Multiple sequence alignment - TraesCS6D01G362500

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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 TraesCS6D01G362500 chr6D 100.000 5214 0 0 1 5214 453005009 453010222 0.000000e+00 9629.0
1 TraesCS6D01G362500 chr6B 91.795 4351 203 75 968 5214 688294040 688298340 0.000000e+00 5915.0
2 TraesCS6D01G362500 chr6B 82.114 369 29 16 612 967 688293661 688294005 1.110000e-71 281.0
3 TraesCS6D01G362500 chr6B 83.871 310 17 15 149 431 688292551 688292854 1.110000e-66 265.0
4 TraesCS6D01G362500 chr6A 92.200 3859 169 52 968 4746 599043041 599046847 0.000000e+00 5337.0
5 TraesCS6D01G362500 chr6A 89.776 313 19 5 4903 5214 599047176 599047476 6.330000e-104 388.0
6 TraesCS6D01G362500 chr6A 80.344 524 43 32 461 967 599042533 599043013 5.000000e-90 342.0
7 TraesCS6D01G362500 chr6A 84.150 347 16 15 66 380 599041574 599041913 3.050000e-77 300.0
8 TraesCS6D01G362500 chr7B 100.000 31 0 0 4505 4535 566837840 566837810 2.030000e-04 58.4


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 TraesCS6D01G362500 chr6D 453005009 453010222 5213 False 9629.000000 9629 100.000000 1 5214 1 chr6D.!!$F1 5213
1 TraesCS6D01G362500 chr6B 688292551 688298340 5789 False 2153.666667 5915 85.926667 149 5214 3 chr6B.!!$F1 5065
2 TraesCS6D01G362500 chr6A 599041574 599047476 5902 False 1591.750000 5337 86.617500 66 5214 4 chr6A.!!$F1 5148

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
558 1223 0.403271 CCATCCATCCATCCTCCCAC 59.597 60.0 0.00 0.0 0.00 4.61 F
766 1825 0.537371 CAGTTTTTGCCCCCGTCTCT 60.537 55.0 0.00 0.0 0.00 3.10 F
1411 2585 0.100325 TGCTGCTTTGTGGTTGTTCG 59.900 50.0 0.00 0.0 0.00 3.95 F
1412 2586 0.380378 GCTGCTTTGTGGTTGTTCGA 59.620 50.0 0.00 0.0 0.00 3.71 F
1784 2964 1.885560 TTTCGAACGGCTCCAATTCA 58.114 45.0 0.00 0.0 0.00 2.57 F
2922 4139 1.008361 ACGTTTTGCGCCAATGATGC 61.008 50.0 4.18 0.0 46.11 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 2566 0.100325 CGAACAACCACAAAGCAGCA 59.900 50.000 0.0 0.0 0.00 4.41 R
2240 3454 1.067565 TGTTACCTCAGAAGCAGCGAG 60.068 52.381 0.0 0.0 0.00 5.03 R
2778 3995 0.540454 TGCTCTGCATCAGAAGGGAG 59.460 55.000 0.0 0.0 40.18 4.30 R
2912 4129 4.266029 CAGAAACGTAAATGCATCATTGGC 59.734 41.667 0.0 0.0 34.04 4.52 R
3715 4935 1.203994 CGATACAGTTTCCCGTGGTCT 59.796 52.381 0.0 0.0 0.00 3.85 R
4801 6079 0.168128 ATCGTTTTAACAGCCGCAGC 59.832 50.000 0.0 0.0 40.32 5.25 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 4.133796 GCCACGCCATTTCAGCCC 62.134 66.667 0.00 0.00 0.00 5.19
23 24 3.814268 CCACGCCATTTCAGCCCG 61.814 66.667 0.00 0.00 0.00 6.13
24 25 4.481112 CACGCCATTTCAGCCCGC 62.481 66.667 0.00 0.00 0.00 6.13
25 26 4.722700 ACGCCATTTCAGCCCGCT 62.723 61.111 0.00 0.00 0.00 5.52
26 27 3.443045 CGCCATTTCAGCCCGCTT 61.443 61.111 0.00 0.00 0.00 4.68
27 28 2.491621 GCCATTTCAGCCCGCTTC 59.508 61.111 0.00 0.00 0.00 3.86
28 29 3.068729 GCCATTTCAGCCCGCTTCC 62.069 63.158 0.00 0.00 0.00 3.46
29 30 2.764314 CCATTTCAGCCCGCTTCCG 61.764 63.158 0.00 0.00 0.00 4.30
39 40 2.048222 CGCTTCCGGCTCACAGAA 60.048 61.111 0.00 0.00 39.13 3.02
40 41 1.667830 CGCTTCCGGCTCACAGAAA 60.668 57.895 0.00 0.00 39.13 2.52
41 42 1.021390 CGCTTCCGGCTCACAGAAAT 61.021 55.000 0.00 0.00 39.13 2.17
42 43 1.739035 CGCTTCCGGCTCACAGAAATA 60.739 52.381 0.00 0.00 39.13 1.40
43 44 2.356135 GCTTCCGGCTCACAGAAATAA 58.644 47.619 0.00 0.00 38.06 1.40
44 45 2.096013 GCTTCCGGCTCACAGAAATAAC 59.904 50.000 0.00 0.00 38.06 1.89
45 46 3.600388 CTTCCGGCTCACAGAAATAACT 58.400 45.455 0.00 0.00 0.00 2.24
46 47 4.755411 CTTCCGGCTCACAGAAATAACTA 58.245 43.478 0.00 0.00 0.00 2.24
47 48 4.811969 TCCGGCTCACAGAAATAACTAA 57.188 40.909 0.00 0.00 0.00 2.24
48 49 4.501071 TCCGGCTCACAGAAATAACTAAC 58.499 43.478 0.00 0.00 0.00 2.34
49 50 4.020928 TCCGGCTCACAGAAATAACTAACA 60.021 41.667 0.00 0.00 0.00 2.41
50 51 4.693566 CCGGCTCACAGAAATAACTAACAA 59.306 41.667 0.00 0.00 0.00 2.83
51 52 5.163854 CCGGCTCACAGAAATAACTAACAAG 60.164 44.000 0.00 0.00 0.00 3.16
52 53 5.637810 CGGCTCACAGAAATAACTAACAAGA 59.362 40.000 0.00 0.00 0.00 3.02
53 54 6.313905 CGGCTCACAGAAATAACTAACAAGAT 59.686 38.462 0.00 0.00 0.00 2.40
54 55 7.491372 CGGCTCACAGAAATAACTAACAAGATA 59.509 37.037 0.00 0.00 0.00 1.98
55 56 9.331282 GGCTCACAGAAATAACTAACAAGATAT 57.669 33.333 0.00 0.00 0.00 1.63
58 59 9.890629 TCACAGAAATAACTAACAAGATATGCT 57.109 29.630 0.00 0.00 0.00 3.79
69 70 8.924303 ACTAACAAGATATGCTAACCACTATGA 58.076 33.333 0.00 0.00 0.00 2.15
86 87 8.061304 ACCACTATGAATTTGGACCAATTATCT 58.939 33.333 7.99 0.00 34.24 1.98
95 96 5.319043 TGGACCAATTATCTGGATAACCC 57.681 43.478 5.33 4.01 38.96 4.11
96 97 4.981647 TGGACCAATTATCTGGATAACCCT 59.018 41.667 5.33 0.00 38.96 4.34
97 98 5.435041 TGGACCAATTATCTGGATAACCCTT 59.565 40.000 5.33 0.00 38.96 3.95
147 164 0.997932 CTTGACGCTGCTTCTGCTAG 59.002 55.000 7.67 0.00 40.48 3.42
231 252 3.011119 TGCTAACAACAACAACCGTTCT 58.989 40.909 0.00 0.00 31.13 3.01
264 292 3.243704 TGGAAAGGCGTTGATTTCTTTGG 60.244 43.478 0.00 0.00 36.03 3.28
268 296 1.418373 GCGTTGATTTCTTTGGTGCC 58.582 50.000 0.00 0.00 0.00 5.01
431 720 3.367025 CACTTTGACTTATCCGGACGAAC 59.633 47.826 6.12 0.00 0.00 3.95
432 721 3.006110 ACTTTGACTTATCCGGACGAACA 59.994 43.478 6.12 0.63 0.00 3.18
433 722 3.880047 TTGACTTATCCGGACGAACAT 57.120 42.857 6.12 0.00 0.00 2.71
435 724 4.987408 TGACTTATCCGGACGAACATAA 57.013 40.909 6.12 0.00 0.00 1.90
436 725 5.327616 TGACTTATCCGGACGAACATAAA 57.672 39.130 6.12 0.00 0.00 1.40
437 726 5.722263 TGACTTATCCGGACGAACATAAAA 58.278 37.500 6.12 0.00 0.00 1.52
438 727 6.342906 TGACTTATCCGGACGAACATAAAAT 58.657 36.000 6.12 0.00 0.00 1.82
439 728 6.819649 TGACTTATCCGGACGAACATAAAATT 59.180 34.615 6.12 0.00 0.00 1.82
441 730 6.259387 ACTTATCCGGACGAACATAAAATTCC 59.741 38.462 6.12 0.00 0.00 3.01
442 731 2.931325 TCCGGACGAACATAAAATTCCG 59.069 45.455 0.00 0.80 44.51 4.30
443 732 2.538132 CCGGACGAACATAAAATTCCGC 60.538 50.000 0.00 0.00 43.75 5.54
471 1136 4.085733 TGGCCGTTAGTTACTTACCAGTA 58.914 43.478 0.00 0.00 34.06 2.74
473 1138 5.187576 TGGCCGTTAGTTACTTACCAGTAAT 59.812 40.000 0.00 0.00 45.38 1.89
485 1150 3.610040 ACCAGTAATCGCAATCAGTCA 57.390 42.857 0.00 0.00 0.00 3.41
487 1152 2.286294 CCAGTAATCGCAATCAGTCAGC 59.714 50.000 0.00 0.00 0.00 4.26
508 1173 0.599204 AGTTCTGTGCGTGTAACCGG 60.599 55.000 0.00 0.00 0.00 5.28
509 1174 1.301087 TTCTGTGCGTGTAACCGGG 60.301 57.895 6.32 0.00 0.00 5.73
510 1175 3.419759 CTGTGCGTGTAACCGGGC 61.420 66.667 6.32 0.00 0.00 6.13
542 1207 7.313646 CGTCCGTCTATTTACTAATCATCCAT 58.686 38.462 0.00 0.00 0.00 3.41
553 1218 5.106577 ACTAATCATCCATCCATCCATCCT 58.893 41.667 0.00 0.00 0.00 3.24
558 1223 0.403271 CCATCCATCCATCCTCCCAC 59.597 60.000 0.00 0.00 0.00 4.61
575 1240 4.410400 CCCCACGCCTCCACCTTC 62.410 72.222 0.00 0.00 0.00 3.46
576 1241 4.410400 CCCACGCCTCCACCTTCC 62.410 72.222 0.00 0.00 0.00 3.46
577 1242 4.410400 CCACGCCTCCACCTTCCC 62.410 72.222 0.00 0.00 0.00 3.97
578 1243 4.410400 CACGCCTCCACCTTCCCC 62.410 72.222 0.00 0.00 0.00 4.81
597 1262 3.452141 TTCCCCCACACCCTCCCTT 62.452 63.158 0.00 0.00 0.00 3.95
658 1717 2.021652 CCCCCTACCCTCCTCCTCT 61.022 68.421 0.00 0.00 0.00 3.69
692 1751 4.179599 CCCTCCCCTCCCCTCCTC 62.180 77.778 0.00 0.00 0.00 3.71
693 1752 4.179599 CCTCCCCTCCCCTCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
694 1753 4.179599 CTCCCCTCCCCTCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
762 1821 2.523168 CCCAGTTTTTGCCCCCGT 60.523 61.111 0.00 0.00 0.00 5.28
766 1825 0.537371 CAGTTTTTGCCCCCGTCTCT 60.537 55.000 0.00 0.00 0.00 3.10
819 1908 6.754206 TCGATTCGTTTCGTTTATTCGATTT 58.246 32.000 5.89 0.00 40.03 2.17
889 1981 2.512515 GGCGTGTCTGGATCTGGC 60.513 66.667 0.00 0.00 0.00 4.85
892 1984 1.599047 CGTGTCTGGATCTGGCCTT 59.401 57.895 3.32 0.00 0.00 4.35
893 1985 0.742281 CGTGTCTGGATCTGGCCTTG 60.742 60.000 3.32 0.00 0.00 3.61
894 1986 1.028868 GTGTCTGGATCTGGCCTTGC 61.029 60.000 3.32 0.00 0.00 4.01
895 1987 1.817099 GTCTGGATCTGGCCTTGCG 60.817 63.158 3.32 0.00 0.00 4.85
896 1988 1.989508 TCTGGATCTGGCCTTGCGA 60.990 57.895 3.32 0.00 0.00 5.10
897 1989 1.523258 CTGGATCTGGCCTTGCGAG 60.523 63.158 3.32 0.00 35.74 5.03
898 1990 2.203126 GGATCTGGCCTTGCGAGG 60.203 66.667 16.53 16.53 46.50 4.63
918 2010 3.528370 CCTCGCGGTCCGAATCCT 61.528 66.667 17.49 0.00 46.81 3.24
919 2011 2.494918 CTCGCGGTCCGAATCCTT 59.505 61.111 17.49 0.00 46.81 3.36
1109 2237 4.273480 CGCCCTTCTCCAATATTGTTACTG 59.727 45.833 14.25 0.00 0.00 2.74
1131 2268 5.296748 TGTATTTTTCTCCTTGCTTTTGGC 58.703 37.500 0.00 0.00 42.22 4.52
1154 2291 4.207891 TGGGAAGTAAGATGCTGACTTC 57.792 45.455 13.86 13.86 45.46 3.01
1242 2379 2.627221 GGGTTCCGTCCTACTATCTTCC 59.373 54.545 0.00 0.00 0.00 3.46
1274 2411 9.678941 GAGTTTTGGTTTACTTGATTTAGAAGG 57.321 33.333 0.00 0.00 0.00 3.46
1275 2412 8.638873 AGTTTTGGTTTACTTGATTTAGAAGGG 58.361 33.333 0.00 0.00 0.00 3.95
1276 2413 7.533289 TTTGGTTTACTTGATTTAGAAGGGG 57.467 36.000 0.00 0.00 0.00 4.79
1277 2414 5.576128 TGGTTTACTTGATTTAGAAGGGGG 58.424 41.667 0.00 0.00 0.00 5.40
1286 2431 1.298953 TTAGAAGGGGGCAGCTTGAT 58.701 50.000 0.00 0.00 0.00 2.57
1288 2433 0.842635 AGAAGGGGGCAGCTTGATAG 59.157 55.000 0.00 0.00 0.00 2.08
1297 2442 3.306641 GGGCAGCTTGATAGGAGTCATAG 60.307 52.174 0.00 0.00 0.00 2.23
1300 2445 4.808558 CAGCTTGATAGGAGTCATAGAGC 58.191 47.826 8.65 8.65 32.34 4.09
1305 2450 3.576118 TGATAGGAGTCATAGAGCTTGCC 59.424 47.826 0.00 0.00 0.00 4.52
1357 2529 4.627467 CACGCTCTAGTGAAATGCTTTAGT 59.373 41.667 0.00 0.00 44.43 2.24
1379 2551 6.120220 AGTTAGTGGAAAATATTTAGCCGCT 58.880 36.000 26.30 26.30 38.39 5.52
1392 2566 3.036429 GCCGCTGGGGTTCTGAGAT 62.036 63.158 12.70 0.00 38.44 2.75
1406 2580 1.884579 CTGAGATGCTGCTTTGTGGTT 59.115 47.619 0.00 0.00 0.00 3.67
1407 2581 1.610038 TGAGATGCTGCTTTGTGGTTG 59.390 47.619 0.00 0.00 0.00 3.77
1411 2585 0.100325 TGCTGCTTTGTGGTTGTTCG 59.900 50.000 0.00 0.00 0.00 3.95
1412 2586 0.380378 GCTGCTTTGTGGTTGTTCGA 59.620 50.000 0.00 0.00 0.00 3.71
1511 2685 2.952310 GTCTATGGCCATTGACCTTTCC 59.048 50.000 36.11 19.12 37.52 3.13
1519 2693 2.558359 CCATTGACCTTTCCTTGACCAC 59.442 50.000 0.00 0.00 0.00 4.16
1558 2732 3.006752 GGATTGGTTGCTGATGGTGAAAA 59.993 43.478 0.00 0.00 0.00 2.29
1783 2963 2.981400 TTTTCGAACGGCTCCAATTC 57.019 45.000 0.00 0.00 0.00 2.17
1784 2964 1.885560 TTTCGAACGGCTCCAATTCA 58.114 45.000 0.00 0.00 0.00 2.57
1786 2966 2.971660 TCGAACGGCTCCAATTCATA 57.028 45.000 0.00 0.00 0.00 2.15
1788 2968 2.093921 TCGAACGGCTCCAATTCATACA 60.094 45.455 0.00 0.00 0.00 2.29
1789 2969 2.675844 CGAACGGCTCCAATTCATACAA 59.324 45.455 0.00 0.00 0.00 2.41
1790 2970 3.312421 CGAACGGCTCCAATTCATACAAT 59.688 43.478 0.00 0.00 0.00 2.71
1791 2971 4.509970 CGAACGGCTCCAATTCATACAATA 59.490 41.667 0.00 0.00 0.00 1.90
1792 2972 5.179368 CGAACGGCTCCAATTCATACAATAT 59.821 40.000 0.00 0.00 0.00 1.28
1793 2973 6.560253 AACGGCTCCAATTCATACAATATC 57.440 37.500 0.00 0.00 0.00 1.63
1794 2974 5.003804 ACGGCTCCAATTCATACAATATCC 58.996 41.667 0.00 0.00 0.00 2.59
1795 2975 4.396166 CGGCTCCAATTCATACAATATCCC 59.604 45.833 0.00 0.00 0.00 3.85
1796 2976 5.324409 GGCTCCAATTCATACAATATCCCA 58.676 41.667 0.00 0.00 0.00 4.37
1797 2977 5.183904 GGCTCCAATTCATACAATATCCCAC 59.816 44.000 0.00 0.00 0.00 4.61
1798 2978 6.006449 GCTCCAATTCATACAATATCCCACT 58.994 40.000 0.00 0.00 0.00 4.00
1799 2979 7.168219 GCTCCAATTCATACAATATCCCACTA 58.832 38.462 0.00 0.00 0.00 2.74
1800 2980 7.335422 GCTCCAATTCATACAATATCCCACTAG 59.665 40.741 0.00 0.00 0.00 2.57
1801 2981 8.275187 TCCAATTCATACAATATCCCACTAGT 57.725 34.615 0.00 0.00 0.00 2.57
1802 2982 8.723365 TCCAATTCATACAATATCCCACTAGTT 58.277 33.333 0.00 0.00 0.00 2.24
1803 2983 9.003658 CCAATTCATACAATATCCCACTAGTTC 57.996 37.037 0.00 0.00 0.00 3.01
1804 2984 9.003658 CAATTCATACAATATCCCACTAGTTCC 57.996 37.037 0.00 0.00 0.00 3.62
1805 2985 7.931015 TTCATACAATATCCCACTAGTTCCT 57.069 36.000 0.00 0.00 0.00 3.36
1808 2988 4.781934 ACAATATCCCACTAGTTCCTTGC 58.218 43.478 0.00 0.00 0.00 4.01
1814 2994 4.843728 TCCCACTAGTTCCTTGCTTTATG 58.156 43.478 0.00 0.00 0.00 1.90
1815 2995 4.288626 TCCCACTAGTTCCTTGCTTTATGT 59.711 41.667 0.00 0.00 0.00 2.29
1818 2998 5.817816 CCACTAGTTCCTTGCTTTATGTAGG 59.182 44.000 0.00 0.00 0.00 3.18
1822 3002 8.599792 ACTAGTTCCTTGCTTTATGTAGGTTTA 58.400 33.333 0.00 0.00 0.00 2.01
1828 3008 5.828299 TGCTTTATGTAGGTTTATGGTGC 57.172 39.130 0.00 0.00 0.00 5.01
1844 3024 3.073274 GGTGCTAACCACATTCCTTCT 57.927 47.619 0.00 0.00 46.75 2.85
1845 3025 3.421844 GGTGCTAACCACATTCCTTCTT 58.578 45.455 0.00 0.00 46.75 2.52
1847 3027 4.082733 GGTGCTAACCACATTCCTTCTTTC 60.083 45.833 0.00 0.00 46.75 2.62
1848 3028 4.518970 GTGCTAACCACATTCCTTCTTTCA 59.481 41.667 0.00 0.00 44.06 2.69
1849 3029 5.183904 GTGCTAACCACATTCCTTCTTTCAT 59.816 40.000 0.00 0.00 44.06 2.57
1850 3030 5.774690 TGCTAACCACATTCCTTCTTTCATT 59.225 36.000 0.00 0.00 0.00 2.57
1851 3031 6.267471 TGCTAACCACATTCCTTCTTTCATTT 59.733 34.615 0.00 0.00 0.00 2.32
1852 3032 7.154656 GCTAACCACATTCCTTCTTTCATTTT 58.845 34.615 0.00 0.00 0.00 1.82
1853 3033 7.657354 GCTAACCACATTCCTTCTTTCATTTTT 59.343 33.333 0.00 0.00 0.00 1.94
1885 3070 2.862536 CCGAGTTGAGTACATGCATCAG 59.137 50.000 0.00 0.00 0.00 2.90
1972 3157 4.481368 TCAGGTTTGCACTTATATCCGT 57.519 40.909 0.00 0.00 0.00 4.69
1994 3180 8.861086 TCCGTCTCTCTGCTAATTTAATTAGAT 58.139 33.333 24.02 0.00 43.85 1.98
1995 3181 8.920665 CCGTCTCTCTGCTAATTTAATTAGATG 58.079 37.037 24.02 16.01 43.85 2.90
2014 3200 5.211973 AGATGCTTATACTTCAGACTCCCA 58.788 41.667 0.00 0.00 0.00 4.37
2015 3201 4.737855 TGCTTATACTTCAGACTCCCAC 57.262 45.455 0.00 0.00 0.00 4.61
2016 3202 4.093743 TGCTTATACTTCAGACTCCCACA 58.906 43.478 0.00 0.00 0.00 4.17
2017 3203 4.716784 TGCTTATACTTCAGACTCCCACAT 59.283 41.667 0.00 0.00 0.00 3.21
2053 3245 9.452287 AAAGCCAAATATTGTTTATGCATTCTT 57.548 25.926 3.54 0.00 0.00 2.52
2076 3268 8.107095 TCTTCCAGTTAACCACATAGCTTATTT 58.893 33.333 0.88 0.00 0.00 1.40
2086 3278 6.594159 ACCACATAGCTTATTTGTGTAGTGTC 59.406 38.462 14.00 0.00 39.23 3.67
2087 3279 6.593770 CCACATAGCTTATTTGTGTAGTGTCA 59.406 38.462 14.00 0.00 39.23 3.58
2088 3280 7.413000 CCACATAGCTTATTTGTGTAGTGTCAC 60.413 40.741 14.00 0.00 39.23 3.67
2107 3299 7.552687 AGTGTCACGATGTTATTAATTGTGGAT 59.447 33.333 0.00 0.00 39.14 3.41
2114 3306 8.187480 CGATGTTATTAATTGTGGATTGTTGGA 58.813 33.333 0.00 0.00 0.00 3.53
2115 3307 9.301153 GATGTTATTAATTGTGGATTGTTGGAC 57.699 33.333 0.00 0.00 0.00 4.02
2123 3315 2.293399 GTGGATTGTTGGACTTGTGGTC 59.707 50.000 0.00 0.00 43.79 4.02
2359 3575 8.829746 AGAGAATGTCCATTGATATAGGCAATA 58.170 33.333 0.00 0.00 34.41 1.90
2563 3780 5.176958 AGTTTAAACTACTTGTACTGCTGCG 59.823 40.000 19.26 0.00 37.52 5.18
2589 3806 7.524717 AATATAAATGATGTTACAGGGGCAC 57.475 36.000 0.00 0.00 0.00 5.01
2922 4139 1.008361 ACGTTTTGCGCCAATGATGC 61.008 50.000 4.18 0.00 46.11 3.91
2935 4152 4.266029 GCCAATGATGCATTTACGTTTCTG 59.734 41.667 0.00 0.00 31.05 3.02
2940 4157 8.365210 CAATGATGCATTTACGTTTCTGTAAAC 58.635 33.333 0.00 0.00 44.51 2.01
3278 4496 1.760613 TCATCCGGGAAGGTGTGTATC 59.239 52.381 0.00 0.00 41.99 2.24
3295 4515 7.123247 GGTGTGTATCTGGACTAACTTTACCTA 59.877 40.741 0.00 0.00 0.00 3.08
3454 4674 8.173130 GTCTTTGGTTGTAATAATTGGACTACG 58.827 37.037 0.00 0.00 0.00 3.51
3455 4675 7.879160 TCTTTGGTTGTAATAATTGGACTACGT 59.121 33.333 0.00 0.00 0.00 3.57
3482 4702 7.173218 TGTCCTGTCATGAAGATTGTTAACTTC 59.827 37.037 7.22 2.95 41.67 3.01
3715 4935 3.503749 GTGACAACCACGCAACCA 58.496 55.556 0.00 0.00 35.86 3.67
3789 5009 5.365025 TCCCTGTTCCAGAATAGAAGAGATG 59.635 44.000 5.79 0.00 36.90 2.90
3805 5025 4.319177 AGAGATGTAAACTTTGCTTCGCT 58.681 39.130 6.12 6.12 0.00 4.93
3809 5029 2.044135 GTAAACTTTGCTTCGCTGCAC 58.956 47.619 0.00 0.00 43.20 4.57
3949 5169 2.435693 ATCCTCCCGTACAGGCAGC 61.436 63.158 0.00 0.00 39.21 5.25
4100 5320 2.168106 CAGAGAGTCAATCCTGGAGTGG 59.832 54.545 22.52 5.87 0.00 4.00
4109 5329 2.262915 CTGGAGTGGGCGAGTCAC 59.737 66.667 6.67 0.00 35.51 3.67
4156 5376 2.125512 GCAAGAGGGTCGCGTGAT 60.126 61.111 5.77 0.00 0.00 3.06
4222 5442 4.567747 GGCAAGAGGAAATAACAGGAAGGA 60.568 45.833 0.00 0.00 0.00 3.36
4260 5487 2.667448 CGAACCTGAGAACGAACGATGA 60.667 50.000 0.14 0.00 0.00 2.92
4263 5490 3.318017 ACCTGAGAACGAACGATGAAAG 58.682 45.455 0.14 0.00 0.00 2.62
4450 5686 1.469308 TGTTGGTTGTTGTTGTCGTCC 59.531 47.619 0.00 0.00 0.00 4.79
4488 5731 1.966845 TAGGGCCAAGTCCTAGCTTT 58.033 50.000 6.18 0.00 39.09 3.51
4625 5875 0.322816 TTGCAACCTCTGGATCTGCC 60.323 55.000 0.00 0.00 31.92 4.85
4695 5945 9.603921 AATTTGCAATTTCCTTGGTTATAGATG 57.396 29.630 0.00 0.00 35.25 2.90
4729 5979 2.807392 TGCGGTATCGTGACGTATATGA 59.193 45.455 4.40 0.00 38.89 2.15
4731 5981 3.601211 GCGGTATCGTGACGTATATGAAC 59.399 47.826 4.40 0.00 38.89 3.18
4976 6403 3.599343 ACGGAAGTAAAATAACCCGGTC 58.401 45.455 0.00 0.00 46.88 4.79
4978 6405 3.369787 CGGAAGTAAAATAACCCGGTCCT 60.370 47.826 0.00 0.00 33.94 3.85
4983 6410 5.005740 AGTAAAATAACCCGGTCCTTGTTC 58.994 41.667 0.00 0.00 0.00 3.18
4986 6413 1.829523 TAACCCGGTCCTTGTTCCCG 61.830 60.000 0.00 0.00 41.37 5.14
5053 6480 3.304190 CGTTTTCACTTTACCCCCGAAAG 60.304 47.826 0.00 0.00 39.38 2.62
5092 6519 3.443925 CTCCAGCGCTCGAGGACA 61.444 66.667 22.68 0.00 0.00 4.02
5093 6520 3.408501 CTCCAGCGCTCGAGGACAG 62.409 68.421 22.68 5.73 0.00 3.51
5094 6521 4.504916 CCAGCGCTCGAGGACAGG 62.505 72.222 15.58 0.00 0.00 4.00
5095 6522 3.443925 CAGCGCTCGAGGACAGGA 61.444 66.667 15.58 0.00 0.00 3.86
5096 6523 3.137459 AGCGCTCGAGGACAGGAG 61.137 66.667 15.58 0.00 0.00 3.69
5097 6524 4.200283 GCGCTCGAGGACAGGAGG 62.200 72.222 15.58 0.00 0.00 4.30
5098 6525 2.438614 CGCTCGAGGACAGGAGGA 60.439 66.667 15.58 0.00 0.00 3.71
5099 6526 1.826054 CGCTCGAGGACAGGAGGAT 60.826 63.158 15.58 0.00 0.00 3.24
5106 6533 1.825474 GAGGACAGGAGGATTTGACGA 59.175 52.381 0.00 0.00 0.00 4.20
5129 6556 2.162008 GTGACGACTCTCTGACTAACCC 59.838 54.545 0.00 0.00 0.00 4.11
5130 6557 2.040012 TGACGACTCTCTGACTAACCCT 59.960 50.000 0.00 0.00 0.00 4.34
5131 6558 3.262660 TGACGACTCTCTGACTAACCCTA 59.737 47.826 0.00 0.00 0.00 3.53
5132 6559 3.872771 GACGACTCTCTGACTAACCCTAG 59.127 52.174 0.00 0.00 0.00 3.02
5133 6560 2.614983 CGACTCTCTGACTAACCCTAGC 59.385 54.545 0.00 0.00 0.00 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.133796 GGGCTGAAATGGCGTGGC 62.134 66.667 0.00 0.00 0.00 5.01
6 7 3.814268 CGGGCTGAAATGGCGTGG 61.814 66.667 0.00 0.00 0.00 4.94
7 8 4.481112 GCGGGCTGAAATGGCGTG 62.481 66.667 0.00 0.00 0.00 5.34
8 9 4.722700 AGCGGGCTGAAATGGCGT 62.723 61.111 0.00 0.00 0.00 5.68
9 10 3.401243 GAAGCGGGCTGAAATGGCG 62.401 63.158 0.00 0.00 0.00 5.69
10 11 2.491621 GAAGCGGGCTGAAATGGC 59.508 61.111 0.00 0.00 0.00 4.40
11 12 2.764314 CGGAAGCGGGCTGAAATGG 61.764 63.158 0.00 0.00 0.00 3.16
12 13 2.764314 CCGGAAGCGGGCTGAAATG 61.764 63.158 0.00 0.00 0.00 2.32
13 14 2.438434 CCGGAAGCGGGCTGAAAT 60.438 61.111 0.00 0.00 0.00 2.17
23 24 2.024176 TATTTCTGTGAGCCGGAAGC 57.976 50.000 5.05 0.00 39.58 3.86
24 25 3.600388 AGTTATTTCTGTGAGCCGGAAG 58.400 45.455 5.05 0.00 39.58 3.46
25 26 3.695830 AGTTATTTCTGTGAGCCGGAA 57.304 42.857 5.05 0.00 36.64 4.30
26 27 4.020928 TGTTAGTTATTTCTGTGAGCCGGA 60.021 41.667 5.05 0.00 0.00 5.14
27 28 4.250464 TGTTAGTTATTTCTGTGAGCCGG 58.750 43.478 0.00 0.00 0.00 6.13
28 29 5.637810 TCTTGTTAGTTATTTCTGTGAGCCG 59.362 40.000 0.00 0.00 0.00 5.52
29 30 7.617041 ATCTTGTTAGTTATTTCTGTGAGCC 57.383 36.000 0.00 0.00 0.00 4.70
32 33 9.890629 AGCATATCTTGTTAGTTATTTCTGTGA 57.109 29.630 0.00 0.00 0.00 3.58
42 43 9.547753 CATAGTGGTTAGCATATCTTGTTAGTT 57.452 33.333 0.00 0.00 0.00 2.24
43 44 8.924303 TCATAGTGGTTAGCATATCTTGTTAGT 58.076 33.333 0.00 0.00 0.00 2.24
44 45 9.764363 TTCATAGTGGTTAGCATATCTTGTTAG 57.236 33.333 0.00 0.00 0.00 2.34
46 47 9.632638 AATTCATAGTGGTTAGCATATCTTGTT 57.367 29.630 0.00 0.00 0.00 2.83
47 48 9.632638 AAATTCATAGTGGTTAGCATATCTTGT 57.367 29.630 0.00 0.00 0.00 3.16
48 49 9.888878 CAAATTCATAGTGGTTAGCATATCTTG 57.111 33.333 0.00 0.00 0.00 3.02
49 50 9.071276 CCAAATTCATAGTGGTTAGCATATCTT 57.929 33.333 0.00 0.00 0.00 2.40
50 51 8.439971 TCCAAATTCATAGTGGTTAGCATATCT 58.560 33.333 0.00 0.00 33.88 1.98
51 52 8.507249 GTCCAAATTCATAGTGGTTAGCATATC 58.493 37.037 0.00 0.00 33.88 1.63
52 53 7.448469 GGTCCAAATTCATAGTGGTTAGCATAT 59.552 37.037 0.00 0.00 33.88 1.78
53 54 6.770785 GGTCCAAATTCATAGTGGTTAGCATA 59.229 38.462 0.00 0.00 33.88 3.14
54 55 5.594317 GGTCCAAATTCATAGTGGTTAGCAT 59.406 40.000 0.00 0.00 33.88 3.79
55 56 4.947388 GGTCCAAATTCATAGTGGTTAGCA 59.053 41.667 0.00 0.00 33.88 3.49
56 57 4.947388 TGGTCCAAATTCATAGTGGTTAGC 59.053 41.667 0.00 0.00 33.88 3.09
57 58 7.645058 ATTGGTCCAAATTCATAGTGGTTAG 57.355 36.000 8.75 0.00 33.88 2.34
58 59 9.707957 ATAATTGGTCCAAATTCATAGTGGTTA 57.292 29.630 8.75 0.00 33.88 2.85
59 60 6.933514 AATTGGTCCAAATTCATAGTGGTT 57.066 33.333 8.75 0.00 33.88 3.67
60 61 8.061304 AGATAATTGGTCCAAATTCATAGTGGT 58.939 33.333 8.75 0.00 33.88 4.16
61 62 8.355169 CAGATAATTGGTCCAAATTCATAGTGG 58.645 37.037 8.75 0.00 32.16 4.00
62 63 8.355169 CCAGATAATTGGTCCAAATTCATAGTG 58.645 37.037 8.75 0.00 33.38 2.74
63 64 8.281531 TCCAGATAATTGGTCCAAATTCATAGT 58.718 33.333 8.75 0.00 39.35 2.12
64 65 8.696043 TCCAGATAATTGGTCCAAATTCATAG 57.304 34.615 8.75 0.00 39.35 2.23
69 70 7.290014 GGGTTATCCAGATAATTGGTCCAAATT 59.710 37.037 8.75 6.47 39.35 1.82
129 130 1.016130 GCTAGCAGAAGCAGCGTCAA 61.016 55.000 10.63 0.00 45.49 3.18
131 132 3.393509 GCTAGCAGAAGCAGCGTC 58.606 61.111 10.63 0.00 45.49 5.19
137 154 1.799383 GTGCCTTGCTAGCAGAAGC 59.201 57.895 18.45 20.60 41.87 3.86
141 158 2.435586 AGCGTGCCTTGCTAGCAG 60.436 61.111 18.45 8.63 41.87 4.24
147 164 0.108804 TACTAGTCAGCGTGCCTTGC 60.109 55.000 0.00 0.00 0.00 4.01
231 252 1.147376 CCTTTCCACCACGTGACCA 59.853 57.895 19.30 0.00 35.23 4.02
264 292 3.183776 TTTTCGTTTCGCCCGGCAC 62.184 57.895 10.77 0.00 0.00 5.01
268 296 2.127003 GCCTTTTCGTTTCGCCCG 60.127 61.111 0.00 0.00 0.00 6.13
431 720 1.067516 CCAGCCAGGCGGAATTTTATG 59.932 52.381 14.05 0.00 0.00 1.90
432 721 1.402787 CCAGCCAGGCGGAATTTTAT 58.597 50.000 14.05 0.00 0.00 1.40
433 722 2.880770 CCAGCCAGGCGGAATTTTA 58.119 52.632 14.05 0.00 0.00 1.52
443 732 0.743345 GTAACTAACGGCCAGCCAGG 60.743 60.000 9.78 0.00 41.84 4.45
485 1150 0.031585 TTACACGCACAGAACTCGCT 59.968 50.000 0.00 0.00 0.00 4.93
487 1152 0.782384 GGTTACACGCACAGAACTCG 59.218 55.000 0.00 0.00 0.00 4.18
493 1158 3.419759 GCCCGGTTACACGCACAG 61.420 66.667 0.00 0.00 0.00 3.66
511 1176 0.381801 TAAATAGACGGACGGACGCC 59.618 55.000 0.77 0.00 37.37 5.68
512 1177 1.064654 AGTAAATAGACGGACGGACGC 59.935 52.381 0.77 0.00 37.37 5.19
513 1178 4.536364 TTAGTAAATAGACGGACGGACG 57.464 45.455 0.00 0.00 40.31 4.79
519 1184 7.453439 TGGATGGATGATTAGTAAATAGACGGA 59.547 37.037 0.00 0.00 0.00 4.69
522 1187 9.606631 GGATGGATGGATGATTAGTAAATAGAC 57.393 37.037 0.00 0.00 0.00 2.59
542 1207 1.385915 GGGTGGGAGGATGGATGGA 60.386 63.158 0.00 0.00 0.00 3.41
558 1223 4.410400 GAAGGTGGAGGCGTGGGG 62.410 72.222 0.00 0.00 0.00 4.96
576 1241 3.339093 GAGGGTGTGGGGGAAGGG 61.339 72.222 0.00 0.00 0.00 3.95
577 1242 3.339093 GGAGGGTGTGGGGGAAGG 61.339 72.222 0.00 0.00 0.00 3.46
578 1243 3.339093 GGGAGGGTGTGGGGGAAG 61.339 72.222 0.00 0.00 0.00 3.46
739 1798 1.006220 GGCAAAAACTGGGCCTTCG 60.006 57.895 4.53 0.00 44.32 3.79
744 1803 4.002506 CGGGGGCAAAAACTGGGC 62.003 66.667 0.00 0.00 0.00 5.36
748 1807 0.250770 GAGAGACGGGGGCAAAAACT 60.251 55.000 0.00 0.00 0.00 2.66
762 1821 1.228003 GCGAGGAGATCCGGAGAGA 60.228 63.158 11.34 0.00 42.08 3.10
794 1883 5.351928 TCGAATAAACGAAACGAATCGAG 57.648 39.130 10.55 0.07 45.48 4.04
819 1908 0.690762 GTACAGGACAGGGGAGCAAA 59.309 55.000 0.00 0.00 0.00 3.68
909 2001 2.225068 GAATCGAGCAAGGATTCGGA 57.775 50.000 8.13 0.00 40.06 4.55
912 2004 0.583917 GGCGAATCGAGCAAGGATTC 59.416 55.000 6.91 11.98 43.95 2.52
918 2010 2.125147 CCTGGGCGAATCGAGCAA 60.125 61.111 6.91 0.00 36.08 3.91
919 2011 4.838152 GCCTGGGCGAATCGAGCA 62.838 66.667 6.91 0.00 36.08 4.26
1109 2237 5.845985 GCCAAAAGCAAGGAGAAAAATAC 57.154 39.130 0.00 0.00 42.97 1.89
1131 2268 4.148128 AGTCAGCATCTTACTTCCCATG 57.852 45.455 0.00 0.00 0.00 3.66
1140 2277 0.806102 GCGGCGAAGTCAGCATCTTA 60.806 55.000 12.98 0.00 36.08 2.10
1154 2291 2.477845 CAAGCAAGAAGAGCGGCG 59.522 61.111 0.51 0.51 37.01 6.46
1268 2405 2.050144 CTATCAAGCTGCCCCCTTCTA 58.950 52.381 0.00 0.00 0.00 2.10
1271 2408 0.624500 TCCTATCAAGCTGCCCCCTT 60.625 55.000 0.00 0.00 0.00 3.95
1272 2409 1.004758 TCCTATCAAGCTGCCCCCT 59.995 57.895 0.00 0.00 0.00 4.79
1273 2410 1.348775 ACTCCTATCAAGCTGCCCCC 61.349 60.000 0.00 0.00 0.00 5.40
1274 2411 0.107643 GACTCCTATCAAGCTGCCCC 59.892 60.000 0.00 0.00 0.00 5.80
1275 2412 0.833287 TGACTCCTATCAAGCTGCCC 59.167 55.000 0.00 0.00 0.00 5.36
1276 2413 2.926778 ATGACTCCTATCAAGCTGCC 57.073 50.000 0.00 0.00 30.82 4.85
1277 2414 4.808558 CTCTATGACTCCTATCAAGCTGC 58.191 47.826 0.00 0.00 30.82 5.25
1286 2431 1.957177 CGGCAAGCTCTATGACTCCTA 59.043 52.381 0.00 0.00 0.00 2.94
1288 2433 0.878086 GCGGCAAGCTCTATGACTCC 60.878 60.000 0.00 0.00 44.04 3.85
1357 2529 5.298276 CCAGCGGCTAAATATTTTCCACTAA 59.702 40.000 5.91 0.00 0.00 2.24
1379 2551 1.203441 AGCAGCATCTCAGAACCCCA 61.203 55.000 0.00 0.00 0.00 4.96
1384 2556 2.156917 CCACAAAGCAGCATCTCAGAA 58.843 47.619 0.00 0.00 0.00 3.02
1392 2566 0.100325 CGAACAACCACAAAGCAGCA 59.900 50.000 0.00 0.00 0.00 4.41
1406 2580 4.272504 GTCTTGACATTTTCCTGTCGAACA 59.727 41.667 0.00 0.00 46.89 3.18
1407 2581 4.319549 GGTCTTGACATTTTCCTGTCGAAC 60.320 45.833 3.08 0.00 46.89 3.95
1411 2585 4.557496 GCTTGGTCTTGACATTTTCCTGTC 60.557 45.833 3.08 0.00 44.70 3.51
1412 2586 3.319122 GCTTGGTCTTGACATTTTCCTGT 59.681 43.478 3.08 0.00 0.00 4.00
1511 2685 9.620823 CCAACTACATTGATTGACGTGGTCAAG 62.621 44.444 15.41 5.51 43.78 3.02
1519 2693 5.123820 ACCAATCCAACTACATTGATTGACG 59.876 40.000 11.51 0.82 41.23 4.35
1558 2732 5.533903 ACAAACAAACATCTCTCAGCTCAAT 59.466 36.000 0.00 0.00 0.00 2.57
1763 2943 2.619177 TGAATTGGAGCCGTTCGAAAAA 59.381 40.909 0.00 0.00 0.00 1.94
1766 2946 2.107950 ATGAATTGGAGCCGTTCGAA 57.892 45.000 0.00 0.00 0.00 3.71
1768 2948 2.276201 TGTATGAATTGGAGCCGTTCG 58.724 47.619 0.00 0.00 0.00 3.95
1769 2949 4.900635 ATTGTATGAATTGGAGCCGTTC 57.099 40.909 0.00 0.00 0.00 3.95
1770 2950 5.473504 GGATATTGTATGAATTGGAGCCGTT 59.526 40.000 0.00 0.00 0.00 4.44
1773 2953 5.183904 GTGGGATATTGTATGAATTGGAGCC 59.816 44.000 0.00 0.00 0.00 4.70
1774 2954 6.006449 AGTGGGATATTGTATGAATTGGAGC 58.994 40.000 0.00 0.00 0.00 4.70
1775 2955 8.378565 ACTAGTGGGATATTGTATGAATTGGAG 58.621 37.037 0.00 0.00 0.00 3.86
1777 2957 8.924511 AACTAGTGGGATATTGTATGAATTGG 57.075 34.615 0.00 0.00 0.00 3.16
1778 2958 9.003658 GGAACTAGTGGGATATTGTATGAATTG 57.996 37.037 0.00 0.00 0.00 2.32
1779 2959 8.949421 AGGAACTAGTGGGATATTGTATGAATT 58.051 33.333 0.00 0.00 36.02 2.17
1780 2960 8.511748 AGGAACTAGTGGGATATTGTATGAAT 57.488 34.615 0.00 0.00 36.02 2.57
1781 2961 7.931015 AGGAACTAGTGGGATATTGTATGAA 57.069 36.000 0.00 0.00 36.02 2.57
1782 2962 7.689313 GCAAGGAACTAGTGGGATATTGTATGA 60.689 40.741 0.00 0.00 38.49 2.15
1783 2963 6.428159 GCAAGGAACTAGTGGGATATTGTATG 59.572 42.308 0.00 0.00 38.49 2.39
1784 2964 6.330250 AGCAAGGAACTAGTGGGATATTGTAT 59.670 38.462 0.00 0.00 38.49 2.29
1786 2966 4.475016 AGCAAGGAACTAGTGGGATATTGT 59.525 41.667 0.00 0.00 38.49 2.71
1788 2968 5.717119 AAGCAAGGAACTAGTGGGATATT 57.283 39.130 0.00 0.00 38.49 1.28
1789 2969 5.717119 AAAGCAAGGAACTAGTGGGATAT 57.283 39.130 0.00 0.00 38.49 1.63
1790 2970 6.157994 ACATAAAGCAAGGAACTAGTGGGATA 59.842 38.462 0.00 0.00 38.49 2.59
1791 2971 5.044846 ACATAAAGCAAGGAACTAGTGGGAT 60.045 40.000 0.00 0.00 38.49 3.85
1792 2972 4.288626 ACATAAAGCAAGGAACTAGTGGGA 59.711 41.667 0.00 0.00 38.49 4.37
1793 2973 4.589908 ACATAAAGCAAGGAACTAGTGGG 58.410 43.478 0.00 0.00 38.49 4.61
1794 2974 5.817816 CCTACATAAAGCAAGGAACTAGTGG 59.182 44.000 0.00 0.00 38.49 4.00
1795 2975 6.407202 ACCTACATAAAGCAAGGAACTAGTG 58.593 40.000 0.00 0.00 38.49 2.74
1796 2976 6.622427 ACCTACATAAAGCAAGGAACTAGT 57.378 37.500 0.00 0.00 38.49 2.57
1797 2977 7.923414 AAACCTACATAAAGCAAGGAACTAG 57.077 36.000 0.00 0.00 38.49 2.57
1798 2978 9.391006 CATAAACCTACATAAAGCAAGGAACTA 57.609 33.333 0.00 0.00 38.49 2.24
1800 2980 7.122204 ACCATAAACCTACATAAAGCAAGGAAC 59.878 37.037 0.00 0.00 33.16 3.62
1801 2981 7.122055 CACCATAAACCTACATAAAGCAAGGAA 59.878 37.037 0.00 0.00 33.16 3.36
1802 2982 6.601613 CACCATAAACCTACATAAAGCAAGGA 59.398 38.462 0.00 0.00 33.16 3.36
1803 2983 6.680378 GCACCATAAACCTACATAAAGCAAGG 60.680 42.308 0.00 0.00 35.14 3.61
1804 2984 6.095440 AGCACCATAAACCTACATAAAGCAAG 59.905 38.462 0.00 0.00 0.00 4.01
1805 2985 5.949354 AGCACCATAAACCTACATAAAGCAA 59.051 36.000 0.00 0.00 0.00 3.91
1808 2988 7.927048 GGTTAGCACCATAAACCTACATAAAG 58.073 38.462 0.00 0.00 43.61 1.85
1851 3031 9.545105 TGTACTCAACTCGGTTTATCTTAAAAA 57.455 29.630 0.00 0.00 0.00 1.94
1852 3032 9.715121 ATGTACTCAACTCGGTTTATCTTAAAA 57.285 29.630 0.00 0.00 0.00 1.52
1853 3033 9.146984 CATGTACTCAACTCGGTTTATCTTAAA 57.853 33.333 0.00 0.00 0.00 1.52
1854 3034 7.277098 GCATGTACTCAACTCGGTTTATCTTAA 59.723 37.037 0.00 0.00 0.00 1.85
1855 3035 6.755141 GCATGTACTCAACTCGGTTTATCTTA 59.245 38.462 0.00 0.00 0.00 2.10
1856 3036 5.581085 GCATGTACTCAACTCGGTTTATCTT 59.419 40.000 0.00 0.00 0.00 2.40
1861 3046 3.120321 TGCATGTACTCAACTCGGTTT 57.880 42.857 0.00 0.00 0.00 3.27
1864 3049 2.862536 CTGATGCATGTACTCAACTCGG 59.137 50.000 2.46 0.00 0.00 4.63
1885 3070 4.253685 TGTCACGATGAAGAAATCCCTTC 58.746 43.478 0.00 0.00 42.09 3.46
1994 3180 4.093743 TGTGGGAGTCTGAAGTATAAGCA 58.906 43.478 0.00 0.00 0.00 3.91
1995 3181 4.737855 TGTGGGAGTCTGAAGTATAAGC 57.262 45.455 0.00 0.00 0.00 3.09
1999 3185 5.249393 ACAAGAATGTGGGAGTCTGAAGTAT 59.751 40.000 0.00 0.00 38.69 2.12
2004 3190 4.437682 AAACAAGAATGTGGGAGTCTGA 57.562 40.909 0.00 0.00 40.46 3.27
2009 3195 5.221422 TGGCTTTTAAACAAGAATGTGGGAG 60.221 40.000 0.00 0.00 40.46 4.30
2010 3196 4.651503 TGGCTTTTAAACAAGAATGTGGGA 59.348 37.500 0.00 0.00 40.46 4.37
2012 3198 6.917217 TTTGGCTTTTAAACAAGAATGTGG 57.083 33.333 0.00 0.00 40.46 4.17
2053 3245 7.120579 CACAAATAAGCTATGTGGTTAACTGGA 59.879 37.037 5.42 0.00 41.25 3.86
2076 3268 8.652463 CAATTAATAACATCGTGACACTACACA 58.348 33.333 3.68 0.00 40.34 3.72
2086 3278 8.797215 CAACAATCCACAATTAATAACATCGTG 58.203 33.333 0.00 0.00 0.00 4.35
2087 3279 7.973388 CCAACAATCCACAATTAATAACATCGT 59.027 33.333 0.00 0.00 0.00 3.73
2088 3280 8.187480 TCCAACAATCCACAATTAATAACATCG 58.813 33.333 0.00 0.00 0.00 3.84
2114 3306 3.213206 TCAAGAATGCAGACCACAAGT 57.787 42.857 0.00 0.00 0.00 3.16
2115 3307 3.817084 TCTTCAAGAATGCAGACCACAAG 59.183 43.478 0.00 0.00 0.00 3.16
2123 3315 3.415212 TGGACCTTCTTCAAGAATGCAG 58.585 45.455 0.00 0.00 33.13 4.41
2240 3454 1.067565 TGTTACCTCAGAAGCAGCGAG 60.068 52.381 0.00 0.00 0.00 5.03
2242 3456 1.728971 CTTGTTACCTCAGAAGCAGCG 59.271 52.381 0.00 0.00 0.00 5.18
2359 3575 4.018779 TGGCCTTAGTTAGTTGCATAACCT 60.019 41.667 3.32 0.00 36.49 3.50
2563 3780 8.082242 GTGCCCCTGTAACATCATTTATATTTC 58.918 37.037 0.00 0.00 0.00 2.17
2589 3806 6.428159 AGGAAAGTACATTTAGCTGTTGACAG 59.572 38.462 6.77 6.77 46.40 3.51
2631 3848 4.400251 CCCTGCATATTGAAGTGAACATGT 59.600 41.667 0.00 0.00 0.00 3.21
2760 3977 7.565398 AGAAGGGAGCTATGATAGACAAAACTA 59.435 37.037 3.13 0.00 0.00 2.24
2772 3989 2.367894 CTGCATCAGAAGGGAGCTATGA 59.632 50.000 0.00 0.00 32.44 2.15
2777 3994 0.814812 GCTCTGCATCAGAAGGGAGC 60.815 60.000 4.79 4.79 40.18 4.70
2778 3995 0.540454 TGCTCTGCATCAGAAGGGAG 59.460 55.000 0.00 0.00 40.18 4.30
2912 4129 4.266029 CAGAAACGTAAATGCATCATTGGC 59.734 41.667 0.00 0.00 34.04 4.52
2922 4139 7.851822 AGCATTGTTTACAGAAACGTAAATG 57.148 32.000 0.00 7.31 46.76 2.32
2935 4152 7.989826 AGATGGATGAAGTTAGCATTGTTTAC 58.010 34.615 0.00 0.00 0.00 2.01
2940 4157 7.330900 AGAAAGATGGATGAAGTTAGCATTG 57.669 36.000 0.00 0.00 0.00 2.82
3112 4330 8.400186 CACAAATTATCATATGCAAGTGTCAGA 58.600 33.333 0.00 0.00 0.00 3.27
3278 4496 7.463961 TGAGAACTAGGTAAAGTTAGTCCAG 57.536 40.000 0.00 0.00 39.78 3.86
3295 4515 4.660168 ACAGGCAGAAATTCATGAGAACT 58.340 39.130 0.00 0.00 36.39 3.01
3348 4568 7.692291 CAGTCAAACACATAATCGAATTGGTAC 59.308 37.037 0.00 0.00 0.00 3.34
3454 4674 5.695851 AACAATCTTCATGACAGGACAAC 57.304 39.130 0.00 0.00 0.00 3.32
3455 4675 6.998074 AGTTAACAATCTTCATGACAGGACAA 59.002 34.615 8.61 0.00 0.00 3.18
3482 4702 3.125316 GGCTGAACCAAGAATAGTGAACG 59.875 47.826 0.00 0.00 38.86 3.95
3667 4887 2.238395 GAGAAGCACTGGGATTCCTTCT 59.762 50.000 3.97 0.74 42.90 2.85
3669 4889 2.026449 CAGAGAAGCACTGGGATTCCTT 60.026 50.000 3.97 0.00 42.90 3.36
3715 4935 1.203994 CGATACAGTTTCCCGTGGTCT 59.796 52.381 0.00 0.00 0.00 3.85
3805 5025 1.913778 TAGAAGGTCCACTACGTGCA 58.086 50.000 0.00 0.00 31.34 4.57
3809 5029 3.770666 CACACATAGAAGGTCCACTACG 58.229 50.000 0.00 0.00 0.00 3.51
3892 5112 1.971357 GTCCTCTCCACAGTCCTTTCA 59.029 52.381 0.00 0.00 0.00 2.69
3949 5169 1.088340 CAACTGCTCTCCTGGATGCG 61.088 60.000 14.29 11.89 0.00 4.73
4222 5442 2.534533 GGGTTCCCTTGTCCCCCT 60.535 66.667 0.00 0.00 35.52 4.79
4245 5472 3.987868 CCTTCTTTCATCGTTCGTTCTCA 59.012 43.478 0.00 0.00 0.00 3.27
4260 5487 3.946907 CGGCGTCGTTCCTTCTTT 58.053 55.556 0.00 0.00 0.00 2.52
4347 5578 1.304381 GGCTGGAGCACCATGGAAA 60.304 57.895 21.47 0.00 45.87 3.13
4466 5709 0.909623 GCTAGGACTTGGCCCTAACA 59.090 55.000 0.00 0.00 35.98 2.41
4488 5731 6.134535 ACCACCTCTAAATTAATCACCACA 57.865 37.500 0.00 0.00 0.00 4.17
4673 5923 7.615365 AGAACATCTATAACCAAGGAAATTGCA 59.385 33.333 0.00 0.00 37.60 4.08
4674 5924 8.000780 AGAACATCTATAACCAAGGAAATTGC 57.999 34.615 0.00 0.00 37.60 3.56
4677 5927 7.615365 TGCAAGAACATCTATAACCAAGGAAAT 59.385 33.333 0.00 0.00 0.00 2.17
4679 5929 6.480763 TGCAAGAACATCTATAACCAAGGAA 58.519 36.000 0.00 0.00 0.00 3.36
4695 5945 0.521291 TACCGCAGCAATGCAAGAAC 59.479 50.000 8.35 0.00 34.41 3.01
4729 5979 4.202111 GGCCATTTCTTGTACAACACAGTT 60.202 41.667 3.59 0.00 38.72 3.16
4731 5981 3.569701 AGGCCATTTCTTGTACAACACAG 59.430 43.478 5.01 0.00 38.72 3.66
4790 6068 1.153706 GCCGCAGCAATTGAGCATT 60.154 52.632 19.14 0.00 39.53 3.56
4791 6069 2.050350 AGCCGCAGCAATTGAGCAT 61.050 52.632 19.14 5.78 43.56 3.79
4801 6079 0.168128 ATCGTTTTAACAGCCGCAGC 59.832 50.000 0.00 0.00 40.32 5.25
4991 6418 2.997315 TCCCTCCTGCCAGTGACG 60.997 66.667 0.00 0.00 0.00 4.35
5004 6431 4.101448 GCTGACATGCCGGTCCCT 62.101 66.667 1.90 0.00 36.97 4.20
5053 6480 2.415491 GCCAGGCGTGATTTTTACTTCC 60.415 50.000 8.24 0.00 0.00 3.46
5091 6518 2.996621 GTCACTTCGTCAAATCCTCCTG 59.003 50.000 0.00 0.00 0.00 3.86
5092 6519 2.352814 CGTCACTTCGTCAAATCCTCCT 60.353 50.000 0.00 0.00 0.00 3.69
5093 6520 1.993370 CGTCACTTCGTCAAATCCTCC 59.007 52.381 0.00 0.00 0.00 4.30
5094 6521 2.662156 GTCGTCACTTCGTCAAATCCTC 59.338 50.000 0.00 0.00 0.00 3.71
5095 6522 2.296471 AGTCGTCACTTCGTCAAATCCT 59.704 45.455 0.00 0.00 0.00 3.24
5096 6523 2.662156 GAGTCGTCACTTCGTCAAATCC 59.338 50.000 0.00 0.00 30.63 3.01
5097 6524 3.566523 AGAGTCGTCACTTCGTCAAATC 58.433 45.455 0.00 0.00 30.63 2.17
5098 6525 3.253677 AGAGAGTCGTCACTTCGTCAAAT 59.746 43.478 0.00 0.00 30.63 2.32
5099 6526 2.617308 AGAGAGTCGTCACTTCGTCAAA 59.383 45.455 0.00 0.00 30.63 2.69
5106 6533 3.502979 GGTTAGTCAGAGAGTCGTCACTT 59.497 47.826 0.00 0.00 30.63 3.16


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

AutoCloner maintained by Alex Coulton.