Multiple sequence alignment - TraesCS5D01G146000

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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 TraesCS5D01G146000 chr5D 100.000 5259 0 0 1 5259 232622668 232617410 0.000000e+00 9712.0
1 TraesCS5D01G146000 chr5D 88.136 118 12 2 3953 4069 507378679 507378795 7.100000e-29 139.0
2 TraesCS5D01G146000 chr5A 94.720 1856 75 13 1746 3599 322613269 322615103 0.000000e+00 2863.0
3 TraesCS5D01G146000 chr5A 89.802 1618 89 36 127 1712 322611538 322613111 0.000000e+00 2004.0
4 TraesCS5D01G146000 chr5A 94.633 1062 41 10 3661 4714 322615310 322616363 0.000000e+00 1631.0
5 TraesCS5D01G146000 chr5A 90.299 134 9 2 1 131 322603511 322603643 7.000000e-39 172.0
6 TraesCS5D01G146000 chr5B 90.073 1793 110 30 3520 5259 272194718 272196495 0.000000e+00 2263.0
7 TraesCS5D01G146000 chr5B 96.386 1245 45 0 2242 3486 272193375 272194619 0.000000e+00 2050.0
8 TraesCS5D01G146000 chr5B 88.965 1169 64 30 560 1712 272191640 272192759 0.000000e+00 1384.0
9 TraesCS5D01G146000 chr5B 92.739 303 17 4 127 428 272191068 272191366 2.910000e-117 433.0
10 TraesCS5D01G146000 chr5B 95.050 202 9 1 1885 2086 272193092 272193292 3.060000e-82 316.0
11 TraesCS5D01G146000 chr5B 95.855 193 6 2 1745 1935 272192913 272193105 1.420000e-80 311.0
12 TraesCS5D01G146000 chr5B 90.000 140 12 2 427 564 272191470 272191609 4.180000e-41 180.0
13 TraesCS5D01G146000 chr5B 90.840 131 8 3 1 131 272190899 272191025 7.000000e-39 172.0
14 TraesCS5D01G146000 chr5B 88.136 118 12 2 3953 4069 637389059 637389175 7.100000e-29 139.0
15 TraesCS5D01G146000 chr5B 89.610 77 4 2 2117 2193 272193293 272193365 1.560000e-15 95.3
16 TraesCS5D01G146000 chr7A 88.136 118 12 2 3953 4069 138661418 138661534 7.100000e-29 139.0
17 TraesCS5D01G146000 chr7D 82.524 103 16 2 3717 3818 99952918 99952817 7.250000e-14 89.8
18 TraesCS5D01G146000 chr7B 81.553 103 17 2 3717 3818 55341222 55341121 3.370000e-12 84.2


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 TraesCS5D01G146000 chr5D 232617410 232622668 5258 True 9712.000000 9712 100.000000 1 5259 1 chr5D.!!$R1 5258
1 TraesCS5D01G146000 chr5A 322611538 322616363 4825 False 2166.000000 2863 93.051667 127 4714 3 chr5A.!!$F2 4587
2 TraesCS5D01G146000 chr5B 272190899 272196495 5596 False 800.477778 2263 92.168667 1 5259 9 chr5B.!!$F2 5258

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
825 1028 0.107848 ACCAGCCGTTATTCCTTCCG 60.108 55.0 0.00 0.00 0.00 4.30 F
847 1054 0.324830 CGTCCTTTCCTCCTCCTCCT 60.325 60.0 0.00 0.00 0.00 3.69 F
1500 1724 0.621082 AAAGGCTAGGGCACTTCCTC 59.379 55.0 9.59 0.00 40.87 3.71 F
2820 3208 0.249657 CGGAGAGCATAGGCACTTCC 60.250 60.0 0.67 4.48 41.23 3.46 F
3348 3736 0.669318 TCATCGAACTGTTGCCCGAC 60.669 55.0 0.00 0.00 33.69 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 2593 1.447317 AAACGTGCTCCACAGGCTTG 61.447 55.0 0.00 0.0 37.69 4.01 R
2493 2881 1.763968 TCAGGTACATCTCTGTCCGG 58.236 55.0 0.00 0.0 36.79 5.14 R
3327 3715 0.389817 CGGGCAACAGTTCGATGAGA 60.390 55.0 0.00 0.0 39.74 3.27 R
3823 4466 0.456995 CCGAGAAGGACGACTTGAGC 60.457 60.0 2.07 0.0 45.00 4.26 R
5099 5753 0.036732 TGCATGTGGGAGGAGAACAC 59.963 55.0 0.00 0.0 35.75 3.32 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
81 82 3.270877 GCGTGGATTTCCTGTCTGTTAT 58.729 45.455 0.00 0.00 36.82 1.89
84 85 4.330074 CGTGGATTTCCTGTCTGTTATGAC 59.670 45.833 0.00 0.00 36.82 3.06
96 97 3.194329 TCTGTTATGACTGACTGAGCCAG 59.806 47.826 0.00 0.00 37.52 4.85
98 99 3.257393 GTTATGACTGACTGAGCCAGTG 58.743 50.000 6.04 2.71 45.44 3.66
99 100 1.346062 ATGACTGACTGAGCCAGTGT 58.654 50.000 6.04 5.54 45.44 3.55
112 113 1.542915 GCCAGTGTCACAGATTGCAAT 59.457 47.619 12.83 12.83 0.00 3.56
120 121 1.464608 CACAGATTGCAATCCGTCGTT 59.535 47.619 31.05 12.62 36.04 3.85
134 181 2.344441 CCGTCGTTGCATTAGTACAGTG 59.656 50.000 0.00 0.00 0.00 3.66
141 188 7.477422 GTCGTTGCATTAGTACAGTGTTATTTG 59.523 37.037 0.00 0.00 0.00 2.32
164 211 6.264832 TGCGATGCAAGGTATTTTCATTTAG 58.735 36.000 0.00 0.00 34.76 1.85
213 260 4.131596 CTGACCGAAGTAAAAGGAACCAA 58.868 43.478 0.00 0.00 0.00 3.67
214 261 3.878699 TGACCGAAGTAAAAGGAACCAAC 59.121 43.478 0.00 0.00 0.00 3.77
215 262 3.878699 GACCGAAGTAAAAGGAACCAACA 59.121 43.478 0.00 0.00 0.00 3.33
216 263 4.271661 ACCGAAGTAAAAGGAACCAACAA 58.728 39.130 0.00 0.00 0.00 2.83
265 312 0.464036 TAGCAACATGGCTAGACCCG 59.536 55.000 0.00 0.00 43.70 5.28
347 394 1.561542 CAGCCTTTGTCCCCTAGTCAT 59.438 52.381 0.00 0.00 0.00 3.06
495 648 3.758023 TGTTGAATTGCACCCTCATACAG 59.242 43.478 0.00 0.00 0.00 2.74
506 659 6.058183 GCACCCTCATACAGAACAATATTCT 58.942 40.000 0.00 0.00 0.00 2.40
507 660 7.147567 TGCACCCTCATACAGAACAATATTCTA 60.148 37.037 0.00 0.00 0.00 2.10
535 688 4.688021 AGCATCCTTCTTCGAATGTACTC 58.312 43.478 0.00 0.00 0.00 2.59
540 693 3.447586 CCTTCTTCGAATGTACTCCTCCA 59.552 47.826 0.00 0.00 0.00 3.86
542 695 4.920640 TCTTCGAATGTACTCCTCCATC 57.079 45.455 0.00 0.00 0.00 3.51
543 696 3.637229 TCTTCGAATGTACTCCTCCATCC 59.363 47.826 0.00 0.00 0.00 3.51
544 697 3.314307 TCGAATGTACTCCTCCATCCT 57.686 47.619 0.00 0.00 0.00 3.24
554 708 7.792032 TGTACTCCTCCATCCTAAAATAAGTG 58.208 38.462 0.00 0.00 0.00 3.16
673 868 4.335594 AGGCACTTGTGTTTCTTTGTACTC 59.664 41.667 2.61 0.00 27.25 2.59
674 869 4.497507 GGCACTTGTGTTTCTTTGTACTCC 60.498 45.833 2.61 0.00 0.00 3.85
675 870 4.335594 GCACTTGTGTTTCTTTGTACTCCT 59.664 41.667 2.61 0.00 0.00 3.69
825 1028 0.107848 ACCAGCCGTTATTCCTTCCG 60.108 55.000 0.00 0.00 0.00 4.30
847 1054 0.324830 CGTCCTTTCCTCCTCCTCCT 60.325 60.000 0.00 0.00 0.00 3.69
883 1090 2.048127 GTGAGCTGTGGGACGTCC 60.048 66.667 27.04 27.04 0.00 4.79
958 1168 1.133419 AGGCAGAGTAGGTAGGTAGGC 60.133 57.143 0.00 0.00 0.00 3.93
962 1172 1.133419 AGAGTAGGTAGGTAGGCAGGC 60.133 57.143 0.00 0.00 0.00 4.85
975 1193 1.006998 AGGCAGGCACCATCCATTTTA 59.993 47.619 0.00 0.00 0.00 1.52
1089 1307 3.169378 TGCAACCCCATGAGCAGA 58.831 55.556 0.00 0.00 32.48 4.26
1240 1458 2.485814 GTCACAAACTCAGGATCCTTGC 59.514 50.000 13.00 0.00 0.00 4.01
1241 1459 1.815003 CACAAACTCAGGATCCTTGCC 59.185 52.381 13.00 0.00 0.00 4.52
1242 1460 1.425066 ACAAACTCAGGATCCTTGCCA 59.575 47.619 13.00 0.00 0.00 4.92
1243 1461 2.089980 CAAACTCAGGATCCTTGCCAG 58.910 52.381 13.00 8.32 0.00 4.85
1257 1475 2.113860 TGCCAGCCAGTTTAGATCAC 57.886 50.000 0.00 0.00 0.00 3.06
1258 1476 1.009829 GCCAGCCAGTTTAGATCACG 58.990 55.000 0.00 0.00 0.00 4.35
1289 1507 0.776810 TCATGGGTTTCAGGCCAAGA 59.223 50.000 5.01 0.00 0.00 3.02
1290 1508 1.146774 TCATGGGTTTCAGGCCAAGAA 59.853 47.619 5.01 5.95 0.00 2.52
1462 1680 1.586422 AGATCGTCCCATGATTTGCG 58.414 50.000 0.00 0.00 0.00 4.85
1468 1686 2.476619 CGTCCCATGATTTGCGTAGATC 59.523 50.000 0.00 0.00 0.00 2.75
1470 1688 1.800586 CCCATGATTTGCGTAGATCCG 59.199 52.381 1.64 0.00 0.00 4.18
1484 1702 5.041940 CGTAGATCCGGTTCTCCTTTAAAG 58.958 45.833 18.31 8.32 0.00 1.85
1491 1715 3.681874 CGGTTCTCCTTTAAAGGCTAGGG 60.682 52.174 26.75 14.41 46.06 3.53
1500 1724 0.621082 AAAGGCTAGGGCACTTCCTC 59.379 55.000 9.59 0.00 40.87 3.71
1516 1740 5.654650 CACTTCCTCTGTTATACTCCTCAGT 59.345 44.000 0.00 0.00 36.55 3.41
1526 1750 9.743057 CTGTTATACTCCTCAGTTTCTGAATAG 57.257 37.037 1.22 4.34 40.18 1.73
1527 1751 8.696374 TGTTATACTCCTCAGTTTCTGAATAGG 58.304 37.037 1.22 0.00 40.18 2.57
1545 1769 7.632861 TGAATAGGTTCATCTGAAAAGATCCA 58.367 34.615 0.00 0.00 39.36 3.41
1547 1771 9.784531 GAATAGGTTCATCTGAAAAGATCCATA 57.215 33.333 0.00 0.00 35.58 2.74
1554 1778 5.114764 TCTGAAAAGATCCATATGTGGCA 57.885 39.130 3.06 0.00 45.63 4.92
1589 1813 5.122869 CACTAGCAGCATTAGTTCAACATGT 59.877 40.000 0.00 0.00 0.00 3.21
1607 1831 9.990360 TCAACATGTTCTGTTTATGTTAGTCTA 57.010 29.630 8.48 0.00 45.98 2.59
1609 1833 9.772973 AACATGTTCTGTTTATGTTAGTCTACA 57.227 29.630 4.92 0.00 45.98 2.74
1610 1834 9.772973 ACATGTTCTGTTTATGTTAGTCTACAA 57.227 29.630 0.00 0.00 32.90 2.41
1634 1858 9.489393 CAAGTTTGAGTTTTATTTTCCTTTTGC 57.511 29.630 0.00 0.00 0.00 3.68
1635 1859 8.208718 AGTTTGAGTTTTATTTTCCTTTTGCC 57.791 30.769 0.00 0.00 0.00 4.52
1637 1861 8.335356 GTTTGAGTTTTATTTTCCTTTTGCCTC 58.665 33.333 0.00 0.00 0.00 4.70
1638 1862 7.118496 TGAGTTTTATTTTCCTTTTGCCTCA 57.882 32.000 0.00 0.00 0.00 3.86
1639 1863 7.560368 TGAGTTTTATTTTCCTTTTGCCTCAA 58.440 30.769 0.00 0.00 0.00 3.02
1640 1864 7.710475 TGAGTTTTATTTTCCTTTTGCCTCAAG 59.290 33.333 0.00 0.00 0.00 3.02
1641 1865 7.791029 AGTTTTATTTTCCTTTTGCCTCAAGA 58.209 30.769 0.00 0.00 0.00 3.02
1642 1866 8.432013 AGTTTTATTTTCCTTTTGCCTCAAGAT 58.568 29.630 0.00 0.00 0.00 2.40
1643 1867 9.056005 GTTTTATTTTCCTTTTGCCTCAAGATT 57.944 29.630 0.00 0.00 0.00 2.40
1644 1868 8.606040 TTTATTTTCCTTTTGCCTCAAGATTG 57.394 30.769 0.00 0.00 0.00 2.67
1653 1877 5.381174 TTGCCTCAAGATTGTTTCATCAG 57.619 39.130 0.00 0.00 0.00 2.90
1674 1898 5.044919 TCAGTTGGTCATTCTGAACCCATAT 60.045 40.000 6.22 0.00 31.76 1.78
1675 1899 5.297776 CAGTTGGTCATTCTGAACCCATATC 59.702 44.000 6.22 2.54 31.76 1.63
1682 1906 6.774656 GTCATTCTGAACCCATATCCTGAATT 59.225 38.462 0.00 0.00 0.00 2.17
1683 1907 7.286316 GTCATTCTGAACCCATATCCTGAATTT 59.714 37.037 0.00 0.00 0.00 1.82
1684 1908 8.501904 TCATTCTGAACCCATATCCTGAATTTA 58.498 33.333 0.00 0.00 0.00 1.40
1685 1909 9.305555 CATTCTGAACCCATATCCTGAATTTAT 57.694 33.333 0.00 0.00 0.00 1.40
1712 1936 4.278170 TGTTGGCAAACTGAAAGAGTATGG 59.722 41.667 0.00 0.00 37.19 2.74
1714 1938 4.922206 TGGCAAACTGAAAGAGTATGGAT 58.078 39.130 0.00 0.00 37.43 3.41
1717 1941 7.118723 TGGCAAACTGAAAGAGTATGGATTAT 58.881 34.615 0.00 0.00 37.43 1.28
1719 1943 9.289782 GGCAAACTGAAAGAGTATGGATTATAT 57.710 33.333 0.00 0.00 37.43 0.86
1750 2099 5.281693 TGTCAACAGAATTATGCTTCACG 57.718 39.130 0.00 0.00 0.00 4.35
1831 2182 4.891756 AGGATATTTTCAGATGTTGCTGGG 59.108 41.667 0.00 0.00 36.55 4.45
1867 2218 2.442236 TGGATGGCCAATCTTTCCTC 57.558 50.000 20.46 6.99 42.49 3.71
1962 2350 1.564348 AGTGTGTGTTTCCCTCTTGGT 59.436 47.619 0.00 0.00 34.77 3.67
2029 2417 3.817647 CCTTAGCTTCAGTTATCATGGCC 59.182 47.826 0.00 0.00 0.00 5.36
2091 2479 2.166870 ACTAATGGGTTCGCGTACATGA 59.833 45.455 17.79 5.30 0.00 3.07
2096 2484 2.132762 GGGTTCGCGTACATGATTAGG 58.867 52.381 17.79 0.00 0.00 2.69
2112 2500 4.412199 TGATTAGGAATGTTTCGGGATCCT 59.588 41.667 12.58 0.00 42.89 3.24
2137 2525 2.286425 CATGTGGGGAGAGGGGGT 60.286 66.667 0.00 0.00 0.00 4.95
2139 2527 1.151361 ATGTGGGGAGAGGGGGTTT 60.151 57.895 0.00 0.00 0.00 3.27
2170 2558 8.180920 GCAAACAAATTGTGATTGGTACTTTTT 58.819 29.630 11.18 0.00 39.69 1.94
2194 2582 7.849804 TTCTTCTTTCTGATGCCTATTGTAC 57.150 36.000 0.00 0.00 0.00 2.90
2205 2593 2.474816 CCTATTGTACGAGCTGAAGCC 58.525 52.381 0.00 0.00 43.38 4.35
2207 2595 2.472695 ATTGTACGAGCTGAAGCCAA 57.527 45.000 0.00 0.00 43.38 4.52
2238 2626 3.368321 CACGTTTGATCATACCGTGTG 57.632 47.619 23.37 16.11 42.72 3.82
2239 2627 2.734606 CACGTTTGATCATACCGTGTGT 59.265 45.455 23.37 9.74 42.72 3.72
2304 2692 4.098960 AGAATAAGACGAATGGTAGCCGAA 59.901 41.667 0.00 0.00 0.00 4.30
2379 2767 2.020559 GCATTCGAACTCGCTGCG 59.979 61.111 17.25 17.25 37.73 5.18
2397 2785 1.666189 GCGAAGTTCTGTTATGGGAGC 59.334 52.381 0.56 0.00 0.00 4.70
2478 2866 7.326454 TGGAAATGACAGAAGACTATCAAGAG 58.674 38.462 0.00 0.00 33.14 2.85
2608 2996 3.495001 GGAGGAAATCGGATTTGTCGATC 59.505 47.826 19.96 9.98 45.20 3.69
2754 3142 7.804147 AGGATCTTTCTGCTCTAAGAATTGAT 58.196 34.615 0.00 0.00 36.12 2.57
2799 3187 1.216710 GAGGAGAAGTGGCGTGAGG 59.783 63.158 0.00 0.00 0.00 3.86
2820 3208 0.249657 CGGAGAGCATAGGCACTTCC 60.250 60.000 0.67 4.48 41.23 3.46
2823 3211 2.158696 GGAGAGCATAGGCACTTCCATT 60.159 50.000 0.67 0.00 41.23 3.16
2826 3214 3.455910 AGAGCATAGGCACTTCCATTGTA 59.544 43.478 0.67 0.00 44.61 2.41
3015 3403 1.875576 GCGATAGAGGTTGATGCAGGG 60.876 57.143 0.00 0.00 39.76 4.45
3108 3496 1.002134 CCCCTCCATGCAAACGAGT 60.002 57.895 0.00 0.00 0.00 4.18
3144 3532 1.065109 CGACACGGTCCATCGCATA 59.935 57.895 0.00 0.00 0.00 3.14
3153 3541 3.149196 GGTCCATCGCATATTGGTCAAT 58.851 45.455 1.65 1.65 34.48 2.57
3183 3571 5.359009 GCAAAGGATTGAGGAAGATGATTCA 59.641 40.000 0.00 0.00 38.94 2.57
3237 3625 0.820871 GACTCAAGTCTCCGAGCCAT 59.179 55.000 2.86 0.00 41.65 4.40
3345 3733 1.338200 ACTCTCATCGAACTGTTGCCC 60.338 52.381 0.00 0.00 0.00 5.36
3348 3736 0.669318 TCATCGAACTGTTGCCCGAC 60.669 55.000 0.00 0.00 33.69 4.79
3351 3739 0.892755 TCGAACTGTTGCCCGACTAT 59.107 50.000 0.00 0.00 0.00 2.12
3460 3848 4.334203 TGGTAGTTGTGTGTAGCAAACTTG 59.666 41.667 0.00 0.00 33.65 3.16
3570 4023 8.136563 AGCATGATATCTGTAGATGAGAATGT 57.863 34.615 3.98 0.00 36.05 2.71
3571 4024 8.035984 AGCATGATATCTGTAGATGAGAATGTG 58.964 37.037 3.98 0.00 36.05 3.21
3572 4025 7.278203 GCATGATATCTGTAGATGAGAATGTGG 59.722 40.741 3.98 0.00 36.05 4.17
3641 4260 6.067263 TGAATAAAGTTCTGAACCAAACGG 57.933 37.500 16.48 0.00 0.00 4.44
3642 4261 5.591067 TGAATAAAGTTCTGAACCAAACGGT 59.409 36.000 16.48 0.00 38.95 4.83
3643 4262 3.775661 AAAGTTCTGAACCAAACGGTG 57.224 42.857 16.48 0.00 36.67 4.94
3644 4263 2.413310 AGTTCTGAACCAAACGGTGT 57.587 45.000 16.48 0.00 36.67 4.16
3645 4264 3.547054 AGTTCTGAACCAAACGGTGTA 57.453 42.857 16.48 0.00 36.67 2.90
3646 4265 4.081322 AGTTCTGAACCAAACGGTGTAT 57.919 40.909 16.48 0.00 36.67 2.29
3649 4268 6.235664 AGTTCTGAACCAAACGGTGTATATT 58.764 36.000 16.48 0.00 36.67 1.28
3651 4270 6.489127 TCTGAACCAAACGGTGTATATTTG 57.511 37.500 0.00 0.00 36.67 2.32
3652 4271 6.231951 TCTGAACCAAACGGTGTATATTTGA 58.768 36.000 0.00 0.00 36.67 2.69
3653 4272 6.711194 TCTGAACCAAACGGTGTATATTTGAA 59.289 34.615 0.00 0.00 36.67 2.69
3655 4274 8.563123 TGAACCAAACGGTGTATATTTGAATA 57.437 30.769 0.00 0.00 36.67 1.75
3657 4276 9.843334 GAACCAAACGGTGTATATTTGAATAAA 57.157 29.630 0.00 0.00 36.67 1.40
3685 4328 2.042464 GATCAGGCACACCCATCTCTA 58.958 52.381 0.00 0.00 36.11 2.43
3823 4466 1.064946 CTACTTCGAGCAGCTCCGG 59.935 63.158 17.16 9.28 0.00 5.14
3901 4544 2.903855 CAGCGGATCACCATGCCC 60.904 66.667 0.00 0.00 35.59 5.36
4246 4889 1.279271 AGGAGGAAGAAACCATCGGTG 59.721 52.381 0.00 0.00 35.34 4.94
4299 4946 2.902846 CCACGTGCGGGGAAACAA 60.903 61.111 10.91 0.00 42.48 2.83
4473 5120 6.959639 AATGCTTTTGGAACTGACTTCTAA 57.040 33.333 0.00 0.00 0.00 2.10
4474 5121 6.566197 ATGCTTTTGGAACTGACTTCTAAG 57.434 37.500 0.00 0.00 31.52 2.18
4475 5122 5.680619 TGCTTTTGGAACTGACTTCTAAGA 58.319 37.500 0.00 0.00 31.52 2.10
4505 5152 9.999009 GGTTAGTGAAGTAAATAGCATAAAACC 57.001 33.333 0.00 0.00 0.00 3.27
4509 5156 7.668052 AGTGAAGTAAATAGCATAAAACCACCA 59.332 33.333 0.00 0.00 0.00 4.17
4520 5167 3.895704 AAAACCACCACATTCTAGGGT 57.104 42.857 0.00 0.00 34.59 4.34
4540 5187 4.231718 GTTTCAGAAAACCACCGCATTA 57.768 40.909 0.00 0.00 39.10 1.90
4636 5283 8.297426 GGTTGAGATGTCGTTAGATCATGTATA 58.703 37.037 0.00 0.00 0.00 1.47
4689 5343 2.781681 ACCTGTAATTTCCTGGTCGG 57.218 50.000 0.00 0.00 29.09 4.79
4693 5347 1.894466 TGTAATTTCCTGGTCGGTCGA 59.106 47.619 0.00 0.00 0.00 4.20
4694 5348 2.498481 TGTAATTTCCTGGTCGGTCGAT 59.502 45.455 0.00 0.00 0.00 3.59
4703 5357 1.407618 TGGTCGGTCGATCCTGTATTG 59.592 52.381 0.95 0.00 0.00 1.90
4709 5363 3.393800 GGTCGATCCTGTATTGATGTGG 58.606 50.000 0.00 0.00 30.42 4.17
4710 5364 3.181465 GGTCGATCCTGTATTGATGTGGT 60.181 47.826 0.00 0.00 30.42 4.16
4712 5366 3.069586 TCGATCCTGTATTGATGTGGTCC 59.930 47.826 0.00 0.00 0.00 4.46
4715 5369 2.092968 TCCTGTATTGATGTGGTCCTGC 60.093 50.000 0.00 0.00 0.00 4.85
4716 5370 2.092753 CCTGTATTGATGTGGTCCTGCT 60.093 50.000 0.00 0.00 0.00 4.24
4718 5372 3.609853 TGTATTGATGTGGTCCTGCTTC 58.390 45.455 0.00 0.00 0.00 3.86
4720 5374 0.684535 TTGATGTGGTCCTGCTTCGA 59.315 50.000 0.00 0.00 0.00 3.71
4745 5399 4.534168 CATATGCTTCTCGCCATCTTTTG 58.466 43.478 0.00 0.00 38.05 2.44
4748 5402 1.806542 GCTTCTCGCCATCTTTTGTGA 59.193 47.619 0.00 0.00 0.00 3.58
4758 5412 6.040955 TCGCCATCTTTTGTGATATAGAGAGT 59.959 38.462 0.00 0.00 0.00 3.24
4768 5422 9.702253 TTTGTGATATAGAGAGTTAGTTCCTCT 57.298 33.333 0.00 0.00 41.91 3.69
4779 5433 5.088026 AGTTAGTTCCTCTTCCACTTAGCT 58.912 41.667 0.00 0.00 0.00 3.32
4787 5441 4.220821 CCTCTTCCACTTAGCTACAACTCA 59.779 45.833 0.00 0.00 0.00 3.41
4794 5448 5.127194 CCACTTAGCTACAACTCATCTACCA 59.873 44.000 0.00 0.00 0.00 3.25
4795 5449 6.183360 CCACTTAGCTACAACTCATCTACCAT 60.183 42.308 0.00 0.00 0.00 3.55
4814 5468 4.101448 GCACCCACGCTCATCCCT 62.101 66.667 0.00 0.00 0.00 4.20
4836 5490 2.743195 GCTGACAAGCTCTACCGTG 58.257 57.895 0.00 0.00 46.60 4.94
4837 5491 0.038159 GCTGACAAGCTCTACCGTGT 60.038 55.000 0.00 0.00 46.60 4.49
4854 5508 2.030457 CGTGTCAATTTCCTCGTATGGC 59.970 50.000 0.00 0.00 0.00 4.40
4882 5536 4.686695 TCCGGACAGGATCAGAGG 57.313 61.111 0.00 0.00 45.98 3.69
4889 5543 1.222936 CAGGATCAGAGGCACCCAC 59.777 63.158 0.00 0.00 0.00 4.61
4905 5559 1.561643 CCACTTCTCTGCCTACCTCA 58.438 55.000 0.00 0.00 0.00 3.86
4914 5568 1.811679 GCCTACCTCAACAGCGAGC 60.812 63.158 0.00 0.00 0.00 5.03
4917 5571 0.798771 CTACCTCAACAGCGAGCGAC 60.799 60.000 0.00 0.00 0.00 5.19
4938 5592 1.318158 GGGCCTGTCTTGGATGCTTG 61.318 60.000 0.84 0.00 0.00 4.01
4959 5613 0.251916 TGACAAGGATGGTAAGCCCG 59.748 55.000 0.00 0.00 35.15 6.13
4976 5630 1.351707 CGCCGACAATCCAAATCCG 59.648 57.895 0.00 0.00 0.00 4.18
5006 5660 1.194781 TCTGACAGGCCCAAGACTCC 61.195 60.000 0.00 0.00 0.00 3.85
5017 5671 1.277557 CCAAGACTCCCAGGTTCTGAG 59.722 57.143 0.00 0.00 32.44 3.35
5042 5696 6.435430 TTTATCTTCAATTCCATGTCACCG 57.565 37.500 0.00 0.00 0.00 4.94
5045 5699 0.037447 TCAATTCCATGTCACCGGCA 59.963 50.000 0.00 0.00 0.00 5.69
5077 5731 1.327303 GTCACCCATTGCACAAAGGA 58.673 50.000 6.22 0.00 31.18 3.36
5082 5736 1.135315 CCCATTGCACAAAGGATGACG 60.135 52.381 6.22 0.00 31.18 4.35
5089 5743 1.135603 CACAAAGGATGACGTGGCATG 60.136 52.381 4.87 4.87 0.00 4.06
5092 5746 0.392998 AAGGATGACGTGGCATGGAC 60.393 55.000 12.05 5.50 0.00 4.02
5099 5753 2.203070 GTGGCATGGACCGCTAGG 60.203 66.667 0.00 0.00 45.13 3.02
5128 5782 2.516695 CACATGCATGCGCCCCTA 60.517 61.111 26.53 0.00 37.32 3.53
5149 5803 4.388577 AGGAAGGACATTACTTGCCTTT 57.611 40.909 0.00 0.00 40.03 3.11
5157 5811 5.279456 GGACATTACTTGCCTTTCCAACAAT 60.279 40.000 0.00 0.00 0.00 2.71
5161 5815 4.961438 ACTTGCCTTTCCAACAATCAAT 57.039 36.364 0.00 0.00 0.00 2.57
5210 5880 8.850454 TGCACTTTCACTCTTTATTTGTTAAC 57.150 30.769 0.00 0.00 0.00 2.01
5219 5889 9.377383 CACTCTTTATTTGTTAACTTACAACGG 57.623 33.333 7.22 0.00 37.72 4.44
5233 5903 3.713826 ACAACGGTGAATTGGTATCCT 57.286 42.857 7.88 0.00 0.00 3.24
5245 5915 5.810080 ATTGGTATCCTGAGGTAGCTAAC 57.190 43.478 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.389859 AAATGCAAAACATAGCAGCAGTA 57.610 34.783 0.00 0.00 44.94 2.74
37 38 3.947910 AATGCAAAACATAGCAGCAGT 57.052 38.095 0.00 0.00 44.94 4.40
38 39 4.668177 GCAAAATGCAAAACATAGCAGCAG 60.668 41.667 0.00 0.00 44.94 4.24
39 40 3.186817 GCAAAATGCAAAACATAGCAGCA 59.813 39.130 0.00 0.00 44.94 4.41
64 65 5.582665 GTCAGTCATAACAGACAGGAAATCC 59.417 44.000 0.00 0.00 40.56 3.01
81 82 0.676184 GACACTGGCTCAGTCAGTCA 59.324 55.000 9.63 0.00 46.09 3.41
84 85 0.390492 TGTGACACTGGCTCAGTCAG 59.610 55.000 4.18 4.18 43.43 3.51
96 97 2.532531 CGGATTGCAATCTGTGACAC 57.467 50.000 31.77 16.82 37.10 3.67
112 113 2.229543 ACTGTACTAATGCAACGACGGA 59.770 45.455 0.00 0.00 0.00 4.69
120 121 5.639931 TCGCAAATAACACTGTACTAATGCA 59.360 36.000 0.00 0.00 0.00 3.96
141 188 6.265577 ACTAAATGAAAATACCTTGCATCGC 58.734 36.000 0.00 0.00 0.00 4.58
191 238 3.735591 TGGTTCCTTTTACTTCGGTCAG 58.264 45.455 0.00 0.00 0.00 3.51
214 261 9.688592 GGATATTCCTTGAAATAGATTGCTTTG 57.311 33.333 0.00 0.00 32.53 2.77
215 262 9.425248 TGGATATTCCTTGAAATAGATTGCTTT 57.575 29.630 0.00 0.00 37.46 3.51
216 263 9.425248 TTGGATATTCCTTGAAATAGATTGCTT 57.575 29.630 0.00 0.00 37.46 3.91
238 285 2.806434 AGCCATGTTGCTATGTTTGGA 58.194 42.857 0.00 0.00 40.56 3.53
247 294 1.221840 CGGGTCTAGCCATGTTGCT 59.778 57.895 1.96 1.96 45.38 3.91
265 312 2.764314 CCTGTGCGGCCATGCTTAC 61.764 63.158 2.24 0.00 35.36 2.34
347 394 6.382282 ACACTGATGAGAGATGAATAGTTGGA 59.618 38.462 0.00 0.00 0.00 3.53
506 659 7.952671 ACATTCGAAGAAGGATGCTATAGTTA 58.047 34.615 3.35 0.00 45.90 2.24
507 660 6.821388 ACATTCGAAGAAGGATGCTATAGTT 58.179 36.000 3.35 0.00 45.90 2.24
535 688 4.511826 GCGACACTTATTTTAGGATGGAGG 59.488 45.833 0.00 0.00 0.00 4.30
544 697 8.810427 CGTCCTAAAATAGCGACACTTATTTTA 58.190 33.333 8.35 8.35 34.91 1.52
554 708 2.545322 CCCTCCGTCCTAAAATAGCGAC 60.545 54.545 0.00 0.00 0.00 5.19
611 805 8.528044 AAGGTGTGGTTACAAATAAGAAAGAA 57.472 30.769 0.00 0.00 38.82 2.52
620 814 5.824097 ACGAGTAAAAGGTGTGGTTACAAAT 59.176 36.000 0.00 0.00 38.82 2.32
626 820 5.280654 TCTTACGAGTAAAAGGTGTGGTT 57.719 39.130 0.00 0.00 0.00 3.67
632 826 4.753610 GTGCCTTTCTTACGAGTAAAAGGT 59.246 41.667 19.50 0.00 36.29 3.50
673 868 7.172361 CCTTCTTCTCTTTTTCTCTTGTGTAGG 59.828 40.741 0.00 0.00 0.00 3.18
674 869 7.172361 CCCTTCTTCTCTTTTTCTCTTGTGTAG 59.828 40.741 0.00 0.00 0.00 2.74
675 870 6.992715 CCCTTCTTCTCTTTTTCTCTTGTGTA 59.007 38.462 0.00 0.00 0.00 2.90
731 926 2.358322 TGCTCCCTTTTCGTTTTCCT 57.642 45.000 0.00 0.00 0.00 3.36
825 1028 0.973496 AGGAGGAGGAAAGGACGAGC 60.973 60.000 0.00 0.00 0.00 5.03
847 1054 2.438614 CACGGAGAGCGAGGAGGA 60.439 66.667 0.00 0.00 0.00 3.71
883 1090 2.236766 GGAATGATGAGCAATGGAGGG 58.763 52.381 0.00 0.00 0.00 4.30
958 1168 2.101783 TGCTAAAATGGATGGTGCCTG 58.898 47.619 0.00 0.00 0.00 4.85
962 1172 4.272489 TCTCCTTGCTAAAATGGATGGTG 58.728 43.478 0.00 0.00 0.00 4.17
975 1193 1.567357 GACCTCCTCTTCTCCTTGCT 58.433 55.000 0.00 0.00 0.00 3.91
1240 1458 2.002586 CACGTGATCTAAACTGGCTGG 58.997 52.381 10.90 0.00 0.00 4.85
1241 1459 2.002586 CCACGTGATCTAAACTGGCTG 58.997 52.381 19.30 0.00 0.00 4.85
1242 1460 1.899814 TCCACGTGATCTAAACTGGCT 59.100 47.619 19.30 0.00 0.00 4.75
1243 1461 2.271800 CTCCACGTGATCTAAACTGGC 58.728 52.381 19.30 0.00 0.00 4.85
1257 1475 2.643551 ACCCATGAAATTAGCTCCACG 58.356 47.619 0.00 0.00 0.00 4.94
1258 1476 4.462483 TGAAACCCATGAAATTAGCTCCAC 59.538 41.667 0.00 0.00 0.00 4.02
1290 1508 6.266103 TCAGAAGTTCAGATGCCATTCTTTTT 59.734 34.615 5.50 0.00 0.00 1.94
1484 1702 1.268283 ACAGAGGAAGTGCCCTAGCC 61.268 60.000 0.00 0.00 36.49 3.93
1491 1715 4.402793 TGAGGAGTATAACAGAGGAAGTGC 59.597 45.833 0.00 0.00 0.00 4.40
1500 1724 9.743057 CTATTCAGAAACTGAGGAGTATAACAG 57.257 37.037 0.00 0.00 41.75 3.16
1526 1750 7.646314 CACATATGGATCTTTTCAGATGAACC 58.354 38.462 7.80 0.00 40.14 3.62
1545 1769 4.221262 AGTGCATCAAGTTTTGCCACATAT 59.779 37.500 0.00 0.00 38.08 1.78
1547 1771 2.366266 AGTGCATCAAGTTTTGCCACAT 59.634 40.909 0.00 0.00 38.08 3.21
1554 1778 3.508793 ATGCTGCTAGTGCATCAAGTTTT 59.491 39.130 16.08 0.00 46.80 2.43
1608 1832 9.489393 GCAAAAGGAAAATAAAACTCAAACTTG 57.511 29.630 0.00 0.00 0.00 3.16
1609 1833 8.673711 GGCAAAAGGAAAATAAAACTCAAACTT 58.326 29.630 0.00 0.00 0.00 2.66
1610 1834 8.046708 AGGCAAAAGGAAAATAAAACTCAAACT 58.953 29.630 0.00 0.00 0.00 2.66
1611 1835 8.208718 AGGCAAAAGGAAAATAAAACTCAAAC 57.791 30.769 0.00 0.00 0.00 2.93
1615 1839 7.926018 TCTTGAGGCAAAAGGAAAATAAAACTC 59.074 33.333 0.00 0.00 0.00 3.01
1616 1840 7.791029 TCTTGAGGCAAAAGGAAAATAAAACT 58.209 30.769 0.00 0.00 0.00 2.66
1620 1844 7.734942 ACAATCTTGAGGCAAAAGGAAAATAA 58.265 30.769 0.00 0.00 0.00 1.40
1625 1849 5.128499 TGAAACAATCTTGAGGCAAAAGGAA 59.872 36.000 0.00 0.00 0.00 3.36
1626 1850 4.648762 TGAAACAATCTTGAGGCAAAAGGA 59.351 37.500 0.00 0.00 0.00 3.36
1627 1851 4.947645 TGAAACAATCTTGAGGCAAAAGG 58.052 39.130 0.00 0.00 0.00 3.11
1630 1854 5.302568 ACTGATGAAACAATCTTGAGGCAAA 59.697 36.000 0.00 0.00 0.00 3.68
1631 1855 4.828939 ACTGATGAAACAATCTTGAGGCAA 59.171 37.500 0.00 0.00 0.00 4.52
1632 1856 4.401022 ACTGATGAAACAATCTTGAGGCA 58.599 39.130 0.00 0.00 0.00 4.75
1633 1857 5.159209 CAACTGATGAAACAATCTTGAGGC 58.841 41.667 0.00 0.00 0.00 4.70
1634 1858 5.242393 ACCAACTGATGAAACAATCTTGAGG 59.758 40.000 0.00 0.00 0.00 3.86
1635 1859 6.016860 TGACCAACTGATGAAACAATCTTGAG 60.017 38.462 0.00 0.00 0.00 3.02
1637 1861 6.075762 TGACCAACTGATGAAACAATCTTG 57.924 37.500 0.00 0.00 0.00 3.02
1638 1862 6.906157 ATGACCAACTGATGAAACAATCTT 57.094 33.333 0.00 0.00 0.00 2.40
1639 1863 6.718454 AGAATGACCAACTGATGAAACAATCT 59.282 34.615 0.00 0.00 0.00 2.40
1640 1864 6.805271 CAGAATGACCAACTGATGAAACAATC 59.195 38.462 0.00 0.00 39.69 2.67
1641 1865 6.491062 TCAGAATGACCAACTGATGAAACAAT 59.509 34.615 0.00 0.00 42.56 2.71
1642 1866 5.827267 TCAGAATGACCAACTGATGAAACAA 59.173 36.000 0.00 0.00 42.56 2.83
1643 1867 5.375773 TCAGAATGACCAACTGATGAAACA 58.624 37.500 0.00 0.00 42.56 2.83
1644 1868 5.947228 TCAGAATGACCAACTGATGAAAC 57.053 39.130 0.00 0.00 42.56 2.78
1674 1898 9.420118 AGTTTGCCAACATATATAAATTCAGGA 57.580 29.630 3.22 0.00 35.05 3.86
1675 1899 9.467258 CAGTTTGCCAACATATATAAATTCAGG 57.533 33.333 3.22 0.00 35.05 3.86
1682 1906 9.461312 ACTCTTTCAGTTTGCCAACATATATAA 57.539 29.630 3.22 0.00 35.05 0.98
1684 1908 7.944729 ACTCTTTCAGTTTGCCAACATATAT 57.055 32.000 3.22 0.00 35.05 0.86
1685 1909 8.892723 CATACTCTTTCAGTTTGCCAACATATA 58.107 33.333 3.22 0.00 36.43 0.86
1688 1912 5.047802 CCATACTCTTTCAGTTTGCCAACAT 60.048 40.000 3.22 0.00 36.43 2.71
1719 1943 7.557358 AGCATAATTCTGTTGACATACAATCCA 59.443 33.333 0.00 0.00 40.76 3.41
1720 1944 7.934457 AGCATAATTCTGTTGACATACAATCC 58.066 34.615 0.00 0.00 40.76 3.01
1721 1945 9.443283 GAAGCATAATTCTGTTGACATACAATC 57.557 33.333 0.00 0.00 40.76 2.67
1722 1946 8.959548 TGAAGCATAATTCTGTTGACATACAAT 58.040 29.630 0.00 0.00 40.76 2.71
1724 1948 7.412891 CGTGAAGCATAATTCTGTTGACATACA 60.413 37.037 0.00 0.00 0.00 2.29
1725 1949 6.901887 CGTGAAGCATAATTCTGTTGACATAC 59.098 38.462 0.00 0.00 0.00 2.39
1727 1951 5.412594 ACGTGAAGCATAATTCTGTTGACAT 59.587 36.000 0.00 0.00 0.00 3.06
1734 2067 3.848019 GCAACACGTGAAGCATAATTCTG 59.152 43.478 25.01 0.00 0.00 3.02
1831 2182 4.441079 CCATCCACCGATACCGTTATATCC 60.441 50.000 0.00 0.00 0.00 2.59
1980 2368 7.791949 TCAAATGAAAAACACAACACAGTTTC 58.208 30.769 0.00 0.00 36.98 2.78
1986 2374 6.720012 AGGTTCAAATGAAAAACACAACAC 57.280 33.333 0.00 0.00 35.58 3.32
2091 2479 5.388599 AAGGATCCCGAAACATTCCTAAT 57.611 39.130 8.55 0.00 35.78 1.73
2096 2484 3.673323 GCACAAAGGATCCCGAAACATTC 60.673 47.826 8.55 0.00 0.00 2.67
2112 2500 2.203408 TCCCCACATGCGCACAAA 60.203 55.556 14.90 0.00 0.00 2.83
2137 2525 9.553064 ACCAATCACAATTTGTTTGCTTATAAA 57.447 25.926 0.00 0.00 39.03 1.40
2139 2527 9.632807 GTACCAATCACAATTTGTTTGCTTATA 57.367 29.630 0.00 0.00 39.03 0.98
2170 2558 6.535150 CGTACAATAGGCATCAGAAAGAAGAA 59.465 38.462 0.00 0.00 0.00 2.52
2172 2560 6.042777 TCGTACAATAGGCATCAGAAAGAAG 58.957 40.000 0.00 0.00 0.00 2.85
2173 2561 5.972935 TCGTACAATAGGCATCAGAAAGAA 58.027 37.500 0.00 0.00 0.00 2.52
2174 2562 5.592054 CTCGTACAATAGGCATCAGAAAGA 58.408 41.667 0.00 0.00 0.00 2.52
2175 2563 4.210120 GCTCGTACAATAGGCATCAGAAAG 59.790 45.833 0.00 0.00 0.00 2.62
2194 2582 2.046507 AGGCTTGGCTTCAGCTCG 60.047 61.111 0.00 0.00 41.70 5.03
2205 2593 1.447317 AAACGTGCTCCACAGGCTTG 61.447 55.000 0.00 0.00 37.69 4.01
2207 2595 1.893808 CAAACGTGCTCCACAGGCT 60.894 57.895 0.00 0.00 37.69 4.58
2238 2626 6.174049 AGGGAACTGCAAAATAAGTAGAGAC 58.826 40.000 0.00 0.00 41.13 3.36
2239 2627 6.374417 AGGGAACTGCAAAATAAGTAGAGA 57.626 37.500 0.00 0.00 41.13 3.10
2304 2692 2.328319 GAGAGATCTGGATCCTTGGCT 58.672 52.381 14.23 5.40 38.58 4.75
2379 2767 4.327680 AGTTGCTCCCATAACAGAACTTC 58.672 43.478 0.00 0.00 0.00 3.01
2397 2785 4.942852 TGGCTGTGGTTATTTCAAAGTTG 58.057 39.130 0.00 0.00 0.00 3.16
2478 2866 2.235402 TGTCCGGACAATTAGGTTCTCC 59.765 50.000 34.60 3.16 38.56 3.71
2487 2875 3.118738 GGTACATCTCTGTCCGGACAATT 60.119 47.826 35.36 18.51 41.33 2.32
2493 2881 1.763968 TCAGGTACATCTCTGTCCGG 58.236 55.000 0.00 0.00 36.79 5.14
2608 2996 3.299585 GATCGCATCGACACACCG 58.700 61.111 0.00 0.00 39.18 4.94
2799 3187 2.280457 GTGCCTATGCTCTCCGGC 60.280 66.667 0.00 0.00 42.78 6.13
3015 3403 5.833082 TCGACTTCAATCCTGTAATCTAGC 58.167 41.667 0.00 0.00 0.00 3.42
3108 3496 1.338655 TCGACGTCAAACATGGACTCA 59.661 47.619 17.16 0.00 33.11 3.41
3144 3532 5.549742 TCCTTTGCAAGAAATTGACCAAT 57.450 34.783 0.00 0.00 0.00 3.16
3153 3541 5.139727 TCTTCCTCAATCCTTTGCAAGAAA 58.860 37.500 0.00 0.00 32.61 2.52
3327 3715 0.389817 CGGGCAACAGTTCGATGAGA 60.390 55.000 0.00 0.00 39.74 3.27
3345 3733 1.926510 TCAACAATGCGAGCATAGTCG 59.073 47.619 11.25 3.51 43.08 4.18
3348 3736 4.464112 CATCATCAACAATGCGAGCATAG 58.536 43.478 11.25 2.72 35.31 2.23
3351 3739 1.402613 CCATCATCAACAATGCGAGCA 59.597 47.619 0.00 0.00 35.17 4.26
3544 3997 9.252635 ACATTCTCATCTACAGATATCATGCTA 57.747 33.333 5.32 0.00 32.63 3.49
3565 4018 8.382030 TGTATACATCATCACATTCCACATTC 57.618 34.615 0.08 0.00 0.00 2.67
3566 4019 8.750515 TTGTATACATCATCACATTCCACATT 57.249 30.769 6.36 0.00 0.00 2.71
3567 4020 8.929260 ATTGTATACATCATCACATTCCACAT 57.071 30.769 6.36 0.00 0.00 3.21
3568 4021 7.992033 TGATTGTATACATCATCACATTCCACA 59.008 33.333 13.80 0.00 0.00 4.17
3569 4022 8.382030 TGATTGTATACATCATCACATTCCAC 57.618 34.615 13.80 0.00 0.00 4.02
3570 4023 8.977267 TTGATTGTATACATCATCACATTCCA 57.023 30.769 16.41 2.75 0.00 3.53
3649 4268 7.661027 TGTGCCTGATCGATCATATTTATTCAA 59.339 33.333 27.43 1.12 36.02 2.69
3651 4270 7.413438 GGTGTGCCTGATCGATCATATTTATTC 60.413 40.741 27.43 13.67 36.02 1.75
3652 4271 6.372659 GGTGTGCCTGATCGATCATATTTATT 59.627 38.462 27.43 0.00 36.02 1.40
3653 4272 5.877012 GGTGTGCCTGATCGATCATATTTAT 59.123 40.000 27.43 0.00 36.02 1.40
3655 4274 4.067896 GGTGTGCCTGATCGATCATATTT 58.932 43.478 27.43 0.00 36.02 1.40
3657 4276 2.027745 GGGTGTGCCTGATCGATCATAT 60.028 50.000 27.43 0.00 36.02 1.78
3658 4277 1.344438 GGGTGTGCCTGATCGATCATA 59.656 52.381 27.43 14.55 36.02 2.15
3685 4328 2.787473 TCTTGCACTCGGATTCCATT 57.213 45.000 3.09 0.00 0.00 3.16
3823 4466 0.456995 CCGAGAAGGACGACTTGAGC 60.457 60.000 2.07 0.00 45.00 4.26
4210 4853 3.157949 CTCCGGCTCTTCCCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
4213 4856 3.157949 CTCCTCCGGCTCTTCCCC 61.158 72.222 0.00 0.00 0.00 4.81
4287 4934 2.570415 TTCTACATTGTTTCCCCGCA 57.430 45.000 0.00 0.00 0.00 5.69
4299 4946 7.287927 ACCTAGCACAGTACATACATTCTACAT 59.712 37.037 0.00 0.00 0.00 2.29
4418 5065 2.160205 CGACACTACCAGAGGTTCTCA 58.840 52.381 0.00 0.00 37.09 3.27
4473 5120 6.152323 TGCTATTTACTTCACTAACCGAGTCT 59.848 38.462 0.00 0.00 35.64 3.24
4474 5121 6.327934 TGCTATTTACTTCACTAACCGAGTC 58.672 40.000 0.00 0.00 35.64 3.36
4475 5122 6.276832 TGCTATTTACTTCACTAACCGAGT 57.723 37.500 0.00 0.00 39.82 4.18
4505 5152 4.286297 TCTGAAACCCTAGAATGTGGTG 57.714 45.455 0.00 0.00 31.32 4.17
4520 5167 4.023536 GTCTAATGCGGTGGTTTTCTGAAA 60.024 41.667 0.00 0.00 0.00 2.69
4570 5217 8.875168 CAACTAGATAAACCCTAGAATCCATCT 58.125 37.037 0.00 0.00 42.48 2.90
4609 5256 5.105351 ACATGATCTAACGACATCTCAACCA 60.105 40.000 0.00 0.00 0.00 3.67
4636 5283 9.887862 AGATTGGATTGATCCCTAACATTATTT 57.112 29.630 7.53 0.00 46.59 1.40
4638 5285 8.672329 TGAGATTGGATTGATCCCTAACATTAT 58.328 33.333 7.53 0.00 46.59 1.28
4639 5286 8.044574 TGAGATTGGATTGATCCCTAACATTA 57.955 34.615 7.53 0.00 46.59 1.90
4643 5296 5.532779 GGTTGAGATTGGATTGATCCCTAAC 59.467 44.000 7.53 4.37 46.59 2.34
4689 5343 4.051922 GACCACATCAATACAGGATCGAC 58.948 47.826 0.00 0.00 0.00 4.20
4693 5347 3.434167 GCAGGACCACATCAATACAGGAT 60.434 47.826 0.00 0.00 0.00 3.24
4694 5348 2.092968 GCAGGACCACATCAATACAGGA 60.093 50.000 0.00 0.00 0.00 3.86
4703 5357 1.363744 CTTCGAAGCAGGACCACATC 58.636 55.000 13.09 0.00 0.00 3.06
4745 5399 8.789762 GGAAGAGGAACTAACTCTCTATATCAC 58.210 40.741 0.00 0.00 44.17 3.06
4748 5402 8.507761 AGTGGAAGAGGAACTAACTCTCTATAT 58.492 37.037 0.00 0.00 44.17 0.86
4758 5412 6.014647 TGTAGCTAAGTGGAAGAGGAACTAA 58.985 40.000 0.00 0.00 41.55 2.24
4764 5418 4.220821 TGAGTTGTAGCTAAGTGGAAGAGG 59.779 45.833 0.00 0.00 0.00 3.69
4768 5422 6.127423 GGTAGATGAGTTGTAGCTAAGTGGAA 60.127 42.308 0.00 0.00 0.00 3.53
4779 5433 3.118408 GGTGCCATGGTAGATGAGTTGTA 60.118 47.826 14.67 0.00 0.00 2.41
4787 5441 1.526887 CGTGGGTGCCATGGTAGAT 59.473 57.895 14.67 0.00 36.92 1.98
4794 5448 2.124570 GATGAGCGTGGGTGCCAT 60.125 61.111 0.00 0.00 35.28 4.40
4795 5449 4.408821 GGATGAGCGTGGGTGCCA 62.409 66.667 0.00 0.00 34.65 4.92
4830 5484 4.426416 CATACGAGGAAATTGACACGGTA 58.574 43.478 0.00 0.00 0.00 4.02
4866 5520 2.060383 TGCCTCTGATCCTGTCCGG 61.060 63.158 0.00 0.00 0.00 5.14
4867 5521 1.142748 GTGCCTCTGATCCTGTCCG 59.857 63.158 0.00 0.00 0.00 4.79
4873 5527 0.107459 GAAGTGGGTGCCTCTGATCC 60.107 60.000 0.00 0.00 0.00 3.36
4882 5536 0.391793 GTAGGCAGAGAAGTGGGTGC 60.392 60.000 0.00 0.00 35.07 5.01
4889 5543 2.676463 GCTGTTGAGGTAGGCAGAGAAG 60.676 54.545 0.00 0.00 0.00 2.85
4914 5568 4.760047 CCAAGACAGGCCCCGTCG 62.760 72.222 15.33 4.53 38.46 5.12
4917 5571 2.124570 CATCCAAGACAGGCCCCG 60.125 66.667 0.00 0.00 0.00 5.73
4924 5578 1.202794 TGTCAGCAAGCATCCAAGACA 60.203 47.619 0.00 0.00 32.70 3.41
4938 5592 1.383523 GGCTTACCATCCTTGTCAGC 58.616 55.000 0.00 0.00 35.26 4.26
4949 5603 2.862674 GATTGTCGGCGGGCTTACCA 62.863 60.000 7.21 0.00 40.22 3.25
4959 5613 0.377203 GTCGGATTTGGATTGTCGGC 59.623 55.000 0.00 0.00 0.00 5.54
4976 5630 1.850377 CCTGTCAGATCTCATGCGTC 58.150 55.000 0.00 0.00 0.00 5.19
5006 5660 4.836825 TGAAGATAAAGCTCAGAACCTGG 58.163 43.478 0.00 0.00 31.51 4.45
5017 5671 6.268566 GGTGACATGGAATTGAAGATAAAGC 58.731 40.000 0.00 0.00 0.00 3.51
5042 5696 1.952296 GTGACCTGGATCATCATTGCC 59.048 52.381 0.00 0.00 0.00 4.52
5077 5731 2.125147 CGGTCCATGCCACGTCAT 60.125 61.111 0.00 0.00 0.00 3.06
5082 5736 2.203070 CCTAGCGGTCCATGCCAC 60.203 66.667 0.00 0.00 0.00 5.01
5089 5743 0.971447 AGGAGAACACCTAGCGGTCC 60.971 60.000 0.00 0.00 43.24 4.46
5092 5746 1.677637 GGGAGGAGAACACCTAGCGG 61.678 65.000 0.00 0.00 40.73 5.52
5099 5753 0.036732 TGCATGTGGGAGGAGAACAC 59.963 55.000 0.00 0.00 35.75 3.32
5128 5782 4.336280 GAAAGGCAAGTAATGTCCTTCCT 58.664 43.478 0.00 0.00 41.61 3.36
5135 5789 5.304101 TGATTGTTGGAAAGGCAAGTAATGT 59.696 36.000 0.00 0.00 0.00 2.71
5141 5795 6.484308 AGAAAATTGATTGTTGGAAAGGCAAG 59.516 34.615 0.00 0.00 0.00 4.01
5210 5880 5.064707 CAGGATACCAATTCACCGTTGTAAG 59.935 44.000 0.00 0.00 37.17 2.34
5216 5886 2.170607 CCTCAGGATACCAATTCACCGT 59.829 50.000 0.00 0.00 37.17 4.83
5217 5887 2.170607 ACCTCAGGATACCAATTCACCG 59.829 50.000 0.00 0.00 37.17 4.94
5219 5889 4.101741 AGCTACCTCAGGATACCAATTCAC 59.898 45.833 0.00 0.00 37.17 3.18
5233 5903 2.353406 GCAACTTCCGTTAGCTACCTCA 60.353 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.