Multiple sequence alignment - TraesCS5D01G350300

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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 TraesCS5D01G350300 chr5D 100.000 2453 0 0 1 2453 434601208 434598756 0.000000e+00 4530
1 TraesCS5D01G350300 chr5D 85.095 946 116 11 642 1572 434567337 434566402 0.000000e+00 942
2 TraesCS5D01G350300 chr5D 85.498 924 105 9 660 1572 434688364 434689269 0.000000e+00 937
3 TraesCS5D01G350300 chr5D 83.621 812 81 21 687 1467 434548965 434548175 0.000000e+00 715
4 TraesCS5D01G350300 chr5D 78.652 890 125 31 540 1400 434479864 434480717 4.640000e-147 531
5 TraesCS5D01G350300 chr5D 82.671 554 62 20 748 1288 434666564 434667096 6.180000e-126 460
6 TraesCS5D01G350300 chr5D 76.087 782 138 35 729 1476 434657441 434656675 1.790000e-96 363
7 TraesCS5D01G350300 chr5D 87.329 292 17 8 3 276 434665603 434665892 1.420000e-82 316
8 TraesCS5D01G350300 chr5D 89.583 240 19 3 2149 2386 434690395 434690630 1.430000e-77 300
9 TraesCS5D01G350300 chr5D 80.364 275 36 13 1590 1849 434566135 434565864 2.490000e-45 193
10 TraesCS5D01G350300 chr5D 87.879 165 12 4 245 402 434665895 434666058 1.160000e-43 187
11 TraesCS5D01G350300 chr5D 78.305 295 33 18 1576 1849 434689520 434689804 7.020000e-36 161
12 TraesCS5D01G350300 chr5D 80.723 166 21 7 1323 1479 434713578 434713415 4.280000e-23 119
13 TraesCS5D01G350300 chr5D 100.000 53 0 0 2109 2161 434599059 434599007 5.580000e-17 99
14 TraesCS5D01G350300 chr5D 100.000 53 0 0 2150 2202 434599100 434599048 5.580000e-17 99
15 TraesCS5D01G350300 chr5A 93.412 850 49 3 727 1572 548658119 548657273 0.000000e+00 1253
16 TraesCS5D01G350300 chr5A 82.395 835 107 23 653 1464 548503571 548504388 0.000000e+00 691
17 TraesCS5D01G350300 chr5A 89.098 266 29 0 1844 2109 548504718 548504983 5.060000e-87 331
18 TraesCS5D01G350300 chr5B 86.907 1054 128 6 531 1578 527769775 527768726 0.000000e+00 1173
19 TraesCS5D01G350300 chr5B 85.564 949 107 11 651 1578 527601659 527600720 0.000000e+00 966
20 TraesCS5D01G350300 chr5B 84.339 862 97 17 738 1575 527492249 527491402 0.000000e+00 809
21 TraesCS5D01G350300 chr5B 89.773 264 27 0 1844 2107 527255842 527256105 3.020000e-89 339
22 TraesCS5D01G350300 chr5B 85.185 324 42 4 1850 2170 527764341 527764021 6.540000e-86 327
23 TraesCS5D01G350300 chr5B 84.561 285 38 5 1845 2129 527599888 527599610 6.680000e-71 278
24 TraesCS5D01G350300 chr5B 87.083 240 24 4 2149 2386 527764083 527763849 5.200000e-67 265
25 TraesCS5D01G350300 chr5B 87.383 214 16 4 574 776 527784173 527783960 4.080000e-58 235
26 TraesCS5D01G350300 chr5B 80.364 275 36 11 1590 1849 527600459 527600188 2.490000e-45 193
27 TraesCS5D01G350300 chr5B 93.137 102 7 0 35 136 527492937 527492836 1.520000e-32 150
28 TraesCS5D01G350300 chr5B 89.744 117 10 2 2271 2386 527599524 527599409 5.470000e-32 148
29 TraesCS5D01G350300 chr7D 87.845 181 18 4 2208 2386 160569990 160569812 2.470000e-50 209
30 TraesCS5D01G350300 chr7D 92.784 97 7 0 674 770 454416219 454416315 9.150000e-30 141
31 TraesCS5D01G350300 chr7A 87.845 181 18 4 2208 2386 161725009 161724831 2.470000e-50 209
32 TraesCS5D01G350300 chr3D 94.845 97 5 0 674 770 536960143 536960239 4.220000e-33 152
33 TraesCS5D01G350300 chr3D 84.314 102 15 1 2278 2378 554178268 554178167 5.580000e-17 99
34 TraesCS5D01G350300 chr3D 84.314 102 15 1 2278 2378 554224475 554224374 5.580000e-17 99
35 TraesCS5D01G350300 chr4B 94.737 95 5 0 676 770 508608047 508607953 5.470000e-32 148
36 TraesCS5D01G350300 chr6A 93.814 97 6 0 674 770 483061844 483061748 1.970000e-31 147


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 TraesCS5D01G350300 chr5D 434598756 434601208 2452 True 1576.00 4530 100.000000 1 2453 3 chr5D.!!$R5 2452
1 TraesCS5D01G350300 chr5D 434548175 434548965 790 True 715.00 715 83.621000 687 1467 1 chr5D.!!$R1 780
2 TraesCS5D01G350300 chr5D 434565864 434567337 1473 True 567.50 942 82.729500 642 1849 2 chr5D.!!$R4 1207
3 TraesCS5D01G350300 chr5D 434479864 434480717 853 False 531.00 531 78.652000 540 1400 1 chr5D.!!$F1 860
4 TraesCS5D01G350300 chr5D 434688364 434690630 2266 False 466.00 937 84.462000 660 2386 3 chr5D.!!$F3 1726
5 TraesCS5D01G350300 chr5D 434656675 434657441 766 True 363.00 363 76.087000 729 1476 1 chr5D.!!$R2 747
6 TraesCS5D01G350300 chr5D 434665603 434667096 1493 False 321.00 460 85.959667 3 1288 3 chr5D.!!$F2 1285
7 TraesCS5D01G350300 chr5A 548657273 548658119 846 True 1253.00 1253 93.412000 727 1572 1 chr5A.!!$R1 845
8 TraesCS5D01G350300 chr5A 548503571 548504983 1412 False 511.00 691 85.746500 653 2109 2 chr5A.!!$F1 1456
9 TraesCS5D01G350300 chr5B 527768726 527769775 1049 True 1173.00 1173 86.907000 531 1578 1 chr5B.!!$R1 1047
10 TraesCS5D01G350300 chr5B 527491402 527492937 1535 True 479.50 809 88.738000 35 1575 2 chr5B.!!$R3 1540
11 TraesCS5D01G350300 chr5B 527599409 527601659 2250 True 396.25 966 85.058250 651 2386 4 chr5B.!!$R4 1735

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
151 152 0.109873 GTGAGAAGCTGTGCATGCAC 60.11 55.0 38.0 38.0 46.33 4.57 F
180 190 0.250038 TGTCTCAGTGTGGCAAGCTC 60.25 55.0 0.0 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1977 0.179468 GCTGGTTAATCCCTACGCCA 59.821 55.0 0.0 0.0 34.77 5.69 R
1799 2685 0.252197 GGGTCACCGAGGCAGTAATT 59.748 55.0 0.0 0.0 0.00 1.40 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
25 26 3.210227 TCTTGCGTTGATCTTTTGACCA 58.790 40.909 0.00 0.00 0.00 4.02
29 30 3.003275 TGCGTTGATCTTTTGACCACTTC 59.997 43.478 0.00 0.00 0.00 3.01
136 137 5.878406 ACCTGGATTAATCTGTAGGTGAG 57.122 43.478 25.22 10.46 35.71 3.51
138 139 5.964477 ACCTGGATTAATCTGTAGGTGAGAA 59.036 40.000 25.22 0.35 35.71 2.87
140 141 5.918608 TGGATTAATCTGTAGGTGAGAAGC 58.081 41.667 14.95 0.00 0.00 3.86
141 142 5.663106 TGGATTAATCTGTAGGTGAGAAGCT 59.337 40.000 14.95 0.00 0.00 3.74
143 144 6.407525 GGATTAATCTGTAGGTGAGAAGCTGT 60.408 42.308 14.95 0.00 0.00 4.40
145 146 1.273606 TCTGTAGGTGAGAAGCTGTGC 59.726 52.381 0.00 0.00 0.00 4.57
146 147 1.001293 CTGTAGGTGAGAAGCTGTGCA 59.999 52.381 0.00 0.00 0.00 4.57
149 150 0.959372 AGGTGAGAAGCTGTGCATGC 60.959 55.000 11.82 11.82 0.00 4.06
151 152 0.109873 GTGAGAAGCTGTGCATGCAC 60.110 55.000 38.00 38.00 46.33 4.57
152 153 1.239296 TGAGAAGCTGTGCATGCACC 61.239 55.000 40.01 28.35 45.63 5.01
153 154 0.959372 GAGAAGCTGTGCATGCACCT 60.959 55.000 40.01 30.64 45.63 4.00
154 155 1.211969 GAAGCTGTGCATGCACCTG 59.788 57.895 40.01 32.67 45.63 4.00
156 157 1.521450 AAGCTGTGCATGCACCTGTC 61.521 55.000 40.01 27.04 45.63 3.51
157 158 1.970114 GCTGTGCATGCACCTGTCT 60.970 57.895 40.01 0.00 45.63 3.41
158 159 1.873863 CTGTGCATGCACCTGTCTG 59.126 57.895 40.01 22.07 45.63 3.51
159 160 1.583495 CTGTGCATGCACCTGTCTGG 61.583 60.000 40.01 20.50 45.63 3.86
180 190 0.250038 TGTCTCAGTGTGGCAAGCTC 60.250 55.000 0.00 0.00 0.00 4.09
238 255 2.028930 GGTACTGCTACTGCTGTTGTCT 60.029 50.000 0.09 0.00 46.76 3.41
243 260 2.564504 TGCTACTGCTGTTGTCTCTGAT 59.435 45.455 0.09 0.00 40.48 2.90
246 263 4.803088 GCTACTGCTGTTGTCTCTGATAAG 59.197 45.833 0.09 0.00 36.03 1.73
280 331 5.183228 GTTATCTTGGCCTTACACTTGCTA 58.817 41.667 3.32 0.00 0.00 3.49
300 351 4.333649 GCTATTAGCACTGCATGTTCTGAA 59.666 41.667 10.83 0.00 41.89 3.02
313 364 1.743958 GTTCTGAAGCTCATGCATGCT 59.256 47.619 22.25 13.77 42.74 3.79
314 365 2.941064 GTTCTGAAGCTCATGCATGCTA 59.059 45.455 22.25 4.78 42.74 3.49
343 394 2.028567 GCCCATGTAGAGTAGAGGATGC 60.029 54.545 0.00 0.00 0.00 3.91
349 406 4.068599 TGTAGAGTAGAGGATGCATCTCG 58.931 47.826 25.28 0.00 36.45 4.04
356 413 2.230025 AGAGGATGCATCTCGGATTACG 59.770 50.000 25.28 0.00 46.11 3.18
357 414 1.964223 AGGATGCATCTCGGATTACGT 59.036 47.619 25.28 0.00 44.69 3.57
374 431 3.603158 ACGTATGTCATAGGCACAACA 57.397 42.857 11.58 0.00 0.00 3.33
378 435 4.201812 CGTATGTCATAGGCACAACAAAGG 60.202 45.833 0.00 0.00 0.00 3.11
384 442 2.689083 GGCACAACAAAGGTTTGCC 58.311 52.632 13.72 13.72 45.17 4.52
387 445 2.079925 GCACAACAAAGGTTTGCCAAA 58.920 42.857 2.27 0.00 41.79 3.28
402 460 8.850156 AGGTTTGCCAAATGATATAGTATGAAC 58.150 33.333 0.00 0.00 37.19 3.18
404 462 9.669353 GTTTGCCAAATGATATAGTATGAACAG 57.331 33.333 0.00 0.00 0.00 3.16
407 465 7.661437 TGCCAAATGATATAGTATGAACAGGTC 59.339 37.037 0.00 0.00 0.00 3.85
468 859 0.615331 AGCTAGGTGTGTGGACCATG 59.385 55.000 0.00 0.00 38.63 3.66
478 869 3.843619 TGTGTGGACCATGGAAGAGATTA 59.156 43.478 21.47 0.00 0.00 1.75
479 870 4.192317 GTGTGGACCATGGAAGAGATTAC 58.808 47.826 21.47 6.25 0.00 1.89
517 909 6.553953 TGAGCAACTCCCACACTAAATATA 57.446 37.500 0.00 0.00 0.00 0.86
520 912 7.071196 TGAGCAACTCCCACACTAAATATATCT 59.929 37.037 0.00 0.00 0.00 1.98
521 913 7.445945 AGCAACTCCCACACTAAATATATCTC 58.554 38.462 0.00 0.00 0.00 2.75
522 914 6.651225 GCAACTCCCACACTAAATATATCTCC 59.349 42.308 0.00 0.00 0.00 3.71
523 915 7.689313 GCAACTCCCACACTAAATATATCTCCA 60.689 40.741 0.00 0.00 0.00 3.86
526 918 7.958583 ACTCCCACACTAAATATATCTCCATCT 59.041 37.037 0.00 0.00 0.00 2.90
528 920 7.955750 TCCCACACTAAATATATCTCCATCTGA 59.044 37.037 0.00 0.00 0.00 3.27
529 921 8.037758 CCCACACTAAATATATCTCCATCTGAC 58.962 40.741 0.00 0.00 0.00 3.51
538 943 4.862902 ATCTCCATCTGACTCGTAATGG 57.137 45.455 0.00 0.00 40.05 3.16
640 1054 4.725490 TGGTCTCCATATCAGTCGTATGA 58.275 43.478 0.00 0.00 32.52 2.15
835 1279 1.912763 GGCCATGTCCCTTGCCAAA 60.913 57.895 0.00 0.00 43.46 3.28
898 1359 3.839323 TCTCCCTCGCCCCTATAAATA 57.161 47.619 0.00 0.00 0.00 1.40
1082 1608 1.219393 GGAAGAGGCTCACCCGAAG 59.781 63.158 18.26 0.00 39.21 3.79
1290 1848 0.389166 GCGATGATGGGAGGATCGTC 60.389 60.000 6.88 6.88 40.85 4.20
1384 1942 1.162800 GGCATTCATGAGCTCCGTCC 61.163 60.000 12.15 0.00 0.00 4.79
1416 1977 2.166254 CAGTTTTGAAGGCAGTGTGGTT 59.834 45.455 0.00 0.00 0.00 3.67
1426 1993 1.839747 AGTGTGGTTGGCGTAGGGA 60.840 57.895 0.00 0.00 0.00 4.20
1486 2060 0.532417 CATGCAGCTGTAGAGGAGCC 60.532 60.000 16.64 0.00 37.12 4.70
1487 2061 1.694133 ATGCAGCTGTAGAGGAGCCC 61.694 60.000 16.64 0.00 37.12 5.19
1488 2062 2.063378 GCAGCTGTAGAGGAGCCCT 61.063 63.158 16.64 0.00 37.12 5.19
1490 2064 1.036707 CAGCTGTAGAGGAGCCCTAC 58.963 60.000 5.25 7.71 37.12 3.18
1492 2066 1.133606 AGCTGTAGAGGAGCCCTACTC 60.134 57.143 0.00 0.00 45.45 2.59
1498 2072 1.853963 GAGGAGCCCTACTCTGTTCA 58.146 55.000 0.14 0.00 45.48 3.18
1499 2073 2.393646 GAGGAGCCCTACTCTGTTCAT 58.606 52.381 0.14 0.00 45.48 2.57
1513 2087 4.005650 TCTGTTCATCTCTGTTCATTGCC 58.994 43.478 0.00 0.00 0.00 4.52
1552 2130 6.091441 CAGTAGCAAGTTCTAGATTGGACAAC 59.909 42.308 7.92 0.00 0.00 3.32
1572 2150 8.455682 GGACAACGAAATTTATGAAGATTACCA 58.544 33.333 0.00 0.00 0.00 3.25
1575 2153 9.236691 CAACGAAATTTATGAAGATTACCATGG 57.763 33.333 11.19 11.19 0.00 3.66
1671 2535 2.290514 TGATTCAGGGTCCAAGCTGAAG 60.291 50.000 12.74 0.00 38.89 3.02
1672 2536 1.140312 TTCAGGGTCCAAGCTGAAGT 58.860 50.000 5.27 0.00 32.80 3.01
1673 2537 1.140312 TCAGGGTCCAAGCTGAAGTT 58.860 50.000 0.00 0.00 0.00 2.66
1674 2538 1.202806 TCAGGGTCCAAGCTGAAGTTG 60.203 52.381 0.00 0.00 0.00 3.16
1678 2542 1.312815 GTCCAAGCTGAAGTTGCACT 58.687 50.000 0.00 0.00 0.00 4.40
1679 2543 2.494059 GTCCAAGCTGAAGTTGCACTA 58.506 47.619 0.00 0.00 0.00 2.74
1688 2574 4.832248 CTGAAGTTGCACTATAGGTCCAA 58.168 43.478 4.43 1.67 0.00 3.53
1698 2584 2.119801 ATAGGTCCAACTTGCAGCTG 57.880 50.000 10.11 10.11 0.00 4.24
1700 2586 2.647297 GTCCAACTTGCAGCTGCC 59.353 61.111 34.64 17.82 41.18 4.85
1708 2594 1.812686 CTTGCAGCTGCCACCATGTT 61.813 55.000 34.64 0.00 41.18 2.71
1714 2600 0.738412 GCTGCCACCATGTTGAATGC 60.738 55.000 0.00 0.00 0.00 3.56
1741 2627 7.450903 ACCATCTTAACAAGCTACACTAGTTT 58.549 34.615 0.00 0.00 0.00 2.66
1749 2635 5.748592 CAAGCTACACTAGTTTGTGGAAAC 58.251 41.667 0.00 0.00 40.67 2.78
1750 2636 4.056050 AGCTACACTAGTTTGTGGAAACG 58.944 43.478 0.00 0.00 45.34 3.60
1758 2644 3.283751 AGTTTGTGGAAACGGTCATGAA 58.716 40.909 0.00 0.00 45.34 2.57
1770 2656 9.490379 GGAAACGGTCATGAAGATATAAATACT 57.510 33.333 0.00 0.00 0.00 2.12
1798 2684 5.877012 ACTCCAACAACATGTCATGATAGTC 59.123 40.000 19.77 0.00 0.00 2.59
1799 2685 5.803552 TCCAACAACATGTCATGATAGTCA 58.196 37.500 19.77 0.00 0.00 3.41
1801 2687 6.885918 TCCAACAACATGTCATGATAGTCAAT 59.114 34.615 19.77 0.00 0.00 2.57
1803 2689 8.676401 CCAACAACATGTCATGATAGTCAATTA 58.324 33.333 19.77 0.00 0.00 1.40
1811 2697 5.403766 GTCATGATAGTCAATTACTGCCTCG 59.596 44.000 0.00 0.00 39.39 4.63
1836 2723 1.204704 CCCGATCATAGCCGCATAGAA 59.795 52.381 0.00 0.00 0.00 2.10
1860 3086 3.198068 ACTCGAATGGACGATCATTTGG 58.802 45.455 16.58 12.12 41.39 3.28
1862 3088 3.867857 TCGAATGGACGATCATTTGGAA 58.132 40.909 16.58 3.22 38.45 3.53
1870 3096 2.030457 ACGATCATTTGGAATCGCGAAC 59.970 45.455 15.24 10.73 39.85 3.95
1886 3112 3.422343 CGCGAACAAGAGTCTGATGAAAC 60.422 47.826 0.00 0.00 0.00 2.78
1946 3172 6.435428 CCAAACTTGGTTGAACTACACATAC 58.565 40.000 0.00 0.00 43.43 2.39
1973 3199 0.832135 TTCTCCCTCACGGCAGAAGT 60.832 55.000 0.00 0.00 0.00 3.01
1983 3209 3.250762 TCACGGCAGAAGTTTCTTCAATG 59.749 43.478 11.27 4.03 34.74 2.82
2001 3227 3.391382 CCCGGTCCCTCGCTTTCT 61.391 66.667 0.00 0.00 0.00 2.52
2044 3270 4.264253 CAACATGAGTCTTGGCCTATTCA 58.736 43.478 3.32 2.52 0.00 2.57
2119 3386 5.593909 CCAGAGTCAACCATTATATTGCCAA 59.406 40.000 0.00 0.00 0.00 4.52
2129 3396 6.210385 ACCATTATATTGCCAACACAGTTTCA 59.790 34.615 0.00 0.00 0.00 2.69
2131 3398 2.888834 ATTGCCAACACAGTTTCACC 57.111 45.000 0.00 0.00 0.00 4.02
2132 3399 1.846007 TTGCCAACACAGTTTCACCT 58.154 45.000 0.00 0.00 0.00 4.00
2133 3400 1.102154 TGCCAACACAGTTTCACCTG 58.898 50.000 0.00 0.00 38.45 4.00
2135 3402 1.065551 GCCAACACAGTTTCACCTGAC 59.934 52.381 0.00 0.00 36.30 3.51
2136 3403 1.330521 CCAACACAGTTTCACCTGACG 59.669 52.381 0.00 0.00 36.30 4.35
2137 3404 2.276201 CAACACAGTTTCACCTGACGA 58.724 47.619 0.00 0.00 36.30 4.20
2138 3405 1.935933 ACACAGTTTCACCTGACGAC 58.064 50.000 0.00 0.00 36.30 4.34
2139 3406 1.480954 ACACAGTTTCACCTGACGACT 59.519 47.619 0.00 0.00 36.30 4.18
2140 3407 2.128035 CACAGTTTCACCTGACGACTC 58.872 52.381 0.00 0.00 36.30 3.36
2141 3408 1.754803 ACAGTTTCACCTGACGACTCA 59.245 47.619 0.00 0.00 36.30 3.41
2142 3409 2.365617 ACAGTTTCACCTGACGACTCAT 59.634 45.455 0.00 0.00 36.30 2.90
2143 3410 3.572682 ACAGTTTCACCTGACGACTCATA 59.427 43.478 0.00 0.00 36.30 2.15
2144 3411 4.220821 ACAGTTTCACCTGACGACTCATAT 59.779 41.667 0.00 0.00 36.30 1.78
2145 3412 4.564372 CAGTTTCACCTGACGACTCATATG 59.436 45.833 0.00 0.00 34.23 1.78
2146 3413 2.871182 TCACCTGACGACTCATATGC 57.129 50.000 0.00 0.00 0.00 3.14
2147 3414 2.099405 TCACCTGACGACTCATATGCA 58.901 47.619 0.00 0.00 0.00 3.96
2148 3415 2.099756 TCACCTGACGACTCATATGCAG 59.900 50.000 0.00 0.00 0.00 4.41
2149 3416 2.103373 ACCTGACGACTCATATGCAGT 58.897 47.619 0.00 2.77 0.00 4.40
2150 3417 2.497675 ACCTGACGACTCATATGCAGTT 59.502 45.455 0.00 0.00 0.00 3.16
2151 3418 3.699538 ACCTGACGACTCATATGCAGTTA 59.300 43.478 0.00 0.00 0.00 2.24
2152 3419 4.342378 ACCTGACGACTCATATGCAGTTAT 59.658 41.667 0.00 0.00 0.00 1.89
2153 3420 5.535030 ACCTGACGACTCATATGCAGTTATA 59.465 40.000 0.00 0.00 0.00 0.98
2154 3421 6.209589 ACCTGACGACTCATATGCAGTTATAT 59.790 38.462 0.00 0.00 0.00 0.86
2155 3422 7.093354 CCTGACGACTCATATGCAGTTATATT 58.907 38.462 0.00 0.00 0.00 1.28
2156 3423 7.062722 CCTGACGACTCATATGCAGTTATATTG 59.937 40.741 0.00 0.00 0.00 1.90
2157 3424 6.366061 TGACGACTCATATGCAGTTATATTGC 59.634 38.462 0.00 3.45 41.86 3.56
2158 3425 5.639506 ACGACTCATATGCAGTTATATTGCC 59.360 40.000 0.00 0.00 40.81 4.52
2159 3426 5.639082 CGACTCATATGCAGTTATATTGCCA 59.361 40.000 0.00 0.00 40.81 4.92
2160 3427 6.147656 CGACTCATATGCAGTTATATTGCCAA 59.852 38.462 0.00 0.00 40.81 4.52
2161 3428 7.206981 ACTCATATGCAGTTATATTGCCAAC 57.793 36.000 0.00 0.00 40.81 3.77
2162 3429 6.772233 ACTCATATGCAGTTATATTGCCAACA 59.228 34.615 0.00 0.00 40.81 3.33
2163 3430 6.969366 TCATATGCAGTTATATTGCCAACAC 58.031 36.000 0.00 0.00 40.81 3.32
2164 3431 6.545298 TCATATGCAGTTATATTGCCAACACA 59.455 34.615 0.00 0.00 40.81 3.72
2165 3432 4.700268 TGCAGTTATATTGCCAACACAG 57.300 40.909 7.14 0.00 40.81 3.66
2166 3433 4.078537 TGCAGTTATATTGCCAACACAGT 58.921 39.130 7.14 0.00 40.81 3.55
2167 3434 4.522405 TGCAGTTATATTGCCAACACAGTT 59.478 37.500 7.14 0.00 40.81 3.16
2168 3435 5.010516 TGCAGTTATATTGCCAACACAGTTT 59.989 36.000 7.14 0.00 40.81 2.66
2169 3436 5.572896 GCAGTTATATTGCCAACACAGTTTC 59.427 40.000 0.00 0.00 35.54 2.78
2170 3437 6.676950 CAGTTATATTGCCAACACAGTTTCA 58.323 36.000 0.00 0.00 0.00 2.69
2171 3438 6.582295 CAGTTATATTGCCAACACAGTTTCAC 59.418 38.462 0.00 0.00 0.00 3.18
2172 3439 2.888834 ATTGCCAACACAGTTTCACC 57.111 45.000 0.00 0.00 0.00 4.02
2173 3440 1.846007 TTGCCAACACAGTTTCACCT 58.154 45.000 0.00 0.00 0.00 4.00
2174 3441 1.102154 TGCCAACACAGTTTCACCTG 58.898 50.000 0.00 0.00 38.45 4.00
2175 3442 1.340502 TGCCAACACAGTTTCACCTGA 60.341 47.619 0.00 0.00 36.30 3.86
2176 3443 1.065551 GCCAACACAGTTTCACCTGAC 59.934 52.381 0.00 0.00 36.30 3.51
2177 3444 1.330521 CCAACACAGTTTCACCTGACG 59.669 52.381 0.00 0.00 36.30 4.35
2178 3445 2.276201 CAACACAGTTTCACCTGACGA 58.724 47.619 0.00 0.00 36.30 4.20
2179 3446 1.935933 ACACAGTTTCACCTGACGAC 58.064 50.000 0.00 0.00 36.30 4.34
2180 3447 1.480954 ACACAGTTTCACCTGACGACT 59.519 47.619 0.00 0.00 36.30 4.18
2181 3448 2.128035 CACAGTTTCACCTGACGACTC 58.872 52.381 0.00 0.00 36.30 3.36
2182 3449 1.754803 ACAGTTTCACCTGACGACTCA 59.245 47.619 0.00 0.00 36.30 3.41
2183 3450 2.365617 ACAGTTTCACCTGACGACTCAT 59.634 45.455 0.00 0.00 36.30 2.90
2184 3451 3.572682 ACAGTTTCACCTGACGACTCATA 59.427 43.478 0.00 0.00 36.30 2.15
2185 3452 4.220821 ACAGTTTCACCTGACGACTCATAT 59.779 41.667 0.00 0.00 36.30 1.78
2186 3453 4.564372 CAGTTTCACCTGACGACTCATATG 59.436 45.833 0.00 0.00 34.23 1.78
2187 3454 2.871182 TCACCTGACGACTCATATGC 57.129 50.000 0.00 0.00 0.00 3.14
2188 3455 2.099405 TCACCTGACGACTCATATGCA 58.901 47.619 0.00 0.00 0.00 3.96
2189 3456 2.099756 TCACCTGACGACTCATATGCAG 59.900 50.000 0.00 0.00 0.00 4.41
2190 3457 2.103373 ACCTGACGACTCATATGCAGT 58.897 47.619 0.00 2.77 0.00 4.40
2191 3458 2.497675 ACCTGACGACTCATATGCAGTT 59.502 45.455 0.00 0.00 0.00 3.16
2192 3459 3.699538 ACCTGACGACTCATATGCAGTTA 59.300 43.478 0.00 0.00 0.00 2.24
2193 3460 4.342378 ACCTGACGACTCATATGCAGTTAT 59.658 41.667 0.00 0.00 0.00 1.89
2194 3461 5.535030 ACCTGACGACTCATATGCAGTTATA 59.465 40.000 0.00 0.00 0.00 0.98
2195 3462 6.209589 ACCTGACGACTCATATGCAGTTATAT 59.790 38.462 0.00 0.00 0.00 0.86
2196 3463 7.093354 CCTGACGACTCATATGCAGTTATATT 58.907 38.462 0.00 0.00 0.00 1.28
2197 3464 7.062722 CCTGACGACTCATATGCAGTTATATTG 59.937 40.741 0.00 0.00 0.00 1.90
2198 3465 6.366061 TGACGACTCATATGCAGTTATATTGC 59.634 38.462 0.00 3.45 41.86 3.56
2199 3466 5.639506 ACGACTCATATGCAGTTATATTGCC 59.360 40.000 0.00 0.00 40.81 4.52
2200 3467 5.639082 CGACTCATATGCAGTTATATTGCCA 59.361 40.000 0.00 0.00 40.81 4.92
2201 3468 6.147656 CGACTCATATGCAGTTATATTGCCAA 59.852 38.462 0.00 0.00 40.81 4.52
2202 3469 7.148356 CGACTCATATGCAGTTATATTGCCAAT 60.148 37.037 0.00 0.00 40.81 3.16
2203 3470 8.413309 ACTCATATGCAGTTATATTGCCAATT 57.587 30.769 0.00 0.00 40.81 2.32
2204 3471 9.519191 ACTCATATGCAGTTATATTGCCAATTA 57.481 29.630 0.00 0.00 40.81 1.40
2211 3478 9.130661 TGCAGTTATATTGCCAATTAATACAGT 57.869 29.630 0.00 0.00 40.81 3.55
2212 3479 9.965824 GCAGTTATATTGCCAATTAATACAGTT 57.034 29.630 0.00 0.00 35.54 3.16
2219 3486 7.994425 TTGCCAATTAATACAGTTTCTCTCA 57.006 32.000 0.00 0.00 0.00 3.27
2220 3487 7.994425 TGCCAATTAATACAGTTTCTCTCAA 57.006 32.000 0.00 0.00 0.00 3.02
2221 3488 8.402798 TGCCAATTAATACAGTTTCTCTCAAA 57.597 30.769 0.00 0.00 0.00 2.69
2222 3489 8.855110 TGCCAATTAATACAGTTTCTCTCAAAA 58.145 29.630 0.00 0.00 0.00 2.44
2331 3628 4.141135 TCTGTAAATGGGTCCAACTTTCCA 60.141 41.667 0.00 0.00 0.00 3.53
2339 3636 3.552068 GGGTCCAACTTTCCATTGAAACG 60.552 47.826 0.00 0.00 35.58 3.60
2391 3688 6.463995 TTGTAAAGCACAAGTCTCCATTTT 57.536 33.333 0.00 0.00 42.29 1.82
2392 3689 6.463995 TGTAAAGCACAAGTCTCCATTTTT 57.536 33.333 0.00 0.00 32.95 1.94
2393 3690 6.272318 TGTAAAGCACAAGTCTCCATTTTTG 58.728 36.000 0.00 0.00 32.95 2.44
2394 3691 5.343307 AAAGCACAAGTCTCCATTTTTGT 57.657 34.783 0.00 0.00 34.31 2.83
2395 3692 6.463995 AAAGCACAAGTCTCCATTTTTGTA 57.536 33.333 0.00 0.00 32.86 2.41
2396 3693 5.438761 AGCACAAGTCTCCATTTTTGTAC 57.561 39.130 0.00 0.00 32.86 2.90
2397 3694 4.887071 AGCACAAGTCTCCATTTTTGTACA 59.113 37.500 0.00 0.00 32.86 2.90
2398 3695 5.359576 AGCACAAGTCTCCATTTTTGTACAA 59.640 36.000 3.59 3.59 32.86 2.41
2399 3696 5.687285 GCACAAGTCTCCATTTTTGTACAAG 59.313 40.000 8.56 0.00 32.86 3.16
2400 3697 6.680378 GCACAAGTCTCCATTTTTGTACAAGT 60.680 38.462 8.56 0.00 32.86 3.16
2401 3698 6.692681 CACAAGTCTCCATTTTTGTACAAGTG 59.307 38.462 8.56 9.13 32.86 3.16
2402 3699 6.601613 ACAAGTCTCCATTTTTGTACAAGTGA 59.398 34.615 8.56 0.87 32.41 3.41
2403 3700 7.122055 ACAAGTCTCCATTTTTGTACAAGTGAA 59.878 33.333 8.56 6.06 32.41 3.18
2404 3701 7.823745 AGTCTCCATTTTTGTACAAGTGAAT 57.176 32.000 8.56 8.00 0.00 2.57
2405 3702 7.875971 AGTCTCCATTTTTGTACAAGTGAATC 58.124 34.615 8.56 0.37 0.00 2.52
2406 3703 7.502226 AGTCTCCATTTTTGTACAAGTGAATCA 59.498 33.333 8.56 0.00 0.00 2.57
2407 3704 8.299570 GTCTCCATTTTTGTACAAGTGAATCAT 58.700 33.333 8.56 0.00 0.00 2.45
2408 3705 9.513906 TCTCCATTTTTGTACAAGTGAATCATA 57.486 29.630 8.56 0.00 0.00 2.15
2418 3715 9.725019 TGTACAAGTGAATCATATTCAAGTTCT 57.275 29.630 4.00 0.00 0.00 3.01
2421 3718 8.734386 ACAAGTGAATCATATTCAAGTTCTTCC 58.266 33.333 4.00 0.00 0.00 3.46
2422 3719 7.545362 AGTGAATCATATTCAAGTTCTTCCG 57.455 36.000 4.00 0.00 0.00 4.30
2423 3720 7.106239 AGTGAATCATATTCAAGTTCTTCCGT 58.894 34.615 4.00 0.00 0.00 4.69
2424 3721 7.607991 AGTGAATCATATTCAAGTTCTTCCGTT 59.392 33.333 4.00 0.00 0.00 4.44
2425 3722 7.905493 GTGAATCATATTCAAGTTCTTCCGTTC 59.095 37.037 4.00 0.00 0.00 3.95
2426 3723 7.824289 TGAATCATATTCAAGTTCTTCCGTTCT 59.176 33.333 0.00 0.00 0.00 3.01
2427 3724 6.968131 TCATATTCAAGTTCTTCCGTTCTG 57.032 37.500 0.00 0.00 0.00 3.02
2428 3725 5.874810 TCATATTCAAGTTCTTCCGTTCTGG 59.125 40.000 0.00 0.00 40.09 3.86
2437 3734 3.289797 TCCGTTCTGGATCTGAGCT 57.710 52.632 0.00 0.00 43.74 4.09
2438 3735 2.437085 TCCGTTCTGGATCTGAGCTA 57.563 50.000 0.00 0.00 43.74 3.32
2439 3736 2.025155 TCCGTTCTGGATCTGAGCTAC 58.975 52.381 0.00 0.00 43.74 3.58
2440 3737 2.028130 CCGTTCTGGATCTGAGCTACT 58.972 52.381 0.00 0.00 42.00 2.57
2441 3738 3.118000 TCCGTTCTGGATCTGAGCTACTA 60.118 47.826 0.00 0.00 43.74 1.82
2442 3739 3.252215 CCGTTCTGGATCTGAGCTACTAG 59.748 52.174 0.00 0.00 42.00 2.57
2443 3740 3.304391 CGTTCTGGATCTGAGCTACTAGC 60.304 52.174 0.00 0.00 42.84 3.42
2444 3741 3.584733 TCTGGATCTGAGCTACTAGCA 57.415 47.619 10.73 0.00 45.56 3.49
2445 3742 4.111255 TCTGGATCTGAGCTACTAGCAT 57.889 45.455 10.73 0.00 45.56 3.79
2446 3743 5.248380 TCTGGATCTGAGCTACTAGCATA 57.752 43.478 10.73 0.00 45.56 3.14
2447 3744 5.825532 TCTGGATCTGAGCTACTAGCATAT 58.174 41.667 10.73 0.00 45.56 1.78
2448 3745 6.963322 TCTGGATCTGAGCTACTAGCATATA 58.037 40.000 10.73 0.00 45.56 0.86
2449 3746 6.826231 TCTGGATCTGAGCTACTAGCATATAC 59.174 42.308 10.73 0.23 45.56 1.47
2450 3747 5.586643 TGGATCTGAGCTACTAGCATATACG 59.413 44.000 10.73 0.00 45.56 3.06
2451 3748 5.818336 GGATCTGAGCTACTAGCATATACGA 59.182 44.000 10.73 0.00 45.56 3.43
2452 3749 6.316640 GGATCTGAGCTACTAGCATATACGAA 59.683 42.308 10.73 0.00 45.56 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.676924 GTCAAAAGATCAACGCAAGAAAGG 59.323 41.667 0.00 0.00 43.62 3.11
1 2 4.676924 GGTCAAAAGATCAACGCAAGAAAG 59.323 41.667 0.00 0.00 43.62 2.62
25 26 7.831193 AGGCAGATTGTACTATGATTTTGAAGT 59.169 33.333 0.00 0.00 0.00 3.01
29 30 6.543465 TCCAGGCAGATTGTACTATGATTTTG 59.457 38.462 0.00 0.00 0.00 2.44
114 115 5.529289 TCTCACCTACAGATTAATCCAGGT 58.471 41.667 20.51 20.51 35.56 4.00
136 137 1.211969 CAGGTGCATGCACAGCTTC 59.788 57.895 42.35 28.48 45.77 3.86
151 152 1.414181 ACACTGAGACAACCAGACAGG 59.586 52.381 0.00 0.00 45.67 4.00
152 153 2.477825 CACACTGAGACAACCAGACAG 58.522 52.381 0.00 0.00 35.69 3.51
153 154 1.138859 CCACACTGAGACAACCAGACA 59.861 52.381 0.00 0.00 35.69 3.41
154 155 1.871080 CCACACTGAGACAACCAGAC 58.129 55.000 0.00 0.00 35.69 3.51
156 157 0.179048 TGCCACACTGAGACAACCAG 60.179 55.000 0.00 0.00 37.64 4.00
157 158 0.254462 TTGCCACACTGAGACAACCA 59.746 50.000 0.00 0.00 0.00 3.67
158 159 0.947244 CTTGCCACACTGAGACAACC 59.053 55.000 0.00 0.00 0.00 3.77
159 160 0.308993 GCTTGCCACACTGAGACAAC 59.691 55.000 0.00 0.00 0.00 3.32
161 162 0.250038 GAGCTTGCCACACTGAGACA 60.250 55.000 0.00 0.00 0.00 3.41
162 163 1.287730 CGAGCTTGCCACACTGAGAC 61.288 60.000 0.00 0.00 0.00 3.36
164 165 2.675056 GCGAGCTTGCCACACTGAG 61.675 63.158 15.66 0.00 0.00 3.35
180 190 1.167851 TCAAATCAGCCTTTCCAGCG 58.832 50.000 0.00 0.00 34.64 5.18
230 247 8.939201 ATATGTGTTCTTATCAGAGACAACAG 57.061 34.615 0.00 0.00 30.72 3.16
280 331 3.128242 GCTTCAGAACATGCAGTGCTAAT 59.872 43.478 17.60 0.00 32.01 1.73
300 351 2.681848 GACAAGTTAGCATGCATGAGCT 59.318 45.455 30.64 22.23 44.55 4.09
313 364 2.829720 ACTCTACATGGGCGACAAGTTA 59.170 45.455 0.00 0.00 32.50 2.24
314 365 1.623811 ACTCTACATGGGCGACAAGTT 59.376 47.619 0.00 0.00 32.50 2.66
343 394 6.258899 CCTATGACATACGTAATCCGAGATG 58.741 44.000 0.00 0.00 40.70 2.90
349 406 4.878439 TGTGCCTATGACATACGTAATCC 58.122 43.478 0.00 0.00 0.00 3.01
356 413 4.700213 ACCTTTGTTGTGCCTATGACATAC 59.300 41.667 0.00 0.00 0.00 2.39
357 414 4.917385 ACCTTTGTTGTGCCTATGACATA 58.083 39.130 0.00 0.00 0.00 2.29
374 431 9.420118 TCATACTATATCATTTGGCAAACCTTT 57.580 29.630 16.00 3.46 36.63 3.11
378 435 9.669353 CTGTTCATACTATATCATTTGGCAAAC 57.331 33.333 16.00 0.00 0.00 2.93
402 460 6.071728 AGCTCATGATTTTTGGTTTAGACCTG 60.072 38.462 3.79 0.00 46.66 4.00
404 462 6.272822 AGCTCATGATTTTTGGTTTAGACC 57.727 37.500 0.00 0.00 46.71 3.85
407 465 8.299570 ACAAGTAGCTCATGATTTTTGGTTTAG 58.700 33.333 0.00 0.00 0.00 1.85
478 869 3.844577 GCTCATGCAACAAGAAGATGT 57.155 42.857 0.00 0.00 39.41 3.06
504 895 8.811017 AGTCAGATGGAGATATATTTAGTGTGG 58.189 37.037 0.00 0.00 0.00 4.17
517 909 4.219115 ACCATTACGAGTCAGATGGAGAT 58.781 43.478 18.28 0.02 41.20 2.75
520 912 5.137551 TCATACCATTACGAGTCAGATGGA 58.862 41.667 18.28 7.01 41.20 3.41
521 913 5.453567 TCATACCATTACGAGTCAGATGG 57.546 43.478 12.48 12.48 43.65 3.51
522 914 9.645059 ATTAATCATACCATTACGAGTCAGATG 57.355 33.333 0.00 0.00 0.00 2.90
523 915 9.862371 GATTAATCATACCATTACGAGTCAGAT 57.138 33.333 10.68 0.00 0.00 2.90
526 918 8.088365 CCTGATTAATCATACCATTACGAGTCA 58.912 37.037 18.26 0.00 36.02 3.41
528 920 6.874134 GCCTGATTAATCATACCATTACGAGT 59.126 38.462 18.26 0.00 36.02 4.18
529 921 6.873605 TGCCTGATTAATCATACCATTACGAG 59.126 38.462 18.26 2.74 36.02 4.18
536 928 3.461458 TGGGTGCCTGATTAATCATACCA 59.539 43.478 28.94 23.05 37.13 3.25
538 943 6.463995 TTTTGGGTGCCTGATTAATCATAC 57.536 37.500 18.26 15.97 36.02 2.39
597 1007 5.487131 ACCATGTGTAAATTAGGGCCATTTT 59.513 36.000 6.18 4.92 0.00 1.82
604 1014 5.110814 TGGAGACCATGTGTAAATTAGGG 57.889 43.478 0.00 0.00 0.00 3.53
607 1017 8.713971 ACTGATATGGAGACCATGTGTAAATTA 58.286 33.333 12.78 0.00 44.84 1.40
742 1171 2.859165 TTTGTCTGGGGTCATCAGTC 57.141 50.000 0.00 0.00 34.15 3.51
835 1279 0.539051 GGTGCAGCTATCCTGACAGT 59.461 55.000 9.07 0.00 44.64 3.55
898 1359 2.356125 GGTGGTGGTGCTAATCTGATGT 60.356 50.000 0.00 0.00 0.00 3.06
1093 1619 1.660560 CCATTGGCTGCTCCTTTCGG 61.661 60.000 0.00 0.00 35.26 4.30
1384 1942 1.300080 CAAAACTGCACGGCCTTGG 60.300 57.895 11.75 0.00 0.00 3.61
1416 1977 0.179468 GCTGGTTAATCCCTACGCCA 59.821 55.000 0.00 0.00 34.77 5.69
1486 2060 5.651387 TGAACAGAGATGAACAGAGTAGG 57.349 43.478 0.00 0.00 0.00 3.18
1487 2061 6.035866 GCAATGAACAGAGATGAACAGAGTAG 59.964 42.308 0.00 0.00 0.00 2.57
1488 2062 5.871524 GCAATGAACAGAGATGAACAGAGTA 59.128 40.000 0.00 0.00 0.00 2.59
1490 2064 4.094590 GGCAATGAACAGAGATGAACAGAG 59.905 45.833 0.00 0.00 0.00 3.35
1492 2066 4.008330 AGGCAATGAACAGAGATGAACAG 58.992 43.478 0.00 0.00 0.00 3.16
1493 2067 3.754850 CAGGCAATGAACAGAGATGAACA 59.245 43.478 0.00 0.00 0.00 3.18
1495 2069 4.290711 TCAGGCAATGAACAGAGATGAA 57.709 40.909 0.00 0.00 34.02 2.57
1496 2070 3.986996 TCAGGCAATGAACAGAGATGA 57.013 42.857 0.00 0.00 34.02 2.92
1498 2072 4.232188 ACATCAGGCAATGAACAGAGAT 57.768 40.909 6.86 0.00 42.53 2.75
1499 2073 3.708403 ACATCAGGCAATGAACAGAGA 57.292 42.857 6.86 0.00 42.53 3.10
1642 2499 1.134551 GGACCCTGAATCAGAGACAGC 60.135 57.143 12.53 0.00 32.44 4.40
1673 2537 2.304470 TGCAAGTTGGACCTATAGTGCA 59.696 45.455 4.75 6.36 46.29 4.57
1674 2538 2.939103 CTGCAAGTTGGACCTATAGTGC 59.061 50.000 4.75 0.11 37.33 4.40
1678 2542 2.680805 GCAGCTGCAAGTTGGACCTATA 60.681 50.000 33.36 0.00 46.15 1.31
1679 2543 1.952367 GCAGCTGCAAGTTGGACCTAT 60.952 52.381 33.36 0.00 46.15 2.57
1688 2574 2.116772 ATGGTGGCAGCTGCAAGT 59.883 55.556 37.63 14.93 44.36 3.16
1698 2584 3.910817 TTGCATTCAACATGGTGGC 57.089 47.368 11.68 7.24 0.00 5.01
1708 2594 4.523943 AGCTTGTTAAGATGGTTGCATTCA 59.476 37.500 0.00 0.00 0.00 2.57
1714 2600 6.874134 ACTAGTGTAGCTTGTTAAGATGGTTG 59.126 38.462 0.00 0.00 29.05 3.77
1741 2627 2.920724 TCTTCATGACCGTTTCCACA 57.079 45.000 0.00 0.00 0.00 4.17
1742 2628 7.548196 TTTATATCTTCATGACCGTTTCCAC 57.452 36.000 0.00 0.00 0.00 4.02
1770 2656 6.353404 TCATGACATGTTGTTGGAGTACTA 57.647 37.500 14.98 0.00 0.00 1.82
1774 2660 5.809001 ACTATCATGACATGTTGTTGGAGT 58.191 37.500 14.98 4.54 0.00 3.85
1775 2661 5.876460 TGACTATCATGACATGTTGTTGGAG 59.124 40.000 14.98 3.97 0.00 3.86
1776 2662 5.803552 TGACTATCATGACATGTTGTTGGA 58.196 37.500 14.98 0.00 0.00 3.53
1778 2664 9.494479 GTAATTGACTATCATGACATGTTGTTG 57.506 33.333 14.98 0.00 0.00 3.33
1798 2684 1.369625 GGTCACCGAGGCAGTAATTG 58.630 55.000 0.00 0.00 0.00 2.32
1799 2685 0.252197 GGGTCACCGAGGCAGTAATT 59.748 55.000 0.00 0.00 0.00 1.40
1801 2687 3.384348 GGGTCACCGAGGCAGTAA 58.616 61.111 0.00 0.00 0.00 2.24
1811 2697 1.006102 CGGCTATGATCGGGTCACC 60.006 63.158 0.00 0.00 40.28 4.02
1828 2715 2.034685 TCCATTCGAGTCCTTCTATGCG 59.965 50.000 0.00 0.00 0.00 4.73
1836 2723 1.763968 TGATCGTCCATTCGAGTCCT 58.236 50.000 0.00 0.00 43.00 3.85
1860 3086 2.596452 TCAGACTCTTGTTCGCGATTC 58.404 47.619 10.88 7.30 0.00 2.52
1862 3088 2.164422 TCATCAGACTCTTGTTCGCGAT 59.836 45.455 10.88 0.00 0.00 4.58
1890 3116 7.732222 ACTGGATTCTAGTCTCAAGAAGATT 57.268 36.000 0.00 0.00 36.46 2.40
1935 3161 5.148651 AGAAGCGGAAAGTATGTGTAGTT 57.851 39.130 0.00 0.00 0.00 2.24
1946 3172 0.737715 CGTGAGGGAGAAGCGGAAAG 60.738 60.000 0.00 0.00 0.00 2.62
1973 3199 0.610785 GGGACCGGGCATTGAAGAAA 60.611 55.000 11.00 0.00 0.00 2.52
2001 3227 2.610374 GCACAAAAGTGGTGTTCGAGTA 59.390 45.455 0.00 0.00 38.51 2.59
2044 3270 1.136891 GCAAGCAACAAAGAACCACCT 59.863 47.619 0.00 0.00 0.00 4.00
2119 3386 1.480954 AGTCGTCAGGTGAAACTGTGT 59.519 47.619 0.00 0.00 39.48 3.72
2129 3396 2.103373 ACTGCATATGAGTCGTCAGGT 58.897 47.619 6.97 0.00 35.66 4.00
2131 3398 7.411264 GCAATATAACTGCATATGAGTCGTCAG 60.411 40.741 6.97 5.60 39.69 3.51
2132 3399 6.366061 GCAATATAACTGCATATGAGTCGTCA 59.634 38.462 6.97 0.00 39.69 4.35
2133 3400 6.183360 GGCAATATAACTGCATATGAGTCGTC 60.183 42.308 6.97 0.00 41.78 4.20
2135 3402 5.639082 TGGCAATATAACTGCATATGAGTCG 59.361 40.000 6.97 0.00 41.78 4.18
2136 3403 7.041167 TGTTGGCAATATAACTGCATATGAGTC 60.041 37.037 6.97 0.00 41.78 3.36
2137 3404 6.772233 TGTTGGCAATATAACTGCATATGAGT 59.228 34.615 6.97 4.52 41.78 3.41
2138 3405 7.080099 GTGTTGGCAATATAACTGCATATGAG 58.920 38.462 6.97 3.87 41.78 2.90
2139 3406 6.545298 TGTGTTGGCAATATAACTGCATATGA 59.455 34.615 6.97 0.00 41.78 2.15
2140 3407 6.737118 TGTGTTGGCAATATAACTGCATATG 58.263 36.000 1.92 0.00 41.78 1.78
2141 3408 6.547141 ACTGTGTTGGCAATATAACTGCATAT 59.453 34.615 1.92 0.00 41.78 1.78
2142 3409 5.885352 ACTGTGTTGGCAATATAACTGCATA 59.115 36.000 1.92 0.00 41.78 3.14
2143 3410 4.706476 ACTGTGTTGGCAATATAACTGCAT 59.294 37.500 1.92 0.00 41.78 3.96
2144 3411 4.078537 ACTGTGTTGGCAATATAACTGCA 58.921 39.130 1.92 0.00 41.78 4.41
2145 3412 4.701956 ACTGTGTTGGCAATATAACTGC 57.298 40.909 1.92 2.30 39.16 4.40
2146 3413 6.582295 GTGAAACTGTGTTGGCAATATAACTG 59.418 38.462 1.92 6.89 0.00 3.16
2147 3414 6.294508 GGTGAAACTGTGTTGGCAATATAACT 60.295 38.462 1.92 0.00 36.74 2.24
2148 3415 5.861787 GGTGAAACTGTGTTGGCAATATAAC 59.138 40.000 1.92 0.82 36.74 1.89
2149 3416 5.772672 AGGTGAAACTGTGTTGGCAATATAA 59.227 36.000 1.92 0.00 36.74 0.98
2150 3417 5.182950 CAGGTGAAACTGTGTTGGCAATATA 59.817 40.000 1.92 0.00 36.74 0.86
2151 3418 4.022068 CAGGTGAAACTGTGTTGGCAATAT 60.022 41.667 1.92 0.00 36.74 1.28
2152 3419 3.317711 CAGGTGAAACTGTGTTGGCAATA 59.682 43.478 1.92 0.00 36.74 1.90
2153 3420 2.101249 CAGGTGAAACTGTGTTGGCAAT 59.899 45.455 1.92 0.00 36.74 3.56
2154 3421 1.476085 CAGGTGAAACTGTGTTGGCAA 59.524 47.619 0.00 0.00 36.74 4.52
2155 3422 1.102154 CAGGTGAAACTGTGTTGGCA 58.898 50.000 0.00 0.00 36.74 4.92
2156 3423 1.065551 GTCAGGTGAAACTGTGTTGGC 59.934 52.381 0.00 0.00 39.48 4.52
2157 3424 1.330521 CGTCAGGTGAAACTGTGTTGG 59.669 52.381 0.00 0.00 39.48 3.77
2158 3425 2.030457 GTCGTCAGGTGAAACTGTGTTG 59.970 50.000 0.00 0.00 39.48 3.33
2159 3426 2.093658 AGTCGTCAGGTGAAACTGTGTT 60.094 45.455 0.00 0.00 39.48 3.32
2160 3427 1.480954 AGTCGTCAGGTGAAACTGTGT 59.519 47.619 0.00 0.00 39.48 3.72
2161 3428 2.128035 GAGTCGTCAGGTGAAACTGTG 58.872 52.381 0.00 0.00 39.48 3.66
2162 3429 1.754803 TGAGTCGTCAGGTGAAACTGT 59.245 47.619 0.00 0.00 39.48 3.55
2163 3430 2.509052 TGAGTCGTCAGGTGAAACTG 57.491 50.000 1.94 0.00 39.84 3.16
2164 3431 4.748892 CATATGAGTCGTCAGGTGAAACT 58.251 43.478 0.00 0.00 35.66 2.66
2165 3432 3.307242 GCATATGAGTCGTCAGGTGAAAC 59.693 47.826 6.97 0.00 35.66 2.78
2166 3433 3.056179 TGCATATGAGTCGTCAGGTGAAA 60.056 43.478 6.97 0.00 35.66 2.69
2167 3434 2.495669 TGCATATGAGTCGTCAGGTGAA 59.504 45.455 6.97 0.00 35.66 3.18
2168 3435 2.099405 TGCATATGAGTCGTCAGGTGA 58.901 47.619 6.97 0.00 35.66 4.02
2169 3436 2.159184 ACTGCATATGAGTCGTCAGGTG 60.159 50.000 6.97 0.00 35.66 4.00
2170 3437 2.103373 ACTGCATATGAGTCGTCAGGT 58.897 47.619 6.97 0.00 35.66 4.00
2171 3438 2.879002 ACTGCATATGAGTCGTCAGG 57.121 50.000 6.97 0.00 35.66 3.86
2172 3439 7.411264 GCAATATAACTGCATATGAGTCGTCAG 60.411 40.741 6.97 5.60 39.69 3.51
2173 3440 6.366061 GCAATATAACTGCATATGAGTCGTCA 59.634 38.462 6.97 0.00 39.69 4.35
2174 3441 6.183360 GGCAATATAACTGCATATGAGTCGTC 60.183 42.308 6.97 0.00 41.78 4.20
2175 3442 5.639506 GGCAATATAACTGCATATGAGTCGT 59.360 40.000 6.97 3.11 41.78 4.34
2176 3443 5.639082 TGGCAATATAACTGCATATGAGTCG 59.361 40.000 6.97 0.00 41.78 4.18
2177 3444 7.439157 TTGGCAATATAACTGCATATGAGTC 57.561 36.000 6.97 0.00 41.78 3.36
2178 3445 8.413309 AATTGGCAATATAACTGCATATGAGT 57.587 30.769 14.05 4.52 41.78 3.41
2185 3452 9.130661 ACTGTATTAATTGGCAATATAACTGCA 57.869 29.630 14.05 11.59 41.78 4.41
2186 3453 9.965824 AACTGTATTAATTGGCAATATAACTGC 57.034 29.630 14.05 8.51 39.16 4.40
2193 3460 9.679661 TGAGAGAAACTGTATTAATTGGCAATA 57.320 29.630 14.05 0.00 0.00 1.90
2194 3461 8.579850 TGAGAGAAACTGTATTAATTGGCAAT 57.420 30.769 6.96 6.96 0.00 3.56
2195 3462 7.994425 TGAGAGAAACTGTATTAATTGGCAA 57.006 32.000 0.68 0.68 0.00 4.52
2196 3463 7.994425 TTGAGAGAAACTGTATTAATTGGCA 57.006 32.000 0.00 0.00 0.00 4.92
2197 3464 9.691362 TTTTTGAGAGAAACTGTATTAATTGGC 57.309 29.630 0.00 0.00 0.00 4.52
2203 3470 9.772973 TGCTACTTTTTGAGAGAAACTGTATTA 57.227 29.630 0.00 0.00 0.00 0.98
2204 3471 8.677148 TGCTACTTTTTGAGAGAAACTGTATT 57.323 30.769 0.00 0.00 0.00 1.89
2205 3472 8.854614 ATGCTACTTTTTGAGAGAAACTGTAT 57.145 30.769 0.00 0.00 0.00 2.29
2206 3473 9.944376 ATATGCTACTTTTTGAGAGAAACTGTA 57.056 29.630 0.00 0.00 0.00 2.74
2207 3474 8.725148 CATATGCTACTTTTTGAGAGAAACTGT 58.275 33.333 0.00 0.00 0.00 3.55
2208 3475 8.180267 CCATATGCTACTTTTTGAGAGAAACTG 58.820 37.037 0.00 0.00 0.00 3.16
2209 3476 8.103305 TCCATATGCTACTTTTTGAGAGAAACT 58.897 33.333 0.00 0.00 0.00 2.66
2210 3477 8.268850 TCCATATGCTACTTTTTGAGAGAAAC 57.731 34.615 0.00 0.00 0.00 2.78
2211 3478 8.896744 CATCCATATGCTACTTTTTGAGAGAAA 58.103 33.333 0.00 0.00 0.00 2.52
2212 3479 7.500227 CCATCCATATGCTACTTTTTGAGAGAA 59.500 37.037 0.00 0.00 0.00 2.87
2213 3480 6.994496 CCATCCATATGCTACTTTTTGAGAGA 59.006 38.462 0.00 0.00 0.00 3.10
2214 3481 6.994496 TCCATCCATATGCTACTTTTTGAGAG 59.006 38.462 0.00 0.00 0.00 3.20
2215 3482 6.899089 TCCATCCATATGCTACTTTTTGAGA 58.101 36.000 0.00 0.00 0.00 3.27
2216 3483 7.309012 CCATCCATCCATATGCTACTTTTTGAG 60.309 40.741 0.00 0.00 0.00 3.02
2217 3484 6.491062 CCATCCATCCATATGCTACTTTTTGA 59.509 38.462 0.00 0.00 0.00 2.69
2218 3485 6.491062 TCCATCCATCCATATGCTACTTTTTG 59.509 38.462 0.00 0.00 0.00 2.44
2219 3486 6.613699 TCCATCCATCCATATGCTACTTTTT 58.386 36.000 0.00 0.00 0.00 1.94
2220 3487 6.204852 TCCATCCATCCATATGCTACTTTT 57.795 37.500 0.00 0.00 0.00 2.27
2221 3488 5.848286 TCCATCCATCCATATGCTACTTT 57.152 39.130 0.00 0.00 0.00 2.66
2222 3489 5.848286 TTCCATCCATCCATATGCTACTT 57.152 39.130 0.00 0.00 0.00 2.24
2303 3600 5.010282 AGTTGGACCCATTTACAGATGAAC 58.990 41.667 0.00 0.00 0.00 3.18
2318 3615 3.638484 CGTTTCAATGGAAAGTTGGACC 58.362 45.455 0.00 0.00 43.35 4.46
2331 3628 3.149196 ACTTGAGGACATGCGTTTCAAT 58.851 40.909 0.00 0.00 32.20 2.57
2339 3636 3.243501 TGCTTTCAAACTTGAGGACATGC 60.244 43.478 0.00 0.00 38.61 4.06
2392 3689 9.725019 AGAACTTGAATATGATTCACTTGTACA 57.275 29.630 1.39 0.00 0.00 2.90
2395 3692 8.734386 GGAAGAACTTGAATATGATTCACTTGT 58.266 33.333 1.39 0.11 0.00 3.16
2396 3693 7.907045 CGGAAGAACTTGAATATGATTCACTTG 59.093 37.037 1.39 0.00 0.00 3.16
2397 3694 7.607991 ACGGAAGAACTTGAATATGATTCACTT 59.392 33.333 1.39 2.73 0.00 3.16
2398 3695 7.106239 ACGGAAGAACTTGAATATGATTCACT 58.894 34.615 1.39 0.00 0.00 3.41
2399 3696 7.308782 ACGGAAGAACTTGAATATGATTCAC 57.691 36.000 1.39 0.00 0.00 3.18
2400 3697 7.824289 AGAACGGAAGAACTTGAATATGATTCA 59.176 33.333 0.00 0.00 0.00 2.57
2401 3698 8.119226 CAGAACGGAAGAACTTGAATATGATTC 58.881 37.037 0.00 0.00 0.00 2.52
2402 3699 7.066284 CCAGAACGGAAGAACTTGAATATGATT 59.934 37.037 0.00 0.00 36.56 2.57
2403 3700 6.540189 CCAGAACGGAAGAACTTGAATATGAT 59.460 38.462 0.00 0.00 36.56 2.45
2404 3701 5.874810 CCAGAACGGAAGAACTTGAATATGA 59.125 40.000 0.00 0.00 36.56 2.15
2405 3702 5.874810 TCCAGAACGGAAGAACTTGAATATG 59.125 40.000 0.00 0.00 42.52 1.78
2406 3703 6.049955 TCCAGAACGGAAGAACTTGAATAT 57.950 37.500 0.00 0.00 42.52 1.28
2407 3704 5.477607 TCCAGAACGGAAGAACTTGAATA 57.522 39.130 0.00 0.00 42.52 1.75
2408 3705 4.351874 TCCAGAACGGAAGAACTTGAAT 57.648 40.909 0.00 0.00 42.52 2.57
2409 3706 3.830744 TCCAGAACGGAAGAACTTGAA 57.169 42.857 0.00 0.00 42.52 2.69
2420 3717 2.028130 AGTAGCTCAGATCCAGAACGG 58.972 52.381 0.00 0.00 0.00 4.44
2421 3718 3.304391 GCTAGTAGCTCAGATCCAGAACG 60.304 52.174 15.16 0.00 38.45 3.95
2422 3719 3.634448 TGCTAGTAGCTCAGATCCAGAAC 59.366 47.826 22.34 0.00 42.97 3.01
2423 3720 3.903467 TGCTAGTAGCTCAGATCCAGAA 58.097 45.455 22.34 0.00 42.97 3.02
2424 3721 3.584733 TGCTAGTAGCTCAGATCCAGA 57.415 47.619 22.34 0.00 42.97 3.86
2425 3722 6.238347 CGTATATGCTAGTAGCTCAGATCCAG 60.238 46.154 22.34 3.30 42.97 3.86
2426 3723 5.586643 CGTATATGCTAGTAGCTCAGATCCA 59.413 44.000 22.34 0.32 42.97 3.41
2427 3724 5.818336 TCGTATATGCTAGTAGCTCAGATCC 59.182 44.000 22.34 4.63 42.97 3.36
2428 3725 6.912203 TCGTATATGCTAGTAGCTCAGATC 57.088 41.667 22.34 8.30 42.97 2.75


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

AutoCloner maintained by Alex Coulton.