Multiple sequence alignment - TraesCS7A01G468300

Loading Multiple Alignment...

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 TraesCS7A01G468300 chr7A 100.000 2285 0 0 1 2285 664415983 664413699 0.000000e+00 4220.0
1 TraesCS7A01G468300 chr7A 88.260 954 82 20 736 1670 664372199 664371257 0.000000e+00 1114.0
2 TraesCS7A01G468300 chr7A 81.025 917 108 41 649 1533 664999448 665000330 0.000000e+00 669.0
3 TraesCS7A01G468300 chr7B 90.915 1453 81 19 639 2057 634580172 634578737 0.000000e+00 1905.0
4 TraesCS7A01G468300 chr7B 88.102 1017 75 26 639 1639 634647719 634646733 0.000000e+00 1166.0
5 TraesCS7A01G468300 chr7B 85.333 675 63 21 639 1288 636983572 636984235 0.000000e+00 665.0
6 TraesCS7A01G468300 chr7B 81.105 905 104 37 649 1528 636940034 636940896 0.000000e+00 662.0
7 TraesCS7A01G468300 chr7B 84.804 612 69 19 1684 2285 634633652 634633055 5.430000e-166 593.0
8 TraesCS7A01G468300 chr7B 92.149 242 16 2 2044 2285 634577146 634576908 2.810000e-89 339.0
9 TraesCS7A01G468300 chr7D 95.050 909 24 4 639 1533 574774515 574773614 0.000000e+00 1410.0
10 TraesCS7A01G468300 chr7D 87.825 1076 85 25 639 1680 574764533 574763470 0.000000e+00 1219.0
11 TraesCS7A01G468300 chr7D 93.307 508 21 5 1532 2037 574773459 574772963 0.000000e+00 737.0
12 TraesCS7A01G468300 chr7D 81.538 910 96 40 649 1528 575408035 575408902 0.000000e+00 684.0
13 TraesCS7A01G468300 chr7D 95.098 204 7 2 153 356 574774714 574774514 3.660000e-83 318.0
14 TraesCS7A01G468300 chr7D 85.763 295 40 2 344 638 587122684 587122976 6.130000e-81 311.0
15 TraesCS7A01G468300 chr7D 84.281 299 41 4 354 647 626249463 626249760 1.030000e-73 287.0
16 TraesCS7A01G468300 chr7D 89.593 221 11 7 2069 2285 574772683 574772471 1.040000e-68 270.0
17 TraesCS7A01G468300 chr5A 86.806 288 37 1 352 638 653929204 653929491 1.020000e-83 320.0
18 TraesCS7A01G468300 chr5A 87.821 156 15 4 4 157 74725814 74725661 1.800000e-41 180.0
19 TraesCS7A01G468300 chr4B 87.319 276 34 1 364 638 507241785 507242060 4.740000e-82 315.0
20 TraesCS7A01G468300 chr3A 85.616 292 35 5 356 645 693197974 693197688 1.330000e-77 300.0
21 TraesCS7A01G468300 chr3A 85.172 290 38 5 356 642 621317510 621317797 2.220000e-75 292.0
22 TraesCS7A01G468300 chr1D 85.246 305 30 11 344 638 343262850 343263149 1.330000e-77 300.0
23 TraesCS7A01G468300 chr6D 84.983 293 41 3 352 641 87389546 87389254 6.170000e-76 294.0
24 TraesCS7A01G468300 chr6D 89.189 148 14 2 4 150 308786090 308785944 1.390000e-42 183.0
25 TraesCS7A01G468300 chr3B 84.564 298 41 5 343 638 603212363 603212657 7.990000e-75 291.0
26 TraesCS7A01G468300 chr3B 85.333 75 9 2 2039 2112 817654396 817654323 2.430000e-10 76.8
27 TraesCS7A01G468300 chr1A 90.345 145 10 4 2 144 402617265 402617407 1.080000e-43 187.0
28 TraesCS7A01G468300 chr2A 88.889 153 13 4 4 154 752072813 752072663 3.880000e-43 185.0
29 TraesCS7A01G468300 chr2A 89.262 149 12 3 4 150 773486889 773487035 1.390000e-42 183.0
30 TraesCS7A01G468300 chr2A 84.810 79 8 4 2050 2127 6009908 6009983 2.430000e-10 76.8
31 TraesCS7A01G468300 chr2B 89.189 148 14 2 4 150 10355192 10355046 1.390000e-42 183.0
32 TraesCS7A01G468300 chrUn 84.293 191 22 5 193 380 51454542 51454727 1.800000e-41 180.0
33 TraesCS7A01G468300 chrUn 88.966 145 11 5 2 144 63263749 63263608 8.390000e-40 174.0
34 TraesCS7A01G468300 chrUn 96.429 56 1 1 170 225 51454267 51454321 8.690000e-15 91.6
35 TraesCS7A01G468300 chr6A 89.655 145 10 5 2 144 25623507 25623366 1.800000e-41 180.0
36 TraesCS7A01G468300 chr6B 87.919 149 15 2 4 150 8641901 8642048 3.020000e-39 172.0
37 TraesCS7A01G468300 chr6B 85.897 78 8 3 2051 2127 634329779 634329854 1.880000e-11 80.5
38 TraesCS7A01G468300 chr5B 85.714 91 9 4 2039 2127 35757815 35757727 2.420000e-15 93.5
39 TraesCS7A01G468300 chr3D 91.045 67 4 2 2048 2112 551624087 551624021 3.130000e-14 89.8
40 TraesCS7A01G468300 chr3D 89.394 66 6 1 2048 2112 499633600 499633665 5.230000e-12 82.4


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 TraesCS7A01G468300 chr7A 664413699 664415983 2284 True 4220.00 4220 100.000 1 2285 1 chr7A.!!$R2 2284
1 TraesCS7A01G468300 chr7A 664371257 664372199 942 True 1114.00 1114 88.260 736 1670 1 chr7A.!!$R1 934
2 TraesCS7A01G468300 chr7A 664999448 665000330 882 False 669.00 669 81.025 649 1533 1 chr7A.!!$F1 884
3 TraesCS7A01G468300 chr7B 634646733 634647719 986 True 1166.00 1166 88.102 639 1639 1 chr7B.!!$R2 1000
4 TraesCS7A01G468300 chr7B 634576908 634580172 3264 True 1122.00 1905 91.532 639 2285 2 chr7B.!!$R3 1646
5 TraesCS7A01G468300 chr7B 636983572 636984235 663 False 665.00 665 85.333 639 1288 1 chr7B.!!$F2 649
6 TraesCS7A01G468300 chr7B 636940034 636940896 862 False 662.00 662 81.105 649 1528 1 chr7B.!!$F1 879
7 TraesCS7A01G468300 chr7B 634633055 634633652 597 True 593.00 593 84.804 1684 2285 1 chr7B.!!$R1 601
8 TraesCS7A01G468300 chr7D 574763470 574764533 1063 True 1219.00 1219 87.825 639 1680 1 chr7D.!!$R1 1041
9 TraesCS7A01G468300 chr7D 575408035 575408902 867 False 684.00 684 81.538 649 1528 1 chr7D.!!$F1 879
10 TraesCS7A01G468300 chr7D 574772471 574774714 2243 True 683.75 1410 93.262 153 2285 4 chr7D.!!$R2 2132

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
48 49 0.253020 AATAAGGTCCGACCCCACCT 60.253 55.0 14.32 0.0 45.59 4.00 F
131 132 0.323629 TTAAGTGGGAGCACGGGAAG 59.676 55.0 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1261 1360 0.609957 TAGTTCTTGGAGACGGCGGA 60.610 55.000 13.24 0.0 0.0 5.54 R
1877 2172 1.071071 CCTGGGTTTACTTGTGTCCGA 59.929 52.381 0.00 0.0 0.0 4.55 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
22 23 4.944962 TCTACGTGGCTTGATTTGATTG 57.055 40.909 0.00 0.00 0.00 2.67
23 24 3.689161 TCTACGTGGCTTGATTTGATTGG 59.311 43.478 0.00 0.00 0.00 3.16
24 25 2.513753 ACGTGGCTTGATTTGATTGGA 58.486 42.857 0.00 0.00 0.00 3.53
25 26 2.890311 ACGTGGCTTGATTTGATTGGAA 59.110 40.909 0.00 0.00 0.00 3.53
26 27 3.244976 CGTGGCTTGATTTGATTGGAAC 58.755 45.455 0.00 0.00 0.00 3.62
27 28 3.305267 CGTGGCTTGATTTGATTGGAACA 60.305 43.478 0.00 0.00 0.00 3.18
42 43 3.414269 TGGAACAAAATAAGGTCCGACC 58.586 45.455 9.81 9.81 34.25 4.79
43 44 2.751259 GGAACAAAATAAGGTCCGACCC 59.249 50.000 14.32 0.00 39.75 4.46
44 45 2.502142 ACAAAATAAGGTCCGACCCC 57.498 50.000 14.32 0.00 39.75 4.95
45 46 1.706305 ACAAAATAAGGTCCGACCCCA 59.294 47.619 14.32 2.49 39.75 4.96
46 47 2.089201 CAAAATAAGGTCCGACCCCAC 58.911 52.381 14.32 0.00 39.75 4.61
47 48 0.622136 AAATAAGGTCCGACCCCACC 59.378 55.000 14.32 0.00 39.75 4.61
48 49 0.253020 AATAAGGTCCGACCCCACCT 60.253 55.000 14.32 0.00 45.59 4.00
49 50 2.122099 AAGGTCCGACCCCACCTT 60.122 61.111 14.32 0.00 46.41 3.50
50 51 2.606826 AGGTCCGACCCCACCTTC 60.607 66.667 14.32 0.00 40.35 3.46
51 52 2.606826 GGTCCGACCCCACCTTCT 60.607 66.667 6.25 0.00 30.04 2.85
52 53 2.222013 GGTCCGACCCCACCTTCTT 61.222 63.158 6.25 0.00 30.04 2.52
53 54 0.906282 GGTCCGACCCCACCTTCTTA 60.906 60.000 6.25 0.00 30.04 2.10
54 55 0.978907 GTCCGACCCCACCTTCTTAA 59.021 55.000 0.00 0.00 0.00 1.85
55 56 1.348696 GTCCGACCCCACCTTCTTAAA 59.651 52.381 0.00 0.00 0.00 1.52
56 57 2.056359 TCCGACCCCACCTTCTTAAAA 58.944 47.619 0.00 0.00 0.00 1.52
57 58 2.645797 TCCGACCCCACCTTCTTAAAAT 59.354 45.455 0.00 0.00 0.00 1.82
58 59 3.014623 CCGACCCCACCTTCTTAAAATC 58.985 50.000 0.00 0.00 0.00 2.17
59 60 3.560453 CCGACCCCACCTTCTTAAAATCA 60.560 47.826 0.00 0.00 0.00 2.57
60 61 3.689649 CGACCCCACCTTCTTAAAATCAG 59.310 47.826 0.00 0.00 0.00 2.90
61 62 4.017126 GACCCCACCTTCTTAAAATCAGG 58.983 47.826 0.00 0.00 0.00 3.86
62 63 3.245622 ACCCCACCTTCTTAAAATCAGGG 60.246 47.826 0.00 0.00 36.85 4.45
63 64 3.365472 CCCACCTTCTTAAAATCAGGGG 58.635 50.000 0.00 0.00 0.00 4.79
64 65 3.365472 CCACCTTCTTAAAATCAGGGGG 58.635 50.000 0.00 0.00 43.81 5.40
65 66 4.316025 CACCTTCTTAAAATCAGGGGGA 57.684 45.455 0.00 0.00 0.00 4.81
66 67 4.273318 CACCTTCTTAAAATCAGGGGGAG 58.727 47.826 0.00 0.00 0.00 4.30
67 68 4.018415 CACCTTCTTAAAATCAGGGGGAGA 60.018 45.833 0.00 0.00 0.00 3.71
68 69 4.796265 ACCTTCTTAAAATCAGGGGGAGAT 59.204 41.667 0.00 0.00 0.00 2.75
69 70 5.136105 CCTTCTTAAAATCAGGGGGAGATG 58.864 45.833 0.00 0.00 0.00 2.90
70 71 5.103940 CCTTCTTAAAATCAGGGGGAGATGA 60.104 44.000 0.00 0.00 0.00 2.92
71 72 6.411320 CCTTCTTAAAATCAGGGGGAGATGAT 60.411 42.308 0.00 0.00 37.77 2.45
72 73 6.596869 TCTTAAAATCAGGGGGAGATGATT 57.403 37.500 0.00 0.00 45.67 2.57
73 74 7.705912 TCTTAAAATCAGGGGGAGATGATTA 57.294 36.000 1.20 0.00 43.56 1.75
74 75 7.749666 TCTTAAAATCAGGGGGAGATGATTAG 58.250 38.462 1.20 0.00 43.56 1.73
75 76 7.572485 TCTTAAAATCAGGGGGAGATGATTAGA 59.428 37.037 1.20 0.00 43.56 2.10
76 77 6.793518 AAAATCAGGGGGAGATGATTAGAT 57.206 37.500 1.20 0.00 43.56 1.98
77 78 6.793518 AAATCAGGGGGAGATGATTAGATT 57.206 37.500 1.20 0.00 43.56 2.40
78 79 7.895144 AAATCAGGGGGAGATGATTAGATTA 57.105 36.000 1.20 0.00 43.56 1.75
79 80 7.507797 AATCAGGGGGAGATGATTAGATTAG 57.492 40.000 0.00 0.00 42.77 1.73
80 81 6.233045 TCAGGGGGAGATGATTAGATTAGA 57.767 41.667 0.00 0.00 0.00 2.10
81 82 6.634041 TCAGGGGGAGATGATTAGATTAGAA 58.366 40.000 0.00 0.00 0.00 2.10
82 83 7.082316 TCAGGGGGAGATGATTAGATTAGAAA 58.918 38.462 0.00 0.00 0.00 2.52
83 84 7.236432 TCAGGGGGAGATGATTAGATTAGAAAG 59.764 40.741 0.00 0.00 0.00 2.62
84 85 7.236432 CAGGGGGAGATGATTAGATTAGAAAGA 59.764 40.741 0.00 0.00 0.00 2.52
85 86 7.796637 AGGGGGAGATGATTAGATTAGAAAGAA 59.203 37.037 0.00 0.00 0.00 2.52
86 87 8.440771 GGGGGAGATGATTAGATTAGAAAGAAA 58.559 37.037 0.00 0.00 0.00 2.52
87 88 9.853177 GGGGAGATGATTAGATTAGAAAGAAAA 57.147 33.333 0.00 0.00 0.00 2.29
111 112 7.619964 AAAAAGAAAGAAGACAACCGTAAGA 57.380 32.000 0.00 0.00 43.02 2.10
112 113 7.803279 AAAAGAAAGAAGACAACCGTAAGAT 57.197 32.000 0.00 0.00 43.02 2.40
113 114 7.803279 AAAGAAAGAAGACAACCGTAAGATT 57.197 32.000 0.00 0.00 43.02 2.40
114 115 8.897872 AAAGAAAGAAGACAACCGTAAGATTA 57.102 30.769 0.00 0.00 43.02 1.75
115 116 8.897872 AAGAAAGAAGACAACCGTAAGATTAA 57.102 30.769 0.00 0.00 43.02 1.40
116 117 8.535690 AGAAAGAAGACAACCGTAAGATTAAG 57.464 34.615 0.00 0.00 43.02 1.85
117 118 8.148999 AGAAAGAAGACAACCGTAAGATTAAGT 58.851 33.333 0.00 0.00 43.02 2.24
118 119 7.653767 AAGAAGACAACCGTAAGATTAAGTG 57.346 36.000 0.00 0.00 43.02 3.16
119 120 6.164176 AGAAGACAACCGTAAGATTAAGTGG 58.836 40.000 0.00 0.00 43.02 4.00
120 121 4.828829 AGACAACCGTAAGATTAAGTGGG 58.171 43.478 0.00 0.00 43.02 4.61
121 122 4.529377 AGACAACCGTAAGATTAAGTGGGA 59.471 41.667 0.00 0.00 43.02 4.37
122 123 4.828829 ACAACCGTAAGATTAAGTGGGAG 58.171 43.478 0.00 0.00 43.02 4.30
123 124 3.538634 ACCGTAAGATTAAGTGGGAGC 57.461 47.619 0.00 0.00 43.02 4.70
124 125 2.835764 ACCGTAAGATTAAGTGGGAGCA 59.164 45.455 0.00 0.00 43.02 4.26
125 126 3.195661 CCGTAAGATTAAGTGGGAGCAC 58.804 50.000 0.00 0.00 43.02 4.40
126 127 2.858344 CGTAAGATTAAGTGGGAGCACG 59.142 50.000 0.00 0.00 43.02 5.34
127 128 2.403252 AAGATTAAGTGGGAGCACGG 57.597 50.000 0.00 0.00 0.00 4.94
128 129 0.541863 AGATTAAGTGGGAGCACGGG 59.458 55.000 0.00 0.00 0.00 5.28
129 130 0.539986 GATTAAGTGGGAGCACGGGA 59.460 55.000 0.00 0.00 0.00 5.14
130 131 0.988832 ATTAAGTGGGAGCACGGGAA 59.011 50.000 0.00 0.00 0.00 3.97
131 132 0.323629 TTAAGTGGGAGCACGGGAAG 59.676 55.000 0.00 0.00 0.00 3.46
132 133 0.543410 TAAGTGGGAGCACGGGAAGA 60.543 55.000 0.00 0.00 0.00 2.87
133 134 1.831652 AAGTGGGAGCACGGGAAGAG 61.832 60.000 0.00 0.00 0.00 2.85
134 135 2.119611 TGGGAGCACGGGAAGAGA 59.880 61.111 0.00 0.00 0.00 3.10
135 136 1.984570 TGGGAGCACGGGAAGAGAG 60.985 63.158 0.00 0.00 0.00 3.20
136 137 2.185608 GGAGCACGGGAAGAGAGC 59.814 66.667 0.00 0.00 0.00 4.09
137 138 2.650116 GGAGCACGGGAAGAGAGCA 61.650 63.158 0.00 0.00 0.00 4.26
138 139 1.153667 GAGCACGGGAAGAGAGCAG 60.154 63.158 0.00 0.00 0.00 4.24
139 140 2.125350 GCACGGGAAGAGAGCAGG 60.125 66.667 0.00 0.00 0.00 4.85
140 141 2.125350 CACGGGAAGAGAGCAGGC 60.125 66.667 0.00 0.00 0.00 4.85
141 142 2.604686 ACGGGAAGAGAGCAGGCA 60.605 61.111 0.00 0.00 0.00 4.75
142 143 2.217038 ACGGGAAGAGAGCAGGCAA 61.217 57.895 0.00 0.00 0.00 4.52
143 144 1.449246 CGGGAAGAGAGCAGGCAAG 60.449 63.158 0.00 0.00 0.00 4.01
144 145 1.748500 GGGAAGAGAGCAGGCAAGC 60.749 63.158 0.00 0.00 0.00 4.01
145 146 1.748500 GGAAGAGAGCAGGCAAGCC 60.749 63.158 2.02 2.02 34.23 4.35
146 147 2.046507 AAGAGAGCAGGCAAGCCG 60.047 61.111 5.28 2.12 41.95 5.52
147 148 3.618780 AAGAGAGCAGGCAAGCCGG 62.619 63.158 6.88 6.88 41.95 6.13
148 149 4.087892 GAGAGCAGGCAAGCCGGA 62.088 66.667 15.46 0.00 41.95 5.14
149 150 3.397613 GAGAGCAGGCAAGCCGGAT 62.398 63.158 15.46 8.74 41.95 4.18
150 151 2.439156 GAGCAGGCAAGCCGGATT 60.439 61.111 15.46 0.00 41.95 3.01
151 152 2.439156 AGCAGGCAAGCCGGATTC 60.439 61.111 15.46 0.00 41.95 2.52
161 162 3.558418 GCAAGCCGGATTCGTCTAATTTA 59.442 43.478 5.05 0.00 33.95 1.40
218 219 7.550712 AGCATAAATTCTTCTTGTCAAATCCC 58.449 34.615 0.00 0.00 0.00 3.85
221 222 2.859165 TCTTCTTGTCAAATCCCGCT 57.141 45.000 0.00 0.00 0.00 5.52
225 226 2.699954 TCTTGTCAAATCCCGCTCTTC 58.300 47.619 0.00 0.00 0.00 2.87
226 227 2.038426 TCTTGTCAAATCCCGCTCTTCA 59.962 45.455 0.00 0.00 0.00 3.02
289 290 7.739498 TCAACTTTTACAATTCTAGGACACC 57.261 36.000 0.00 0.00 0.00 4.16
337 338 3.370527 GCTAGCTGGGTAATTGAGGACAA 60.371 47.826 7.70 0.00 40.42 3.18
372 373 9.647797 TGTATTATAACTAGAATAATGCCCGTG 57.352 33.333 17.78 0.00 33.49 4.94
373 374 7.611213 ATTATAACTAGAATAATGCCCGTGC 57.389 36.000 0.00 0.00 38.26 5.34
374 375 1.865865 ACTAGAATAATGCCCGTGCG 58.134 50.000 0.00 0.00 41.78 5.34
375 376 1.138266 ACTAGAATAATGCCCGTGCGT 59.862 47.619 0.00 0.00 41.78 5.24
377 378 0.732571 AGAATAATGCCCGTGCGTTG 59.267 50.000 7.64 0.00 46.06 4.10
378 379 0.865639 GAATAATGCCCGTGCGTTGC 60.866 55.000 7.64 0.00 46.06 4.17
379 380 1.590610 AATAATGCCCGTGCGTTGCA 61.591 50.000 7.64 8.11 46.06 4.08
380 381 1.590610 ATAATGCCCGTGCGTTGCAA 61.591 50.000 7.64 0.00 46.06 4.08
381 382 2.465097 TAATGCCCGTGCGTTGCAAC 62.465 55.000 19.89 19.89 46.06 4.17
383 384 4.980903 GCCCGTGCGTTGCAACAG 62.981 66.667 28.01 20.60 41.47 3.16
384 385 3.276091 CCCGTGCGTTGCAACAGA 61.276 61.111 28.01 11.66 41.47 3.41
385 386 2.712539 CCGTGCGTTGCAACAGAA 59.287 55.556 28.01 13.44 41.47 3.02
386 387 1.282570 CCGTGCGTTGCAACAGAAT 59.717 52.632 28.01 0.00 41.47 2.40
387 388 0.515127 CCGTGCGTTGCAACAGAATA 59.485 50.000 28.01 7.20 41.47 1.75
388 389 1.130373 CCGTGCGTTGCAACAGAATAT 59.870 47.619 28.01 0.00 41.47 1.28
389 390 2.350192 CCGTGCGTTGCAACAGAATATA 59.650 45.455 28.01 4.13 41.47 0.86
390 391 3.181515 CCGTGCGTTGCAACAGAATATAA 60.182 43.478 28.01 2.35 41.47 0.98
391 392 4.399112 CGTGCGTTGCAACAGAATATAAA 58.601 39.130 28.01 0.84 41.47 1.40
392 393 5.027737 CGTGCGTTGCAACAGAATATAAAT 58.972 37.500 28.01 0.00 41.47 1.40
393 394 6.188871 CGTGCGTTGCAACAGAATATAAATA 58.811 36.000 28.01 0.00 41.47 1.40
394 395 6.850823 CGTGCGTTGCAACAGAATATAAATAT 59.149 34.615 28.01 0.00 41.47 1.28
395 396 7.375808 CGTGCGTTGCAACAGAATATAAATATT 59.624 33.333 28.01 0.00 41.47 1.28
396 397 9.658475 GTGCGTTGCAACAGAATATAAATATTA 57.342 29.630 28.01 0.00 41.47 0.98
414 415 8.657074 AAATATTATAGCACGTTAGCTTGTGA 57.343 30.769 15.18 0.00 43.70 3.58
415 416 8.833231 AATATTATAGCACGTTAGCTTGTGAT 57.167 30.769 15.18 12.01 43.70 3.06
416 417 8.833231 ATATTATAGCACGTTAGCTTGTGATT 57.167 30.769 15.18 6.79 43.70 2.57
417 418 6.978343 TTATAGCACGTTAGCTTGTGATTT 57.022 33.333 15.18 8.21 43.70 2.17
418 419 8.657074 ATTATAGCACGTTAGCTTGTGATTTA 57.343 30.769 15.18 7.41 43.70 1.40
419 420 8.657074 TTATAGCACGTTAGCTTGTGATTTAT 57.343 30.769 15.18 11.38 43.70 1.40
420 421 5.470845 AGCACGTTAGCTTGTGATTTATC 57.529 39.130 15.18 0.00 43.70 1.75
421 422 5.178797 AGCACGTTAGCTTGTGATTTATCT 58.821 37.500 15.18 1.91 43.70 1.98
422 423 6.338146 AGCACGTTAGCTTGTGATTTATCTA 58.662 36.000 15.18 0.00 43.70 1.98
423 424 6.986817 AGCACGTTAGCTTGTGATTTATCTAT 59.013 34.615 15.18 0.00 43.70 1.98
424 425 7.169982 AGCACGTTAGCTTGTGATTTATCTATC 59.830 37.037 15.18 0.00 43.70 2.08
425 426 7.042725 GCACGTTAGCTTGTGATTTATCTATCA 60.043 37.037 15.18 0.00 38.36 2.15
426 427 8.817100 CACGTTAGCTTGTGATTTATCTATCAA 58.183 33.333 7.45 0.00 38.36 2.57
427 428 9.547753 ACGTTAGCTTGTGATTTATCTATCAAT 57.452 29.630 0.00 0.00 36.37 2.57
588 589 6.499106 AAATGAAAGGTTGGATGAAAAGGT 57.501 33.333 0.00 0.00 0.00 3.50
589 590 4.935352 TGAAAGGTTGGATGAAAAGGTG 57.065 40.909 0.00 0.00 0.00 4.00
590 591 4.541705 TGAAAGGTTGGATGAAAAGGTGA 58.458 39.130 0.00 0.00 0.00 4.02
591 592 5.147032 TGAAAGGTTGGATGAAAAGGTGAT 58.853 37.500 0.00 0.00 0.00 3.06
592 593 5.010922 TGAAAGGTTGGATGAAAAGGTGATG 59.989 40.000 0.00 0.00 0.00 3.07
593 594 4.387026 AGGTTGGATGAAAAGGTGATGA 57.613 40.909 0.00 0.00 0.00 2.92
594 595 4.739793 AGGTTGGATGAAAAGGTGATGAA 58.260 39.130 0.00 0.00 0.00 2.57
595 596 4.768968 AGGTTGGATGAAAAGGTGATGAAG 59.231 41.667 0.00 0.00 0.00 3.02
596 597 4.766891 GGTTGGATGAAAAGGTGATGAAGA 59.233 41.667 0.00 0.00 0.00 2.87
597 598 5.105997 GGTTGGATGAAAAGGTGATGAAGAG 60.106 44.000 0.00 0.00 0.00 2.85
598 599 5.503634 TGGATGAAAAGGTGATGAAGAGA 57.496 39.130 0.00 0.00 0.00 3.10
599 600 5.879763 TGGATGAAAAGGTGATGAAGAGAA 58.120 37.500 0.00 0.00 0.00 2.87
600 601 6.306199 TGGATGAAAAGGTGATGAAGAGAAA 58.694 36.000 0.00 0.00 0.00 2.52
601 602 6.777091 TGGATGAAAAGGTGATGAAGAGAAAA 59.223 34.615 0.00 0.00 0.00 2.29
602 603 7.040201 TGGATGAAAAGGTGATGAAGAGAAAAG 60.040 37.037 0.00 0.00 0.00 2.27
603 604 7.040132 GGATGAAAAGGTGATGAAGAGAAAAGT 60.040 37.037 0.00 0.00 0.00 2.66
604 605 7.031226 TGAAAAGGTGATGAAGAGAAAAGTG 57.969 36.000 0.00 0.00 0.00 3.16
605 606 6.828273 TGAAAAGGTGATGAAGAGAAAAGTGA 59.172 34.615 0.00 0.00 0.00 3.41
606 607 7.339212 TGAAAAGGTGATGAAGAGAAAAGTGAA 59.661 33.333 0.00 0.00 0.00 3.18
607 608 7.645058 AAAGGTGATGAAGAGAAAAGTGAAA 57.355 32.000 0.00 0.00 0.00 2.69
608 609 7.830099 AAGGTGATGAAGAGAAAAGTGAAAT 57.170 32.000 0.00 0.00 0.00 2.17
609 610 7.211966 AGGTGATGAAGAGAAAAGTGAAATG 57.788 36.000 0.00 0.00 0.00 2.32
610 611 6.208204 AGGTGATGAAGAGAAAAGTGAAATGG 59.792 38.462 0.00 0.00 0.00 3.16
611 612 6.385033 GTGATGAAGAGAAAAGTGAAATGGG 58.615 40.000 0.00 0.00 0.00 4.00
612 613 6.207417 GTGATGAAGAGAAAAGTGAAATGGGA 59.793 38.462 0.00 0.00 0.00 4.37
613 614 6.777091 TGATGAAGAGAAAAGTGAAATGGGAA 59.223 34.615 0.00 0.00 0.00 3.97
614 615 6.391227 TGAAGAGAAAAGTGAAATGGGAAC 57.609 37.500 0.00 0.00 0.00 3.62
615 616 6.129179 TGAAGAGAAAAGTGAAATGGGAACT 58.871 36.000 0.00 0.00 0.00 3.01
616 617 6.607198 TGAAGAGAAAAGTGAAATGGGAACTT 59.393 34.615 0.00 0.00 35.70 2.66
617 618 7.124147 TGAAGAGAAAAGTGAAATGGGAACTTT 59.876 33.333 0.00 0.00 44.01 2.66
618 619 8.533569 AAGAGAAAAGTGAAATGGGAACTTTA 57.466 30.769 0.85 0.00 41.93 1.85
619 620 7.941919 AGAGAAAAGTGAAATGGGAACTTTAC 58.058 34.615 0.85 0.00 41.93 2.01
620 621 6.735130 AGAAAAGTGAAATGGGAACTTTACG 58.265 36.000 0.85 0.00 41.93 3.18
621 622 6.320418 AGAAAAGTGAAATGGGAACTTTACGT 59.680 34.615 0.00 0.00 41.93 3.57
622 623 6.459670 AAAGTGAAATGGGAACTTTACGTT 57.540 33.333 0.00 0.00 41.19 3.99
623 624 6.459670 AAGTGAAATGGGAACTTTACGTTT 57.540 33.333 0.00 0.00 35.56 3.60
624 625 6.459670 AGTGAAATGGGAACTTTACGTTTT 57.540 33.333 0.00 0.00 35.56 2.43
625 626 6.869695 AGTGAAATGGGAACTTTACGTTTTT 58.130 32.000 0.00 0.00 35.56 1.94
720 729 3.428725 GCCAACATGTTTGAACACAGTGA 60.429 43.478 13.55 0.00 42.51 3.41
724 733 4.016444 ACATGTTTGAACACAGTGAAGGT 58.984 39.130 7.81 0.00 42.51 3.50
779 799 4.459337 CAGAACAGTAAACCTTCCATTCCC 59.541 45.833 0.00 0.00 0.00 3.97
786 806 1.886422 ACCTTCCATTCCCCTCTCTC 58.114 55.000 0.00 0.00 0.00 3.20
884 959 3.370103 CCCAAGCAAATGCCAAGAATCAT 60.370 43.478 0.94 0.00 43.38 2.45
1098 1191 4.722700 GTGCTGGTGGTGGGCGAT 62.723 66.667 0.00 0.00 0.00 4.58
1247 1346 2.317609 CCGTCAACCAGTTCAGGCG 61.318 63.158 0.00 0.00 0.00 5.52
1369 1472 1.480954 GGGTACTTGAGGAGCGATTCA 59.519 52.381 0.00 0.00 0.00 2.57
1659 1947 3.472652 TCAGTGGACGCATGTTTACTTT 58.527 40.909 0.00 0.00 0.00 2.66
1674 1962 5.769662 TGTTTACTTTTCATGATGCAGAGGT 59.230 36.000 0.00 0.00 0.00 3.85
1675 1963 6.265196 TGTTTACTTTTCATGATGCAGAGGTT 59.735 34.615 0.00 0.00 0.00 3.50
1676 1964 4.778534 ACTTTTCATGATGCAGAGGTTG 57.221 40.909 0.00 0.00 0.00 3.77
1677 1965 4.401022 ACTTTTCATGATGCAGAGGTTGA 58.599 39.130 0.00 0.00 0.00 3.18
1678 1966 4.458295 ACTTTTCATGATGCAGAGGTTGAG 59.542 41.667 0.00 0.00 0.00 3.02
1679 1967 3.986996 TTCATGATGCAGAGGTTGAGA 57.013 42.857 0.00 0.00 0.00 3.27
1680 1968 3.986996 TCATGATGCAGAGGTTGAGAA 57.013 42.857 0.00 0.00 0.00 2.87
1681 1969 3.603532 TCATGATGCAGAGGTTGAGAAC 58.396 45.455 0.00 0.00 0.00 3.01
1705 1993 7.108847 ACTTGAGATATAAGCCCATCTATTGC 58.891 38.462 0.00 0.00 31.63 3.56
1899 2194 2.501261 GGACACAAGTAAACCCAGGTC 58.499 52.381 0.00 0.00 0.00 3.85
1919 2215 9.626045 CCAGGTCTTTTTGTTGTTCTATAAATC 57.374 33.333 0.00 0.00 0.00 2.17
1941 2237 6.425210 TCTTAGCCATTATGTCTATGCAGT 57.575 37.500 0.00 0.00 0.00 4.40
1954 2250 5.106436 TGTCTATGCAGTGAAGAAATGCTTG 60.106 40.000 0.00 0.00 40.62 4.01
1981 2277 8.552865 GGTTTCTTGTAGAAAGAAGAAGAAGAC 58.447 37.037 2.28 0.00 44.07 3.01
1982 2278 7.932120 TTCTTGTAGAAAGAAGAAGAAGACG 57.068 36.000 0.00 0.00 39.38 4.18
1983 2279 7.273320 TCTTGTAGAAAGAAGAAGAAGACGA 57.727 36.000 0.00 0.00 32.42 4.20
1984 2280 7.713750 TCTTGTAGAAAGAAGAAGAAGACGAA 58.286 34.615 0.00 0.00 32.42 3.85
1985 2281 7.863375 TCTTGTAGAAAGAAGAAGAAGACGAAG 59.137 37.037 0.00 0.00 32.42 3.79
2058 3959 8.119891 TCTTGCTTTCTTAAAATATACCCCCTT 58.880 33.333 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.336433 CCAATCAAATCAAGCCACGTAGAT 59.664 41.667 0.00 0.00 0.00 1.98
1 2 3.689161 CCAATCAAATCAAGCCACGTAGA 59.311 43.478 0.00 0.00 0.00 2.59
2 3 3.689161 TCCAATCAAATCAAGCCACGTAG 59.311 43.478 0.00 0.00 0.00 3.51
3 4 3.680490 TCCAATCAAATCAAGCCACGTA 58.320 40.909 0.00 0.00 0.00 3.57
4 5 2.513753 TCCAATCAAATCAAGCCACGT 58.486 42.857 0.00 0.00 0.00 4.49
5 6 3.244976 GTTCCAATCAAATCAAGCCACG 58.755 45.455 0.00 0.00 0.00 4.94
6 7 4.255833 TGTTCCAATCAAATCAAGCCAC 57.744 40.909 0.00 0.00 0.00 5.01
7 8 4.952071 TTGTTCCAATCAAATCAAGCCA 57.048 36.364 0.00 0.00 0.00 4.75
8 9 6.806388 ATTTTGTTCCAATCAAATCAAGCC 57.194 33.333 0.00 0.00 35.25 4.35
9 10 8.445493 CCTTATTTTGTTCCAATCAAATCAAGC 58.555 33.333 0.00 0.00 35.25 4.01
10 11 9.492973 ACCTTATTTTGTTCCAATCAAATCAAG 57.507 29.630 0.00 0.00 35.25 3.02
11 12 9.487790 GACCTTATTTTGTTCCAATCAAATCAA 57.512 29.630 0.00 0.00 35.25 2.57
12 13 8.093927 GGACCTTATTTTGTTCCAATCAAATCA 58.906 33.333 0.00 0.00 35.25 2.57
13 14 7.275560 CGGACCTTATTTTGTTCCAATCAAATC 59.724 37.037 0.00 0.00 35.25 2.17
14 15 7.039363 TCGGACCTTATTTTGTTCCAATCAAAT 60.039 33.333 0.00 0.00 35.25 2.32
15 16 6.265649 TCGGACCTTATTTTGTTCCAATCAAA 59.734 34.615 0.00 0.00 33.76 2.69
16 17 5.770663 TCGGACCTTATTTTGTTCCAATCAA 59.229 36.000 0.00 0.00 0.00 2.57
17 18 5.182380 GTCGGACCTTATTTTGTTCCAATCA 59.818 40.000 0.00 0.00 0.00 2.57
18 19 5.392703 GGTCGGACCTTATTTTGTTCCAATC 60.393 44.000 19.92 0.00 34.73 2.67
19 20 4.461431 GGTCGGACCTTATTTTGTTCCAAT 59.539 41.667 19.92 0.00 34.73 3.16
20 21 3.822167 GGTCGGACCTTATTTTGTTCCAA 59.178 43.478 19.92 0.00 34.73 3.53
21 22 3.414269 GGTCGGACCTTATTTTGTTCCA 58.586 45.455 19.92 0.00 34.73 3.53
22 23 2.751259 GGGTCGGACCTTATTTTGTTCC 59.249 50.000 25.39 1.74 38.64 3.62
23 24 2.751259 GGGGTCGGACCTTATTTTGTTC 59.249 50.000 25.39 5.74 38.64 3.18
24 25 2.108601 TGGGGTCGGACCTTATTTTGTT 59.891 45.455 25.39 0.00 38.64 2.83
25 26 1.706305 TGGGGTCGGACCTTATTTTGT 59.294 47.619 25.39 0.00 38.64 2.83
26 27 2.089201 GTGGGGTCGGACCTTATTTTG 58.911 52.381 25.39 0.00 38.64 2.44
27 28 1.005097 GGTGGGGTCGGACCTTATTTT 59.995 52.381 25.39 0.00 38.64 1.82
28 29 0.622136 GGTGGGGTCGGACCTTATTT 59.378 55.000 25.39 0.00 38.64 1.40
29 30 0.253020 AGGTGGGGTCGGACCTTATT 60.253 55.000 25.39 6.54 39.75 1.40
30 31 1.394963 AGGTGGGGTCGGACCTTAT 59.605 57.895 25.39 6.17 39.75 1.73
31 32 2.864049 AGGTGGGGTCGGACCTTA 59.136 61.111 25.39 12.68 39.75 2.69
32 33 2.122099 AAGGTGGGGTCGGACCTT 60.122 61.111 25.39 9.74 45.92 3.50
33 34 2.606826 GAAGGTGGGGTCGGACCT 60.607 66.667 25.39 5.58 44.94 3.85
34 35 0.906282 TAAGAAGGTGGGGTCGGACC 60.906 60.000 19.06 19.06 37.60 4.46
35 36 0.978907 TTAAGAAGGTGGGGTCGGAC 59.021 55.000 0.00 0.00 0.00 4.79
36 37 1.732117 TTTAAGAAGGTGGGGTCGGA 58.268 50.000 0.00 0.00 0.00 4.55
37 38 2.572209 TTTTAAGAAGGTGGGGTCGG 57.428 50.000 0.00 0.00 0.00 4.79
38 39 3.681593 TGATTTTAAGAAGGTGGGGTCG 58.318 45.455 0.00 0.00 0.00 4.79
39 40 4.017126 CCTGATTTTAAGAAGGTGGGGTC 58.983 47.826 0.00 0.00 0.00 4.46
40 41 3.245622 CCCTGATTTTAAGAAGGTGGGGT 60.246 47.826 0.00 0.00 0.00 4.95
41 42 3.365472 CCCTGATTTTAAGAAGGTGGGG 58.635 50.000 0.00 0.00 0.00 4.96
42 43 3.365472 CCCCTGATTTTAAGAAGGTGGG 58.635 50.000 0.00 0.00 0.00 4.61
43 44 3.011257 TCCCCCTGATTTTAAGAAGGTGG 59.989 47.826 0.00 0.00 0.00 4.61
44 45 4.018415 TCTCCCCCTGATTTTAAGAAGGTG 60.018 45.833 0.00 0.00 0.00 4.00
45 46 4.183916 TCTCCCCCTGATTTTAAGAAGGT 58.816 43.478 0.00 0.00 0.00 3.50
46 47 4.862641 TCTCCCCCTGATTTTAAGAAGG 57.137 45.455 0.00 0.00 0.00 3.46
47 48 6.006275 TCATCTCCCCCTGATTTTAAGAAG 57.994 41.667 0.00 0.00 0.00 2.85
48 49 6.596869 ATCATCTCCCCCTGATTTTAAGAA 57.403 37.500 0.00 0.00 0.00 2.52
49 50 6.596869 AATCATCTCCCCCTGATTTTAAGA 57.403 37.500 0.00 0.00 38.60 2.10
50 51 7.749666 TCTAATCATCTCCCCCTGATTTTAAG 58.250 38.462 3.40 0.00 41.22 1.85
51 52 7.705912 TCTAATCATCTCCCCCTGATTTTAA 57.294 36.000 3.40 0.00 41.22 1.52
52 53 7.895144 ATCTAATCATCTCCCCCTGATTTTA 57.105 36.000 3.40 0.00 41.22 1.52
53 54 6.793518 ATCTAATCATCTCCCCCTGATTTT 57.206 37.500 3.40 0.00 41.22 1.82
54 55 6.793518 AATCTAATCATCTCCCCCTGATTT 57.206 37.500 3.40 0.00 41.22 2.17
55 56 7.259391 TCTAATCTAATCATCTCCCCCTGATT 58.741 38.462 3.57 3.57 42.92 2.57
56 57 6.820205 TCTAATCTAATCATCTCCCCCTGAT 58.180 40.000 0.00 0.00 33.59 2.90
57 58 6.233045 TCTAATCTAATCATCTCCCCCTGA 57.767 41.667 0.00 0.00 0.00 3.86
58 59 6.942163 TTCTAATCTAATCATCTCCCCCTG 57.058 41.667 0.00 0.00 0.00 4.45
59 60 7.316841 TCTTTCTAATCTAATCATCTCCCCCT 58.683 38.462 0.00 0.00 0.00 4.79
60 61 7.560796 TCTTTCTAATCTAATCATCTCCCCC 57.439 40.000 0.00 0.00 0.00 5.40
61 62 9.853177 TTTTCTTTCTAATCTAATCATCTCCCC 57.147 33.333 0.00 0.00 0.00 4.81
87 88 7.619964 TCTTACGGTTGTCTTCTTTCTTTTT 57.380 32.000 0.00 0.00 0.00 1.94
88 89 7.803279 ATCTTACGGTTGTCTTCTTTCTTTT 57.197 32.000 0.00 0.00 0.00 2.27
89 90 7.803279 AATCTTACGGTTGTCTTCTTTCTTT 57.197 32.000 0.00 0.00 0.00 2.52
90 91 8.897872 TTAATCTTACGGTTGTCTTCTTTCTT 57.102 30.769 0.00 0.00 0.00 2.52
91 92 8.148999 ACTTAATCTTACGGTTGTCTTCTTTCT 58.851 33.333 0.00 0.00 0.00 2.52
92 93 8.221766 CACTTAATCTTACGGTTGTCTTCTTTC 58.778 37.037 0.00 0.00 0.00 2.62
93 94 7.172703 CCACTTAATCTTACGGTTGTCTTCTTT 59.827 37.037 0.00 0.00 0.00 2.52
94 95 6.649557 CCACTTAATCTTACGGTTGTCTTCTT 59.350 38.462 0.00 0.00 0.00 2.52
95 96 6.164176 CCACTTAATCTTACGGTTGTCTTCT 58.836 40.000 0.00 0.00 0.00 2.85
96 97 5.350640 CCCACTTAATCTTACGGTTGTCTTC 59.649 44.000 0.00 0.00 0.00 2.87
97 98 5.012354 TCCCACTTAATCTTACGGTTGTCTT 59.988 40.000 0.00 0.00 0.00 3.01
98 99 4.529377 TCCCACTTAATCTTACGGTTGTCT 59.471 41.667 0.00 0.00 0.00 3.41
99 100 4.824289 TCCCACTTAATCTTACGGTTGTC 58.176 43.478 0.00 0.00 0.00 3.18
100 101 4.828829 CTCCCACTTAATCTTACGGTTGT 58.171 43.478 0.00 0.00 0.00 3.32
101 102 3.621715 GCTCCCACTTAATCTTACGGTTG 59.378 47.826 0.00 0.00 0.00 3.77
102 103 3.262405 TGCTCCCACTTAATCTTACGGTT 59.738 43.478 0.00 0.00 0.00 4.44
103 104 2.835764 TGCTCCCACTTAATCTTACGGT 59.164 45.455 0.00 0.00 0.00 4.83
104 105 3.195661 GTGCTCCCACTTAATCTTACGG 58.804 50.000 0.00 0.00 38.93 4.02
105 106 2.858344 CGTGCTCCCACTTAATCTTACG 59.142 50.000 0.00 0.00 39.86 3.18
106 107 3.195661 CCGTGCTCCCACTTAATCTTAC 58.804 50.000 0.00 0.00 39.86 2.34
107 108 2.169769 CCCGTGCTCCCACTTAATCTTA 59.830 50.000 0.00 0.00 39.86 2.10
108 109 1.065418 CCCGTGCTCCCACTTAATCTT 60.065 52.381 0.00 0.00 39.86 2.40
109 110 0.541863 CCCGTGCTCCCACTTAATCT 59.458 55.000 0.00 0.00 39.86 2.40
110 111 0.539986 TCCCGTGCTCCCACTTAATC 59.460 55.000 0.00 0.00 39.86 1.75
111 112 0.988832 TTCCCGTGCTCCCACTTAAT 59.011 50.000 0.00 0.00 39.86 1.40
112 113 0.323629 CTTCCCGTGCTCCCACTTAA 59.676 55.000 0.00 0.00 39.86 1.85
113 114 0.543410 TCTTCCCGTGCTCCCACTTA 60.543 55.000 0.00 0.00 39.86 2.24
114 115 1.831652 CTCTTCCCGTGCTCCCACTT 61.832 60.000 0.00 0.00 39.86 3.16
115 116 2.203788 TCTTCCCGTGCTCCCACT 60.204 61.111 0.00 0.00 39.86 4.00
116 117 2.232298 CTCTCTTCCCGTGCTCCCAC 62.232 65.000 0.00 0.00 38.62 4.61
117 118 1.984570 CTCTCTTCCCGTGCTCCCA 60.985 63.158 0.00 0.00 0.00 4.37
118 119 2.896443 CTCTCTTCCCGTGCTCCC 59.104 66.667 0.00 0.00 0.00 4.30
119 120 2.185608 GCTCTCTTCCCGTGCTCC 59.814 66.667 0.00 0.00 0.00 4.70
120 121 1.153667 CTGCTCTCTTCCCGTGCTC 60.154 63.158 0.00 0.00 0.00 4.26
121 122 2.654079 CCTGCTCTCTTCCCGTGCT 61.654 63.158 0.00 0.00 0.00 4.40
122 123 2.125350 CCTGCTCTCTTCCCGTGC 60.125 66.667 0.00 0.00 0.00 5.34
123 124 2.125350 GCCTGCTCTCTTCCCGTG 60.125 66.667 0.00 0.00 0.00 4.94
124 125 2.177594 CTTGCCTGCTCTCTTCCCGT 62.178 60.000 0.00 0.00 0.00 5.28
125 126 1.449246 CTTGCCTGCTCTCTTCCCG 60.449 63.158 0.00 0.00 0.00 5.14
126 127 1.748500 GCTTGCCTGCTCTCTTCCC 60.749 63.158 0.00 0.00 0.00 3.97
127 128 1.748500 GGCTTGCCTGCTCTCTTCC 60.749 63.158 4.11 0.00 0.00 3.46
128 129 2.105466 CGGCTTGCCTGCTCTCTTC 61.105 63.158 10.12 0.00 0.00 2.87
129 130 2.046507 CGGCTTGCCTGCTCTCTT 60.047 61.111 10.12 0.00 0.00 2.85
130 131 4.093291 CCGGCTTGCCTGCTCTCT 62.093 66.667 10.12 0.00 0.00 3.10
131 132 2.883267 AATCCGGCTTGCCTGCTCTC 62.883 60.000 10.12 0.00 0.00 3.20
132 133 2.883267 GAATCCGGCTTGCCTGCTCT 62.883 60.000 10.12 0.00 0.00 4.09
133 134 2.439156 AATCCGGCTTGCCTGCTC 60.439 61.111 10.12 0.00 0.00 4.26
134 135 2.439156 GAATCCGGCTTGCCTGCT 60.439 61.111 10.12 0.00 0.00 4.24
135 136 3.880846 CGAATCCGGCTTGCCTGC 61.881 66.667 10.12 0.00 0.00 4.85
136 137 2.436646 ACGAATCCGGCTTGCCTG 60.437 61.111 10.12 3.29 40.78 4.85
137 138 2.125106 GACGAATCCGGCTTGCCT 60.125 61.111 10.12 0.00 41.56 4.75
143 144 4.117685 AGTGTAAATTAGACGAATCCGGC 58.882 43.478 0.00 0.00 46.21 6.13
144 145 9.125906 CTTATAGTGTAAATTAGACGAATCCGG 57.874 37.037 0.00 0.00 40.78 5.14
145 146 9.125906 CCTTATAGTGTAAATTAGACGAATCCG 57.874 37.037 0.00 0.00 42.50 4.18
161 162 7.739825 AGATGCATGTATGTTCCTTATAGTGT 58.260 34.615 2.46 0.00 0.00 3.55
250 251 0.376852 GTTGAAACAGCTCGTGCACA 59.623 50.000 18.64 3.15 42.74 4.57
251 252 0.657840 AGTTGAAACAGCTCGTGCAC 59.342 50.000 12.58 6.82 42.74 4.57
289 290 2.994990 ACTCGGCTAGCTAGAGTCG 58.005 57.895 28.22 21.38 45.91 4.18
354 355 2.210116 CGCACGGGCATTATTCTAGTT 58.790 47.619 11.77 0.00 41.24 2.24
355 356 1.138266 ACGCACGGGCATTATTCTAGT 59.862 47.619 11.77 0.00 41.24 2.57
356 357 1.865865 ACGCACGGGCATTATTCTAG 58.134 50.000 11.77 0.00 41.24 2.43
357 358 1.937223 CAACGCACGGGCATTATTCTA 59.063 47.619 11.77 0.00 41.24 2.10
358 359 0.732571 CAACGCACGGGCATTATTCT 59.267 50.000 11.77 0.00 41.24 2.40
359 360 0.865639 GCAACGCACGGGCATTATTC 60.866 55.000 11.77 0.00 41.24 1.75
360 361 1.138671 GCAACGCACGGGCATTATT 59.861 52.632 11.77 0.00 41.24 1.40
361 362 1.590610 TTGCAACGCACGGGCATTAT 61.591 50.000 11.77 0.00 38.71 1.28
362 363 2.261586 TTGCAACGCACGGGCATTA 61.262 52.632 11.77 0.00 38.71 1.90
363 364 3.600694 TTGCAACGCACGGGCATT 61.601 55.556 11.77 0.00 38.71 3.56
364 365 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
366 367 4.980903 CTGTTGCAACGCACGGGC 62.981 66.667 23.79 0.00 38.71 6.13
367 368 2.128853 ATTCTGTTGCAACGCACGGG 62.129 55.000 23.79 9.89 38.71 5.28
368 369 0.515127 TATTCTGTTGCAACGCACGG 59.485 50.000 23.79 6.92 38.71 4.94
369 370 2.525750 ATATTCTGTTGCAACGCACG 57.474 45.000 23.79 12.38 38.71 5.34
370 371 8.560576 AATATTTATATTCTGTTGCAACGCAC 57.439 30.769 23.79 1.83 38.71 5.34
388 389 9.752961 TCACAAGCTAACGTGCTATAATATTTA 57.247 29.630 0.23 0.00 43.24 1.40
389 390 8.657074 TCACAAGCTAACGTGCTATAATATTT 57.343 30.769 0.23 0.00 43.24 1.40
390 391 8.833231 ATCACAAGCTAACGTGCTATAATATT 57.167 30.769 0.23 0.00 43.24 1.28
391 392 8.833231 AATCACAAGCTAACGTGCTATAATAT 57.167 30.769 0.23 0.00 43.24 1.28
392 393 8.657074 AAATCACAAGCTAACGTGCTATAATA 57.343 30.769 0.23 0.00 43.24 0.98
393 394 7.553881 AAATCACAAGCTAACGTGCTATAAT 57.446 32.000 0.23 0.00 43.24 1.28
394 395 6.978343 AAATCACAAGCTAACGTGCTATAA 57.022 33.333 0.23 0.00 43.24 0.98
395 396 8.141909 AGATAAATCACAAGCTAACGTGCTATA 58.858 33.333 0.23 1.05 43.24 1.31
396 397 6.986817 AGATAAATCACAAGCTAACGTGCTAT 59.013 34.615 0.23 3.96 43.24 2.97
397 398 6.338146 AGATAAATCACAAGCTAACGTGCTA 58.662 36.000 0.23 0.00 43.24 3.49
398 399 5.178797 AGATAAATCACAAGCTAACGTGCT 58.821 37.500 6.08 0.00 46.40 4.40
399 400 5.470845 AGATAAATCACAAGCTAACGTGC 57.529 39.130 6.08 0.00 33.03 5.34
400 401 8.352752 TGATAGATAAATCACAAGCTAACGTG 57.647 34.615 0.00 4.83 30.92 4.49
401 402 8.942338 TTGATAGATAAATCACAAGCTAACGT 57.058 30.769 0.00 0.00 35.63 3.99
562 563 9.320295 ACCTTTTCATCCAACCTTTCATTTATA 57.680 29.630 0.00 0.00 0.00 0.98
563 564 8.096414 CACCTTTTCATCCAACCTTTCATTTAT 58.904 33.333 0.00 0.00 0.00 1.40
564 565 7.288852 TCACCTTTTCATCCAACCTTTCATTTA 59.711 33.333 0.00 0.00 0.00 1.40
565 566 6.099557 TCACCTTTTCATCCAACCTTTCATTT 59.900 34.615 0.00 0.00 0.00 2.32
566 567 5.602145 TCACCTTTTCATCCAACCTTTCATT 59.398 36.000 0.00 0.00 0.00 2.57
567 568 5.147032 TCACCTTTTCATCCAACCTTTCAT 58.853 37.500 0.00 0.00 0.00 2.57
568 569 4.541705 TCACCTTTTCATCCAACCTTTCA 58.458 39.130 0.00 0.00 0.00 2.69
569 570 5.243730 TCATCACCTTTTCATCCAACCTTTC 59.756 40.000 0.00 0.00 0.00 2.62
570 571 5.147032 TCATCACCTTTTCATCCAACCTTT 58.853 37.500 0.00 0.00 0.00 3.11
571 572 4.739793 TCATCACCTTTTCATCCAACCTT 58.260 39.130 0.00 0.00 0.00 3.50
572 573 4.387026 TCATCACCTTTTCATCCAACCT 57.613 40.909 0.00 0.00 0.00 3.50
573 574 4.766891 TCTTCATCACCTTTTCATCCAACC 59.233 41.667 0.00 0.00 0.00 3.77
574 575 5.707298 TCTCTTCATCACCTTTTCATCCAAC 59.293 40.000 0.00 0.00 0.00 3.77
575 576 5.879763 TCTCTTCATCACCTTTTCATCCAA 58.120 37.500 0.00 0.00 0.00 3.53
576 577 5.503634 TCTCTTCATCACCTTTTCATCCA 57.496 39.130 0.00 0.00 0.00 3.41
577 578 6.824305 TTTCTCTTCATCACCTTTTCATCC 57.176 37.500 0.00 0.00 0.00 3.51
578 579 7.806960 CACTTTTCTCTTCATCACCTTTTCATC 59.193 37.037 0.00 0.00 0.00 2.92
579 580 7.503566 TCACTTTTCTCTTCATCACCTTTTCAT 59.496 33.333 0.00 0.00 0.00 2.57
580 581 6.828273 TCACTTTTCTCTTCATCACCTTTTCA 59.172 34.615 0.00 0.00 0.00 2.69
581 582 7.264373 TCACTTTTCTCTTCATCACCTTTTC 57.736 36.000 0.00 0.00 0.00 2.29
582 583 7.645058 TTCACTTTTCTCTTCATCACCTTTT 57.355 32.000 0.00 0.00 0.00 2.27
583 584 7.645058 TTTCACTTTTCTCTTCATCACCTTT 57.355 32.000 0.00 0.00 0.00 3.11
584 585 7.255730 CCATTTCACTTTTCTCTTCATCACCTT 60.256 37.037 0.00 0.00 0.00 3.50
585 586 6.208204 CCATTTCACTTTTCTCTTCATCACCT 59.792 38.462 0.00 0.00 0.00 4.00
586 587 6.385033 CCATTTCACTTTTCTCTTCATCACC 58.615 40.000 0.00 0.00 0.00 4.02
587 588 6.207417 TCCCATTTCACTTTTCTCTTCATCAC 59.793 38.462 0.00 0.00 0.00 3.06
588 589 6.306199 TCCCATTTCACTTTTCTCTTCATCA 58.694 36.000 0.00 0.00 0.00 3.07
589 590 6.824305 TCCCATTTCACTTTTCTCTTCATC 57.176 37.500 0.00 0.00 0.00 2.92
590 591 6.779539 AGTTCCCATTTCACTTTTCTCTTCAT 59.220 34.615 0.00 0.00 0.00 2.57
591 592 6.129179 AGTTCCCATTTCACTTTTCTCTTCA 58.871 36.000 0.00 0.00 0.00 3.02
592 593 6.641169 AGTTCCCATTTCACTTTTCTCTTC 57.359 37.500 0.00 0.00 0.00 2.87
593 594 7.423844 AAAGTTCCCATTTCACTTTTCTCTT 57.576 32.000 0.00 0.00 37.44 2.85
594 595 7.255139 CGTAAAGTTCCCATTTCACTTTTCTCT 60.255 37.037 2.10 0.00 40.44 3.10
595 596 6.856426 CGTAAAGTTCCCATTTCACTTTTCTC 59.144 38.462 2.10 0.00 40.44 2.87
596 597 6.320418 ACGTAAAGTTCCCATTTCACTTTTCT 59.680 34.615 2.10 0.00 40.44 2.52
597 598 6.500910 ACGTAAAGTTCCCATTTCACTTTTC 58.499 36.000 2.10 0.00 40.44 2.29
598 599 6.459670 ACGTAAAGTTCCCATTTCACTTTT 57.540 33.333 2.10 0.00 40.44 2.27
599 600 6.459670 AACGTAAAGTTCCCATTTCACTTT 57.540 33.333 0.00 0.00 39.16 2.66
600 601 6.459670 AAACGTAAAGTTCCCATTTCACTT 57.540 33.333 0.00 0.00 43.37 3.16
601 602 6.459670 AAAACGTAAAGTTCCCATTTCACT 57.540 33.333 0.00 0.00 43.37 3.41
623 624 7.503991 CGACACGCATTTCTACTACTTAAAAA 58.496 34.615 0.00 0.00 0.00 1.94
624 625 7.041187 CGACACGCATTTCTACTACTTAAAA 57.959 36.000 0.00 0.00 0.00 1.52
625 626 6.621737 CGACACGCATTTCTACTACTTAAA 57.378 37.500 0.00 0.00 0.00 1.52
720 729 1.152546 GTGGCTGGGGTCAAACCTT 60.153 57.895 0.00 0.00 38.64 3.50
724 733 2.112297 GTCGTGGCTGGGGTCAAA 59.888 61.111 0.00 0.00 0.00 2.69
779 799 5.104776 TGAGAGAGAGAGAAAGAGAGAGAGG 60.105 48.000 0.00 0.00 0.00 3.69
786 806 4.078537 TGTGGTGAGAGAGAGAGAAAGAG 58.921 47.826 0.00 0.00 0.00 2.85
869 944 5.410067 CCGTGTTTATGATTCTTGGCATTT 58.590 37.500 0.00 0.00 0.00 2.32
990 1080 1.141881 CTCCCTCATCGTCGGTTGG 59.858 63.158 0.00 0.00 0.00 3.77
1098 1191 3.699955 CTCGCATTCCTCGTCGCCA 62.700 63.158 0.00 0.00 0.00 5.69
1261 1360 0.609957 TAGTTCTTGGAGACGGCGGA 60.610 55.000 13.24 0.00 0.00 5.54
1369 1472 5.126067 ACTCAACTAGTCAACAGCACAAAT 58.874 37.500 0.00 0.00 30.33 2.32
1659 1947 3.986996 TCTCAACCTCTGCATCATGAA 57.013 42.857 0.00 0.00 0.00 2.57
1674 1962 6.560003 TGGGCTTATATCTCAAGTTCTCAA 57.440 37.500 0.00 0.00 0.00 3.02
1675 1963 6.556495 AGATGGGCTTATATCTCAAGTTCTCA 59.444 38.462 0.00 0.00 0.00 3.27
1676 1964 7.003402 AGATGGGCTTATATCTCAAGTTCTC 57.997 40.000 0.00 0.00 0.00 2.87
1677 1965 8.677870 ATAGATGGGCTTATATCTCAAGTTCT 57.322 34.615 0.00 0.00 35.42 3.01
1678 1966 9.160496 CAATAGATGGGCTTATATCTCAAGTTC 57.840 37.037 0.00 0.00 35.42 3.01
1679 1967 7.609532 GCAATAGATGGGCTTATATCTCAAGTT 59.390 37.037 0.00 0.00 35.42 2.66
1680 1968 7.037730 AGCAATAGATGGGCTTATATCTCAAGT 60.038 37.037 0.00 0.00 35.42 3.16
1681 1969 7.337167 AGCAATAGATGGGCTTATATCTCAAG 58.663 38.462 0.00 0.00 35.42 3.02
1705 1993 9.777575 AAATGAACAAGCAAAAAGAAATGAAAG 57.222 25.926 0.00 0.00 0.00 2.62
1858 2153 3.068873 CCGAGATAGAGCTAGCCACTTTT 59.931 47.826 12.13 3.08 0.00 2.27
1877 2172 1.071071 CCTGGGTTTACTTGTGTCCGA 59.929 52.381 0.00 0.00 0.00 4.55
1919 2215 6.226052 TCACTGCATAGACATAATGGCTAAG 58.774 40.000 0.00 0.00 42.08 2.18
1954 2250 7.715686 TCTTCTTCTTCTTTCTACAAGAAACCC 59.284 37.037 0.00 0.00 39.13 4.11
1981 2277 4.273480 TCAGCCAAAGAGACTTTTTCTTCG 59.727 41.667 0.00 0.00 33.92 3.79
1982 2278 5.757850 TCAGCCAAAGAGACTTTTTCTTC 57.242 39.130 0.00 0.00 33.92 2.87
1983 2279 6.721704 ATTCAGCCAAAGAGACTTTTTCTT 57.278 33.333 0.00 0.00 36.49 2.52
1984 2280 6.721704 AATTCAGCCAAAGAGACTTTTTCT 57.278 33.333 0.00 0.00 37.23 2.52
1985 2281 7.708322 AGAAAATTCAGCCAAAGAGACTTTTTC 59.292 33.333 0.00 0.00 28.47 2.29
2110 4011 8.757789 CGGCTCTTGTAAATGAACGTATTTATA 58.242 33.333 6.75 2.46 35.61 0.98
2111 4012 7.279313 ACGGCTCTTGTAAATGAACGTATTTAT 59.721 33.333 6.75 0.00 35.61 1.40
2211 4112 9.571816 AATGTCCATTTGGTGTTTTGAATTATT 57.428 25.926 0.00 0.00 36.34 1.40
2213 4119 8.970859 AAATGTCCATTTGGTGTTTTGAATTA 57.029 26.923 4.52 0.00 39.36 1.40
2216 4122 7.560368 ACTAAATGTCCATTTGGTGTTTTGAA 58.440 30.769 17.52 0.00 46.22 2.69


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

AutoCloner maintained by Alex Coulton.