Multiple sequence alignment - TraesCS2D01G461400

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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 TraesCS2D01G461400 chr2D 100.000 2252 0 0 1 2252 567676908 567679159 0.000000e+00 4159.0
1 TraesCS2D01G461400 chr2D 88.762 525 57 2 1729 2252 87829873 87830396 1.890000e-180 641.0
2 TraesCS2D01G461400 chr2D 79.032 558 68 26 904 1433 567641939 567642475 9.960000e-89 337.0
3 TraesCS2D01G461400 chr2D 93.458 214 11 2 928 1141 567805955 567806165 4.670000e-82 315.0
4 TraesCS2D01G461400 chr2D 92.500 120 9 0 707 826 567802790 567802909 2.970000e-39 172.0
5 TraesCS2D01G461400 chr2D 80.237 253 24 10 3 253 333219048 333218820 1.380000e-37 167.0
6 TraesCS2D01G461400 chr2D 92.381 105 6 2 3 106 192162151 192162048 5.010000e-32 148.0
7 TraesCS2D01G461400 chr2D 96.386 83 3 0 818 900 567804072 567804154 1.080000e-28 137.0
8 TraesCS2D01G461400 chr2D 97.143 35 1 0 1430 1464 567678295 567678329 2.420000e-05 60.2
9 TraesCS2D01G461400 chr2D 97.143 35 1 0 1388 1422 567678337 567678371 2.420000e-05 60.2
10 TraesCS2D01G461400 chr2A 92.495 1066 61 8 685 1732 707235507 707236571 0.000000e+00 1507.0
11 TraesCS2D01G461400 chr2A 90.879 899 38 18 535 1402 707221654 707222539 0.000000e+00 1166.0
12 TraesCS2D01G461400 chr2A 89.122 524 56 1 1729 2252 66767826 66767304 0.000000e+00 651.0
13 TraesCS2D01G461400 chr2A 85.007 667 52 15 791 1433 707105042 707105684 3.160000e-178 634.0
14 TraesCS2D01G461400 chr2A 93.636 330 15 3 1394 1720 707222675 707223001 2.600000e-134 488.0
15 TraesCS2D01G461400 chr2A 83.096 491 54 19 939 1404 707077419 707077905 9.620000e-114 420.0
16 TraesCS2D01G461400 chr2A 78.364 550 74 25 894 1430 707064204 707064721 4.670000e-82 315.0
17 TraesCS2D01G461400 chr2A 79.032 248 26 11 3 249 54880124 54880346 1.800000e-31 147.0
18 TraesCS2D01G461400 chr2A 88.889 99 11 0 440 538 749432978 749433076 3.040000e-24 122.0
19 TraesCS2D01G461400 chr2A 100.000 32 0 0 1391 1422 707222714 707222745 2.420000e-05 60.2
20 TraesCS2D01G461400 chr2A 97.143 35 1 0 1430 1464 707236220 707236254 2.420000e-05 60.2
21 TraesCS2D01G461400 chr2A 97.143 35 1 0 1388 1422 707236262 707236296 2.420000e-05 60.2
22 TraesCS2D01G461400 chr2A 100.000 29 0 0 1436 1464 707222675 707222703 1.000000e-03 54.7
23 TraesCS2D01G461400 chr2B 92.023 1053 53 10 707 1732 680445795 680446843 0.000000e+00 1450.0
24 TraesCS2D01G461400 chr2B 88.593 526 54 4 1728 2252 730178651 730179171 3.160000e-178 634.0
25 TraesCS2D01G461400 chr2B 84.322 472 51 13 982 1433 680322523 680322991 7.380000e-120 440.0
26 TraesCS2D01G461400 chr2B 80.652 491 58 16 962 1433 680408945 680409417 1.660000e-91 346.0
27 TraesCS2D01G461400 chr2B 80.744 457 52 16 896 1344 680308624 680309052 7.760000e-85 324.0
28 TraesCS2D01G461400 chr2B 83.871 155 6 7 250 403 680443368 680443504 1.820000e-26 130.0
29 TraesCS2D01G461400 chr2B 89.216 102 8 3 3 102 788302178 788302278 8.450000e-25 124.0
30 TraesCS2D01G461400 chr2B 88.571 105 9 3 3 105 788360812 788360709 8.450000e-25 124.0
31 TraesCS2D01G461400 chr2B 88.571 105 9 3 3 105 788383832 788383729 8.450000e-25 124.0
32 TraesCS2D01G461400 chr2B 88.571 105 9 3 3 105 788414190 788414087 8.450000e-25 124.0
33 TraesCS2D01G461400 chr2B 85.841 113 16 0 146 258 788302285 788302397 1.090000e-23 121.0
34 TraesCS2D01G461400 chr2B 85.841 113 16 0 146 258 788360705 788360593 1.090000e-23 121.0
35 TraesCS2D01G461400 chr2B 85.841 113 16 0 146 258 788383725 788383613 1.090000e-23 121.0
36 TraesCS2D01G461400 chr2B 85.841 113 16 0 146 258 788414083 788413971 1.090000e-23 121.0
37 TraesCS2D01G461400 chr2B 96.970 33 1 0 1430 1462 680446498 680446530 3.120000e-04 56.5
38 TraesCS2D01G461400 chr6D 89.524 525 54 1 1729 2252 20134466 20134990 0.000000e+00 664.0
39 TraesCS2D01G461400 chr6D 92.929 99 7 0 440 538 17273499 17273597 6.480000e-31 145.0
40 TraesCS2D01G461400 chr6D 80.833 120 17 4 135 254 18089816 18089929 3.080000e-14 89.8
41 TraesCS2D01G461400 chr7D 89.484 523 54 1 1731 2252 136414289 136414811 0.000000e+00 660.0
42 TraesCS2D01G461400 chr7D 88.679 106 11 1 433 538 597962573 597962469 6.530000e-26 128.0
43 TraesCS2D01G461400 chr7B 89.143 525 56 1 1729 2252 748331722 748331198 0.000000e+00 652.0
44 TraesCS2D01G461400 chr5D 89.143 525 54 3 1729 2252 220673942 220674464 0.000000e+00 651.0
45 TraesCS2D01G461400 chr3D 88.571 525 59 1 1729 2252 562513983 562514507 8.770000e-179 636.0
46 TraesCS2D01G461400 chr3D 89.167 120 13 0 141 260 445753421 445753302 1.390000e-32 150.0
47 TraesCS2D01G461400 chr4B 88.381 525 59 2 1729 2252 624724706 624725229 4.080000e-177 630.0
48 TraesCS2D01G461400 chr6A 77.778 252 28 16 4 254 15698712 15698936 1.820000e-26 130.0
49 TraesCS2D01G461400 chr6A 88.679 106 9 3 3 106 537322342 537322238 2.350000e-25 126.0
50 TraesCS2D01G461400 chr6A 84.906 106 13 3 3 107 614935374 614935271 1.100000e-18 104.0
51 TraesCS2D01G461400 chr7A 88.889 99 11 0 440 538 28120699 28120797 3.040000e-24 122.0
52 TraesCS2D01G461400 chr4D 86.598 97 12 1 440 536 434928547 434928452 3.060000e-19 106.0
53 TraesCS2D01G461400 chr1B 79.310 116 21 3 137 250 170573042 170573156 6.670000e-11 78.7
54 TraesCS2D01G461400 chr3A 79.070 129 14 12 136 257 750588571 750588449 2.400000e-10 76.8


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 TraesCS2D01G461400 chr2D 567676908 567679159 2251 False 1426.466667 4159 98.095333 1 2252 3 chr2D.!!$F3 2251
1 TraesCS2D01G461400 chr2D 87829873 87830396 523 False 641.000000 641 88.762000 1729 2252 1 chr2D.!!$F1 523
2 TraesCS2D01G461400 chr2D 567641939 567642475 536 False 337.000000 337 79.032000 904 1433 1 chr2D.!!$F2 529
3 TraesCS2D01G461400 chr2D 567802790 567806165 3375 False 208.000000 315 94.114667 707 1141 3 chr2D.!!$F4 434
4 TraesCS2D01G461400 chr2A 66767304 66767826 522 True 651.000000 651 89.122000 1729 2252 1 chr2A.!!$R1 523
5 TraesCS2D01G461400 chr2A 707105042 707105684 642 False 634.000000 634 85.007000 791 1433 1 chr2A.!!$F4 642
6 TraesCS2D01G461400 chr2A 707235507 707236571 1064 False 542.466667 1507 95.593667 685 1732 3 chr2A.!!$F7 1047
7 TraesCS2D01G461400 chr2A 707221654 707223001 1347 False 442.225000 1166 96.128750 535 1720 4 chr2A.!!$F6 1185
8 TraesCS2D01G461400 chr2A 707064204 707064721 517 False 315.000000 315 78.364000 894 1430 1 chr2A.!!$F2 536
9 TraesCS2D01G461400 chr2B 730178651 730179171 520 False 634.000000 634 88.593000 1728 2252 1 chr2B.!!$F4 524
10 TraesCS2D01G461400 chr2B 680443368 680446843 3475 False 545.500000 1450 90.954667 250 1732 3 chr2B.!!$F5 1482
11 TraesCS2D01G461400 chr6D 20134466 20134990 524 False 664.000000 664 89.524000 1729 2252 1 chr6D.!!$F3 523
12 TraesCS2D01G461400 chr7D 136414289 136414811 522 False 660.000000 660 89.484000 1731 2252 1 chr7D.!!$F1 521
13 TraesCS2D01G461400 chr7B 748331198 748331722 524 True 652.000000 652 89.143000 1729 2252 1 chr7B.!!$R1 523
14 TraesCS2D01G461400 chr5D 220673942 220674464 522 False 651.000000 651 89.143000 1729 2252 1 chr5D.!!$F1 523
15 TraesCS2D01G461400 chr3D 562513983 562514507 524 False 636.000000 636 88.571000 1729 2252 1 chr3D.!!$F1 523
16 TraesCS2D01G461400 chr4B 624724706 624725229 523 False 630.000000 630 88.381000 1729 2252 1 chr4B.!!$F1 523

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
606 1978 0.106769 TGTTTTGGCTGCAGGAGACA 60.107 50.0 17.12 0.0 38.27 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 7211 0.677288 CTAGACACACCACCGGAACA 59.323 55.0 9.46 0.0 0.0 3.18 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
39 40 3.584406 TTTTTGTATGCCGGGATGTTG 57.416 42.857 20.08 0.00 0.00 3.33
40 41 2.208132 TTTGTATGCCGGGATGTTGT 57.792 45.000 20.08 0.00 0.00 3.32
41 42 1.745232 TTGTATGCCGGGATGTTGTC 58.255 50.000 20.08 4.55 0.00 3.18
42 43 0.908910 TGTATGCCGGGATGTTGTCT 59.091 50.000 20.08 0.00 0.00 3.41
43 44 1.280710 TGTATGCCGGGATGTTGTCTT 59.719 47.619 20.08 0.00 0.00 3.01
44 45 2.290641 TGTATGCCGGGATGTTGTCTTT 60.291 45.455 20.08 0.00 0.00 2.52
45 46 1.176527 ATGCCGGGATGTTGTCTTTG 58.823 50.000 8.05 0.00 0.00 2.77
46 47 0.109532 TGCCGGGATGTTGTCTTTGA 59.890 50.000 2.18 0.00 0.00 2.69
47 48 1.271871 TGCCGGGATGTTGTCTTTGAT 60.272 47.619 2.18 0.00 0.00 2.57
48 49 1.133025 GCCGGGATGTTGTCTTTGATG 59.867 52.381 2.18 0.00 0.00 3.07
49 50 1.745087 CCGGGATGTTGTCTTTGATGG 59.255 52.381 0.00 0.00 0.00 3.51
50 51 1.133025 CGGGATGTTGTCTTTGATGGC 59.867 52.381 0.00 0.00 0.00 4.40
51 52 1.133025 GGGATGTTGTCTTTGATGGCG 59.867 52.381 0.00 0.00 0.00 5.69
52 53 1.133025 GGATGTTGTCTTTGATGGCGG 59.867 52.381 0.00 0.00 0.00 6.13
53 54 1.812571 GATGTTGTCTTTGATGGCGGT 59.187 47.619 0.00 0.00 0.00 5.68
54 55 1.686355 TGTTGTCTTTGATGGCGGTT 58.314 45.000 0.00 0.00 0.00 4.44
55 56 2.852449 TGTTGTCTTTGATGGCGGTTA 58.148 42.857 0.00 0.00 0.00 2.85
56 57 2.811431 TGTTGTCTTTGATGGCGGTTAG 59.189 45.455 0.00 0.00 0.00 2.34
57 58 3.071479 GTTGTCTTTGATGGCGGTTAGA 58.929 45.455 0.00 0.00 0.00 2.10
58 59 2.972625 TGTCTTTGATGGCGGTTAGAG 58.027 47.619 0.00 0.00 0.00 2.43
59 60 2.301870 TGTCTTTGATGGCGGTTAGAGT 59.698 45.455 0.00 0.00 0.00 3.24
60 61 2.673368 GTCTTTGATGGCGGTTAGAGTG 59.327 50.000 0.00 0.00 0.00 3.51
61 62 2.301870 TCTTTGATGGCGGTTAGAGTGT 59.698 45.455 0.00 0.00 0.00 3.55
62 63 2.851263 TTGATGGCGGTTAGAGTGTT 57.149 45.000 0.00 0.00 0.00 3.32
63 64 2.093306 TGATGGCGGTTAGAGTGTTG 57.907 50.000 0.00 0.00 0.00 3.33
64 65 1.346395 TGATGGCGGTTAGAGTGTTGT 59.654 47.619 0.00 0.00 0.00 3.32
65 66 2.224426 TGATGGCGGTTAGAGTGTTGTT 60.224 45.455 0.00 0.00 0.00 2.83
66 67 1.588674 TGGCGGTTAGAGTGTTGTTG 58.411 50.000 0.00 0.00 0.00 3.33
67 68 1.134340 TGGCGGTTAGAGTGTTGTTGT 60.134 47.619 0.00 0.00 0.00 3.32
68 69 1.944709 GGCGGTTAGAGTGTTGTTGTT 59.055 47.619 0.00 0.00 0.00 2.83
69 70 2.286772 GGCGGTTAGAGTGTTGTTGTTG 60.287 50.000 0.00 0.00 0.00 3.33
70 71 2.853281 GCGGTTAGAGTGTTGTTGTTGC 60.853 50.000 0.00 0.00 0.00 4.17
71 72 2.612212 CGGTTAGAGTGTTGTTGTTGCT 59.388 45.455 0.00 0.00 0.00 3.91
72 73 3.805422 CGGTTAGAGTGTTGTTGTTGCTA 59.195 43.478 0.00 0.00 0.00 3.49
73 74 4.084537 CGGTTAGAGTGTTGTTGTTGCTAG 60.085 45.833 0.00 0.00 0.00 3.42
74 75 4.814771 GGTTAGAGTGTTGTTGTTGCTAGT 59.185 41.667 0.00 0.00 0.00 2.57
75 76 5.277345 GGTTAGAGTGTTGTTGTTGCTAGTG 60.277 44.000 0.00 0.00 0.00 2.74
76 77 4.137116 AGAGTGTTGTTGTTGCTAGTGA 57.863 40.909 0.00 0.00 0.00 3.41
77 78 3.871594 AGAGTGTTGTTGTTGCTAGTGAC 59.128 43.478 0.00 0.00 0.00 3.67
78 79 3.871594 GAGTGTTGTTGTTGCTAGTGACT 59.128 43.478 0.00 0.00 0.00 3.41
79 80 3.623060 AGTGTTGTTGTTGCTAGTGACTG 59.377 43.478 0.00 0.00 0.00 3.51
80 81 3.621268 GTGTTGTTGTTGCTAGTGACTGA 59.379 43.478 0.00 0.00 0.00 3.41
81 82 4.273480 GTGTTGTTGTTGCTAGTGACTGAT 59.727 41.667 0.00 0.00 0.00 2.90
82 83 4.511454 TGTTGTTGTTGCTAGTGACTGATC 59.489 41.667 0.00 0.00 0.00 2.92
83 84 4.335400 TGTTGTTGCTAGTGACTGATCA 57.665 40.909 0.00 0.00 0.00 2.92
91 92 2.261361 TGACTGATCACCGTGGCG 59.739 61.111 0.00 0.00 0.00 5.69
123 124 7.671495 TTTTGTTCAGAGATTGAATCGATCA 57.329 32.000 12.62 0.00 46.85 2.92
124 125 7.854557 TTTGTTCAGAGATTGAATCGATCAT 57.145 32.000 12.62 0.00 46.85 2.45
125 126 7.474398 TTGTTCAGAGATTGAATCGATCATC 57.526 36.000 12.62 7.34 46.85 2.92
126 127 6.576185 TGTTCAGAGATTGAATCGATCATCA 58.424 36.000 12.62 0.00 46.85 3.07
127 128 7.215085 TGTTCAGAGATTGAATCGATCATCAT 58.785 34.615 12.62 0.00 46.85 2.45
128 129 7.384387 TGTTCAGAGATTGAATCGATCATCATC 59.616 37.037 12.62 1.99 46.85 2.92
129 130 6.989659 TCAGAGATTGAATCGATCATCATCA 58.010 36.000 12.62 0.00 38.03 3.07
130 131 7.091443 TCAGAGATTGAATCGATCATCATCAG 58.909 38.462 12.62 0.00 38.03 2.90
131 132 7.039923 TCAGAGATTGAATCGATCATCATCAGA 60.040 37.037 12.62 1.87 38.03 3.27
132 133 7.599245 CAGAGATTGAATCGATCATCATCAGAA 59.401 37.037 12.62 0.00 38.03 3.02
133 134 7.815549 AGAGATTGAATCGATCATCATCAGAAG 59.184 37.037 12.62 0.00 38.03 2.85
134 135 7.668492 AGATTGAATCGATCATCATCAGAAGA 58.332 34.615 12.62 0.00 38.03 2.87
135 136 8.315482 AGATTGAATCGATCATCATCAGAAGAT 58.685 33.333 12.62 0.00 38.03 2.40
136 137 8.850007 ATTGAATCGATCATCATCAGAAGATT 57.150 30.769 0.00 0.00 38.03 2.40
137 138 8.672823 TTGAATCGATCATCATCAGAAGATTT 57.327 30.769 0.00 0.00 38.03 2.17
138 139 8.672823 TGAATCGATCATCATCAGAAGATTTT 57.327 30.769 0.00 0.00 32.70 1.82
139 140 9.117183 TGAATCGATCATCATCAGAAGATTTTT 57.883 29.630 0.00 0.00 32.70 1.94
167 168 4.822036 TTTTTGACCGTGTGTATCCTTG 57.178 40.909 0.00 0.00 0.00 3.61
168 169 3.755112 TTTGACCGTGTGTATCCTTGA 57.245 42.857 0.00 0.00 0.00 3.02
169 170 3.973206 TTGACCGTGTGTATCCTTGAT 57.027 42.857 0.00 0.00 0.00 2.57
170 171 3.245518 TGACCGTGTGTATCCTTGATG 57.754 47.619 0.00 0.00 0.00 3.07
171 172 2.565391 TGACCGTGTGTATCCTTGATGT 59.435 45.455 0.00 0.00 0.00 3.06
172 173 3.187700 GACCGTGTGTATCCTTGATGTC 58.812 50.000 0.00 0.00 0.00 3.06
173 174 2.832129 ACCGTGTGTATCCTTGATGTCT 59.168 45.455 0.00 0.00 0.00 3.41
174 175 3.260884 ACCGTGTGTATCCTTGATGTCTT 59.739 43.478 0.00 0.00 0.00 3.01
175 176 4.253685 CCGTGTGTATCCTTGATGTCTTT 58.746 43.478 0.00 0.00 0.00 2.52
176 177 4.093408 CCGTGTGTATCCTTGATGTCTTTG 59.907 45.833 0.00 0.00 0.00 2.77
177 178 4.093408 CGTGTGTATCCTTGATGTCTTTGG 59.907 45.833 0.00 0.00 0.00 3.28
178 179 5.245531 GTGTGTATCCTTGATGTCTTTGGA 58.754 41.667 0.00 0.00 0.00 3.53
179 180 5.122396 GTGTGTATCCTTGATGTCTTTGGAC 59.878 44.000 0.00 0.00 42.42 4.02
180 181 5.013079 TGTGTATCCTTGATGTCTTTGGACT 59.987 40.000 0.00 0.00 42.54 3.85
181 182 5.940470 GTGTATCCTTGATGTCTTTGGACTT 59.060 40.000 0.00 0.00 42.54 3.01
182 183 6.092807 GTGTATCCTTGATGTCTTTGGACTTC 59.907 42.308 0.00 0.00 42.99 3.01
183 184 4.982241 TCCTTGATGTCTTTGGACTTCT 57.018 40.909 11.39 0.00 43.06 2.85
184 185 5.310409 TCCTTGATGTCTTTGGACTTCTT 57.690 39.130 11.39 0.00 43.06 2.52
185 186 5.065914 TCCTTGATGTCTTTGGACTTCTTG 58.934 41.667 11.39 6.06 43.06 3.02
186 187 4.823989 CCTTGATGTCTTTGGACTTCTTGT 59.176 41.667 11.39 0.00 43.06 3.16
187 188 5.300286 CCTTGATGTCTTTGGACTTCTTGTT 59.700 40.000 11.39 0.00 43.06 2.83
188 189 5.756195 TGATGTCTTTGGACTTCTTGTTG 57.244 39.130 11.39 0.00 43.06 3.33
189 190 4.580167 TGATGTCTTTGGACTTCTTGTTGG 59.420 41.667 11.39 0.00 43.06 3.77
190 191 3.963129 TGTCTTTGGACTTCTTGTTGGT 58.037 40.909 0.00 0.00 42.54 3.67
191 192 5.105567 TGTCTTTGGACTTCTTGTTGGTA 57.894 39.130 0.00 0.00 42.54 3.25
192 193 4.879545 TGTCTTTGGACTTCTTGTTGGTAC 59.120 41.667 0.00 0.00 42.54 3.34
193 194 4.879545 GTCTTTGGACTTCTTGTTGGTACA 59.120 41.667 0.00 0.00 39.24 2.90
194 195 5.007724 GTCTTTGGACTTCTTGTTGGTACAG 59.992 44.000 0.00 0.00 38.51 2.74
195 196 4.764050 TTGGACTTCTTGTTGGTACAGA 57.236 40.909 0.00 0.00 42.39 3.41
196 197 4.336889 TGGACTTCTTGTTGGTACAGAG 57.663 45.455 0.00 0.00 42.39 3.35
197 198 3.964688 TGGACTTCTTGTTGGTACAGAGA 59.035 43.478 0.00 0.00 42.39 3.10
198 199 4.202223 TGGACTTCTTGTTGGTACAGAGAC 60.202 45.833 0.00 0.00 42.39 3.36
199 200 4.308265 GACTTCTTGTTGGTACAGAGACC 58.692 47.826 0.00 0.00 42.39 3.85
200 201 3.243771 ACTTCTTGTTGGTACAGAGACCG 60.244 47.826 0.00 0.00 42.99 4.79
201 202 2.589720 TCTTGTTGGTACAGAGACCGA 58.410 47.619 0.00 0.00 42.99 4.69
202 203 2.557056 TCTTGTTGGTACAGAGACCGAG 59.443 50.000 0.00 0.00 42.99 4.63
203 204 1.991121 TGTTGGTACAGAGACCGAGT 58.009 50.000 0.00 0.00 42.99 4.18
204 205 1.611977 TGTTGGTACAGAGACCGAGTG 59.388 52.381 0.00 0.00 42.99 3.51
205 206 1.612463 GTTGGTACAGAGACCGAGTGT 59.388 52.381 0.00 0.00 42.99 3.55
206 207 2.816087 GTTGGTACAGAGACCGAGTGTA 59.184 50.000 0.00 0.00 42.99 2.90
207 208 3.144657 TGGTACAGAGACCGAGTGTAA 57.855 47.619 0.00 0.00 42.99 2.41
208 209 3.693807 TGGTACAGAGACCGAGTGTAAT 58.306 45.455 0.00 0.00 42.99 1.89
209 210 4.084287 TGGTACAGAGACCGAGTGTAATT 58.916 43.478 0.00 0.00 42.99 1.40
210 211 4.082408 TGGTACAGAGACCGAGTGTAATTG 60.082 45.833 0.00 0.00 42.99 2.32
211 212 3.594603 ACAGAGACCGAGTGTAATTGG 57.405 47.619 0.00 0.00 0.00 3.16
212 213 2.897969 ACAGAGACCGAGTGTAATTGGT 59.102 45.455 0.00 0.00 39.85 3.67
213 214 4.084287 ACAGAGACCGAGTGTAATTGGTA 58.916 43.478 0.00 0.00 37.06 3.25
214 215 4.710375 ACAGAGACCGAGTGTAATTGGTAT 59.290 41.667 0.00 0.00 37.06 2.73
215 216 5.163540 ACAGAGACCGAGTGTAATTGGTATC 60.164 44.000 5.47 5.47 42.86 2.24
216 217 5.202004 AGAGACCGAGTGTAATTGGTATCT 58.798 41.667 9.44 9.44 46.16 1.98
217 218 5.903810 GAGACCGAGTGTAATTGGTATCTT 58.096 41.667 6.21 0.00 40.45 2.40
218 219 5.903810 AGACCGAGTGTAATTGGTATCTTC 58.096 41.667 0.00 0.00 37.06 2.87
219 220 5.421056 AGACCGAGTGTAATTGGTATCTTCA 59.579 40.000 0.00 0.00 37.06 3.02
220 221 6.098409 AGACCGAGTGTAATTGGTATCTTCAT 59.902 38.462 0.00 0.00 37.06 2.57
221 222 7.287005 AGACCGAGTGTAATTGGTATCTTCATA 59.713 37.037 0.00 0.00 37.06 2.15
222 223 7.788026 ACCGAGTGTAATTGGTATCTTCATAA 58.212 34.615 0.00 0.00 35.01 1.90
223 224 8.429641 ACCGAGTGTAATTGGTATCTTCATAAT 58.570 33.333 0.00 0.00 35.01 1.28
224 225 9.923143 CCGAGTGTAATTGGTATCTTCATAATA 57.077 33.333 0.00 0.00 0.00 0.98
256 257 7.767250 ATTCCCTTTCTCGAAAAAGAAGAAT 57.233 32.000 12.83 15.44 38.30 2.40
279 280 1.954382 GTGAAACCTTCCGCCTTCTTT 59.046 47.619 0.00 0.00 0.00 2.52
309 310 2.559698 TCGTCAATTGCTCCAAGGAA 57.440 45.000 0.00 0.00 0.00 3.36
310 311 2.426522 TCGTCAATTGCTCCAAGGAAG 58.573 47.619 0.00 0.00 0.00 3.46
311 312 2.154462 CGTCAATTGCTCCAAGGAAGT 58.846 47.619 0.00 0.00 0.00 3.01
314 315 4.215399 CGTCAATTGCTCCAAGGAAGTAAA 59.785 41.667 0.00 0.00 0.00 2.01
315 316 5.106157 CGTCAATTGCTCCAAGGAAGTAAAT 60.106 40.000 0.00 0.00 0.00 1.40
316 317 6.325596 GTCAATTGCTCCAAGGAAGTAAATC 58.674 40.000 0.00 0.00 0.00 2.17
317 318 6.009589 TCAATTGCTCCAAGGAAGTAAATCA 58.990 36.000 0.00 0.00 0.00 2.57
318 319 5.904362 ATTGCTCCAAGGAAGTAAATCAC 57.096 39.130 0.00 0.00 0.00 3.06
319 320 4.640771 TGCTCCAAGGAAGTAAATCACT 57.359 40.909 0.00 0.00 40.05 3.41
320 321 4.579869 TGCTCCAAGGAAGTAAATCACTC 58.420 43.478 0.00 0.00 36.04 3.51
321 322 4.287067 TGCTCCAAGGAAGTAAATCACTCT 59.713 41.667 0.00 0.00 36.04 3.24
322 323 4.633565 GCTCCAAGGAAGTAAATCACTCTG 59.366 45.833 0.00 0.00 36.04 3.35
323 324 5.799213 CTCCAAGGAAGTAAATCACTCTGT 58.201 41.667 0.00 0.00 36.04 3.41
324 325 5.794894 TCCAAGGAAGTAAATCACTCTGTC 58.205 41.667 0.00 0.00 36.04 3.51
325 326 5.544176 TCCAAGGAAGTAAATCACTCTGTCT 59.456 40.000 0.00 0.00 36.04 3.41
326 327 6.724441 TCCAAGGAAGTAAATCACTCTGTCTA 59.276 38.462 0.00 0.00 36.04 2.59
327 328 7.234782 TCCAAGGAAGTAAATCACTCTGTCTAA 59.765 37.037 0.00 0.00 36.04 2.10
328 329 8.043710 CCAAGGAAGTAAATCACTCTGTCTAAT 58.956 37.037 0.00 0.00 36.04 1.73
329 330 9.442047 CAAGGAAGTAAATCACTCTGTCTAATT 57.558 33.333 0.00 0.00 36.04 1.40
361 362 3.121058 CCAAACCAAAATCAACGATTGCG 60.121 43.478 0.00 0.00 44.79 4.85
387 389 3.304764 TTCTCGCGGTCGACTGACG 62.305 63.158 28.38 26.57 46.49 4.35
398 400 1.069924 CGACTGACGAGAAGCAGCAG 61.070 60.000 0.00 0.00 45.77 4.24
403 405 0.811915 GACGAGAAGCAGCAGGACTA 59.188 55.000 0.00 0.00 0.00 2.59
405 407 0.814457 CGAGAAGCAGCAGGACTACT 59.186 55.000 0.00 0.00 0.00 2.57
406 408 1.203523 CGAGAAGCAGCAGGACTACTT 59.796 52.381 0.00 0.00 34.49 2.24
407 409 2.615869 GAGAAGCAGCAGGACTACTTG 58.384 52.381 0.00 0.00 31.77 3.16
408 410 1.277557 AGAAGCAGCAGGACTACTTGG 59.722 52.381 0.00 0.00 31.77 3.61
409 411 0.322008 AAGCAGCAGGACTACTTGGC 60.322 55.000 0.00 0.00 30.34 4.52
410 412 1.197430 AGCAGCAGGACTACTTGGCT 61.197 55.000 0.00 0.00 0.00 4.75
411 413 1.023513 GCAGCAGGACTACTTGGCTG 61.024 60.000 7.52 7.52 33.86 4.85
412 414 1.023513 CAGCAGGACTACTTGGCTGC 61.024 60.000 0.00 0.00 38.01 5.25
413 415 1.197430 AGCAGGACTACTTGGCTGCT 61.197 55.000 0.00 0.00 42.41 4.24
414 416 0.742635 GCAGGACTACTTGGCTGCTC 60.743 60.000 0.00 0.00 35.26 4.26
415 417 0.107945 CAGGACTACTTGGCTGCTCC 60.108 60.000 0.00 0.00 0.00 4.70
416 418 0.252467 AGGACTACTTGGCTGCTCCT 60.252 55.000 0.00 0.00 35.26 3.69
417 419 1.007238 AGGACTACTTGGCTGCTCCTA 59.993 52.381 0.00 0.00 35.26 2.94
418 420 1.410882 GGACTACTTGGCTGCTCCTAG 59.589 57.143 0.00 5.75 42.42 3.02
419 421 1.410882 GACTACTTGGCTGCTCCTAGG 59.589 57.143 0.82 0.82 41.25 3.02
420 422 1.273324 ACTACTTGGCTGCTCCTAGGT 60.273 52.381 9.08 0.00 41.25 3.08
421 423 1.834263 CTACTTGGCTGCTCCTAGGTT 59.166 52.381 9.08 0.00 41.25 3.50
422 424 1.952621 ACTTGGCTGCTCCTAGGTTA 58.047 50.000 9.08 0.00 41.25 2.85
423 425 1.555533 ACTTGGCTGCTCCTAGGTTAC 59.444 52.381 9.08 0.00 41.25 2.50
424 426 0.909623 TTGGCTGCTCCTAGGTTACC 59.090 55.000 9.08 5.48 35.26 2.85
425 427 0.252513 TGGCTGCTCCTAGGTTACCA 60.253 55.000 9.08 8.05 35.26 3.25
426 428 0.178301 GGCTGCTCCTAGGTTACCAC 59.822 60.000 9.08 0.00 0.00 4.16
427 429 0.179108 GCTGCTCCTAGGTTACCACG 60.179 60.000 9.08 0.00 0.00 4.94
428 430 1.183549 CTGCTCCTAGGTTACCACGT 58.816 55.000 9.08 0.00 0.00 4.49
429 431 0.892755 TGCTCCTAGGTTACCACGTG 59.107 55.000 9.08 9.08 0.00 4.49
430 432 0.459759 GCTCCTAGGTTACCACGTGC 60.460 60.000 10.91 0.00 0.00 5.34
431 433 0.892755 CTCCTAGGTTACCACGTGCA 59.107 55.000 10.91 0.00 0.00 4.57
432 434 0.604578 TCCTAGGTTACCACGTGCAC 59.395 55.000 10.91 6.82 0.00 4.57
433 435 0.319083 CCTAGGTTACCACGTGCACA 59.681 55.000 18.64 0.00 0.00 4.57
434 436 1.066430 CCTAGGTTACCACGTGCACAT 60.066 52.381 18.64 0.00 0.00 3.21
435 437 1.999735 CTAGGTTACCACGTGCACATG 59.000 52.381 18.64 12.53 0.00 3.21
493 607 8.242729 AGATATATCCAGATGATACAATCGCA 57.757 34.615 9.18 0.00 38.75 5.10
495 609 9.138062 GATATATCCAGATGATACAATCGCATC 57.862 37.037 0.81 0.00 38.75 3.91
498 612 3.989817 CCAGATGATACAATCGCATCGAA 59.010 43.478 0.00 0.00 42.36 3.71
516 630 3.560068 TCGAAAGAAAGTCTGGTCTTTGC 59.440 43.478 13.82 7.23 42.67 3.68
518 632 4.023707 CGAAAGAAAGTCTGGTCTTTGCAT 60.024 41.667 13.82 0.00 42.67 3.96
519 633 5.179368 CGAAAGAAAGTCTGGTCTTTGCATA 59.821 40.000 13.82 0.00 42.67 3.14
520 634 6.566197 AAAGAAAGTCTGGTCTTTGCATAG 57.434 37.500 9.83 0.00 41.42 2.23
521 635 5.234466 AGAAAGTCTGGTCTTTGCATAGT 57.766 39.130 4.00 0.00 37.70 2.12
522 636 5.625150 AGAAAGTCTGGTCTTTGCATAGTT 58.375 37.500 4.00 0.00 37.70 2.24
524 638 6.876257 AGAAAGTCTGGTCTTTGCATAGTTAG 59.124 38.462 4.00 2.30 37.70 2.34
525 639 6.360370 AAGTCTGGTCTTTGCATAGTTAGA 57.640 37.500 4.00 4.38 0.00 2.10
526 640 6.552445 AGTCTGGTCTTTGCATAGTTAGAT 57.448 37.500 4.00 0.00 0.00 1.98
545 1889 3.201297 CACACAGCCACGTGCACA 61.201 61.111 18.64 0.00 44.83 4.57
564 1923 4.751060 CACATGTGCTAAGCAATCCAAAT 58.249 39.130 13.94 0.00 41.47 2.32
598 1970 2.608016 GCTCCTAAGTTGTTTTGGCTGC 60.608 50.000 0.00 0.00 32.46 5.25
604 1976 1.032014 GTTGTTTTGGCTGCAGGAGA 58.968 50.000 17.12 0.00 0.00 3.71
605 1977 1.032014 TTGTTTTGGCTGCAGGAGAC 58.968 50.000 17.12 0.00 0.00 3.36
606 1978 0.106769 TGTTTTGGCTGCAGGAGACA 60.107 50.000 17.12 0.00 38.27 3.41
607 1979 0.312102 GTTTTGGCTGCAGGAGACAC 59.688 55.000 17.12 0.00 40.58 3.67
609 1981 3.535629 TTGGCTGCAGGAGACACGG 62.536 63.158 17.12 0.00 40.58 4.94
610 1982 3.695606 GGCTGCAGGAGACACGGA 61.696 66.667 17.12 0.00 0.00 4.69
611 1983 2.343758 GCTGCAGGAGACACGGAA 59.656 61.111 17.12 0.00 0.00 4.30
612 1984 2.029844 GCTGCAGGAGACACGGAAC 61.030 63.158 17.12 0.00 0.00 3.62
631 2003 1.808945 ACGCCTGATTTTCTTCTGCAG 59.191 47.619 7.63 7.63 0.00 4.41
640 2692 9.064706 CCTGATTTTCTTCTGCAGAATACATAT 57.935 33.333 28.57 17.49 41.42 1.78
641 2693 9.880064 CTGATTTTCTTCTGCAGAATACATATG 57.120 33.333 28.57 15.39 41.42 1.78
642 2694 8.843262 TGATTTTCTTCTGCAGAATACATATGG 58.157 33.333 28.57 14.68 41.42 2.74
645 2697 5.059161 TCTTCTGCAGAATACATATGGCAC 58.941 41.667 28.57 0.00 33.01 5.01
646 2698 4.818005 CTTCTGCAGAATACATATGGCACA 59.182 41.667 28.57 2.14 36.52 4.57
647 2699 5.049612 CTTCTGCAGAATACATATGGCACAG 60.050 44.000 28.57 8.64 35.77 3.66
933 4995 0.804544 GTACACGCGATGCTAAGCCA 60.805 55.000 15.93 0.00 0.00 4.75
1155 6228 1.112916 AGAAGGTTTTGGGGTTGCCG 61.113 55.000 0.00 0.00 0.00 5.69
1679 6935 3.618690 AACTACTAAGGGCAAGCAGAG 57.381 47.619 0.00 0.00 0.00 3.35
1683 6939 5.151454 ACTACTAAGGGCAAGCAGAGATAT 58.849 41.667 0.00 0.00 0.00 1.63
1870 7126 7.305474 GCTCCGATTTTAGATGTTTCTTCAAA 58.695 34.615 0.00 0.00 33.17 2.69
1949 7205 0.179026 GAATAAGGTCTTCCCCGCCC 60.179 60.000 0.00 0.00 0.00 6.13
1955 7211 4.431524 TCTTCCCCGCCCATCCCT 62.432 66.667 0.00 0.00 0.00 4.20
1978 7235 0.821517 CCGGTGGTGTGTCTAGCATA 59.178 55.000 0.00 0.00 0.00 3.14
2005 7262 0.597637 GACGTGTGGAGGTGTGTCTG 60.598 60.000 0.00 0.00 0.00 3.51
2026 7283 1.546029 CGGCGGATCTATCCTTGATGA 59.454 52.381 0.00 0.00 44.93 2.92
2034 7291 6.206243 CGGATCTATCCTTGATGAATTTGCTT 59.794 38.462 7.39 0.00 44.93 3.91
2042 7299 4.380841 TGATGAATTTGCTTGGATCTGC 57.619 40.909 0.00 0.00 0.00 4.26
2051 7308 2.028112 TGCTTGGATCTGCTCGTAGTTT 60.028 45.455 0.00 0.00 0.00 2.66
2071 7328 3.547054 TGTCTACGGGTGTGTTTCTTT 57.453 42.857 0.00 0.00 0.00 2.52
2112 7369 1.437986 GCTACTCTTCATCGGCGGT 59.562 57.895 7.21 0.00 0.00 5.68
2118 7375 1.375396 CTTCATCGGCGGTGGTTGA 60.375 57.895 21.45 6.79 0.00 3.18
2126 7383 1.742411 CGGCGGTGGTTGATGTTCTAT 60.742 52.381 0.00 0.00 0.00 1.98
2136 7393 2.710377 TGATGTTCTATTGCGCTGGTT 58.290 42.857 9.73 0.00 0.00 3.67
2153 7410 1.425448 GGTTCTATGGGGCCTTAGCAT 59.575 52.381 0.84 0.14 42.56 3.79
2171 7428 2.732366 CATGACGACTTCCCGACTATG 58.268 52.381 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.894126 ACAACATCCCGGCATACAAAAA 59.106 40.909 0.00 0.00 0.00 1.94
20 21 2.490115 GACAACATCCCGGCATACAAAA 59.510 45.455 0.00 0.00 0.00 2.44
21 22 2.088423 GACAACATCCCGGCATACAAA 58.912 47.619 0.00 0.00 0.00 2.83
22 23 1.280710 AGACAACATCCCGGCATACAA 59.719 47.619 0.00 0.00 0.00 2.41
23 24 0.908910 AGACAACATCCCGGCATACA 59.091 50.000 0.00 0.00 0.00 2.29
24 25 2.038387 AAGACAACATCCCGGCATAC 57.962 50.000 0.00 0.00 0.00 2.39
25 26 2.026729 TCAAAGACAACATCCCGGCATA 60.027 45.455 0.00 0.00 0.00 3.14
26 27 1.176527 CAAAGACAACATCCCGGCAT 58.823 50.000 0.00 0.00 0.00 4.40
27 28 0.109532 TCAAAGACAACATCCCGGCA 59.890 50.000 0.00 0.00 0.00 5.69
28 29 1.133025 CATCAAAGACAACATCCCGGC 59.867 52.381 0.00 0.00 0.00 6.13
29 30 1.745087 CCATCAAAGACAACATCCCGG 59.255 52.381 0.00 0.00 0.00 5.73
30 31 1.133025 GCCATCAAAGACAACATCCCG 59.867 52.381 0.00 0.00 0.00 5.14
31 32 1.133025 CGCCATCAAAGACAACATCCC 59.867 52.381 0.00 0.00 0.00 3.85
32 33 1.133025 CCGCCATCAAAGACAACATCC 59.867 52.381 0.00 0.00 0.00 3.51
33 34 1.812571 ACCGCCATCAAAGACAACATC 59.187 47.619 0.00 0.00 0.00 3.06
34 35 1.909700 ACCGCCATCAAAGACAACAT 58.090 45.000 0.00 0.00 0.00 2.71
35 36 1.686355 AACCGCCATCAAAGACAACA 58.314 45.000 0.00 0.00 0.00 3.33
36 37 3.071479 TCTAACCGCCATCAAAGACAAC 58.929 45.455 0.00 0.00 0.00 3.32
37 38 3.244422 ACTCTAACCGCCATCAAAGACAA 60.244 43.478 0.00 0.00 0.00 3.18
38 39 2.301870 ACTCTAACCGCCATCAAAGACA 59.698 45.455 0.00 0.00 0.00 3.41
39 40 2.673368 CACTCTAACCGCCATCAAAGAC 59.327 50.000 0.00 0.00 0.00 3.01
40 41 2.301870 ACACTCTAACCGCCATCAAAGA 59.698 45.455 0.00 0.00 0.00 2.52
41 42 2.699954 ACACTCTAACCGCCATCAAAG 58.300 47.619 0.00 0.00 0.00 2.77
42 43 2.811431 CAACACTCTAACCGCCATCAAA 59.189 45.455 0.00 0.00 0.00 2.69
43 44 2.224426 ACAACACTCTAACCGCCATCAA 60.224 45.455 0.00 0.00 0.00 2.57
44 45 1.346395 ACAACACTCTAACCGCCATCA 59.654 47.619 0.00 0.00 0.00 3.07
45 46 2.094762 ACAACACTCTAACCGCCATC 57.905 50.000 0.00 0.00 0.00 3.51
46 47 2.151202 CAACAACACTCTAACCGCCAT 58.849 47.619 0.00 0.00 0.00 4.40
47 48 1.134340 ACAACAACACTCTAACCGCCA 60.134 47.619 0.00 0.00 0.00 5.69
48 49 1.589803 ACAACAACACTCTAACCGCC 58.410 50.000 0.00 0.00 0.00 6.13
49 50 2.853281 GCAACAACAACACTCTAACCGC 60.853 50.000 0.00 0.00 0.00 5.68
50 51 2.612212 AGCAACAACAACACTCTAACCG 59.388 45.455 0.00 0.00 0.00 4.44
51 52 4.814771 ACTAGCAACAACAACACTCTAACC 59.185 41.667 0.00 0.00 0.00 2.85
52 53 5.522460 TCACTAGCAACAACAACACTCTAAC 59.478 40.000 0.00 0.00 0.00 2.34
53 54 5.522460 GTCACTAGCAACAACAACACTCTAA 59.478 40.000 0.00 0.00 0.00 2.10
54 55 5.047847 GTCACTAGCAACAACAACACTCTA 58.952 41.667 0.00 0.00 0.00 2.43
55 56 3.871594 GTCACTAGCAACAACAACACTCT 59.128 43.478 0.00 0.00 0.00 3.24
56 57 3.871594 AGTCACTAGCAACAACAACACTC 59.128 43.478 0.00 0.00 0.00 3.51
57 58 3.623060 CAGTCACTAGCAACAACAACACT 59.377 43.478 0.00 0.00 0.00 3.55
58 59 3.621268 TCAGTCACTAGCAACAACAACAC 59.379 43.478 0.00 0.00 0.00 3.32
59 60 3.867857 TCAGTCACTAGCAACAACAACA 58.132 40.909 0.00 0.00 0.00 3.33
60 61 4.511454 TGATCAGTCACTAGCAACAACAAC 59.489 41.667 0.00 0.00 0.00 3.32
61 62 4.702831 TGATCAGTCACTAGCAACAACAA 58.297 39.130 0.00 0.00 0.00 2.83
62 63 4.335400 TGATCAGTCACTAGCAACAACA 57.665 40.909 0.00 0.00 0.00 3.33
74 75 2.261361 CGCCACGGTGATCAGTCA 59.739 61.111 10.28 0.00 0.00 3.41
75 76 2.509336 CCGCCACGGTGATCAGTC 60.509 66.667 10.28 0.00 42.73 3.51
76 77 4.082523 CCCGCCACGGTGATCAGT 62.083 66.667 10.28 0.00 46.80 3.41
77 78 3.605749 AACCCGCCACGGTGATCAG 62.606 63.158 10.28 0.00 46.80 2.90
78 79 2.684192 AAAACCCGCCACGGTGATCA 62.684 55.000 10.28 0.00 46.80 2.92
79 80 1.520600 AAAAACCCGCCACGGTGATC 61.521 55.000 10.28 0.00 46.80 2.92
80 81 1.529713 AAAAACCCGCCACGGTGAT 60.530 52.632 10.28 0.00 46.80 3.06
81 82 2.124236 AAAAACCCGCCACGGTGA 60.124 55.556 10.28 0.00 46.80 4.02
98 99 8.098220 TGATCGATTCAATCTCTGAACAAAAA 57.902 30.769 0.00 0.00 46.80 1.94
99 100 7.671495 TGATCGATTCAATCTCTGAACAAAA 57.329 32.000 0.00 0.00 46.80 2.44
100 101 7.550196 TGATGATCGATTCAATCTCTGAACAAA 59.450 33.333 0.00 0.00 46.80 2.83
101 102 7.043565 TGATGATCGATTCAATCTCTGAACAA 58.956 34.615 0.00 0.00 46.80 2.83
102 103 6.576185 TGATGATCGATTCAATCTCTGAACA 58.424 36.000 0.00 0.00 46.80 3.18
103 104 7.384387 TGATGATGATCGATTCAATCTCTGAAC 59.616 37.037 0.00 0.00 46.80 3.18
105 106 6.989659 TGATGATGATCGATTCAATCTCTGA 58.010 36.000 0.00 0.00 38.03 3.27
106 107 7.091443 TCTGATGATGATCGATTCAATCTCTG 58.909 38.462 0.00 0.34 38.03 3.35
107 108 7.229581 TCTGATGATGATCGATTCAATCTCT 57.770 36.000 0.00 0.00 38.03 3.10
108 109 7.813627 TCTTCTGATGATGATCGATTCAATCTC 59.186 37.037 0.00 0.00 38.03 2.75
109 110 7.668492 TCTTCTGATGATGATCGATTCAATCT 58.332 34.615 0.00 0.00 38.03 2.40
110 111 7.886405 TCTTCTGATGATGATCGATTCAATC 57.114 36.000 0.00 4.65 38.03 2.67
111 112 8.850007 AATCTTCTGATGATGATCGATTCAAT 57.150 30.769 0.00 0.00 36.47 2.57
112 113 8.672823 AAATCTTCTGATGATGATCGATTCAA 57.327 30.769 0.00 0.00 36.47 2.69
113 114 8.672823 AAAATCTTCTGATGATGATCGATTCA 57.327 30.769 0.00 0.00 36.47 2.57
146 147 4.452825 TCAAGGATACACACGGTCAAAAA 58.547 39.130 0.00 0.00 41.41 1.94
147 148 4.074627 TCAAGGATACACACGGTCAAAA 57.925 40.909 0.00 0.00 41.41 2.44
148 149 3.755112 TCAAGGATACACACGGTCAAA 57.245 42.857 0.00 0.00 41.41 2.69
149 150 3.007506 ACATCAAGGATACACACGGTCAA 59.992 43.478 0.00 0.00 41.41 3.18
150 151 2.565391 ACATCAAGGATACACACGGTCA 59.435 45.455 0.00 0.00 41.41 4.02
151 152 3.119101 AGACATCAAGGATACACACGGTC 60.119 47.826 0.00 0.00 41.41 4.79
152 153 2.832129 AGACATCAAGGATACACACGGT 59.168 45.455 0.00 0.00 41.41 4.83
153 154 3.526931 AGACATCAAGGATACACACGG 57.473 47.619 0.00 0.00 41.41 4.94
154 155 4.093408 CCAAAGACATCAAGGATACACACG 59.907 45.833 0.00 0.00 41.41 4.49
155 156 5.122396 GTCCAAAGACATCAAGGATACACAC 59.878 44.000 0.00 0.00 42.99 3.82
156 157 5.013079 AGTCCAAAGACATCAAGGATACACA 59.987 40.000 0.00 0.00 46.15 3.72
157 158 5.491982 AGTCCAAAGACATCAAGGATACAC 58.508 41.667 0.00 0.00 46.15 2.90
158 159 5.762179 AGTCCAAAGACATCAAGGATACA 57.238 39.130 0.00 0.00 46.15 2.29
159 160 6.410540 AGAAGTCCAAAGACATCAAGGATAC 58.589 40.000 1.84 0.00 46.15 2.24
160 161 6.627087 AGAAGTCCAAAGACATCAAGGATA 57.373 37.500 1.84 0.00 46.15 2.59
161 162 5.511386 AGAAGTCCAAAGACATCAAGGAT 57.489 39.130 1.84 0.00 46.15 3.24
162 163 4.982241 AGAAGTCCAAAGACATCAAGGA 57.018 40.909 1.84 0.00 46.15 3.36
163 164 4.823989 ACAAGAAGTCCAAAGACATCAAGG 59.176 41.667 1.84 0.00 46.15 3.61
164 165 6.204359 CAACAAGAAGTCCAAAGACATCAAG 58.796 40.000 1.84 0.00 46.15 3.02
165 166 5.067674 CCAACAAGAAGTCCAAAGACATCAA 59.932 40.000 1.84 0.00 46.15 2.57
166 167 4.580167 CCAACAAGAAGTCCAAAGACATCA 59.420 41.667 1.84 0.00 46.15 3.07
167 168 4.580580 ACCAACAAGAAGTCCAAAGACATC 59.419 41.667 0.00 0.00 46.15 3.06
168 169 4.536765 ACCAACAAGAAGTCCAAAGACAT 58.463 39.130 0.00 0.00 46.15 3.06
169 170 3.963129 ACCAACAAGAAGTCCAAAGACA 58.037 40.909 0.00 0.00 46.15 3.41
170 171 4.879545 TGTACCAACAAGAAGTCCAAAGAC 59.120 41.667 0.00 0.00 36.54 3.01
171 172 5.104693 TCTGTACCAACAAGAAGTCCAAAGA 60.105 40.000 0.00 0.00 34.49 2.52
172 173 5.123227 TCTGTACCAACAAGAAGTCCAAAG 58.877 41.667 0.00 0.00 34.49 2.77
173 174 5.104693 TCTCTGTACCAACAAGAAGTCCAAA 60.105 40.000 0.00 0.00 34.49 3.28
174 175 4.407621 TCTCTGTACCAACAAGAAGTCCAA 59.592 41.667 0.00 0.00 34.49 3.53
175 176 3.964688 TCTCTGTACCAACAAGAAGTCCA 59.035 43.478 0.00 0.00 34.49 4.02
176 177 4.308265 GTCTCTGTACCAACAAGAAGTCC 58.692 47.826 0.00 0.00 34.49 3.85
177 178 4.308265 GGTCTCTGTACCAACAAGAAGTC 58.692 47.826 0.00 0.00 39.50 3.01
178 179 3.243771 CGGTCTCTGTACCAACAAGAAGT 60.244 47.826 0.00 0.00 39.71 3.01
179 180 3.005472 TCGGTCTCTGTACCAACAAGAAG 59.995 47.826 0.00 0.00 39.71 2.85
180 181 2.960384 TCGGTCTCTGTACCAACAAGAA 59.040 45.455 0.00 0.00 39.71 2.52
181 182 2.557056 CTCGGTCTCTGTACCAACAAGA 59.443 50.000 0.00 0.00 39.71 3.02
182 183 2.296471 ACTCGGTCTCTGTACCAACAAG 59.704 50.000 0.00 0.00 39.71 3.16
183 184 2.035449 CACTCGGTCTCTGTACCAACAA 59.965 50.000 0.00 0.00 39.71 2.83
184 185 1.611977 CACTCGGTCTCTGTACCAACA 59.388 52.381 0.00 0.00 39.71 3.33
185 186 1.612463 ACACTCGGTCTCTGTACCAAC 59.388 52.381 0.00 0.00 39.71 3.77
186 187 1.991121 ACACTCGGTCTCTGTACCAA 58.009 50.000 0.00 0.00 39.71 3.67
187 188 2.865119 TACACTCGGTCTCTGTACCA 57.135 50.000 0.00 0.00 39.71 3.25
188 189 4.421948 CAATTACACTCGGTCTCTGTACC 58.578 47.826 0.00 0.00 36.08 3.34
189 190 4.082354 ACCAATTACACTCGGTCTCTGTAC 60.082 45.833 0.00 0.00 0.00 2.90
190 191 4.084287 ACCAATTACACTCGGTCTCTGTA 58.916 43.478 0.00 0.00 0.00 2.74
191 192 2.897969 ACCAATTACACTCGGTCTCTGT 59.102 45.455 0.00 0.00 0.00 3.41
192 193 3.594603 ACCAATTACACTCGGTCTCTG 57.405 47.619 0.00 0.00 0.00 3.35
193 194 5.202004 AGATACCAATTACACTCGGTCTCT 58.798 41.667 0.00 0.00 31.99 3.10
194 195 5.517322 AGATACCAATTACACTCGGTCTC 57.483 43.478 0.00 0.00 32.81 3.36
195 196 5.421056 TGAAGATACCAATTACACTCGGTCT 59.579 40.000 0.00 0.00 32.81 3.85
196 197 5.657474 TGAAGATACCAATTACACTCGGTC 58.343 41.667 0.00 0.00 32.81 4.79
197 198 5.670792 TGAAGATACCAATTACACTCGGT 57.329 39.130 0.00 0.00 35.46 4.69
198 199 8.833231 ATTATGAAGATACCAATTACACTCGG 57.167 34.615 0.00 0.00 0.00 4.63
229 230 9.953565 TTCTTCTTTTTCGAGAAAGGGAATATA 57.046 29.630 23.65 4.52 37.27 0.86
230 231 8.863872 TTCTTCTTTTTCGAGAAAGGGAATAT 57.136 30.769 23.65 0.00 37.27 1.28
231 232 8.863872 ATTCTTCTTTTTCGAGAAAGGGAATA 57.136 30.769 27.57 16.05 37.50 1.75
232 233 7.767250 ATTCTTCTTTTTCGAGAAAGGGAAT 57.233 32.000 25.63 25.63 37.27 3.01
233 234 7.582667 AATTCTTCTTTTTCGAGAAAGGGAA 57.417 32.000 23.65 24.09 37.27 3.97
234 235 7.068226 ACAAATTCTTCTTTTTCGAGAAAGGGA 59.932 33.333 23.65 19.03 37.27 4.20
235 236 7.168135 CACAAATTCTTCTTTTTCGAGAAAGGG 59.832 37.037 23.65 17.50 37.27 3.95
236 237 7.915397 TCACAAATTCTTCTTTTTCGAGAAAGG 59.085 33.333 23.65 11.95 37.27 3.11
237 238 8.841444 TCACAAATTCTTCTTTTTCGAGAAAG 57.159 30.769 19.57 19.57 35.38 2.62
238 239 9.632807 TTTCACAAATTCTTCTTTTTCGAGAAA 57.367 25.926 0.78 0.78 35.38 2.52
239 240 9.072294 GTTTCACAAATTCTTCTTTTTCGAGAA 57.928 29.630 0.00 0.00 34.63 2.87
240 241 7.700656 GGTTTCACAAATTCTTCTTTTTCGAGA 59.299 33.333 0.00 0.00 0.00 4.04
241 242 7.702348 AGGTTTCACAAATTCTTCTTTTTCGAG 59.298 33.333 0.00 0.00 0.00 4.04
242 243 7.543756 AGGTTTCACAAATTCTTCTTTTTCGA 58.456 30.769 0.00 0.00 0.00 3.71
243 244 7.755582 AGGTTTCACAAATTCTTCTTTTTCG 57.244 32.000 0.00 0.00 0.00 3.46
244 245 8.604035 GGAAGGTTTCACAAATTCTTCTTTTTC 58.396 33.333 0.00 0.00 35.63 2.29
245 246 7.277760 CGGAAGGTTTCACAAATTCTTCTTTTT 59.722 33.333 0.00 0.00 35.63 1.94
246 247 6.756542 CGGAAGGTTTCACAAATTCTTCTTTT 59.243 34.615 0.00 0.00 35.63 2.27
247 248 6.273071 CGGAAGGTTTCACAAATTCTTCTTT 58.727 36.000 0.00 0.00 35.63 2.52
248 249 5.736207 GCGGAAGGTTTCACAAATTCTTCTT 60.736 40.000 0.00 0.00 35.63 2.52
256 257 1.679153 GAAGGCGGAAGGTTTCACAAA 59.321 47.619 0.00 0.00 0.00 2.83
279 280 2.287547 GCAATTGACGAAGAAACAGCCA 60.288 45.455 10.34 0.00 0.00 4.75
284 285 3.896648 TGGAGCAATTGACGAAGAAAC 57.103 42.857 10.34 0.00 0.00 2.78
315 316 9.085645 TGGAGTTTAACTAATTAGACAGAGTGA 57.914 33.333 19.38 0.00 29.66 3.41
316 317 9.706691 TTGGAGTTTAACTAATTAGACAGAGTG 57.293 33.333 19.38 0.00 29.66 3.51
319 320 9.498176 GGTTTGGAGTTTAACTAATTAGACAGA 57.502 33.333 19.38 0.00 29.66 3.41
320 321 9.280174 TGGTTTGGAGTTTAACTAATTAGACAG 57.720 33.333 19.38 0.00 29.66 3.51
321 322 9.629878 TTGGTTTGGAGTTTAACTAATTAGACA 57.370 29.630 19.38 3.29 29.66 3.41
328 329 9.589111 GTTGATTTTGGTTTGGAGTTTAACTAA 57.411 29.630 0.00 0.00 0.00 2.24
329 330 7.916450 CGTTGATTTTGGTTTGGAGTTTAACTA 59.084 33.333 0.00 0.00 0.00 2.24
330 331 6.754675 CGTTGATTTTGGTTTGGAGTTTAACT 59.245 34.615 0.00 0.00 0.00 2.24
331 332 6.752815 TCGTTGATTTTGGTTTGGAGTTTAAC 59.247 34.615 0.00 0.00 0.00 2.01
332 333 6.864342 TCGTTGATTTTGGTTTGGAGTTTAA 58.136 32.000 0.00 0.00 0.00 1.52
387 389 2.615869 CAAGTAGTCCTGCTGCTTCTC 58.384 52.381 0.00 0.00 45.02 2.87
398 400 1.410882 CTAGGAGCAGCCAAGTAGTCC 59.589 57.143 0.00 0.00 40.02 3.85
403 405 1.555533 GTAACCTAGGAGCAGCCAAGT 59.444 52.381 17.98 0.00 40.02 3.16
405 407 0.909623 GGTAACCTAGGAGCAGCCAA 59.090 55.000 17.98 0.00 40.02 4.52
406 408 0.252513 TGGTAACCTAGGAGCAGCCA 60.253 55.000 17.98 12.79 40.02 4.75
407 409 0.178301 GTGGTAACCTAGGAGCAGCC 59.822 60.000 17.98 10.34 0.00 4.85
408 410 0.179108 CGTGGTAACCTAGGAGCAGC 60.179 60.000 17.98 9.81 0.00 5.25
409 411 1.135083 CACGTGGTAACCTAGGAGCAG 60.135 57.143 17.98 6.67 0.00 4.24
410 412 0.892755 CACGTGGTAACCTAGGAGCA 59.107 55.000 17.98 7.06 0.00 4.26
411 413 0.459759 GCACGTGGTAACCTAGGAGC 60.460 60.000 17.98 3.98 0.00 4.70
412 414 0.892755 TGCACGTGGTAACCTAGGAG 59.107 55.000 17.98 0.06 0.00 3.69
413 415 0.604578 GTGCACGTGGTAACCTAGGA 59.395 55.000 17.98 0.00 0.00 2.94
414 416 0.319083 TGTGCACGTGGTAACCTAGG 59.681 55.000 18.88 7.41 0.00 3.02
415 417 1.999735 CATGTGCACGTGGTAACCTAG 59.000 52.381 28.05 2.13 0.00 3.02
416 418 1.345089 ACATGTGCACGTGGTAACCTA 59.655 47.619 35.60 6.33 37.19 3.08
417 419 0.107831 ACATGTGCACGTGGTAACCT 59.892 50.000 35.60 16.32 37.19 3.50
418 420 0.237235 CACATGTGCACGTGGTAACC 59.763 55.000 35.60 0.00 37.19 2.85
419 421 3.746108 CACATGTGCACGTGGTAAC 57.254 52.632 35.60 0.18 37.19 2.50
469 583 9.138062 GATGCGATTGTATCATCTGGATATATC 57.862 37.037 3.96 3.96 40.49 1.63
471 585 7.013274 TCGATGCGATTGTATCATCTGGATATA 59.987 37.037 11.14 0.00 40.49 0.86
472 586 5.981915 CGATGCGATTGTATCATCTGGATAT 59.018 40.000 11.14 0.00 40.49 1.63
480 594 6.258727 ACTTTCTTTCGATGCGATTGTATCAT 59.741 34.615 11.14 0.00 37.08 2.45
485 599 3.997021 AGACTTTCTTTCGATGCGATTGT 59.003 39.130 0.00 0.00 35.23 2.71
486 600 4.329489 CAGACTTTCTTTCGATGCGATTG 58.671 43.478 0.00 0.00 35.23 2.67
488 602 2.932614 CCAGACTTTCTTTCGATGCGAT 59.067 45.455 0.00 0.00 35.23 4.58
489 603 2.288825 ACCAGACTTTCTTTCGATGCGA 60.289 45.455 0.00 0.00 0.00 5.10
490 604 2.069273 ACCAGACTTTCTTTCGATGCG 58.931 47.619 0.00 0.00 0.00 4.73
493 607 4.214332 GCAAAGACCAGACTTTCTTTCGAT 59.786 41.667 6.02 0.00 39.54 3.59
495 609 3.312421 TGCAAAGACCAGACTTTCTTTCG 59.688 43.478 6.02 4.65 39.54 3.46
498 612 5.625150 ACTATGCAAAGACCAGACTTTCTT 58.375 37.500 0.00 0.00 37.91 2.52
501 615 6.769512 TCTAACTATGCAAAGACCAGACTTT 58.230 36.000 0.00 0.00 40.16 2.66
502 616 6.360370 TCTAACTATGCAAAGACCAGACTT 57.640 37.500 0.00 0.00 0.00 3.01
503 617 6.344500 CATCTAACTATGCAAAGACCAGACT 58.656 40.000 0.00 0.00 0.00 3.24
516 630 3.310774 GTGGCTGTGTGCATCTAACTATG 59.689 47.826 0.00 0.00 45.15 2.23
518 632 2.673893 CGTGGCTGTGTGCATCTAACTA 60.674 50.000 0.00 0.00 45.15 2.24
519 633 1.813513 GTGGCTGTGTGCATCTAACT 58.186 50.000 0.00 0.00 45.15 2.24
520 634 0.443869 CGTGGCTGTGTGCATCTAAC 59.556 55.000 0.00 0.00 45.15 2.34
521 635 0.034756 ACGTGGCTGTGTGCATCTAA 59.965 50.000 0.00 0.00 45.15 2.10
522 636 0.670239 CACGTGGCTGTGTGCATCTA 60.670 55.000 7.95 0.00 45.15 1.98
524 638 2.557805 CACGTGGCTGTGTGCATC 59.442 61.111 7.95 0.00 45.15 3.91
530 644 2.253154 CATGTGCACGTGGCTGTG 59.747 61.111 28.05 4.34 45.15 3.66
531 645 2.203195 ACATGTGCACGTGGCTGT 60.203 55.556 35.60 19.65 45.15 4.40
542 1886 3.853831 TTGGATTGCTTAGCACATGTG 57.146 42.857 21.83 21.83 38.71 3.21
543 1887 6.528537 TTATTTGGATTGCTTAGCACATGT 57.471 33.333 6.34 0.00 38.71 3.21
544 1888 7.830940 TTTTATTTGGATTGCTTAGCACATG 57.169 32.000 6.34 0.00 38.71 3.21
545 1889 8.096414 ACTTTTTATTTGGATTGCTTAGCACAT 58.904 29.630 6.34 3.95 38.71 3.21
564 1923 6.826741 ACAACTTAGGAGCAGTCAACTTTTTA 59.173 34.615 0.00 0.00 0.00 1.52
598 1970 2.432628 GGCGTTCCGTGTCTCCTG 60.433 66.667 0.00 0.00 0.00 3.86
604 1976 0.872388 GAAAATCAGGCGTTCCGTGT 59.128 50.000 0.00 0.00 37.47 4.49
605 1977 1.156736 AGAAAATCAGGCGTTCCGTG 58.843 50.000 0.00 0.00 37.47 4.94
606 1978 1.804748 GAAGAAAATCAGGCGTTCCGT 59.195 47.619 0.00 0.00 37.47 4.69
607 1979 2.076863 AGAAGAAAATCAGGCGTTCCG 58.923 47.619 0.00 0.00 37.47 4.30
609 1981 2.226437 TGCAGAAGAAAATCAGGCGTTC 59.774 45.455 0.00 0.00 0.00 3.95
610 1982 2.227388 CTGCAGAAGAAAATCAGGCGTT 59.773 45.455 8.42 0.00 0.00 4.84
611 1983 1.808945 CTGCAGAAGAAAATCAGGCGT 59.191 47.619 8.42 0.00 0.00 5.68
612 1984 2.079158 TCTGCAGAAGAAAATCAGGCG 58.921 47.619 15.67 0.00 29.54 5.52
622 1994 5.059161 GTGCCATATGTATTCTGCAGAAGA 58.941 41.667 31.14 25.74 37.48 2.87
631 2003 8.623903 TCATTTCTTTCTGTGCCATATGTATTC 58.376 33.333 1.24 0.00 0.00 1.75
640 2692 5.076182 TGGTTATCATTTCTTTCTGTGCCA 58.924 37.500 0.00 0.00 0.00 4.92
641 2693 5.643379 TGGTTATCATTTCTTTCTGTGCC 57.357 39.130 0.00 0.00 0.00 5.01
785 2868 3.066342 CCGTCGATCACCACTGTATAGTT 59.934 47.826 0.00 0.00 34.07 2.24
933 4995 0.308993 GCTGCGTTTGAGTGAGCTTT 59.691 50.000 0.00 0.00 0.00 3.51
1129 6202 1.298859 CCCAAAACCTTCTCCTCGCG 61.299 60.000 0.00 0.00 0.00 5.87
1542 6787 9.725019 TGTGATCAAGTGATGAAGTAGTAAATT 57.275 29.630 0.00 0.00 42.54 1.82
1616 6872 5.800438 GGTTTCTGTTAATGAAAATCGGAGC 59.200 40.000 7.77 0.00 35.54 4.70
1679 6935 5.975344 TCATGTGTCGTCGTTTCCTAATATC 59.025 40.000 0.00 0.00 0.00 1.63
1683 6939 3.646611 TCATGTGTCGTCGTTTCCTAA 57.353 42.857 0.00 0.00 0.00 2.69
1815 7071 4.760220 AAGGGCCGGGATCCACCT 62.760 66.667 15.23 12.07 38.98 4.00
1870 7126 3.888930 CAGGACACACACCCTAACAAAAT 59.111 43.478 0.00 0.00 0.00 1.82
1924 7180 3.901844 CGGGGAAGACCTTATTCCATCTA 59.098 47.826 7.02 0.00 46.77 1.98
1949 7205 1.377202 CACCACCGGAACAGGGATG 60.377 63.158 9.46 0.00 35.02 3.51
1955 7211 0.677288 CTAGACACACCACCGGAACA 59.323 55.000 9.46 0.00 0.00 3.18
1978 7235 2.520020 TCCACACGTCCACCGACT 60.520 61.111 0.00 0.00 40.70 4.18
2026 7283 2.440409 ACGAGCAGATCCAAGCAAATT 58.560 42.857 5.37 0.00 0.00 1.82
2034 7291 2.826128 AGACAAACTACGAGCAGATCCA 59.174 45.455 0.00 0.00 0.00 3.41
2051 7308 3.547054 AAAGAAACACACCCGTAGACA 57.453 42.857 0.00 0.00 0.00 3.41
2059 7316 4.217767 GGATCCAACCTAAAGAAACACACC 59.782 45.833 6.95 0.00 0.00 4.16
2060 7317 5.070685 AGGATCCAACCTAAAGAAACACAC 58.929 41.667 15.82 0.00 38.65 3.82
2071 7328 4.202182 CGTAAATCGGAAGGATCCAACCTA 60.202 45.833 15.82 9.08 46.97 3.08
2112 7369 2.419673 CAGCGCAATAGAACATCAACCA 59.580 45.455 11.47 0.00 0.00 3.67
2118 7375 2.991250 AGAACCAGCGCAATAGAACAT 58.009 42.857 11.47 0.00 0.00 2.71
2126 7383 1.077787 CCCCATAGAACCAGCGCAA 60.078 57.895 11.47 0.00 0.00 4.85
2136 7393 1.699634 GTCATGCTAAGGCCCCATAGA 59.300 52.381 0.00 0.00 37.74 1.98
2153 7410 1.830279 ACATAGTCGGGAAGTCGTCA 58.170 50.000 0.00 0.00 0.00 4.35
2171 7428 3.304190 CCGGGCAAAACTTGTTGTAGTAC 60.304 47.826 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.