 798232923 0.000000e+00 1301
6 TraesCS3A01G501200 chr3B 86.349 630 30 13 1608 2237 69989676 69990249 8.710000e-179 636
7 TraesCS3A01G501200 chr3B 81.492 362 58 6 257 614 798251445 798251801 2.810000e-74 289
8 TraesCS3A01G501200 chr2A 95.404 631 5 1 1607 2237 89921404 89922010 0.000000e+00 983
9 TraesCS3A01G501200 chr2A 94.762 630 9 1 1608 2237 89797562 89796957 0.000000e+00 959
10 TraesCS3A01G501200 chr5B 93.968 630 14 12 1608 2237 9576798 9576193 0.000000e+00 931
11 TraesCS3A01G501200 chr4B 90.317 630 36 13 1608 2237 487298794 487298190 0.000000e+00 802
12 TraesCS3A01G501200 chr2D 90.063 634 30 15 1612 2237 339730467 339729859 0.000000e+00 791
13 TraesCS3A01G501200 chr1A 89.498 638 35 14 1608 2237 540662853 540662240 0.000000e+00 778
14 TraesCS3A01G501200 chr7B 89.382 631 43 13 1607 2237 704057858 704057252 0.000000e+00 773
15 TraesCS3A01G501200 chr3D 87.079 712 55 23 927 1609 594684636 594685339 0.000000e+00 771
16 TraesCS3A01G501200 chr3D 86.094 640 60 11 248 877 594771580 594772200 0.000000e+00 662
17 TraesCS3A01G501200 chr3D 84.006 669 68 21 223 877 594642706 594643349 6.830000e-170 606
18 TraesCS3A01G501200 chr3D 90.930 441 28 8 241 679 594683924 594684354 1.150000e-162 582
19 TraesCS3A01G501200 chr3D 84.095 591 57 22 1046 1609 594772952 594773532 9.090000e-149 536
20 TraesCS3A01G501200 chr3D 84.956 565 42 23 927 1463 594643370 594643919 1.180000e-147 532
21 TraesCS3A01G501200 chr3D 84.956 565 42 23 927 1463 594772221 594772770 1.180000e-147 532
22 TraesCS3A01G501200 chr3D 83.587 591 60 22 1046 1609 594644101 594644681 9.160000e-144 520
23 TraesCS3A01G501200 chr3D 90.726 248 20 2 631 877 594684370 594684615 5.960000e-86 327
24 TraesCS3A01G501200 chr3D 79.508 366 64 8 262 621 594800082 594800442 1.330000e-62 250
25 TraesCS3A01G501200 chr2B 88.050 636 44 12 1608 2235 49665238 49664627 0.000000e+00 725
26 TraesCS3A01G501200 chr1B 87.619 630 38 7 1608 2237 113092436 113091847 0.000000e+00 695
27 TraesCS3A01G501200 chr5D 86.882 465 35 6 1604 2067 313795108 313795547 4.290000e-137 497


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 TraesCS3A01G501200 chr3A 725460567 725462803 2236 False 4132.000000 4132 100.000000 1 2237 1 chr3A.!!$F2 2236
1 TraesCS3A01G501200 chr3A 725555803 725557185 1382 False 1349.000000 1349 84.908000 248 1609 1 chr3A.!!$F4 1361
2 TraesCS3A01G501200 chr3A 725598351 725599733 1382 False 1349.000000 1349 84.908000 248 1609 1 chr3A.!!$F5 1361
3 TraesCS3A01G501200 chr3A 41411474 41412089 615 False 760.000000 760 88.924000 1605 2237 1 chr3A.!!$F1 632
4 TraesCS3A01G501200 chr3B 798231579 798232923 1344 False 1301.000000 1301 84.577000 256 1609 1 chr3B.!!$F2 1353
5 TraesCS3A01G501200 chr3B 69989676 69990249 573 False 636.000000 636 86.349000 1608 2237 1 chr3B.!!$F1 629
6 TraesCS3A01G501200 chr2A 89921404 89922010 606 False 983.000000 983 95.404000 1607 2237 1 chr2A.!!$F1 630
7 TraesCS3A01G501200 chr2A 89796957 89797562 605 True 959.000000 959 94.762000 1608 2237 1 chr2A.!!$R1 629
8 TraesCS3A01G501200 chr5B 9576193 9576798 605 True 931.000000 931 93.968000 1608 2237 1 chr5B.!!$R1 629
9 TraesCS3A01G501200 chr4B 487298190 487298794 604 True 802.000000 802 90.317000 1608 2237 1 chr4B.!!$R1 629
10 TraesCS3A01G501200 chr2D 339729859 339730467 608 True 791.000000 791 90.063000 1612 2237 1 chr2D.!!$R1 625
11 TraesCS3A01G501200 chr1A 540662240 540662853 613 True 778.000000 778 89.498000 1608 2237 1 chr1A.!!$R1 629
12 TraesCS3A01G501200 chr7B 704057252 704057858 606 True 773.000000 773 89.382000 1607 2237 1 chr7B.!!$R1 630
13 TraesCS3A01G501200 chr3D 594771580 594773532 1952 False 576.666667 662 85.048333 248 1609 3 chr3D.!!$F4 1361
14 TraesCS3A01G501200 chr3D 594683924 594685339 1415 False 560.000000 771 89.578333 241 1609 3 chr3D.!!$F3 1368
15 TraesCS3A01G501200 chr3D 594642706 594644681 1975 False 552.666667 606 84.183000 223 1609 3 chr3D.!!$F2 1386
16 TraesCS3A01G501200 chr2B 49664627 49665238 611 True 725.000000 725 88.050000 1608 2235 1 chr2B.!!$R1 627
17 TraesCS3A01G501200 chr1B 113091847 113092436 589 True 695.000000 695 87.619000 1608 2237 1 chr1B.!!$R1 629

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
879 985 0.03563 GACACAGGATCAGCAGCCTT 60.036 55.0 0.0 0.0 30.41 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 3280 4.521062 GATGCAGCTCGCCTCCGT 62.521 66.667 0.0 0.0 41.33 4.69 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
30 31 8.902540 ATGTTGAATGTAGTTTGTACTTCTGA 57.097 30.769 0.00 0.00 35.78 3.27
31 32 8.902540 TGTTGAATGTAGTTTGTACTTCTGAT 57.097 30.769 0.00 0.00 35.78 2.90
32 33 8.773645 TGTTGAATGTAGTTTGTACTTCTGATG 58.226 33.333 0.00 0.00 35.78 3.07
33 34 8.988934 GTTGAATGTAGTTTGTACTTCTGATGA 58.011 33.333 0.00 0.00 35.78 2.92
34 35 9.554395 TTGAATGTAGTTTGTACTTCTGATGAA 57.446 29.630 0.00 0.00 35.78 2.57
35 36 8.988934 TGAATGTAGTTTGTACTTCTGATGAAC 58.011 33.333 0.00 0.00 35.78 3.18
36 37 7.582435 ATGTAGTTTGTACTTCTGATGAACG 57.418 36.000 0.00 0.00 35.78 3.95
37 38 6.509656 TGTAGTTTGTACTTCTGATGAACGT 58.490 36.000 0.00 0.00 35.78 3.99
38 39 6.982141 TGTAGTTTGTACTTCTGATGAACGTT 59.018 34.615 0.00 0.00 35.78 3.99
39 40 6.920569 AGTTTGTACTTCTGATGAACGTTT 57.079 33.333 0.46 0.00 0.00 3.60
40 41 8.971321 GTAGTTTGTACTTCTGATGAACGTTTA 58.029 33.333 0.46 0.00 35.78 2.01
41 42 8.603242 AGTTTGTACTTCTGATGAACGTTTAT 57.397 30.769 5.09 5.09 0.00 1.40
42 43 9.701098 AGTTTGTACTTCTGATGAACGTTTATA 57.299 29.630 5.44 0.00 0.00 0.98
70 71 6.806388 ATTTGGATTCCTTTCACAAAATGC 57.194 33.333 3.95 0.00 35.06 3.56
71 72 5.549742 TTGGATTCCTTTCACAAAATGCT 57.450 34.783 3.95 0.00 0.00 3.79
72 73 5.549742 TGGATTCCTTTCACAAAATGCTT 57.450 34.783 3.95 0.00 0.00 3.91
73 74 5.540911 TGGATTCCTTTCACAAAATGCTTC 58.459 37.500 3.95 0.00 0.00 3.86
74 75 4.622740 GGATTCCTTTCACAAAATGCTTCG 59.377 41.667 0.00 0.00 0.00 3.79
75 76 3.011949 TCCTTTCACAAAATGCTTCGC 57.988 42.857 0.00 0.00 0.00 4.70
76 77 2.360483 TCCTTTCACAAAATGCTTCGCA 59.640 40.909 0.00 0.00 44.86 5.10
77 78 2.727798 CCTTTCACAAAATGCTTCGCAG 59.272 45.455 0.00 0.00 43.65 5.18
78 79 3.550639 CCTTTCACAAAATGCTTCGCAGA 60.551 43.478 0.00 0.00 43.65 4.26
79 80 3.921119 TTCACAAAATGCTTCGCAGAT 57.079 38.095 0.00 0.00 43.65 2.90
80 81 3.476295 TCACAAAATGCTTCGCAGATC 57.524 42.857 0.00 0.00 43.65 2.75
81 82 2.813172 TCACAAAATGCTTCGCAGATCA 59.187 40.909 0.00 0.00 43.65 2.92
82 83 2.912967 CACAAAATGCTTCGCAGATCAC 59.087 45.455 0.00 0.00 43.65 3.06
83 84 2.553602 ACAAAATGCTTCGCAGATCACA 59.446 40.909 0.00 0.00 43.65 3.58
84 85 2.907910 AAATGCTTCGCAGATCACAC 57.092 45.000 0.00 0.00 43.65 3.82
85 86 1.812235 AATGCTTCGCAGATCACACA 58.188 45.000 0.00 0.00 43.65 3.72
86 87 1.812235 ATGCTTCGCAGATCACACAA 58.188 45.000 0.00 0.00 43.65 3.33
87 88 1.812235 TGCTTCGCAGATCACACAAT 58.188 45.000 0.00 0.00 35.04 2.71
88 89 1.733912 TGCTTCGCAGATCACACAATC 59.266 47.619 0.00 0.00 35.04 2.67
89 90 2.005451 GCTTCGCAGATCACACAATCT 58.995 47.619 0.00 0.00 36.41 2.40
90 91 2.030213 GCTTCGCAGATCACACAATCTC 59.970 50.000 0.00 0.00 33.68 2.75
91 92 2.299993 TCGCAGATCACACAATCTCC 57.700 50.000 0.00 0.00 33.68 3.71
92 93 1.134699 TCGCAGATCACACAATCTCCC 60.135 52.381 0.00 0.00 33.68 4.30
93 94 1.405933 CGCAGATCACACAATCTCCCA 60.406 52.381 0.00 0.00 33.68 4.37
94 95 2.744166 CGCAGATCACACAATCTCCCAT 60.744 50.000 0.00 0.00 33.68 4.00
95 96 2.617308 GCAGATCACACAATCTCCCATG 59.383 50.000 0.00 0.00 33.68 3.66
96 97 3.683564 GCAGATCACACAATCTCCCATGA 60.684 47.826 0.00 0.00 33.68 3.07
97 98 4.520179 CAGATCACACAATCTCCCATGAA 58.480 43.478 0.00 0.00 33.68 2.57
98 99 4.334759 CAGATCACACAATCTCCCATGAAC 59.665 45.833 0.00 0.00 33.68 3.18
99 100 3.786368 TCACACAATCTCCCATGAACA 57.214 42.857 0.00 0.00 0.00 3.18
100 101 4.305539 TCACACAATCTCCCATGAACAT 57.694 40.909 0.00 0.00 0.00 2.71
101 102 4.264253 TCACACAATCTCCCATGAACATC 58.736 43.478 0.00 0.00 0.00 3.06
102 103 4.011698 CACACAATCTCCCATGAACATCA 58.988 43.478 0.00 0.00 0.00 3.07
103 104 4.012374 ACACAATCTCCCATGAACATCAC 58.988 43.478 0.00 0.00 0.00 3.06
104 105 4.263639 ACACAATCTCCCATGAACATCACT 60.264 41.667 0.00 0.00 0.00 3.41
105 106 4.703575 CACAATCTCCCATGAACATCACTT 59.296 41.667 0.00 0.00 0.00 3.16
106 107 5.882000 CACAATCTCCCATGAACATCACTTA 59.118 40.000 0.00 0.00 0.00 2.24
107 108 6.544931 CACAATCTCCCATGAACATCACTTAT 59.455 38.462 0.00 0.00 0.00 1.73
108 109 6.769822 ACAATCTCCCATGAACATCACTTATC 59.230 38.462 0.00 0.00 0.00 1.75
109 110 5.955961 TCTCCCATGAACATCACTTATCA 57.044 39.130 0.00 0.00 0.00 2.15
110 111 6.505048 TCTCCCATGAACATCACTTATCAT 57.495 37.500 0.00 0.00 32.94 2.45
111 112 6.528321 TCTCCCATGAACATCACTTATCATC 58.472 40.000 0.00 0.00 30.39 2.92
112 113 6.328410 TCTCCCATGAACATCACTTATCATCT 59.672 38.462 0.00 0.00 30.39 2.90
113 114 6.293698 TCCCATGAACATCACTTATCATCTG 58.706 40.000 0.00 0.00 30.39 2.90
114 115 6.100134 TCCCATGAACATCACTTATCATCTGA 59.900 38.462 0.00 0.00 30.39 3.27
115 116 6.940867 CCCATGAACATCACTTATCATCTGAT 59.059 38.462 0.00 0.00 38.51 2.90
116 117 7.094762 CCCATGAACATCACTTATCATCTGATG 60.095 40.741 11.42 11.42 44.63 3.07
117 118 7.660208 CCATGAACATCACTTATCATCTGATGA 59.340 37.037 21.55 21.55 42.65 2.92
118 119 8.496751 CATGAACATCACTTATCATCTGATGAC 58.503 37.037 21.71 6.09 42.65 3.06
119 120 6.988580 TGAACATCACTTATCATCTGATGACC 59.011 38.462 21.71 1.73 42.65 4.02
120 121 6.490241 ACATCACTTATCATCTGATGACCA 57.510 37.500 21.71 10.58 42.65 4.02
121 122 6.892485 ACATCACTTATCATCTGATGACCAA 58.108 36.000 21.71 16.62 42.65 3.67
122 123 7.341030 ACATCACTTATCATCTGATGACCAAA 58.659 34.615 21.71 14.75 42.65 3.28
123 124 7.830697 ACATCACTTATCATCTGATGACCAAAA 59.169 33.333 21.71 12.63 42.65 2.44
124 125 7.854557 TCACTTATCATCTGATGACCAAAAG 57.145 36.000 21.71 21.07 43.01 2.27
125 126 6.317140 TCACTTATCATCTGATGACCAAAAGC 59.683 38.462 21.71 0.00 43.01 3.51
126 127 5.591877 ACTTATCATCTGATGACCAAAAGCC 59.408 40.000 21.71 0.00 43.01 4.35
127 128 3.726557 TCATCTGATGACCAAAAGCCT 57.273 42.857 16.06 0.00 33.59 4.58
128 129 3.614092 TCATCTGATGACCAAAAGCCTC 58.386 45.455 16.06 0.00 33.59 4.70
129 130 3.009363 TCATCTGATGACCAAAAGCCTCA 59.991 43.478 16.06 0.00 33.59 3.86
130 131 3.507162 TCTGATGACCAAAAGCCTCAA 57.493 42.857 0.00 0.00 0.00 3.02
131 132 3.149196 TCTGATGACCAAAAGCCTCAAC 58.851 45.455 0.00 0.00 0.00 3.18
132 133 2.886523 CTGATGACCAAAAGCCTCAACA 59.113 45.455 0.00 0.00 0.00 3.33
133 134 3.295093 TGATGACCAAAAGCCTCAACAA 58.705 40.909 0.00 0.00 0.00 2.83
134 135 3.896888 TGATGACCAAAAGCCTCAACAAT 59.103 39.130 0.00 0.00 0.00 2.71
135 136 3.731652 TGACCAAAAGCCTCAACAATG 57.268 42.857 0.00 0.00 0.00 2.82
136 137 3.030291 TGACCAAAAGCCTCAACAATGT 58.970 40.909 0.00 0.00 0.00 2.71
137 138 4.211125 TGACCAAAAGCCTCAACAATGTA 58.789 39.130 0.00 0.00 0.00 2.29
138 139 4.037446 TGACCAAAAGCCTCAACAATGTAC 59.963 41.667 0.00 0.00 0.00 2.90
139 140 4.215109 ACCAAAAGCCTCAACAATGTACT 58.785 39.130 0.00 0.00 0.00 2.73
140 141 4.037923 ACCAAAAGCCTCAACAATGTACTG 59.962 41.667 0.00 0.00 0.00 2.74
141 142 4.549458 CAAAAGCCTCAACAATGTACTGG 58.451 43.478 0.00 0.00 0.00 4.00
142 143 3.508845 AAGCCTCAACAATGTACTGGT 57.491 42.857 0.00 0.00 0.00 4.00
143 144 3.508845 AGCCTCAACAATGTACTGGTT 57.491 42.857 0.00 0.00 0.00 3.67
144 145 4.634012 AGCCTCAACAATGTACTGGTTA 57.366 40.909 0.00 0.00 0.00 2.85
145 146 4.980573 AGCCTCAACAATGTACTGGTTAA 58.019 39.130 0.00 0.00 0.00 2.01
146 147 5.381757 AGCCTCAACAATGTACTGGTTAAA 58.618 37.500 0.00 0.00 0.00 1.52
147 148 6.010219 AGCCTCAACAATGTACTGGTTAAAT 58.990 36.000 0.00 0.00 0.00 1.40
148 149 6.493458 AGCCTCAACAATGTACTGGTTAAATT 59.507 34.615 0.00 0.00 0.00 1.82
149 150 7.015195 AGCCTCAACAATGTACTGGTTAAATTT 59.985 33.333 0.00 0.00 0.00 1.82
150 151 7.655732 GCCTCAACAATGTACTGGTTAAATTTT 59.344 33.333 0.00 0.00 0.00 1.82
151 152 9.541143 CCTCAACAATGTACTGGTTAAATTTTT 57.459 29.630 0.00 0.00 0.00 1.94
180 181 9.788960 AAAATAAGAATCTAATGAACGAAAGCC 57.211 29.630 0.00 0.00 0.00 4.35
181 182 8.506168 AATAAGAATCTAATGAACGAAAGCCA 57.494 30.769 0.00 0.00 0.00 4.75
182 183 5.803020 AGAATCTAATGAACGAAAGCCAC 57.197 39.130 0.00 0.00 0.00 5.01
183 184 4.330074 AGAATCTAATGAACGAAAGCCACG 59.670 41.667 0.00 0.00 0.00 4.94
184 185 2.343101 TCTAATGAACGAAAGCCACGG 58.657 47.619 0.00 0.00 34.93 4.94
185 186 0.800012 TAATGAACGAAAGCCACGGC 59.200 50.000 0.00 0.00 42.33 5.68
195 196 3.276846 GCCACGGCGAGTTTGTGT 61.277 61.111 16.62 0.00 31.75 3.72
196 197 2.631428 CCACGGCGAGTTTGTGTG 59.369 61.111 16.62 0.00 31.75 3.82
197 198 1.885388 CCACGGCGAGTTTGTGTGA 60.885 57.895 16.62 0.00 32.39 3.58
198 199 1.227999 CCACGGCGAGTTTGTGTGAT 61.228 55.000 16.62 0.00 32.39 3.06
199 200 0.110688 CACGGCGAGTTTGTGTGATG 60.111 55.000 16.62 0.00 32.39 3.07
200 201 0.249699 ACGGCGAGTTTGTGTGATGA 60.250 50.000 16.62 0.00 0.00 2.92
201 202 0.439985 CGGCGAGTTTGTGTGATGAG 59.560 55.000 0.00 0.00 0.00 2.90
202 203 1.795768 GGCGAGTTTGTGTGATGAGA 58.204 50.000 0.00 0.00 0.00 3.27
203 204 2.350522 GGCGAGTTTGTGTGATGAGAT 58.649 47.619 0.00 0.00 0.00 2.75
204 205 2.349886 GGCGAGTTTGTGTGATGAGATC 59.650 50.000 0.00 0.00 0.00 2.75
205 206 3.257393 GCGAGTTTGTGTGATGAGATCT 58.743 45.455 0.00 0.00 0.00 2.75
206 207 4.424626 GCGAGTTTGTGTGATGAGATCTA 58.575 43.478 0.00 0.00 0.00 1.98
207 208 4.502282 GCGAGTTTGTGTGATGAGATCTAG 59.498 45.833 0.00 0.00 0.00 2.43
208 209 5.645624 CGAGTTTGTGTGATGAGATCTAGT 58.354 41.667 0.00 0.00 0.00 2.57
209 210 6.096036 CGAGTTTGTGTGATGAGATCTAGTT 58.904 40.000 0.00 0.00 0.00 2.24
210 211 6.587990 CGAGTTTGTGTGATGAGATCTAGTTT 59.412 38.462 0.00 0.00 0.00 2.66
211 212 7.201393 CGAGTTTGTGTGATGAGATCTAGTTTC 60.201 40.741 0.00 0.00 0.00 2.78
212 213 6.587990 AGTTTGTGTGATGAGATCTAGTTTCG 59.412 38.462 0.00 0.00 0.00 3.46
213 214 5.897377 TGTGTGATGAGATCTAGTTTCGA 57.103 39.130 0.00 0.00 0.00 3.71
214 215 6.456795 TGTGTGATGAGATCTAGTTTCGAT 57.543 37.500 0.00 0.00 0.00 3.59
215 216 6.499172 TGTGTGATGAGATCTAGTTTCGATC 58.501 40.000 0.00 0.00 38.01 3.69
216 217 5.918011 GTGTGATGAGATCTAGTTTCGATCC 59.082 44.000 0.00 0.00 38.39 3.36
217 218 5.594317 TGTGATGAGATCTAGTTTCGATCCA 59.406 40.000 0.00 0.00 38.39 3.41
218 219 6.096846 TGTGATGAGATCTAGTTTCGATCCAA 59.903 38.462 0.00 0.00 38.39 3.53
219 220 6.419413 GTGATGAGATCTAGTTTCGATCCAAC 59.581 42.308 0.00 0.00 38.39 3.77
220 221 5.263968 TGAGATCTAGTTTCGATCCAACC 57.736 43.478 0.00 0.00 38.39 3.77
221 222 4.956700 TGAGATCTAGTTTCGATCCAACCT 59.043 41.667 0.00 0.00 38.39 3.50
225 226 5.334724 TCTAGTTTCGATCCAACCTAACC 57.665 43.478 0.00 0.00 0.00 2.85
233 234 4.341235 TCGATCCAACCTAACCTACAGATG 59.659 45.833 0.00 0.00 0.00 2.90
236 237 3.451178 TCCAACCTAACCTACAGATGAGC 59.549 47.826 0.00 0.00 0.00 4.26
297 301 4.558178 GCACATGAAACATGGACAAATCA 58.442 39.130 14.70 0.00 0.00 2.57
378 382 5.949354 TCCACACGAATAAATCATTTTCCCT 59.051 36.000 0.00 0.00 0.00 4.20
457 461 0.688087 CCCCTCTACTCTGGGTCACC 60.688 65.000 0.00 0.00 41.82 4.02
488 492 2.103094 TGCATGACCAGCAGTATCCTAC 59.897 50.000 0.00 0.00 37.02 3.18
489 493 2.366916 GCATGACCAGCAGTATCCTACT 59.633 50.000 0.00 0.00 40.28 2.57
490 494 3.553922 GCATGACCAGCAGTATCCTACTC 60.554 52.174 0.00 0.00 36.76 2.59
491 495 2.667470 TGACCAGCAGTATCCTACTCC 58.333 52.381 0.00 0.00 36.76 3.85
492 496 2.245028 TGACCAGCAGTATCCTACTCCT 59.755 50.000 0.00 0.00 36.76 3.69
493 497 3.462205 TGACCAGCAGTATCCTACTCCTA 59.538 47.826 0.00 0.00 36.76 2.94
496 500 4.355588 ACCAGCAGTATCCTACTCCTATCT 59.644 45.833 0.00 0.00 36.76 1.98
501 505 5.186797 GCAGTATCCTACTCCTATCTGCAAT 59.813 44.000 0.00 0.00 43.99 3.56
525 538 3.181456 CCAAGGAAAATTCAACAGGCCAA 60.181 43.478 5.01 0.00 0.00 4.52
549 568 0.472471 CACAACCAGTACCACCCACT 59.528 55.000 0.00 0.00 0.00 4.00
577 598 2.299297 ACACTACAGACTAACAGGTGGC 59.701 50.000 0.00 0.00 0.00 5.01
667 753 1.130561 GCGTAACTGTCAATGGAAGCC 59.869 52.381 0.00 0.00 0.00 4.35
683 769 0.892755 AGCCCAGATCGTTGTCGTTA 59.107 50.000 0.00 0.00 38.33 3.18
684 770 1.274167 AGCCCAGATCGTTGTCGTTAA 59.726 47.619 0.00 0.00 38.33 2.01
718 804 2.165167 CAGGTGACCATGTGCTTCAAT 58.835 47.619 3.63 0.00 0.00 2.57
719 805 2.094906 CAGGTGACCATGTGCTTCAATG 60.095 50.000 3.63 0.00 0.00 2.82
822 908 3.261083 GGGCTCTCCTCCCCTATAAAAT 58.739 50.000 0.00 0.00 38.30 1.82
834 920 4.204012 CCCTATAAAATGGTCGCCAAGAA 58.796 43.478 2.68 0.00 36.95 2.52
849 935 2.036346 CCAAGAACCCTGCTTTTCCAAG 59.964 50.000 0.00 0.00 0.00 3.61
865 964 4.350368 TCCAAGCAGAAACATAGACACA 57.650 40.909 0.00 0.00 0.00 3.72
877 983 0.826715 TAGACACAGGATCAGCAGCC 59.173 55.000 0.00 0.00 0.00 4.85
878 984 0.908656 AGACACAGGATCAGCAGCCT 60.909 55.000 0.00 0.00 33.99 4.58
879 985 0.035630 GACACAGGATCAGCAGCCTT 60.036 55.000 0.00 0.00 30.41 4.35
881 987 1.030488 CACAGGATCAGCAGCCTTGG 61.030 60.000 0.00 0.00 30.41 3.61
882 988 2.119655 CAGGATCAGCAGCCTTGGC 61.120 63.158 2.97 2.97 30.41 4.52
883 989 2.274760 GGATCAGCAGCCTTGGCT 59.725 61.111 8.56 8.56 43.77 4.75
884 990 1.823041 GGATCAGCAGCCTTGGCTC 60.823 63.158 11.72 7.04 40.23 4.70
885 991 1.224039 GATCAGCAGCCTTGGCTCT 59.776 57.895 11.72 9.15 40.23 4.09
887 993 2.268167 ATCAGCAGCCTTGGCTCTCC 62.268 60.000 11.72 3.51 40.23 3.71
888 994 2.610233 AGCAGCCTTGGCTCTCCT 60.610 61.111 11.72 5.76 36.81 3.69
890 996 2.588989 CAGCCTTGGCTCTCCTCC 59.411 66.667 11.72 0.00 0.00 4.30
891 997 2.690510 AGCCTTGGCTCTCCTCCC 60.691 66.667 8.56 0.00 0.00 4.30
892 998 3.803162 GCCTTGGCTCTCCTCCCC 61.803 72.222 4.11 0.00 0.00 4.81
894 1000 1.314867 CCTTGGCTCTCCTCCCCTA 59.685 63.158 0.00 0.00 0.00 3.53
895 1001 0.104725 CCTTGGCTCTCCTCCCCTAT 60.105 60.000 0.00 0.00 0.00 2.57
896 1002 1.150135 CCTTGGCTCTCCTCCCCTATA 59.850 57.143 0.00 0.00 0.00 1.31
897 1003 2.427889 CCTTGGCTCTCCTCCCCTATAA 60.428 54.545 0.00 0.00 0.00 0.98
898 1004 3.318313 CTTGGCTCTCCTCCCCTATAAA 58.682 50.000 0.00 0.00 0.00 1.40
1148 2516 1.151668 CAAGGTGTGAAGAAGGAGCG 58.848 55.000 0.00 0.00 0.00 5.03
1258 2626 3.288964 TGTTAACCGGGAACAACAATGT 58.711 40.909 18.75 0.00 43.14 2.71
1259 2627 3.066900 TGTTAACCGGGAACAACAATGTG 59.933 43.478 18.75 0.00 40.46 3.21
1265 2633 2.406130 GGGAACAACAATGTGTGCATG 58.594 47.619 0.00 0.00 40.46 4.06
1284 2652 3.314307 TGAGATCCCGTATGTTCTCCT 57.686 47.619 0.00 0.00 34.93 3.69
1297 2665 7.361885 CCGTATGTTCTCCTATTAGCTTACGAT 60.362 40.741 7.19 0.00 34.30 3.73
1317 2685 3.140325 TCAAGGTTGGAGCTTAGGTTG 57.860 47.619 0.00 0.00 33.64 3.77
1438 2833 4.647564 AGGGATGAAGTTCATTGTCACT 57.352 40.909 19.19 11.41 37.20 3.41
1481 2886 7.366551 CCCTACTTTGTTGGATTACTATTCCCT 60.367 40.741 0.05 0.00 30.33 4.20
1482 2887 8.711170 CCTACTTTGTTGGATTACTATTCCCTA 58.289 37.037 0.00 0.00 30.33 3.53
1483 2888 9.543783 CTACTTTGTTGGATTACTATTCCCTAC 57.456 37.037 0.00 0.00 31.87 3.18
1484 2889 8.159229 ACTTTGTTGGATTACTATTCCCTACT 57.841 34.615 0.00 0.00 31.87 2.57
1485 2890 8.612145 ACTTTGTTGGATTACTATTCCCTACTT 58.388 33.333 0.00 0.00 31.87 2.24
1486 2891 8.801882 TTTGTTGGATTACTATTCCCTACTTG 57.198 34.615 0.00 0.00 31.87 3.16
1487 2892 7.743116 TGTTGGATTACTATTCCCTACTTGA 57.257 36.000 0.00 0.00 31.87 3.02
1488 2893 7.562135 TGTTGGATTACTATTCCCTACTTGAC 58.438 38.462 0.00 0.00 31.87 3.18
1489 2894 7.402071 TGTTGGATTACTATTCCCTACTTGACT 59.598 37.037 0.00 0.00 31.87 3.41
1490 2895 7.598759 TGGATTACTATTCCCTACTTGACTC 57.401 40.000 0.00 0.00 31.87 3.36
1491 2896 6.264744 TGGATTACTATTCCCTACTTGACTCG 59.735 42.308 0.00 0.00 31.87 4.18
1492 2897 6.294620 GGATTACTATTCCCTACTTGACTCGG 60.295 46.154 0.00 0.00 0.00 4.63
1555 2960 6.109359 CCTACATCACCCTCAAAAAGACTAG 58.891 44.000 0.00 0.00 0.00 2.57
1570 2975 9.360093 CAAAAAGACTAGGTCTACATCAACTAG 57.640 37.037 0.41 0.00 42.59 2.57
1619 3024 2.789323 ACCCATATACTCCCTCCGTT 57.211 50.000 0.00 0.00 0.00 4.44
1833 3239 4.572571 TGTGAACCACCACCGCCC 62.573 66.667 0.00 0.00 36.26 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.990360 TCAGAAGTACAAACTACATTCAACATA 57.010 29.630 0.00 0.00 33.75 2.29
5 6 8.902540 TCAGAAGTACAAACTACATTCAACAT 57.097 30.769 0.00 0.00 33.75 2.71
6 7 8.773645 CATCAGAAGTACAAACTACATTCAACA 58.226 33.333 0.00 0.00 33.75 3.33
7 8 8.988934 TCATCAGAAGTACAAACTACATTCAAC 58.011 33.333 0.00 0.00 33.75 3.18
8 9 9.554395 TTCATCAGAAGTACAAACTACATTCAA 57.446 29.630 0.00 0.00 33.75 2.69
9 10 8.988934 GTTCATCAGAAGTACAAACTACATTCA 58.011 33.333 0.00 0.00 33.75 2.57
10 11 8.162880 CGTTCATCAGAAGTACAAACTACATTC 58.837 37.037 0.00 0.00 33.75 2.67
11 12 7.656137 ACGTTCATCAGAAGTACAAACTACATT 59.344 33.333 0.00 0.00 33.75 2.71
12 13 7.152645 ACGTTCATCAGAAGTACAAACTACAT 58.847 34.615 0.00 0.00 33.75 2.29
13 14 6.509656 ACGTTCATCAGAAGTACAAACTACA 58.490 36.000 0.00 0.00 33.75 2.74
14 15 7.404139 AACGTTCATCAGAAGTACAAACTAC 57.596 36.000 0.00 0.00 33.75 2.73
15 16 9.701098 ATAAACGTTCATCAGAAGTACAAACTA 57.299 29.630 0.00 0.00 33.75 2.24
16 17 6.920569 AAACGTTCATCAGAAGTACAAACT 57.079 33.333 0.00 0.00 37.65 2.66
44 45 8.782144 GCATTTTGTGAAAGGAATCCAAATTTA 58.218 29.630 0.61 0.00 0.00 1.40
45 46 7.503230 AGCATTTTGTGAAAGGAATCCAAATTT 59.497 29.630 0.61 0.00 0.00 1.82
46 47 6.999871 AGCATTTTGTGAAAGGAATCCAAATT 59.000 30.769 0.61 0.00 0.00 1.82
47 48 6.536447 AGCATTTTGTGAAAGGAATCCAAAT 58.464 32.000 0.61 0.00 0.00 2.32
48 49 5.927819 AGCATTTTGTGAAAGGAATCCAAA 58.072 33.333 0.61 0.00 0.00 3.28
49 50 5.549742 AGCATTTTGTGAAAGGAATCCAA 57.450 34.783 0.61 0.00 0.00 3.53
50 51 5.540911 GAAGCATTTTGTGAAAGGAATCCA 58.459 37.500 0.61 0.00 0.00 3.41
51 52 4.622740 CGAAGCATTTTGTGAAAGGAATCC 59.377 41.667 0.00 0.00 0.00 3.01
52 53 5.752098 CGAAGCATTTTGTGAAAGGAATC 57.248 39.130 0.00 0.00 0.00 2.52
70 71 2.606725 GGAGATTGTGTGATCTGCGAAG 59.393 50.000 0.00 0.00 36.54 3.79
71 72 2.621338 GGAGATTGTGTGATCTGCGAA 58.379 47.619 0.00 0.00 36.54 4.70
72 73 1.134699 GGGAGATTGTGTGATCTGCGA 60.135 52.381 0.00 0.00 43.16 5.10
73 74 1.293924 GGGAGATTGTGTGATCTGCG 58.706 55.000 0.00 0.00 43.16 5.18
74 75 2.408271 TGGGAGATTGTGTGATCTGC 57.592 50.000 0.00 0.00 41.97 4.26
75 76 4.146745 TCATGGGAGATTGTGTGATCTG 57.853 45.455 0.00 0.00 36.54 2.90
76 77 4.019051 TGTTCATGGGAGATTGTGTGATCT 60.019 41.667 0.00 0.00 39.04 2.75
77 78 4.264253 TGTTCATGGGAGATTGTGTGATC 58.736 43.478 0.00 0.00 0.00 2.92
78 79 4.305539 TGTTCATGGGAGATTGTGTGAT 57.694 40.909 0.00 0.00 0.00 3.06
79 80 3.786368 TGTTCATGGGAGATTGTGTGA 57.214 42.857 0.00 0.00 0.00 3.58
80 81 4.011698 TGATGTTCATGGGAGATTGTGTG 58.988 43.478 0.00 0.00 0.00 3.82
81 82 4.012374 GTGATGTTCATGGGAGATTGTGT 58.988 43.478 0.00 0.00 0.00 3.72
82 83 4.267536 AGTGATGTTCATGGGAGATTGTG 58.732 43.478 0.00 0.00 0.00 3.33
83 84 4.581309 AGTGATGTTCATGGGAGATTGT 57.419 40.909 0.00 0.00 0.00 2.71
84 85 6.769341 TGATAAGTGATGTTCATGGGAGATTG 59.231 38.462 0.00 0.00 0.00 2.67
85 86 6.903516 TGATAAGTGATGTTCATGGGAGATT 58.096 36.000 0.00 0.00 0.00 2.40
86 87 6.505048 TGATAAGTGATGTTCATGGGAGAT 57.495 37.500 0.00 0.00 0.00 2.75
87 88 5.955961 TGATAAGTGATGTTCATGGGAGA 57.044 39.130 0.00 0.00 0.00 3.71
88 89 6.427242 CAGATGATAAGTGATGTTCATGGGAG 59.573 42.308 0.00 0.00 0.00 4.30
89 90 6.100134 TCAGATGATAAGTGATGTTCATGGGA 59.900 38.462 0.00 0.00 0.00 4.37
90 91 6.293698 TCAGATGATAAGTGATGTTCATGGG 58.706 40.000 0.00 0.00 0.00 4.00
91 92 7.660208 TCATCAGATGATAAGTGATGTTCATGG 59.340 37.037 9.21 0.00 45.23 3.66
92 93 8.496751 GTCATCAGATGATAAGTGATGTTCATG 58.503 37.037 16.37 0.00 45.23 3.07
93 94 7.660617 GGTCATCAGATGATAAGTGATGTTCAT 59.339 37.037 16.37 0.00 45.23 2.57
94 95 6.988580 GGTCATCAGATGATAAGTGATGTTCA 59.011 38.462 16.37 0.00 45.23 3.18
95 96 6.988580 TGGTCATCAGATGATAAGTGATGTTC 59.011 38.462 16.37 0.00 45.23 3.18
96 97 6.892485 TGGTCATCAGATGATAAGTGATGTT 58.108 36.000 16.37 0.00 45.23 2.71
97 98 6.490241 TGGTCATCAGATGATAAGTGATGT 57.510 37.500 16.37 0.00 45.23 3.06
98 99 7.797038 TTTGGTCATCAGATGATAAGTGATG 57.203 36.000 16.37 3.40 46.01 3.07
99 100 7.013083 GCTTTTGGTCATCAGATGATAAGTGAT 59.987 37.037 16.37 0.00 42.04 3.06
100 101 6.317140 GCTTTTGGTCATCAGATGATAAGTGA 59.683 38.462 16.37 1.63 42.04 3.41
101 102 6.459298 GGCTTTTGGTCATCAGATGATAAGTG 60.459 42.308 16.37 11.28 42.04 3.16
102 103 5.591877 GGCTTTTGGTCATCAGATGATAAGT 59.408 40.000 16.37 0.00 42.04 2.24
103 104 5.826737 AGGCTTTTGGTCATCAGATGATAAG 59.173 40.000 16.37 16.11 42.04 1.73
104 105 5.759059 AGGCTTTTGGTCATCAGATGATAA 58.241 37.500 16.37 11.69 42.04 1.75
105 106 5.104402 TGAGGCTTTTGGTCATCAGATGATA 60.104 40.000 16.37 6.33 42.04 2.15
106 107 4.205587 GAGGCTTTTGGTCATCAGATGAT 58.794 43.478 16.37 0.00 42.04 2.45
107 108 3.009363 TGAGGCTTTTGGTCATCAGATGA 59.991 43.478 9.21 9.21 36.84 2.92
108 109 3.349927 TGAGGCTTTTGGTCATCAGATG 58.650 45.455 3.71 3.71 0.00 2.90
109 110 3.726557 TGAGGCTTTTGGTCATCAGAT 57.273 42.857 0.00 0.00 0.00 2.90
110 111 3.149196 GTTGAGGCTTTTGGTCATCAGA 58.851 45.455 0.00 0.00 0.00 3.27
111 112 2.886523 TGTTGAGGCTTTTGGTCATCAG 59.113 45.455 0.00 0.00 0.00 2.90
112 113 2.942804 TGTTGAGGCTTTTGGTCATCA 58.057 42.857 0.00 0.00 0.00 3.07
113 114 4.240096 CATTGTTGAGGCTTTTGGTCATC 58.760 43.478 0.00 0.00 0.00 2.92
114 115 3.642848 ACATTGTTGAGGCTTTTGGTCAT 59.357 39.130 0.00 0.00 0.00 3.06
115 116 3.030291 ACATTGTTGAGGCTTTTGGTCA 58.970 40.909 0.00 0.00 0.00 4.02
116 117 3.733443 ACATTGTTGAGGCTTTTGGTC 57.267 42.857 0.00 0.00 0.00 4.02
117 118 4.037923 CAGTACATTGTTGAGGCTTTTGGT 59.962 41.667 0.00 0.00 0.00 3.67
118 119 4.549458 CAGTACATTGTTGAGGCTTTTGG 58.451 43.478 0.00 0.00 0.00 3.28
119 120 4.037923 ACCAGTACATTGTTGAGGCTTTTG 59.962 41.667 0.00 0.00 0.00 2.44
120 121 4.215109 ACCAGTACATTGTTGAGGCTTTT 58.785 39.130 0.00 0.00 0.00 2.27
121 122 3.832527 ACCAGTACATTGTTGAGGCTTT 58.167 40.909 0.00 0.00 0.00 3.51
122 123 3.508845 ACCAGTACATTGTTGAGGCTT 57.491 42.857 0.00 0.00 0.00 4.35
123 124 3.508845 AACCAGTACATTGTTGAGGCT 57.491 42.857 0.00 0.00 0.00 4.58
124 125 5.699097 TTTAACCAGTACATTGTTGAGGC 57.301 39.130 0.00 0.00 0.00 4.70
125 126 9.541143 AAAAATTTAACCAGTACATTGTTGAGG 57.459 29.630 0.00 0.00 0.00 3.86
154 155 9.788960 GGCTTTCGTTCATTAGATTCTTATTTT 57.211 29.630 0.00 0.00 0.00 1.82
155 156 8.956426 TGGCTTTCGTTCATTAGATTCTTATTT 58.044 29.630 0.00 0.00 0.00 1.40
156 157 8.398665 GTGGCTTTCGTTCATTAGATTCTTATT 58.601 33.333 0.00 0.00 0.00 1.40
157 158 7.254455 CGTGGCTTTCGTTCATTAGATTCTTAT 60.254 37.037 0.00 0.00 0.00 1.73
158 159 6.035650 CGTGGCTTTCGTTCATTAGATTCTTA 59.964 38.462 0.00 0.00 0.00 2.10
159 160 5.163854 CGTGGCTTTCGTTCATTAGATTCTT 60.164 40.000 0.00 0.00 0.00 2.52
160 161 4.330074 CGTGGCTTTCGTTCATTAGATTCT 59.670 41.667 0.00 0.00 0.00 2.40
161 162 4.494199 CCGTGGCTTTCGTTCATTAGATTC 60.494 45.833 0.00 0.00 0.00 2.52
162 163 3.374058 CCGTGGCTTTCGTTCATTAGATT 59.626 43.478 0.00 0.00 0.00 2.40
163 164 2.936498 CCGTGGCTTTCGTTCATTAGAT 59.064 45.455 0.00 0.00 0.00 1.98
164 165 2.343101 CCGTGGCTTTCGTTCATTAGA 58.657 47.619 0.00 0.00 0.00 2.10
165 166 1.202031 GCCGTGGCTTTCGTTCATTAG 60.202 52.381 2.98 0.00 38.26 1.73
166 167 0.800012 GCCGTGGCTTTCGTTCATTA 59.200 50.000 2.98 0.00 38.26 1.90
167 168 1.579429 GCCGTGGCTTTCGTTCATT 59.421 52.632 2.98 0.00 38.26 2.57
168 169 2.677003 CGCCGTGGCTTTCGTTCAT 61.677 57.895 9.55 0.00 39.32 2.57
169 170 3.342627 CGCCGTGGCTTTCGTTCA 61.343 61.111 9.55 0.00 39.32 3.18
170 171 3.011760 CTCGCCGTGGCTTTCGTTC 62.012 63.158 9.55 0.00 39.32 3.95
171 172 3.041940 CTCGCCGTGGCTTTCGTT 61.042 61.111 9.55 0.00 39.32 3.85
172 173 3.802418 AACTCGCCGTGGCTTTCGT 62.802 57.895 9.55 0.00 39.32 3.85
173 174 2.604174 AAACTCGCCGTGGCTTTCG 61.604 57.895 9.55 0.00 39.32 3.46
174 175 1.082104 CAAACTCGCCGTGGCTTTC 60.082 57.895 9.55 0.00 39.32 2.62
175 176 1.822186 ACAAACTCGCCGTGGCTTT 60.822 52.632 9.55 0.00 39.32 3.51
176 177 2.203153 ACAAACTCGCCGTGGCTT 60.203 55.556 9.55 0.00 39.32 4.35
177 178 2.972505 CACAAACTCGCCGTGGCT 60.973 61.111 9.55 0.00 39.32 4.75
178 179 3.276846 ACACAAACTCGCCGTGGC 61.277 61.111 0.00 0.00 34.91 5.01
179 180 1.227999 ATCACACAAACTCGCCGTGG 61.228 55.000 0.00 0.00 34.91 4.94
180 181 0.110688 CATCACACAAACTCGCCGTG 60.111 55.000 0.00 0.00 36.70 4.94
181 182 0.249699 TCATCACACAAACTCGCCGT 60.250 50.000 0.00 0.00 0.00 5.68
182 183 0.439985 CTCATCACACAAACTCGCCG 59.560 55.000 0.00 0.00 0.00 6.46
183 184 1.795768 TCTCATCACACAAACTCGCC 58.204 50.000 0.00 0.00 0.00 5.54
184 185 3.257393 AGATCTCATCACACAAACTCGC 58.743 45.455 0.00 0.00 0.00 5.03
185 186 5.645624 ACTAGATCTCATCACACAAACTCG 58.354 41.667 0.00 0.00 0.00 4.18
186 187 7.201393 CGAAACTAGATCTCATCACACAAACTC 60.201 40.741 0.00 0.00 0.00 3.01
187 188 6.587990 CGAAACTAGATCTCATCACACAAACT 59.412 38.462 0.00 0.00 0.00 2.66
188 189 6.586463 TCGAAACTAGATCTCATCACACAAAC 59.414 38.462 0.00 0.00 0.00 2.93
189 190 6.687604 TCGAAACTAGATCTCATCACACAAA 58.312 36.000 0.00 0.00 0.00 2.83
190 191 6.267496 TCGAAACTAGATCTCATCACACAA 57.733 37.500 0.00 0.00 0.00 3.33
191 192 5.897377 TCGAAACTAGATCTCATCACACA 57.103 39.130 0.00 0.00 0.00 3.72
192 193 5.918011 GGATCGAAACTAGATCTCATCACAC 59.082 44.000 0.00 0.00 42.91 3.82
193 194 5.594317 TGGATCGAAACTAGATCTCATCACA 59.406 40.000 0.00 0.00 42.91 3.58
194 195 6.078202 TGGATCGAAACTAGATCTCATCAC 57.922 41.667 0.00 0.00 42.91 3.06
195 196 6.461648 GGTTGGATCGAAACTAGATCTCATCA 60.462 42.308 0.00 0.00 42.91 3.07
196 197 5.923684 GGTTGGATCGAAACTAGATCTCATC 59.076 44.000 0.00 0.00 42.91 2.92
197 198 5.600484 AGGTTGGATCGAAACTAGATCTCAT 59.400 40.000 6.18 0.00 42.91 2.90
198 199 4.956700 AGGTTGGATCGAAACTAGATCTCA 59.043 41.667 6.18 1.19 42.91 3.27
199 200 5.523438 AGGTTGGATCGAAACTAGATCTC 57.477 43.478 6.18 0.00 42.91 2.75
200 201 6.183360 GGTTAGGTTGGATCGAAACTAGATCT 60.183 42.308 13.98 0.00 42.91 2.75
201 202 5.984323 GGTTAGGTTGGATCGAAACTAGATC 59.016 44.000 13.98 9.50 42.68 2.75
202 203 5.661759 AGGTTAGGTTGGATCGAAACTAGAT 59.338 40.000 13.98 3.61 0.00 1.98
203 204 5.021458 AGGTTAGGTTGGATCGAAACTAGA 58.979 41.667 13.98 4.82 0.00 2.43
204 205 5.340439 AGGTTAGGTTGGATCGAAACTAG 57.660 43.478 13.98 0.00 0.00 2.57
205 206 5.716228 TGTAGGTTAGGTTGGATCGAAACTA 59.284 40.000 10.85 10.85 0.00 2.24
206 207 4.529377 TGTAGGTTAGGTTGGATCGAAACT 59.471 41.667 12.93 12.93 0.00 2.66
207 208 4.824289 TGTAGGTTAGGTTGGATCGAAAC 58.176 43.478 0.00 0.00 0.00 2.78
208 209 4.773674 TCTGTAGGTTAGGTTGGATCGAAA 59.226 41.667 0.00 0.00 0.00 3.46
209 210 4.346730 TCTGTAGGTTAGGTTGGATCGAA 58.653 43.478 0.00 0.00 0.00 3.71
210 211 3.972133 TCTGTAGGTTAGGTTGGATCGA 58.028 45.455 0.00 0.00 0.00 3.59
211 212 4.341235 TCATCTGTAGGTTAGGTTGGATCG 59.659 45.833 0.00 0.00 0.00 3.69
212 213 5.740513 GCTCATCTGTAGGTTAGGTTGGATC 60.741 48.000 0.00 0.00 0.00 3.36
213 214 4.101741 GCTCATCTGTAGGTTAGGTTGGAT 59.898 45.833 0.00 0.00 0.00 3.41
214 215 3.451178 GCTCATCTGTAGGTTAGGTTGGA 59.549 47.826 0.00 0.00 0.00 3.53
215 216 3.197766 TGCTCATCTGTAGGTTAGGTTGG 59.802 47.826 0.00 0.00 0.00 3.77
216 217 4.471904 TGCTCATCTGTAGGTTAGGTTG 57.528 45.455 0.00 0.00 0.00 3.77
217 218 6.136857 TCTATGCTCATCTGTAGGTTAGGTT 58.863 40.000 0.00 0.00 0.00 3.50
218 219 5.706447 TCTATGCTCATCTGTAGGTTAGGT 58.294 41.667 0.00 0.00 0.00 3.08
219 220 6.849085 ATCTATGCTCATCTGTAGGTTAGG 57.151 41.667 0.00 0.00 0.00 2.69
220 221 7.890515 TGAATCTATGCTCATCTGTAGGTTAG 58.109 38.462 0.00 0.00 0.00 2.34
221 222 7.839680 TGAATCTATGCTCATCTGTAGGTTA 57.160 36.000 0.00 0.00 0.00 2.85
225 226 6.645827 CAGGTTGAATCTATGCTCATCTGTAG 59.354 42.308 0.00 0.00 0.00 2.74
233 234 9.748708 GAGATATATCAGGTTGAATCTATGCTC 57.251 37.037 15.08 0.00 25.65 4.26
488 492 2.158711 TCCTTGGCATTGCAGATAGGAG 60.159 50.000 11.39 0.00 0.00 3.69
489 493 1.845791 TCCTTGGCATTGCAGATAGGA 59.154 47.619 11.39 12.45 0.00 2.94
490 494 2.353357 TCCTTGGCATTGCAGATAGG 57.647 50.000 11.39 10.45 0.00 2.57
491 495 4.724074 TTTTCCTTGGCATTGCAGATAG 57.276 40.909 11.39 1.72 0.00 2.08
492 496 5.187381 TGAATTTTCCTTGGCATTGCAGATA 59.813 36.000 11.39 0.00 0.00 1.98
493 497 4.020039 TGAATTTTCCTTGGCATTGCAGAT 60.020 37.500 11.39 0.00 0.00 2.90
496 500 3.766068 TGAATTTTCCTTGGCATTGCA 57.234 38.095 11.39 0.00 0.00 4.08
501 505 2.224257 GCCTGTTGAATTTTCCTTGGCA 60.224 45.455 0.00 0.00 37.91 4.92
525 538 2.570302 GGGTGGTACTGGTTGTGTATCT 59.430 50.000 0.00 0.00 0.00 1.98
549 568 5.417894 CCTGTTAGTCTGTAGTGTATGTGGA 59.582 44.000 0.00 0.00 0.00 4.02
577 598 4.559063 CGCCAGGGCTCTCATGGG 62.559 72.222 8.91 0.00 46.67 4.00
643 729 0.179225 CCATTGACAGTTACGCACGC 60.179 55.000 0.00 0.00 0.00 5.34
718 804 0.032952 GGTTCGCTACCACTCACACA 59.967 55.000 2.10 0.00 46.92 3.72
719 805 2.823628 GGTTCGCTACCACTCACAC 58.176 57.895 2.10 0.00 46.92 3.82
822 908 2.429930 CAGGGTTCTTGGCGACCA 59.570 61.111 0.00 0.00 37.68 4.02
849 935 4.507710 TGATCCTGTGTCTATGTTTCTGC 58.492 43.478 0.00 0.00 0.00 4.26
860 959 0.035630 AAGGCTGCTGATCCTGTGTC 60.036 55.000 0.00 0.00 32.00 3.67
865 964 2.274760 GCCAAGGCTGCTGATCCT 59.725 61.111 3.29 0.00 38.26 3.24
877 983 2.704190 TATAGGGGAGGAGAGCCAAG 57.296 55.000 0.00 0.00 36.29 3.61
878 984 3.431411 TTTATAGGGGAGGAGAGCCAA 57.569 47.619 0.00 0.00 36.29 4.52
879 985 3.046374 GTTTTATAGGGGAGGAGAGCCA 58.954 50.000 0.00 0.00 36.29 4.75
881 987 2.699321 ACGTTTTATAGGGGAGGAGAGC 59.301 50.000 0.00 0.00 0.00 4.09
882 988 3.958798 TGACGTTTTATAGGGGAGGAGAG 59.041 47.826 0.00 0.00 0.00 3.20
883 989 3.958798 CTGACGTTTTATAGGGGAGGAGA 59.041 47.826 0.00 0.00 0.00 3.71
884 990 3.492829 GCTGACGTTTTATAGGGGAGGAG 60.493 52.174 0.00 0.00 0.00 3.69
885 991 2.433239 GCTGACGTTTTATAGGGGAGGA 59.567 50.000 0.00 0.00 0.00 3.71
887 993 3.132289 TCAGCTGACGTTTTATAGGGGAG 59.868 47.826 13.74 0.00 0.00 4.30
888 994 3.101437 TCAGCTGACGTTTTATAGGGGA 58.899 45.455 13.74 0.00 0.00 4.81
890 996 4.755411 TCTTCAGCTGACGTTTTATAGGG 58.245 43.478 18.03 0.00 0.00 3.53
891 997 5.637810 TGTTCTTCAGCTGACGTTTTATAGG 59.362 40.000 18.03 0.00 0.00 2.57
892 998 6.366332 AGTGTTCTTCAGCTGACGTTTTATAG 59.634 38.462 18.03 8.74 0.00 1.31
894 1000 5.057149 AGTGTTCTTCAGCTGACGTTTTAT 58.943 37.500 18.03 0.00 0.00 1.40
895 1001 4.439057 AGTGTTCTTCAGCTGACGTTTTA 58.561 39.130 18.03 0.00 0.00 1.52
896 1002 3.270877 AGTGTTCTTCAGCTGACGTTTT 58.729 40.909 18.03 0.00 0.00 2.43
897 1003 2.906354 AGTGTTCTTCAGCTGACGTTT 58.094 42.857 18.03 0.00 0.00 3.60
898 1004 2.604046 AGTGTTCTTCAGCTGACGTT 57.396 45.000 18.03 0.00 0.00 3.99
999 1116 0.183492 GCCCACAGCAGAATCCCATA 59.817 55.000 0.00 0.00 42.97 2.74
1148 2516 1.208706 CTTCTTCTTCTCCCTCCCCC 58.791 60.000 0.00 0.00 0.00 5.40
1258 2626 1.762370 ACATACGGGATCTCATGCACA 59.238 47.619 0.00 0.00 0.00 4.57
1259 2627 2.533266 ACATACGGGATCTCATGCAC 57.467 50.000 0.00 0.00 0.00 4.57
1265 2633 5.986501 AATAGGAGAACATACGGGATCTC 57.013 43.478 0.00 0.00 38.04 2.75
1284 2652 6.474140 TCCAACCTTGATCGTAAGCTAATA 57.526 37.500 0.00 0.00 37.18 0.98
1297 2665 2.708861 TCAACCTAAGCTCCAACCTTGA 59.291 45.455 0.00 0.00 0.00 3.02
1317 2685 6.093404 TGTGACGACAGTAGAAATCTCATTC 58.907 40.000 0.00 0.00 0.00 2.67
1362 2757 5.913137 TCATGGAATACAACCAACCAATC 57.087 39.130 0.00 0.00 40.93 2.67
1363 2758 6.440010 TGAATCATGGAATACAACCAACCAAT 59.560 34.615 0.00 0.00 40.93 3.16
1364 2759 5.777223 TGAATCATGGAATACAACCAACCAA 59.223 36.000 0.00 0.00 40.93 3.67
1481 2886 1.199327 CGAGTCAAGCCGAGTCAAGTA 59.801 52.381 8.78 0.00 43.35 2.24
1482 2887 0.039074 CGAGTCAAGCCGAGTCAAGT 60.039 55.000 8.78 0.00 43.35 3.16
1483 2888 0.734253 CCGAGTCAAGCCGAGTCAAG 60.734 60.000 8.78 0.00 43.35 3.02
1484 2889 1.289066 CCGAGTCAAGCCGAGTCAA 59.711 57.895 8.78 0.00 43.35 3.18
1485 2890 1.461091 AACCGAGTCAAGCCGAGTCA 61.461 55.000 8.78 0.00 43.35 3.41
1486 2891 0.733223 GAACCGAGTCAAGCCGAGTC 60.733 60.000 0.00 0.00 40.25 3.36
1487 2892 1.289380 GAACCGAGTCAAGCCGAGT 59.711 57.895 0.00 0.00 0.00 4.18
1488 2893 1.009389 GTGAACCGAGTCAAGCCGAG 61.009 60.000 0.00 0.00 0.00 4.63
1489 2894 1.006571 GTGAACCGAGTCAAGCCGA 60.007 57.895 0.00 0.00 0.00 5.54
1490 2895 0.242825 TAGTGAACCGAGTCAAGCCG 59.757 55.000 0.00 0.00 0.00 5.52
1491 2896 1.272769 ACTAGTGAACCGAGTCAAGCC 59.727 52.381 0.00 0.00 0.00 4.35
1492 2897 2.726832 ACTAGTGAACCGAGTCAAGC 57.273 50.000 0.00 0.00 0.00 4.01
1555 2960 4.586841 AGATGCTCCTAGTTGATGTAGACC 59.413 45.833 0.00 0.00 0.00 3.85
1619 3024 1.673920 GCAGTGGACAACTTTTTCCGA 59.326 47.619 0.00 0.00 36.83 4.55
1874 3280 4.521062 GATGCAGCTCGCCTCCGT 62.521 66.667 0.00 0.00 41.33 4.69


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

AutoCloner maintained by Alex Coulton.