Multiple sequence alignment - TraesCS7D01G487400

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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 TraesCS7D01G487400 chr7D 100.000 3261 0 0 1 3261 597655337 597652077 0.000000e+00 6023
1 TraesCS7D01G487400 chr7D 78.751 1313 215 40 1008 2267 597619803 597621104 0.000000e+00 821
2 TraesCS7D01G487400 chr7D 79.120 1250 197 40 1184 2386 597965351 597966583 0.000000e+00 804
3 TraesCS7D01G487400 chr7D 78.464 1328 211 44 1007 2267 597570247 597568928 0.000000e+00 798
4 TraesCS7D01G487400 chr7D 78.446 1313 214 38 1011 2267 597546423 597545124 0.000000e+00 793
5 TraesCS7D01G487400 chr7D 98.985 197 2 0 1 197 472862522 472862326 1.440000e-93 353
6 TraesCS7D01G487400 chr7B 90.297 2999 239 25 306 3261 676423424 676426413 0.000000e+00 3879
7 TraesCS7D01G487400 chr7B 78.212 1432 231 51 1011 2384 676211026 676209618 0.000000e+00 841
8 TraesCS7D01G487400 chr7B 78.341 1302 206 42 1029 2267 676534931 676533643 0.000000e+00 773
9 TraesCS7D01G487400 chr7B 79.376 1154 186 35 1153 2267 676862177 676861037 0.000000e+00 765
10 TraesCS7D01G487400 chr7B 83.130 575 95 2 1742 2316 676215556 676214984 1.040000e-144 523
11 TraesCS7D01G487400 chr7B 77.323 635 115 18 2492 3103 686123501 686122873 6.700000e-92 348
12 TraesCS7D01G487400 chr7B 93.966 116 7 0 189 304 676418207 676418322 3.340000e-40 176
13 TraesCS7D01G487400 chr7A 83.571 1960 246 40 472 2368 690399246 690401192 0.000000e+00 1766
14 TraesCS7D01G487400 chr7A 92.683 1066 76 1 1565 2628 690412962 690414027 0.000000e+00 1535
15 TraesCS7D01G487400 chr7A 95.975 795 30 1 744 1536 690412173 690412967 0.000000e+00 1290
16 TraesCS7D01G487400 chr7A 77.978 1444 235 50 1011 2386 690195791 690194363 0.000000e+00 828
17 TraesCS7D01G487400 chr7A 78.208 1317 220 38 1007 2267 690517275 690518580 0.000000e+00 780
18 TraesCS7D01G487400 chr7A 95.320 406 18 1 306 710 690411779 690412184 0.000000e+00 643
19 TraesCS7D01G487400 chr7A 84.932 584 74 5 2692 3261 690414067 690414650 2.180000e-161 579
20 TraesCS7D01G487400 chr7A 76.866 536 70 31 1007 1493 690438750 690439280 1.500000e-63 254
21 TraesCS7D01G487400 chr5D 77.267 805 149 21 2480 3259 540032357 540031562 2.990000e-120 442
22 TraesCS7D01G487400 chr5D 96.585 205 7 0 1 205 98590415 98590619 1.120000e-89 340
23 TraesCS7D01G487400 chr5D 75.920 598 111 25 2686 3256 142947901 142947310 3.210000e-70 276
24 TraesCS7D01G487400 chr2B 77.990 627 112 21 2488 3094 396407409 396406789 1.430000e-98 370
25 TraesCS7D01G487400 chr2B 77.458 661 121 16 2453 3094 608482429 608481778 1.430000e-98 370
26 TraesCS7D01G487400 chr2B 75.000 848 162 32 2453 3256 146929519 146930360 2.410000e-91 346
27 TraesCS7D01G487400 chr6D 99.482 193 1 0 1 193 129455131 129455323 5.180000e-93 351
28 TraesCS7D01G487400 chr6D 97.537 203 5 0 1 203 98045817 98045615 6.700000e-92 348
29 TraesCS7D01G487400 chr6D 74.049 447 92 16 2456 2882 123038887 123038445 9.360000e-36 161
30 TraesCS7D01G487400 chr3D 99.482 193 1 0 1 193 581738159 581737967 5.180000e-93 351
31 TraesCS7D01G487400 chr2D 99.482 193 1 0 1 193 338660208 338660400 5.180000e-93 351
32 TraesCS7D01G487400 chr1D 97.512 201 5 0 1 201 475768884 475769084 8.660000e-91 344
33 TraesCS7D01G487400 chr1D 76.847 609 116 18 2453 3048 430069245 430069841 1.460000e-83 320
34 TraesCS7D01G487400 chr1D 73.370 368 76 13 2453 2800 301510362 301510727 2.060000e-22 117
35 TraesCS7D01G487400 chr4D 98.953 191 2 0 1 191 53477460 53477650 3.120000e-90 342
36 TraesCS7D01G487400 chr4D 79.545 220 33 7 2453 2660 447946492 447946273 2.620000e-31 147
37 TraesCS7D01G487400 chr4A 95.327 214 6 4 1 214 532365526 532365735 1.450000e-88 337
38 TraesCS7D01G487400 chr4A 77.642 492 92 15 2615 3094 687826232 687825747 1.920000e-72 283
39 TraesCS7D01G487400 chr5B 75.821 670 127 24 2614 3256 381386875 381387536 1.140000e-79 307
40 TraesCS7D01G487400 chr6B 75.836 538 118 11 1665 2196 172368480 172367949 2.500000e-66 263
41 TraesCS7D01G487400 chr3B 78.607 402 75 10 2700 3094 166564996 166565393 4.180000e-64 255
42 TraesCS7D01G487400 chr4B 84.252 127 19 1 2453 2578 560882101 560881975 4.420000e-24 122
43 TraesCS7D01G487400 chr3A 77.228 202 37 6 2453 2646 79438927 79439127 3.440000e-20 110


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 TraesCS7D01G487400 chr7D 597652077 597655337 3260 True 6023.00 6023 100.0000 1 3261 1 chr7D.!!$R4 3260
1 TraesCS7D01G487400 chr7D 597619803 597621104 1301 False 821.00 821 78.7510 1008 2267 1 chr7D.!!$F1 1259
2 TraesCS7D01G487400 chr7D 597965351 597966583 1232 False 804.00 804 79.1200 1184 2386 1 chr7D.!!$F2 1202
3 TraesCS7D01G487400 chr7D 597568928 597570247 1319 True 798.00 798 78.4640 1007 2267 1 chr7D.!!$R3 1260
4 TraesCS7D01G487400 chr7D 597545124 597546423 1299 True 793.00 793 78.4460 1011 2267 1 chr7D.!!$R2 1256
5 TraesCS7D01G487400 chr7B 676423424 676426413 2989 False 3879.00 3879 90.2970 306 3261 1 chr7B.!!$F2 2955
6 TraesCS7D01G487400 chr7B 676533643 676534931 1288 True 773.00 773 78.3410 1029 2267 1 chr7B.!!$R1 1238
7 TraesCS7D01G487400 chr7B 676861037 676862177 1140 True 765.00 765 79.3760 1153 2267 1 chr7B.!!$R2 1114
8 TraesCS7D01G487400 chr7B 676209618 676215556 5938 True 682.00 841 80.6710 1011 2384 2 chr7B.!!$R4 1373
9 TraesCS7D01G487400 chr7B 686122873 686123501 628 True 348.00 348 77.3230 2492 3103 1 chr7B.!!$R3 611
10 TraesCS7D01G487400 chr7A 690399246 690401192 1946 False 1766.00 1766 83.5710 472 2368 1 chr7A.!!$F1 1896
11 TraesCS7D01G487400 chr7A 690411779 690414650 2871 False 1011.75 1535 92.2275 306 3261 4 chr7A.!!$F4 2955
12 TraesCS7D01G487400 chr7A 690194363 690195791 1428 True 828.00 828 77.9780 1011 2386 1 chr7A.!!$R1 1375
13 TraesCS7D01G487400 chr7A 690517275 690518580 1305 False 780.00 780 78.2080 1007 2267 1 chr7A.!!$F3 1260
14 TraesCS7D01G487400 chr7A 690438750 690439280 530 False 254.00 254 76.8660 1007 1493 1 chr7A.!!$F2 486
15 TraesCS7D01G487400 chr5D 540031562 540032357 795 True 442.00 442 77.2670 2480 3259 1 chr5D.!!$R2 779
16 TraesCS7D01G487400 chr5D 142947310 142947901 591 True 276.00 276 75.9200 2686 3256 1 chr5D.!!$R1 570
17 TraesCS7D01G487400 chr2B 396406789 396407409 620 True 370.00 370 77.9900 2488 3094 1 chr2B.!!$R1 606
18 TraesCS7D01G487400 chr2B 608481778 608482429 651 True 370.00 370 77.4580 2453 3094 1 chr2B.!!$R2 641
19 TraesCS7D01G487400 chr2B 146929519 146930360 841 False 346.00 346 75.0000 2453 3256 1 chr2B.!!$F1 803
20 TraesCS7D01G487400 chr1D 430069245 430069841 596 False 320.00 320 76.8470 2453 3048 1 chr1D.!!$F2 595
21 TraesCS7D01G487400 chr5B 381386875 381387536 661 False 307.00 307 75.8210 2614 3256 1 chr5B.!!$F1 642
22 TraesCS7D01G487400 chr6B 172367949 172368480 531 True 263.00 263 75.8360 1665 2196 1 chr6B.!!$R1 531

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
272 273 0.104672 TCCACCCTTGAACTCAGGGA 60.105 55.0 12.15 3.0 45.01 4.20 F
282 283 0.252284 AACTCAGGGACTCCACGGAT 60.252 55.0 0.00 0.0 34.60 4.18 F
290 291 0.741221 GACTCCACGGATGCCAAGTC 60.741 60.0 0.00 0.0 0.00 3.01 F
1789 5436 0.179000 GCGTCCAGGAGGTGATCAAT 59.821 55.0 10.89 0.0 35.89 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1240 4786 1.337703 TGAAGTACACCTACGTGCGTT 59.662 47.619 1.66 0.00 44.40 4.84 R
1789 5436 1.511305 GATCGTCTTGGCACCGAGA 59.489 57.895 2.24 2.24 33.66 4.04 R
2191 5838 3.384668 CCCATTAGCGATGACACTGTAG 58.615 50.000 4.88 0.00 38.03 2.74 R
2681 6372 0.655733 CAGCGTTCGTGTGACCTTTT 59.344 50.000 0.00 0.00 0.00 2.27 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
24 25 7.725610 GAAACATAACCATCTTTGATCAACG 57.274 36.000 7.89 6.62 0.00 4.10
25 26 7.447374 AAACATAACCATCTTTGATCAACGA 57.553 32.000 16.08 16.08 0.00 3.85
26 27 6.668541 ACATAACCATCTTTGATCAACGAG 57.331 37.500 18.24 10.23 0.00 4.18
28 29 3.340814 ACCATCTTTGATCAACGAGCT 57.659 42.857 18.24 2.03 0.00 4.09
29 30 4.471904 ACCATCTTTGATCAACGAGCTA 57.528 40.909 18.24 0.00 0.00 3.32
30 31 4.437239 ACCATCTTTGATCAACGAGCTAG 58.563 43.478 18.24 8.24 0.00 3.42
31 32 4.081420 ACCATCTTTGATCAACGAGCTAGT 60.081 41.667 18.24 10.56 0.00 2.57
32 33 4.505922 CCATCTTTGATCAACGAGCTAGTC 59.494 45.833 18.24 0.00 0.00 2.59
33 34 4.783764 TCTTTGATCAACGAGCTAGTCA 57.216 40.909 7.89 0.00 0.00 3.41
34 35 5.134202 TCTTTGATCAACGAGCTAGTCAA 57.866 39.130 7.89 0.00 0.00 3.18
35 36 5.164233 TCTTTGATCAACGAGCTAGTCAAG 58.836 41.667 7.89 0.00 0.00 3.02
36 37 4.521130 TTGATCAACGAGCTAGTCAAGT 57.479 40.909 3.38 0.00 0.00 3.16
38 39 5.236655 TGATCAACGAGCTAGTCAAGTAG 57.763 43.478 0.00 0.00 0.00 2.57
39 40 4.941873 TGATCAACGAGCTAGTCAAGTAGA 59.058 41.667 0.00 0.00 0.00 2.59
41 42 3.690139 TCAACGAGCTAGTCAAGTAGAGG 59.310 47.826 0.00 0.00 0.00 3.69
42 43 2.018515 ACGAGCTAGTCAAGTAGAGGC 58.981 52.381 0.00 0.00 0.00 4.70
45 46 3.815962 CGAGCTAGTCAAGTAGAGGCATA 59.184 47.826 0.00 0.00 0.00 3.14
46 47 4.319911 CGAGCTAGTCAAGTAGAGGCATAC 60.320 50.000 0.00 0.00 0.00 2.39
47 48 4.798882 AGCTAGTCAAGTAGAGGCATACT 58.201 43.478 0.00 0.00 37.61 2.12
48 49 5.942961 AGCTAGTCAAGTAGAGGCATACTA 58.057 41.667 3.23 0.00 34.90 1.82
49 50 6.001460 AGCTAGTCAAGTAGAGGCATACTAG 58.999 44.000 0.00 0.00 38.50 2.57
51 52 6.293735 GCTAGTCAAGTAGAGGCATACTAGTG 60.294 46.154 5.39 0.00 38.02 2.74
52 53 5.756918 AGTCAAGTAGAGGCATACTAGTGA 58.243 41.667 5.39 2.59 34.90 3.41
53 54 5.591067 AGTCAAGTAGAGGCATACTAGTGAC 59.409 44.000 17.97 17.97 40.57 3.67
54 55 5.357314 GTCAAGTAGAGGCATACTAGTGACA 59.643 44.000 19.41 0.00 40.28 3.58
55 56 5.357314 TCAAGTAGAGGCATACTAGTGACAC 59.643 44.000 5.39 0.00 34.90 3.67
56 57 5.118729 AGTAGAGGCATACTAGTGACACT 57.881 43.478 13.68 13.68 34.21 3.55
58 59 4.243793 AGAGGCATACTAGTGACACTCT 57.756 45.455 12.39 10.40 0.00 3.24
59 60 3.951037 AGAGGCATACTAGTGACACTCTG 59.049 47.826 12.39 9.04 33.23 3.35
60 61 3.697045 GAGGCATACTAGTGACACTCTGT 59.303 47.826 12.39 14.35 0.00 3.41
61 62 4.090090 AGGCATACTAGTGACACTCTGTT 58.910 43.478 12.39 0.00 0.00 3.16
62 63 4.528596 AGGCATACTAGTGACACTCTGTTT 59.471 41.667 12.39 5.23 0.00 2.83
64 65 5.230942 GCATACTAGTGACACTCTGTTTGT 58.769 41.667 12.39 5.61 0.00 2.83
65 66 5.346281 GCATACTAGTGACACTCTGTTTGTC 59.654 44.000 12.39 9.81 43.22 3.18
66 67 6.682746 CATACTAGTGACACTCTGTTTGTCT 58.317 40.000 12.39 0.00 43.30 3.41
67 68 7.575155 GCATACTAGTGACACTCTGTTTGTCTA 60.575 40.741 12.39 0.00 43.30 2.59
69 70 6.682746 ACTAGTGACACTCTGTTTGTCTATG 58.317 40.000 12.39 0.00 43.30 2.23
70 71 5.537300 AGTGACACTCTGTTTGTCTATGT 57.463 39.130 1.07 0.00 43.30 2.29
71 72 6.650427 AGTGACACTCTGTTTGTCTATGTA 57.350 37.500 1.07 0.00 43.30 2.29
72 73 7.233389 AGTGACACTCTGTTTGTCTATGTAT 57.767 36.000 1.07 0.00 43.30 2.29
73 74 7.671302 AGTGACACTCTGTTTGTCTATGTATT 58.329 34.615 1.07 0.00 43.30 1.89
76 77 7.598869 TGACACTCTGTTTGTCTATGTATTCAC 59.401 37.037 11.01 0.00 43.30 3.18
77 78 7.441836 ACACTCTGTTTGTCTATGTATTCACA 58.558 34.615 0.00 0.00 39.52 3.58
78 79 7.385205 ACACTCTGTTTGTCTATGTATTCACAC 59.615 37.037 0.00 0.00 37.54 3.82
80 81 8.097038 ACTCTGTTTGTCTATGTATTCACACAT 58.903 33.333 0.00 0.00 41.88 3.21
81 82 8.255394 TCTGTTTGTCTATGTATTCACACATG 57.745 34.615 0.00 0.00 39.46 3.21
83 84 9.150348 CTGTTTGTCTATGTATTCACACATGTA 57.850 33.333 0.00 0.00 39.46 2.29
84 85 9.665719 TGTTTGTCTATGTATTCACACATGTAT 57.334 29.630 0.00 0.00 39.46 2.29
86 87 9.883142 TTTGTCTATGTATTCACACATGTATCA 57.117 29.630 0.00 0.00 39.46 2.15
87 88 9.883142 TTGTCTATGTATTCACACATGTATCAA 57.117 29.630 0.00 0.00 39.46 2.57
88 89 9.533253 TGTCTATGTATTCACACATGTATCAAG 57.467 33.333 0.00 0.00 39.46 3.02
93 94 8.039603 TGTATTCACACATGTATCAAGTTTCC 57.960 34.615 0.00 0.00 0.00 3.13
94 95 5.605564 TTCACACATGTATCAAGTTTCCG 57.394 39.130 0.00 0.00 0.00 4.30
96 97 3.751175 CACACATGTATCAAGTTTCCGGT 59.249 43.478 0.00 0.00 0.00 5.28
97 98 4.215399 CACACATGTATCAAGTTTCCGGTT 59.785 41.667 0.00 0.00 0.00 4.44
98 99 5.410132 CACACATGTATCAAGTTTCCGGTTA 59.590 40.000 0.00 0.00 0.00 2.85
99 100 5.998981 ACACATGTATCAAGTTTCCGGTTAA 59.001 36.000 0.00 0.00 0.00 2.01
100 101 6.657541 ACACATGTATCAAGTTTCCGGTTAAT 59.342 34.615 0.00 0.00 0.00 1.40
101 102 7.825270 ACACATGTATCAAGTTTCCGGTTAATA 59.175 33.333 0.00 0.00 0.00 0.98
102 103 8.120465 CACATGTATCAAGTTTCCGGTTAATAC 58.880 37.037 0.00 0.00 0.00 1.89
103 104 7.825270 ACATGTATCAAGTTTCCGGTTAATACA 59.175 33.333 0.00 0.88 34.10 2.29
104 105 8.670135 CATGTATCAAGTTTCCGGTTAATACAA 58.330 33.333 0.00 0.00 33.52 2.41
105 106 8.795842 TGTATCAAGTTTCCGGTTAATACAAT 57.204 30.769 0.00 0.00 0.00 2.71
107 108 9.712359 GTATCAAGTTTCCGGTTAATACAATTC 57.288 33.333 0.00 0.00 0.00 2.17
108 109 7.989416 TCAAGTTTCCGGTTAATACAATTCT 57.011 32.000 0.00 0.00 0.00 2.40
109 110 9.675464 ATCAAGTTTCCGGTTAATACAATTCTA 57.325 29.630 0.00 0.00 0.00 2.10
110 111 9.158233 TCAAGTTTCCGGTTAATACAATTCTAG 57.842 33.333 0.00 0.00 0.00 2.43
111 112 7.549615 AGTTTCCGGTTAATACAATTCTAGC 57.450 36.000 0.00 0.00 0.00 3.42
113 114 7.773690 AGTTTCCGGTTAATACAATTCTAGCAT 59.226 33.333 0.00 0.00 0.00 3.79
114 115 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
116 117 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
118 119 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
185 186 8.701643 ATTATTACCTCTAGGGCATATTTCCT 57.298 34.615 0.20 0.00 40.27 3.36
186 187 8.520119 TTATTACCTCTAGGGCATATTTCCTT 57.480 34.615 0.20 0.00 40.27 3.36
187 188 4.984146 ACCTCTAGGGCATATTTCCTTC 57.016 45.455 0.20 0.00 40.27 3.46
188 189 4.307259 ACCTCTAGGGCATATTTCCTTCA 58.693 43.478 0.20 0.00 40.27 3.02
189 190 4.726825 ACCTCTAGGGCATATTTCCTTCAA 59.273 41.667 0.20 0.00 40.27 2.69
190 191 5.373854 ACCTCTAGGGCATATTTCCTTCAAT 59.626 40.000 0.20 0.00 40.27 2.57
191 192 6.126068 ACCTCTAGGGCATATTTCCTTCAATT 60.126 38.462 0.20 0.00 40.27 2.32
192 193 6.779539 CCTCTAGGGCATATTTCCTTCAATTT 59.220 38.462 0.00 0.00 34.75 1.82
193 194 7.040132 CCTCTAGGGCATATTTCCTTCAATTTC 60.040 40.741 0.00 0.00 34.75 2.17
194 195 5.520376 AGGGCATATTTCCTTCAATTTCG 57.480 39.130 0.00 0.00 0.00 3.46
195 196 4.956075 AGGGCATATTTCCTTCAATTTCGT 59.044 37.500 0.00 0.00 0.00 3.85
197 198 5.163561 GGGCATATTTCCTTCAATTTCGTCA 60.164 40.000 0.00 0.00 0.00 4.35
198 199 6.329496 GGCATATTTCCTTCAATTTCGTCAA 58.671 36.000 0.00 0.00 0.00 3.18
199 200 6.980397 GGCATATTTCCTTCAATTTCGTCAAT 59.020 34.615 0.00 0.00 0.00 2.57
200 201 7.043192 GGCATATTTCCTTCAATTTCGTCAATG 60.043 37.037 0.00 0.00 0.00 2.82
201 202 7.489113 GCATATTTCCTTCAATTTCGTCAATGT 59.511 33.333 0.00 0.00 0.00 2.71
203 204 7.642071 ATTTCCTTCAATTTCGTCAATGTTG 57.358 32.000 0.00 0.00 0.00 3.33
204 205 4.545610 TCCTTCAATTTCGTCAATGTTGC 58.454 39.130 0.00 0.00 0.00 4.17
205 206 3.361644 CCTTCAATTTCGTCAATGTTGCG 59.638 43.478 4.11 4.11 0.00 4.85
206 207 2.927429 TCAATTTCGTCAATGTTGCGG 58.073 42.857 8.77 0.00 0.00 5.69
207 208 1.386412 CAATTTCGTCAATGTTGCGGC 59.614 47.619 0.00 0.00 0.00 6.53
208 209 0.454285 ATTTCGTCAATGTTGCGGCG 60.454 50.000 0.51 0.51 0.00 6.46
209 210 2.450960 TTTCGTCAATGTTGCGGCGG 62.451 55.000 9.78 0.00 0.00 6.13
213 214 4.114997 CAATGTTGCGGCGGGGAC 62.115 66.667 9.78 0.00 0.00 4.46
227 228 2.340443 GGACGGCGAGATCCCATC 59.660 66.667 16.62 0.00 0.00 3.51
229 230 2.518587 ACGGCGAGATCCCATCGA 60.519 61.111 16.62 0.00 42.76 3.59
230 231 2.256764 CGGCGAGATCCCATCGAG 59.743 66.667 0.00 0.00 42.76 4.04
232 233 2.569354 GGCGAGATCCCATCGAGCT 61.569 63.158 7.00 0.00 42.76 4.09
236 237 3.529948 AGATCCCATCGAGCTCTGT 57.470 52.632 12.85 0.00 28.47 3.41
238 239 1.133513 AGATCCCATCGAGCTCTGTCT 60.134 52.381 12.85 0.82 28.47 3.41
239 240 2.107378 AGATCCCATCGAGCTCTGTCTA 59.893 50.000 12.85 0.00 28.47 2.59
240 241 1.974265 TCCCATCGAGCTCTGTCTAG 58.026 55.000 12.85 0.00 0.00 2.43
241 242 0.958091 CCCATCGAGCTCTGTCTAGG 59.042 60.000 12.85 4.98 0.00 3.02
243 244 1.686355 CATCGAGCTCTGTCTAGGGT 58.314 55.000 12.85 0.00 0.00 4.34
244 245 1.606668 CATCGAGCTCTGTCTAGGGTC 59.393 57.143 12.85 0.00 0.00 4.46
245 246 2.018544 CGAGCTCTGTCTAGGGTCG 58.981 63.158 12.85 3.72 42.69 4.79
246 247 1.731093 GAGCTCTGTCTAGGGTCGC 59.269 63.158 6.43 0.00 0.00 5.19
247 248 2.054140 GAGCTCTGTCTAGGGTCGCG 62.054 65.000 6.43 0.00 0.00 5.87
248 249 2.409651 CTCTGTCTAGGGTCGCGC 59.590 66.667 0.00 0.00 0.00 6.86
249 250 3.127352 CTCTGTCTAGGGTCGCGCC 62.127 68.421 0.00 6.06 0.00 6.53
250 251 3.141488 CTGTCTAGGGTCGCGCCT 61.141 66.667 17.07 13.90 37.43 5.52
253 254 2.044252 TCTAGGGTCGCGCCTTCT 60.044 61.111 10.66 7.01 37.43 2.85
254 255 2.119655 TCTAGGGTCGCGCCTTCTC 61.120 63.158 10.66 0.00 37.43 2.87
256 257 3.949885 TAGGGTCGCGCCTTCTCCA 62.950 63.158 10.66 0.00 37.43 3.86
261 262 4.394712 CGCGCCTTCTCCACCCTT 62.395 66.667 0.00 0.00 0.00 3.95
264 265 1.374947 CGCCTTCTCCACCCTTGAA 59.625 57.895 0.00 0.00 0.00 2.69
265 266 0.955919 CGCCTTCTCCACCCTTGAAC 60.956 60.000 0.00 0.00 0.00 3.18
266 267 0.402121 GCCTTCTCCACCCTTGAACT 59.598 55.000 0.00 0.00 0.00 3.01
268 269 1.699634 CCTTCTCCACCCTTGAACTCA 59.300 52.381 0.00 0.00 0.00 3.41
269 270 2.289945 CCTTCTCCACCCTTGAACTCAG 60.290 54.545 0.00 0.00 0.00 3.35
270 271 1.352083 TCTCCACCCTTGAACTCAGG 58.648 55.000 0.00 0.00 0.00 3.86
272 273 0.104672 TCCACCCTTGAACTCAGGGA 60.105 55.000 12.15 3.00 45.01 4.20
274 275 1.059913 CACCCTTGAACTCAGGGACT 58.940 55.000 12.15 0.00 45.01 3.85
277 278 1.352083 CCTTGAACTCAGGGACTCCA 58.648 55.000 1.67 0.00 45.01 3.86
278 279 1.002544 CCTTGAACTCAGGGACTCCAC 59.997 57.143 1.67 0.00 45.01 4.02
279 280 0.679505 TTGAACTCAGGGACTCCACG 59.320 55.000 0.00 0.00 34.60 4.94
280 281 1.185618 TGAACTCAGGGACTCCACGG 61.186 60.000 0.00 0.00 34.60 4.94
281 282 0.898789 GAACTCAGGGACTCCACGGA 60.899 60.000 0.00 0.00 34.60 4.69
282 283 0.252284 AACTCAGGGACTCCACGGAT 60.252 55.000 0.00 0.00 34.60 4.18
284 285 2.187946 CAGGGACTCCACGGATGC 59.812 66.667 0.00 0.00 34.60 3.91
285 286 3.083997 AGGGACTCCACGGATGCC 61.084 66.667 0.00 0.00 34.83 4.40
286 287 3.399181 GGGACTCCACGGATGCCA 61.399 66.667 0.00 0.00 0.00 4.92
287 288 2.668632 GGACTCCACGGATGCCAA 59.331 61.111 0.00 0.00 0.00 4.52
288 289 1.450312 GGACTCCACGGATGCCAAG 60.450 63.158 0.00 0.00 0.00 3.61
289 290 1.296715 GACTCCACGGATGCCAAGT 59.703 57.895 0.00 0.00 0.00 3.16
290 291 0.741221 GACTCCACGGATGCCAAGTC 60.741 60.000 0.00 0.00 0.00 3.01
291 292 1.811266 CTCCACGGATGCCAAGTCG 60.811 63.158 0.00 0.00 0.00 4.18
293 294 2.100631 CCACGGATGCCAAGTCGAC 61.101 63.158 7.70 7.70 0.00 4.20
295 296 3.554692 CGGATGCCAAGTCGACGC 61.555 66.667 10.46 8.48 0.00 5.19
296 297 3.554692 GGATGCCAAGTCGACGCG 61.555 66.667 10.46 3.53 0.00 6.01
298 299 3.071459 GATGCCAAGTCGACGCGTG 62.071 63.158 20.70 9.70 0.00 5.34
498 500 8.310406 TCTCAATATACTCATTAAATGTGGCG 57.690 34.615 0.00 0.00 0.00 5.69
517 523 7.607250 TGTGGCGAATATTAAAATGTTTCCTT 58.393 30.769 0.00 0.00 0.00 3.36
551 565 9.014297 CCTGATGTTAGAAAAACTTACAAGGAT 57.986 33.333 0.00 0.00 40.64 3.24
1240 4786 1.881973 ACTTCTACGGTAAGTGCACGA 59.118 47.619 12.01 0.00 35.87 4.35
1542 5120 6.474819 CATGCAACAAAATATATGGGCATG 57.525 37.500 21.77 21.77 45.37 4.06
1626 5267 1.102154 TTTTGTGTGTGGTCAGCTGG 58.898 50.000 15.13 0.00 0.00 4.85
1789 5436 0.179000 GCGTCCAGGAGGTGATCAAT 59.821 55.000 10.89 0.00 35.89 2.57
1873 5520 3.181445 TGAGTGGGCACAAGACTAACAAT 60.181 43.478 0.00 0.00 0.00 2.71
2191 5838 2.079925 GTTCACATGACAGAGAAGGCC 58.920 52.381 0.00 0.00 0.00 5.19
2311 5961 1.241165 TGCTGCAACCAAGATCTGTG 58.759 50.000 0.00 0.00 0.00 3.66
2399 6053 2.417787 GGATCTGTTGCTGGAATTTGGC 60.418 50.000 0.00 0.00 0.00 4.52
2402 6056 2.170166 CTGTTGCTGGAATTTGGCCTA 58.830 47.619 3.32 0.00 0.00 3.93
2403 6057 1.892474 TGTTGCTGGAATTTGGCCTAC 59.108 47.619 3.32 0.00 0.00 3.18
2474 6128 5.455326 CCTTTGTCCCATACTGCTAGCTTAT 60.455 44.000 17.23 9.72 0.00 1.73
2478 6132 6.075315 TGTCCCATACTGCTAGCTTATTAGA 58.925 40.000 17.23 8.45 0.00 2.10
2520 6179 2.817844 GAGGTTGTTTCCCCACATGTAC 59.182 50.000 0.00 0.00 0.00 2.90
2523 6182 2.879646 GTTGTTTCCCCACATGTACGAA 59.120 45.455 0.00 0.00 0.00 3.85
2669 6359 1.261480 AGGTCACACGAGAGCTGAAT 58.739 50.000 0.00 0.00 44.08 2.57
2702 6400 2.916502 AAGGTCACACGAACGCTGCA 62.917 55.000 0.00 0.00 32.39 4.41
2717 6415 3.730761 GCACCTTCGGCTGCTGTG 61.731 66.667 8.55 0.25 30.89 3.66
2736 6434 4.103103 GTTTGCTTCGCCTCCCGC 62.103 66.667 0.00 0.00 36.73 6.13
2786 6490 1.153549 CGCCTTCTCCTGTGCCTAC 60.154 63.158 0.00 0.00 0.00 3.18
2823 6527 1.621992 TCTCCAGAGAGACACACCAC 58.378 55.000 0.00 0.00 44.42 4.16
2846 6551 1.063972 CACTTGCAACACACCACCG 59.936 57.895 0.00 0.00 0.00 4.94
2847 6552 1.078072 ACTTGCAACACACCACCGA 60.078 52.632 0.00 0.00 0.00 4.69
2864 6572 0.600557 CGAGTTCCTGAGCACTGAGT 59.399 55.000 0.00 0.00 0.00 3.41
2890 6598 2.365617 GCTACGATCTTCTCCATCCCAA 59.634 50.000 0.00 0.00 0.00 4.12
2927 6636 3.388024 TGCAAGTAAGGATAGTAGGCCTG 59.612 47.826 17.99 0.00 34.00 4.85
2952 6661 5.182001 CGAAAACCCATCTCTTTGAGTCATT 59.818 40.000 0.00 0.00 0.00 2.57
2955 6664 7.693969 AAACCCATCTCTTTGAGTCATTTAG 57.306 36.000 0.00 0.00 0.00 1.85
2960 6669 6.418101 CATCTCTTTGAGTCATTTAGGGGAA 58.582 40.000 0.00 0.00 0.00 3.97
3049 6758 1.141881 CCGACGATCACTTCCCCAG 59.858 63.158 0.00 0.00 0.00 4.45
3072 6781 1.186917 TAACTTCTTCCCCGACGCCA 61.187 55.000 0.00 0.00 0.00 5.69
3139 6863 3.999001 ACTGCTCAGTGTGTGTTCATATG 59.001 43.478 1.15 0.00 40.75 1.78
3214 6940 5.698832 TGTTCTGTTGAAGTTCACAAGTTG 58.301 37.500 4.68 0.00 32.15 3.16
3252 6978 7.672239 ACCTACTCTCTATTAGATTGGATGACC 59.328 40.741 0.00 0.00 32.41 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.447374 TCGTTGATCAAAGATGGTTATGTTT 57.553 32.000 18.50 0.00 30.61 2.83
2 3 6.403636 GCTCGTTGATCAAAGATGGTTATGTT 60.404 38.462 21.83 0.00 0.00 2.71
4 5 5.295292 AGCTCGTTGATCAAAGATGGTTATG 59.705 40.000 21.83 11.16 0.00 1.90
8 9 3.340814 AGCTCGTTGATCAAAGATGGT 57.659 42.857 21.83 17.63 0.00 3.55
9 10 4.437239 ACTAGCTCGTTGATCAAAGATGG 58.563 43.478 21.83 14.18 0.00 3.51
10 11 5.105063 TGACTAGCTCGTTGATCAAAGATG 58.895 41.667 21.83 16.63 0.00 2.90
11 12 5.330455 TGACTAGCTCGTTGATCAAAGAT 57.670 39.130 21.83 12.82 0.00 2.40
12 13 4.783764 TGACTAGCTCGTTGATCAAAGA 57.216 40.909 20.62 20.62 0.00 2.52
13 14 4.926238 ACTTGACTAGCTCGTTGATCAAAG 59.074 41.667 10.35 12.64 0.00 2.77
14 15 4.883083 ACTTGACTAGCTCGTTGATCAAA 58.117 39.130 10.35 0.00 0.00 2.69
15 16 4.521130 ACTTGACTAGCTCGTTGATCAA 57.479 40.909 3.38 3.38 0.00 2.57
16 17 4.941873 TCTACTTGACTAGCTCGTTGATCA 59.058 41.667 0.00 0.00 0.00 2.92
18 19 4.336993 CCTCTACTTGACTAGCTCGTTGAT 59.663 45.833 0.00 0.00 0.00 2.57
19 20 3.690139 CCTCTACTTGACTAGCTCGTTGA 59.310 47.826 0.00 0.00 0.00 3.18
20 21 3.732471 GCCTCTACTTGACTAGCTCGTTG 60.732 52.174 0.00 0.00 0.00 4.10
21 22 2.424246 GCCTCTACTTGACTAGCTCGTT 59.576 50.000 0.00 0.00 0.00 3.85
22 23 2.018515 GCCTCTACTTGACTAGCTCGT 58.981 52.381 0.00 0.00 0.00 4.18
23 24 2.017782 TGCCTCTACTTGACTAGCTCG 58.982 52.381 0.00 0.00 0.00 5.03
24 25 4.825085 AGTATGCCTCTACTTGACTAGCTC 59.175 45.833 0.00 0.00 0.00 4.09
25 26 4.798882 AGTATGCCTCTACTTGACTAGCT 58.201 43.478 0.00 0.00 0.00 3.32
26 27 5.766174 ACTAGTATGCCTCTACTTGACTAGC 59.234 44.000 0.00 0.00 38.86 3.42
28 29 6.766944 GTCACTAGTATGCCTCTACTTGACTA 59.233 42.308 0.00 0.00 36.95 2.59
29 30 5.591067 GTCACTAGTATGCCTCTACTTGACT 59.409 44.000 0.00 0.00 36.95 3.41
30 31 5.357314 TGTCACTAGTATGCCTCTACTTGAC 59.643 44.000 0.00 11.98 38.64 3.18
31 32 5.357314 GTGTCACTAGTATGCCTCTACTTGA 59.643 44.000 0.00 0.18 33.96 3.02
32 33 5.358442 AGTGTCACTAGTATGCCTCTACTTG 59.642 44.000 2.87 0.00 33.96 3.16
33 34 5.511363 AGTGTCACTAGTATGCCTCTACTT 58.489 41.667 2.87 0.00 33.96 2.24
34 35 5.104277 AGAGTGTCACTAGTATGCCTCTACT 60.104 44.000 5.21 0.00 36.04 2.57
35 36 5.008217 CAGAGTGTCACTAGTATGCCTCTAC 59.992 48.000 5.21 0.00 0.00 2.59
36 37 5.126779 CAGAGTGTCACTAGTATGCCTCTA 58.873 45.833 5.21 0.00 0.00 2.43
38 39 3.697045 ACAGAGTGTCACTAGTATGCCTC 59.303 47.826 5.21 0.00 0.00 4.70
39 40 3.702792 ACAGAGTGTCACTAGTATGCCT 58.297 45.455 5.21 0.00 0.00 4.75
41 42 5.230942 ACAAACAGAGTGTCACTAGTATGC 58.769 41.667 5.21 0.00 0.00 3.14
42 43 6.682746 AGACAAACAGAGTGTCACTAGTATG 58.317 40.000 5.21 5.56 46.44 2.39
45 46 6.265649 ACATAGACAAACAGAGTGTCACTAGT 59.734 38.462 5.21 5.11 46.44 2.57
46 47 6.682746 ACATAGACAAACAGAGTGTCACTAG 58.317 40.000 5.21 4.44 46.44 2.57
47 48 6.650427 ACATAGACAAACAGAGTGTCACTA 57.350 37.500 5.21 0.00 46.44 2.74
48 49 5.537300 ACATAGACAAACAGAGTGTCACT 57.463 39.130 4.81 4.81 46.44 3.41
49 50 7.598869 TGAATACATAGACAAACAGAGTGTCAC 59.401 37.037 7.26 0.00 46.44 3.67
51 52 7.598869 TGTGAATACATAGACAAACAGAGTGTC 59.401 37.037 0.00 0.00 44.75 3.67
52 53 7.385205 GTGTGAATACATAGACAAACAGAGTGT 59.615 37.037 0.00 0.00 39.39 3.55
53 54 7.384932 TGTGTGAATACATAGACAAACAGAGTG 59.615 37.037 0.00 0.00 39.39 3.51
54 55 7.441836 TGTGTGAATACATAGACAAACAGAGT 58.558 34.615 0.00 0.00 39.39 3.24
55 56 7.889589 TGTGTGAATACATAGACAAACAGAG 57.110 36.000 0.00 0.00 39.39 3.35
56 57 7.877612 ACATGTGTGAATACATAGACAAACAGA 59.122 33.333 0.00 0.00 39.17 3.41
58 59 7.977789 ACATGTGTGAATACATAGACAAACA 57.022 32.000 0.00 0.00 39.17 2.83
60 61 9.883142 TGATACATGTGTGAATACATAGACAAA 57.117 29.630 9.11 0.00 39.17 2.83
61 62 9.883142 TTGATACATGTGTGAATACATAGACAA 57.117 29.630 9.11 0.00 39.17 3.18
62 63 9.533253 CTTGATACATGTGTGAATACATAGACA 57.467 33.333 9.11 0.00 39.17 3.41
67 68 8.677300 GGAAACTTGATACATGTGTGAATACAT 58.323 33.333 9.11 0.00 41.77 2.29
69 70 7.180079 CGGAAACTTGATACATGTGTGAATAC 58.820 38.462 9.11 0.00 0.00 1.89
70 71 6.315144 CCGGAAACTTGATACATGTGTGAATA 59.685 38.462 9.11 0.00 0.00 1.75
71 72 5.123820 CCGGAAACTTGATACATGTGTGAAT 59.876 40.000 9.11 0.00 0.00 2.57
72 73 4.454161 CCGGAAACTTGATACATGTGTGAA 59.546 41.667 9.11 0.70 0.00 3.18
73 74 4.000325 CCGGAAACTTGATACATGTGTGA 59.000 43.478 9.11 0.00 0.00 3.58
76 77 6.489127 TTAACCGGAAACTTGATACATGTG 57.511 37.500 9.46 0.00 0.00 3.21
77 78 7.825270 TGTATTAACCGGAAACTTGATACATGT 59.175 33.333 9.46 2.69 28.53 3.21
78 79 8.203937 TGTATTAACCGGAAACTTGATACATG 57.796 34.615 9.46 0.00 28.53 3.21
80 81 8.795842 ATTGTATTAACCGGAAACTTGATACA 57.204 30.769 9.46 11.96 30.33 2.29
81 82 9.712359 GAATTGTATTAACCGGAAACTTGATAC 57.288 33.333 9.46 9.36 0.00 2.24
83 84 8.575649 AGAATTGTATTAACCGGAAACTTGAT 57.424 30.769 9.46 0.00 0.00 2.57
84 85 7.989416 AGAATTGTATTAACCGGAAACTTGA 57.011 32.000 9.46 0.00 0.00 3.02
86 87 7.608761 TGCTAGAATTGTATTAACCGGAAACTT 59.391 33.333 9.46 0.00 0.00 2.66
87 88 7.107542 TGCTAGAATTGTATTAACCGGAAACT 58.892 34.615 9.46 0.00 0.00 2.66
88 89 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
90 91 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
91 92 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
92 93 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
159 160 9.799223 AGGAAATATGCCCTAGAGGTAATAATA 57.201 33.333 0.00 0.00 38.26 0.98
160 161 8.701643 AGGAAATATGCCCTAGAGGTAATAAT 57.298 34.615 0.00 0.00 38.26 1.28
162 163 7.737607 TGAAGGAAATATGCCCTAGAGGTAATA 59.262 37.037 0.00 0.00 38.26 0.98
163 164 6.562608 TGAAGGAAATATGCCCTAGAGGTAAT 59.437 38.462 0.00 0.00 38.26 1.89
164 165 5.908831 TGAAGGAAATATGCCCTAGAGGTAA 59.091 40.000 0.00 0.00 38.26 2.85
165 166 5.473273 TGAAGGAAATATGCCCTAGAGGTA 58.527 41.667 0.00 0.00 38.26 3.08
166 167 4.307259 TGAAGGAAATATGCCCTAGAGGT 58.693 43.478 0.00 0.00 38.26 3.85
167 168 4.982241 TGAAGGAAATATGCCCTAGAGG 57.018 45.455 0.00 0.00 39.47 3.69
168 169 7.308229 CGAAATTGAAGGAAATATGCCCTAGAG 60.308 40.741 0.00 0.00 31.36 2.43
170 171 6.263168 ACGAAATTGAAGGAAATATGCCCTAG 59.737 38.462 0.00 0.00 31.36 3.02
171 172 6.126409 ACGAAATTGAAGGAAATATGCCCTA 58.874 36.000 0.00 0.00 31.36 3.53
173 174 5.163561 TGACGAAATTGAAGGAAATATGCCC 60.164 40.000 0.00 0.00 0.00 5.36
174 175 5.890334 TGACGAAATTGAAGGAAATATGCC 58.110 37.500 0.00 0.00 0.00 4.40
177 178 9.357652 CAACATTGACGAAATTGAAGGAAATAT 57.642 29.630 0.00 0.00 0.00 1.28
179 180 6.146021 GCAACATTGACGAAATTGAAGGAAAT 59.854 34.615 0.00 0.00 0.00 2.17
180 181 5.461737 GCAACATTGACGAAATTGAAGGAAA 59.538 36.000 0.00 0.00 0.00 3.13
182 183 4.545610 GCAACATTGACGAAATTGAAGGA 58.454 39.130 0.00 0.00 0.00 3.36
183 184 3.361644 CGCAACATTGACGAAATTGAAGG 59.638 43.478 0.00 0.00 32.28 3.46
185 186 3.304257 CCGCAACATTGACGAAATTGAA 58.696 40.909 9.13 0.00 32.28 2.69
186 187 2.920227 GCCGCAACATTGACGAAATTGA 60.920 45.455 9.13 0.00 32.28 2.57
187 188 1.386412 GCCGCAACATTGACGAAATTG 59.614 47.619 9.13 0.00 32.28 2.32
188 189 1.696988 GCCGCAACATTGACGAAATT 58.303 45.000 9.13 0.00 32.28 1.82
189 190 0.454285 CGCCGCAACATTGACGAAAT 60.454 50.000 9.13 0.00 32.28 2.17
190 191 1.082431 CGCCGCAACATTGACGAAA 60.082 52.632 9.13 0.00 32.28 3.46
191 192 2.553770 CGCCGCAACATTGACGAA 59.446 55.556 9.13 0.00 32.28 3.85
192 193 3.418913 CCGCCGCAACATTGACGA 61.419 61.111 9.13 0.00 32.28 4.20
193 194 4.459331 CCCGCCGCAACATTGACG 62.459 66.667 0.00 0.00 0.00 4.35
194 195 4.114997 CCCCGCCGCAACATTGAC 62.115 66.667 0.00 0.00 0.00 3.18
195 196 4.337177 TCCCCGCCGCAACATTGA 62.337 61.111 0.00 0.00 0.00 2.57
213 214 2.256764 CTCGATGGGATCTCGCCG 59.743 66.667 0.53 0.53 36.11 6.46
215 216 1.080839 GAGCTCGATGGGATCTCGC 60.081 63.158 0.00 0.00 36.11 5.03
217 218 1.269448 GACAGAGCTCGATGGGATCTC 59.731 57.143 8.37 0.00 38.02 2.75
219 220 1.327303 AGACAGAGCTCGATGGGATC 58.673 55.000 8.37 0.00 0.00 3.36
220 221 2.513753 CTAGACAGAGCTCGATGGGAT 58.486 52.381 8.37 0.00 0.00 3.85
221 222 1.477740 CCTAGACAGAGCTCGATGGGA 60.478 57.143 8.37 0.00 0.00 4.37
222 223 0.958091 CCTAGACAGAGCTCGATGGG 59.042 60.000 8.37 3.43 0.00 4.00
224 225 1.606668 GACCCTAGACAGAGCTCGATG 59.393 57.143 8.37 4.61 0.00 3.84
225 226 1.812324 CGACCCTAGACAGAGCTCGAT 60.812 57.143 8.37 0.00 0.00 3.59
226 227 0.462225 CGACCCTAGACAGAGCTCGA 60.462 60.000 8.37 0.00 0.00 4.04
227 228 2.018544 CGACCCTAGACAGAGCTCG 58.981 63.158 8.37 6.04 0.00 5.03
229 230 2.115911 CGCGACCCTAGACAGAGCT 61.116 63.158 0.00 0.00 0.00 4.09
230 231 2.409651 CGCGACCCTAGACAGAGC 59.590 66.667 0.00 0.00 0.00 4.09
232 233 3.138798 GGCGCGACCCTAGACAGA 61.139 66.667 12.10 0.00 0.00 3.41
233 234 2.615262 GAAGGCGCGACCCTAGACAG 62.615 65.000 9.25 0.00 40.58 3.51
234 235 2.678934 AAGGCGCGACCCTAGACA 60.679 61.111 9.25 0.00 40.58 3.41
235 236 2.104530 GAAGGCGCGACCCTAGAC 59.895 66.667 9.25 0.00 40.58 2.59
236 237 2.044252 AGAAGGCGCGACCCTAGA 60.044 61.111 9.25 0.00 40.58 2.43
238 239 3.145551 GGAGAAGGCGCGACCCTA 61.146 66.667 9.25 0.00 40.58 3.53
244 245 4.394712 AAGGGTGGAGAAGGCGCG 62.395 66.667 0.00 0.00 0.00 6.86
245 246 2.747855 CAAGGGTGGAGAAGGCGC 60.748 66.667 0.00 0.00 0.00 6.53
246 247 0.955919 GTTCAAGGGTGGAGAAGGCG 60.956 60.000 0.00 0.00 0.00 5.52
247 248 0.402121 AGTTCAAGGGTGGAGAAGGC 59.598 55.000 0.00 0.00 0.00 4.35
248 249 1.699634 TGAGTTCAAGGGTGGAGAAGG 59.300 52.381 0.00 0.00 0.00 3.46
249 250 2.289945 CCTGAGTTCAAGGGTGGAGAAG 60.290 54.545 0.00 0.00 0.00 2.85
250 251 1.699634 CCTGAGTTCAAGGGTGGAGAA 59.300 52.381 0.00 0.00 0.00 2.87
253 254 0.104672 TCCCTGAGTTCAAGGGTGGA 60.105 55.000 8.33 0.00 43.21 4.02
254 255 0.036875 GTCCCTGAGTTCAAGGGTGG 59.963 60.000 8.33 0.00 43.21 4.61
256 257 1.353091 GAGTCCCTGAGTTCAAGGGT 58.647 55.000 8.33 0.00 43.21 4.34
257 258 0.615850 GGAGTCCCTGAGTTCAAGGG 59.384 60.000 0.00 1.82 44.06 3.95
259 260 1.337260 CGTGGAGTCCCTGAGTTCAAG 60.337 57.143 6.74 0.00 0.00 3.02
260 261 0.679505 CGTGGAGTCCCTGAGTTCAA 59.320 55.000 6.74 0.00 0.00 2.69
261 262 1.185618 CCGTGGAGTCCCTGAGTTCA 61.186 60.000 6.74 0.00 0.00 3.18
264 265 0.972983 CATCCGTGGAGTCCCTGAGT 60.973 60.000 6.74 0.00 0.00 3.41
265 266 1.819229 CATCCGTGGAGTCCCTGAG 59.181 63.158 6.74 0.00 0.00 3.35
266 267 2.359169 GCATCCGTGGAGTCCCTGA 61.359 63.158 6.74 0.46 0.00 3.86
268 269 3.083997 GGCATCCGTGGAGTCCCT 61.084 66.667 6.74 0.00 0.00 4.20
269 270 2.876368 CTTGGCATCCGTGGAGTCCC 62.876 65.000 6.74 0.00 0.00 4.46
270 271 1.450312 CTTGGCATCCGTGGAGTCC 60.450 63.158 0.73 0.73 0.00 3.85
272 273 1.296715 GACTTGGCATCCGTGGAGT 59.703 57.895 0.00 0.00 0.00 3.85
274 275 2.264480 CGACTTGGCATCCGTGGA 59.736 61.111 0.00 0.00 0.00 4.02
277 278 2.126071 CGTCGACTTGGCATCCGT 60.126 61.111 14.70 0.00 0.00 4.69
278 279 3.554692 GCGTCGACTTGGCATCCG 61.555 66.667 14.70 0.00 0.00 4.18
279 280 3.554692 CGCGTCGACTTGGCATCC 61.555 66.667 14.70 0.00 0.00 3.51
280 281 2.809601 ACGCGTCGACTTGGCATC 60.810 61.111 14.70 0.00 0.00 3.91
281 282 3.112075 CACGCGTCGACTTGGCAT 61.112 61.111 9.86 0.00 0.00 4.40
295 296 1.473257 CCATATATCATCCCCGCCACG 60.473 57.143 0.00 0.00 0.00 4.94
296 297 1.559682 ACCATATATCATCCCCGCCAC 59.440 52.381 0.00 0.00 0.00 5.01
298 299 1.837439 TGACCATATATCATCCCCGCC 59.163 52.381 0.00 0.00 0.00 6.13
299 300 3.733337 GATGACCATATATCATCCCCGC 58.267 50.000 14.33 0.00 44.51 6.13
335 337 4.507756 ACCGACTAAAAACTTACAACGACC 59.492 41.667 0.00 0.00 0.00 4.79
551 565 6.854496 ATAGTCAGCTTTGAAAACGTGTTA 57.146 33.333 0.00 0.00 0.00 2.41
1240 4786 1.337703 TGAAGTACACCTACGTGCGTT 59.662 47.619 1.66 0.00 44.40 4.84
1552 5130 6.080648 TGTGTGATATATGGTAAGGACGAC 57.919 41.667 0.00 0.00 0.00 4.34
1618 5259 2.117941 GACGTTTGGTGCCAGCTGAC 62.118 60.000 17.39 3.38 0.00 3.51
1626 5267 1.569479 GCTGAGGAGACGTTTGGTGC 61.569 60.000 0.00 0.00 0.00 5.01
1789 5436 1.511305 GATCGTCTTGGCACCGAGA 59.489 57.895 2.24 2.24 33.66 4.04
1873 5520 3.531538 GAATTGGTCATAGTCCGCAGAA 58.468 45.455 0.00 0.00 0.00 3.02
2191 5838 3.384668 CCCATTAGCGATGACACTGTAG 58.615 50.000 4.88 0.00 38.03 2.74
2311 5961 0.736325 TTCCAAGAAGCTAGCGCGTC 60.736 55.000 9.55 8.47 43.71 5.19
2520 6179 3.486708 CGTCTCTCCTCTTCTCATGTTCG 60.487 52.174 0.00 0.00 0.00 3.95
2523 6182 3.080300 ACGTCTCTCCTCTTCTCATGT 57.920 47.619 0.00 0.00 0.00 3.21
2612 6302 5.539582 TGCGTCGCTAAAATTTAGACAAT 57.460 34.783 19.50 0.00 32.57 2.71
2681 6372 0.655733 CAGCGTTCGTGTGACCTTTT 59.344 50.000 0.00 0.00 0.00 2.27
2684 6375 2.661866 GCAGCGTTCGTGTGACCT 60.662 61.111 0.00 0.00 0.00 3.85
2736 6434 3.119245 TGACGGGAGATAAAACGAAGAGG 60.119 47.826 0.00 0.00 0.00 3.69
2823 6527 1.067985 TGGTGTGTTGCAAGTGTTGTG 60.068 47.619 0.00 0.00 0.00 3.33
2846 6551 2.829741 AACTCAGTGCTCAGGAACTC 57.170 50.000 0.00 0.00 34.60 3.01
2847 6552 3.006323 CAGTAACTCAGTGCTCAGGAACT 59.994 47.826 0.00 0.00 43.88 3.01
2864 6572 4.278669 GGATGGAGAAGATCGTAGCAGTAA 59.721 45.833 0.00 0.00 0.00 2.24
2912 6621 1.789523 TTCGCAGGCCTACTATCCTT 58.210 50.000 3.98 0.00 0.00 3.36
2927 6636 2.814336 ACTCAAAGAGATGGGTTTTCGC 59.186 45.455 0.31 0.00 26.31 4.70
2952 6661 3.631250 GCTCATCACCATTTTCCCCTAA 58.369 45.455 0.00 0.00 0.00 2.69
2955 6664 0.740737 CGCTCATCACCATTTTCCCC 59.259 55.000 0.00 0.00 0.00 4.81
2960 6669 2.030007 CCACAAACGCTCATCACCATTT 60.030 45.455 0.00 0.00 0.00 2.32
3049 6758 1.568606 GTCGGGGAAGAAGTTATCGC 58.431 55.000 0.00 0.00 0.00 4.58
3072 6781 2.878406 CCATGTTGTCGAAGAGGTTGTT 59.122 45.455 0.00 0.00 36.95 2.83
3154 6878 4.464112 GCTAAACAAGAAACTTAGCACGG 58.536 43.478 7.91 0.00 44.48 4.94
3214 6940 7.938140 ATAGAGAGTAGGTGAATAGCATCTC 57.062 40.000 0.00 0.00 39.20 2.75


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

AutoCloner maintained by Alex Coulton.