Multiple sequence alignment - TraesCS3B01G068300

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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 TraesCS3B01G068300 chr3B 100.000 5520 0 0 1 5520 40530789 40525270 0.000000e+00 10194
1 TraesCS3B01G068300 chr3A 92.865 3728 175 24 1856 5520 32175996 32172297 0.000000e+00 5326
2 TraesCS3B01G068300 chr3A 89.669 1781 100 31 1 1773 32177699 32175995 0.000000e+00 2193
3 TraesCS3B01G068300 chr3D 93.805 3406 156 20 1855 5235 23084645 23081270 0.000000e+00 5070
4 TraesCS3B01G068300 chr3D 92.013 1252 56 18 356 1574 23086247 23085007 0.000000e+00 1718
5 TraesCS3B01G068300 chr3D 95.610 205 5 4 1572 1775 23084847 23084646 5.330000e-85 326
6 TraesCS3B01G068300 chr3D 86.688 308 18 4 5234 5520 23081176 23080871 2.480000e-83 320
7 TraesCS3B01G068300 chr3D 79.365 315 24 14 8 304 23086534 23086243 3.400000e-42 183
8 TraesCS3B01G068300 chr5D 94.792 96 3 2 1771 1865 504792930 504793024 1.240000e-31 148
9 TraesCS3B01G068300 chr5D 96.629 89 2 1 1772 1860 56448461 56448548 4.460000e-31 147
10 TraesCS3B01G068300 chr5D 91.919 99 6 2 1772 1870 487170901 487170805 2.680000e-28 137
11 TraesCS3B01G068300 chr5B 94.845 97 2 3 1767 1862 665559934 665560028 1.240000e-31 148
12 TraesCS3B01G068300 chr7B 96.629 89 2 1 1772 1860 263113386 263113299 4.460000e-31 147
13 TraesCS3B01G068300 chr7B 89.720 107 8 3 1759 1865 450586564 450586461 3.470000e-27 134
14 TraesCS3B01G068300 chr4D 93.750 96 4 2 1769 1863 10971528 10971622 5.760000e-30 143
15 TraesCS3B01G068300 chr2B 92.079 101 6 2 1771 1871 142917033 142917131 2.070000e-29 141
16 TraesCS3B01G068300 chr4B 90.385 104 7 3 1772 1874 273251782 273251681 3.470000e-27 134


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 TraesCS3B01G068300 chr3B 40525270 40530789 5519 True 10194.0 10194 100.0000 1 5520 1 chr3B.!!$R1 5519
1 TraesCS3B01G068300 chr3A 32172297 32177699 5402 True 3759.5 5326 91.2670 1 5520 2 chr3A.!!$R1 5519
2 TraesCS3B01G068300 chr3D 23080871 23086534 5663 True 1523.4 5070 89.4962 8 5520 5 chr3D.!!$R1 5512

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
501 522 0.036294 GTTGACTGGGAGGCTGGTAC 60.036 60.000 0.0 0.0 0.00 3.34 F
673 716 0.036765 TCATTTGAGACGTTCCCCCG 60.037 55.000 0.0 0.0 0.00 5.73 F
1657 1895 0.174162 GCGAATCAGCCCTGCAAAAT 59.826 50.000 0.0 0.0 0.00 1.82 F
2497 2752 0.322975 AGTCAAGAGCAATCTGCCGT 59.677 50.000 0.0 0.0 46.52 5.68 F
3166 3433 0.868406 CCGCAGAAACAACCTCTCAC 59.132 55.000 0.0 0.0 0.00 3.51 F
3589 3859 1.000060 GCTGCTCATTCACCAAAGCAA 60.000 47.619 0.0 0.0 43.61 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2273 0.317479 ACACACACGCTAGGAACCTC 59.683 55.000 0.00 0.0 0.00 3.85 R
2557 2812 1.339055 TGTTCAATGGAAGCCCTCTCG 60.339 52.381 0.00 0.0 32.62 4.04 R
3579 3849 1.068895 TGAATGCCACTTGCTTTGGTG 59.931 47.619 1.52 0.0 42.00 4.17 R
3715 3985 0.392461 TATGTTGAGAACCTGGCGGC 60.392 55.000 0.00 0.0 0.00 6.53 R
4495 4765 1.675641 GTTGGTTGATGAGCCGCCT 60.676 57.895 0.00 0.0 0.00 5.52 R
5110 5386 2.302733 TGTGTTCATTCCTGCTCTGCTA 59.697 45.455 0.00 0.0 0.00 3.49 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
49 50 8.391106 GTGATAGTTGTACCTTGAAATAAGCTG 58.609 37.037 0.00 0.00 0.00 4.24
113 116 1.227205 CATCGCTCCAGCAGGACTC 60.227 63.158 0.00 0.00 39.61 3.36
126 129 2.810852 GCAGGACTCCAAACTTTCTGAG 59.189 50.000 0.00 0.00 0.00 3.35
129 132 4.991687 CAGGACTCCAAACTTTCTGAGTAC 59.008 45.833 0.00 5.35 38.15 2.73
130 133 4.902448 AGGACTCCAAACTTTCTGAGTACT 59.098 41.667 0.00 0.00 42.77 2.73
131 134 5.367060 AGGACTCCAAACTTTCTGAGTACTT 59.633 40.000 0.00 0.00 44.68 2.24
132 135 5.467063 GGACTCCAAACTTTCTGAGTACTTG 59.533 44.000 0.00 0.00 38.15 3.16
133 136 6.235231 ACTCCAAACTTTCTGAGTACTTGA 57.765 37.500 0.00 0.00 37.72 3.02
134 137 6.831976 ACTCCAAACTTTCTGAGTACTTGAT 58.168 36.000 0.00 0.00 37.72 2.57
135 138 7.963532 ACTCCAAACTTTCTGAGTACTTGATA 58.036 34.615 0.00 0.00 37.72 2.15
136 139 7.873505 ACTCCAAACTTTCTGAGTACTTGATAC 59.126 37.037 0.00 0.00 37.72 2.24
138 141 8.429641 TCCAAACTTTCTGAGTACTTGATACTT 58.570 33.333 0.00 0.00 44.64 2.24
139 142 9.057089 CCAAACTTTCTGAGTACTTGATACTTT 57.943 33.333 0.00 0.00 44.64 2.66
217 222 5.741011 TGTTCTAACAAGTTCCAACTCTGT 58.259 37.500 0.00 0.00 38.57 3.41
248 253 6.929606 AGAAATGAAGCATAATACTCGGTACC 59.070 38.462 0.16 0.16 0.00 3.34
311 332 4.163458 CAGCACATGCATTCACTTTGTA 57.837 40.909 6.64 0.00 45.16 2.41
329 350 9.866936 CACTTTGTACTATACGCTGTTTTAAAA 57.133 29.630 0.00 0.00 0.00 1.52
344 365 6.041511 TGTTTTAAAAAGGAAACCCTAACGC 58.958 36.000 1.31 0.00 32.65 4.84
410 431 4.532834 GAGGTATCCTCTGTCTGAAGTCT 58.467 47.826 8.38 0.00 46.41 3.24
437 458 0.321653 GGTCAGGCTGGTGGTACAAG 60.322 60.000 15.73 0.00 44.16 3.16
478 499 0.734889 CCATCACTCATCCCGTTTGC 59.265 55.000 0.00 0.00 0.00 3.68
484 505 0.609131 CTCATCCCGTTTGCCTGGTT 60.609 55.000 0.00 0.00 0.00 3.67
485 506 0.893270 TCATCCCGTTTGCCTGGTTG 60.893 55.000 0.00 0.00 0.00 3.77
486 507 0.893270 CATCCCGTTTGCCTGGTTGA 60.893 55.000 0.00 0.00 0.00 3.18
487 508 0.893727 ATCCCGTTTGCCTGGTTGAC 60.894 55.000 0.00 0.00 0.00 3.18
488 509 1.528309 CCCGTTTGCCTGGTTGACT 60.528 57.895 0.00 0.00 0.00 3.41
489 510 1.654220 CCGTTTGCCTGGTTGACTG 59.346 57.895 0.00 0.00 0.00 3.51
490 511 1.654220 CGTTTGCCTGGTTGACTGG 59.346 57.895 0.00 0.00 40.89 4.00
491 512 1.795170 CGTTTGCCTGGTTGACTGGG 61.795 60.000 0.00 0.00 38.54 4.45
492 513 0.467290 GTTTGCCTGGTTGACTGGGA 60.467 55.000 0.00 0.00 38.54 4.37
493 514 0.178992 TTTGCCTGGTTGACTGGGAG 60.179 55.000 0.00 0.00 39.57 4.30
494 515 2.067932 TTGCCTGGTTGACTGGGAGG 62.068 60.000 0.00 0.00 39.57 4.30
495 516 2.352805 CCTGGTTGACTGGGAGGC 59.647 66.667 0.00 0.00 34.73 4.70
496 517 2.227036 CCTGGTTGACTGGGAGGCT 61.227 63.158 0.00 0.00 34.73 4.58
497 518 1.002868 CTGGTTGACTGGGAGGCTG 60.003 63.158 0.00 0.00 0.00 4.85
498 519 2.352805 GGTTGACTGGGAGGCTGG 59.647 66.667 0.00 0.00 0.00 4.85
499 520 2.529744 GGTTGACTGGGAGGCTGGT 61.530 63.158 0.00 0.00 0.00 4.00
500 521 1.198759 GGTTGACTGGGAGGCTGGTA 61.199 60.000 0.00 0.00 0.00 3.25
501 522 0.036294 GTTGACTGGGAGGCTGGTAC 60.036 60.000 0.00 0.00 0.00 3.34
502 523 0.472925 TTGACTGGGAGGCTGGTACA 60.473 55.000 0.00 0.00 0.00 2.90
503 524 0.472925 TGACTGGGAGGCTGGTACAA 60.473 55.000 0.00 0.00 38.70 2.41
504 525 0.250513 GACTGGGAGGCTGGTACAAG 59.749 60.000 0.00 0.00 38.70 3.16
505 526 1.201429 ACTGGGAGGCTGGTACAAGG 61.201 60.000 0.00 0.00 38.70 3.61
541 584 4.019321 AGGTCTGATGCTAAACTTGCCTTA 60.019 41.667 0.00 0.00 0.00 2.69
668 711 4.682860 TCCGTTACTTCATTTGAGACGTTC 59.317 41.667 0.00 0.00 0.00 3.95
672 715 2.084546 CTTCATTTGAGACGTTCCCCC 58.915 52.381 0.00 0.00 0.00 5.40
673 716 0.036765 TCATTTGAGACGTTCCCCCG 60.037 55.000 0.00 0.00 0.00 5.73
674 717 0.321298 CATTTGAGACGTTCCCCCGT 60.321 55.000 0.00 0.00 45.18 5.28
701 745 5.585047 GTCGATTGGTTACTAAAAGAGGCAT 59.415 40.000 0.00 0.00 0.00 4.40
836 889 5.561679 ACCCTCCAGATTTACTTCACTTTC 58.438 41.667 0.00 0.00 0.00 2.62
884 937 6.763610 TGTTCTCTCTGTCTTTTCCTTTTCTC 59.236 38.462 0.00 0.00 0.00 2.87
886 939 7.130681 TCTCTCTGTCTTTTCCTTTTCTCTT 57.869 36.000 0.00 0.00 0.00 2.85
894 947 5.532779 TCTTTTCCTTTTCTCTTTCTCTGCC 59.467 40.000 0.00 0.00 0.00 4.85
917 970 6.153000 GCCTCTTATCTAATTCTATCGTCCCA 59.847 42.308 0.00 0.00 0.00 4.37
919 972 8.194104 CCTCTTATCTAATTCTATCGTCCCATG 58.806 40.741 0.00 0.00 0.00 3.66
953 1006 3.668447 TGGTTCTCACTTTCAGCATCTC 58.332 45.455 0.00 0.00 0.00 2.75
965 1018 2.015587 CAGCATCTCCTCTTTGCTTCC 58.984 52.381 0.00 0.00 43.94 3.46
1023 1076 0.175073 GGGTGGGCTTACAGTACTCG 59.825 60.000 0.00 0.00 0.00 4.18
1025 1078 0.459759 GTGGGCTTACAGTACTCGCC 60.460 60.000 11.62 11.62 39.98 5.54
1041 1094 2.109799 CCTGCATACAGCTCCGGG 59.890 66.667 0.00 0.00 45.94 5.73
1058 1111 2.294074 CGGGTTCACTTCTTCAACCAA 58.706 47.619 2.66 0.00 41.33 3.67
1218 1271 5.503357 CGAGTTTGAAACCGTGAAAGATTCA 60.503 40.000 4.14 0.00 37.33 2.57
1263 1316 5.179555 CCAGGTACTTGCTGTCTTAGTTTTC 59.820 44.000 0.00 0.00 34.60 2.29
1363 1416 1.598962 GCCTCTGCTGCAGTCAACA 60.599 57.895 27.24 8.57 32.61 3.33
1387 1440 4.785376 AGGAGTGTTCCAGTTCCATTCTAT 59.215 41.667 0.00 0.00 46.64 1.98
1439 1492 3.751175 TGCTTGTTACATAGTTCAGCCAC 59.249 43.478 2.59 0.00 0.00 5.01
1445 1498 7.429636 TGTTACATAGTTCAGCCACTTTAAC 57.570 36.000 0.00 0.00 0.00 2.01
1446 1499 7.221450 TGTTACATAGTTCAGCCACTTTAACT 58.779 34.615 0.00 0.00 36.26 2.24
1453 1506 4.002906 TCAGCCACTTTAACTCGTTGAT 57.997 40.909 0.00 0.00 0.00 2.57
1456 1509 6.869695 TCAGCCACTTTAACTCGTTGATATA 58.130 36.000 0.00 0.00 0.00 0.86
1463 1516 9.999009 CACTTTAACTCGTTGATATACACTCTA 57.001 33.333 0.00 0.00 0.00 2.43
1485 1555 9.294030 CTCTATGATTGGTTACAAGAAAATTGC 57.706 33.333 0.00 0.00 40.49 3.56
1529 1605 5.509972 CACGCTTACTCGAATGAGATATAGC 59.490 44.000 0.00 0.00 45.57 2.97
1544 1620 5.902760 AGATATAGCCTCCTGTCTCAAGAT 58.097 41.667 0.00 0.00 0.00 2.40
1550 1626 3.430651 GCCTCCTGTCTCAAGATTCTCAG 60.431 52.174 0.00 0.00 0.00 3.35
1551 1627 3.430651 CCTCCTGTCTCAAGATTCTCAGC 60.431 52.174 0.00 0.00 0.00 4.26
1552 1628 3.168292 TCCTGTCTCAAGATTCTCAGCA 58.832 45.455 0.00 0.00 0.00 4.41
1553 1629 3.056250 TCCTGTCTCAAGATTCTCAGCAC 60.056 47.826 0.00 0.00 0.00 4.40
1554 1630 2.922387 CTGTCTCAAGATTCTCAGCACG 59.078 50.000 0.00 0.00 0.00 5.34
1657 1895 0.174162 GCGAATCAGCCCTGCAAAAT 59.826 50.000 0.00 0.00 0.00 1.82
1735 1974 1.715785 ATGGTTTTGACAGGGGGTTG 58.284 50.000 0.00 0.00 0.00 3.77
1741 1980 1.434513 TTGACAGGGGGTTGATGGCT 61.435 55.000 0.00 0.00 0.00 4.75
1775 2014 7.897575 AACATGCTTAGCTGCTTATATACTC 57.102 36.000 7.79 0.00 0.00 2.59
1776 2015 6.402222 ACATGCTTAGCTGCTTATATACTCC 58.598 40.000 7.79 0.00 0.00 3.85
1777 2016 5.407407 TGCTTAGCTGCTTATATACTCCC 57.593 43.478 7.79 0.00 0.00 4.30
1778 2017 5.087323 TGCTTAGCTGCTTATATACTCCCT 58.913 41.667 7.79 0.00 0.00 4.20
1779 2018 5.186021 TGCTTAGCTGCTTATATACTCCCTC 59.814 44.000 7.79 0.00 0.00 4.30
1780 2019 5.394773 GCTTAGCTGCTTATATACTCCCTCC 60.395 48.000 7.79 0.00 0.00 4.30
1781 2020 3.093057 AGCTGCTTATATACTCCCTCCG 58.907 50.000 0.00 0.00 0.00 4.63
1782 2021 2.826725 GCTGCTTATATACTCCCTCCGT 59.173 50.000 0.00 0.00 0.00 4.69
1783 2022 3.119424 GCTGCTTATATACTCCCTCCGTC 60.119 52.174 0.00 0.00 0.00 4.79
1784 2023 3.428532 TGCTTATATACTCCCTCCGTCC 58.571 50.000 0.00 0.00 0.00 4.79
1785 2024 2.759535 GCTTATATACTCCCTCCGTCCC 59.240 54.545 0.00 0.00 0.00 4.46
1786 2025 3.816842 GCTTATATACTCCCTCCGTCCCA 60.817 52.174 0.00 0.00 0.00 4.37
1787 2026 4.611367 CTTATATACTCCCTCCGTCCCAT 58.389 47.826 0.00 0.00 0.00 4.00
1788 2027 5.763355 CTTATATACTCCCTCCGTCCCATA 58.237 45.833 0.00 0.00 0.00 2.74
1789 2028 4.687262 ATATACTCCCTCCGTCCCATAA 57.313 45.455 0.00 0.00 0.00 1.90
1790 2029 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
1791 2030 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
1792 2031 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
1793 2032 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
1794 2033 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
1795 2034 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
1796 2035 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
1797 2036 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
1799 2038 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
1800 2039 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
1801 2040 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
1802 2041 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
1803 2042 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
1849 2088 3.720949 CGTCTTACAATATGGGACGGA 57.279 47.619 0.00 0.00 43.69 4.69
1850 2089 3.639538 CGTCTTACAATATGGGACGGAG 58.360 50.000 0.00 0.00 43.69 4.63
1851 2090 3.317149 CGTCTTACAATATGGGACGGAGA 59.683 47.826 0.00 0.00 43.69 3.71
1852 2091 4.556898 CGTCTTACAATATGGGACGGAGAG 60.557 50.000 0.00 0.00 43.69 3.20
1853 2092 4.583489 GTCTTACAATATGGGACGGAGAGA 59.417 45.833 0.00 0.00 0.00 3.10
1854 2093 4.827835 TCTTACAATATGGGACGGAGAGAG 59.172 45.833 0.00 0.00 0.00 3.20
1890 2134 0.457851 TGGTTTCCAAAGCAACACCG 59.542 50.000 1.45 0.00 42.72 4.94
1952 2197 6.261826 CAGGATTTCCTCCACATCAATAGTTC 59.738 42.308 0.00 0.00 46.65 3.01
1961 2206 4.570369 CCACATCAATAGTTCGTGCATACA 59.430 41.667 0.00 0.00 0.00 2.29
2071 2316 8.726068 TGTCAATGCTTCTTCAAAACGATTATA 58.274 29.630 0.00 0.00 0.00 0.98
2155 2400 6.628844 GCTTTAACCTCAAATTGCTCCATCAT 60.629 38.462 0.00 0.00 0.00 2.45
2184 2429 7.436673 TGGTTTGTAAATGAAATGCAACACTAC 59.563 33.333 0.00 0.00 0.00 2.73
2238 2493 9.507329 AAATGAATAGCTCTTCAGTAGAAACAA 57.493 29.630 18.13 0.00 38.47 2.83
2285 2540 9.248291 CAAATACAAGTATATCATGGTTTTGCC 57.752 33.333 0.00 0.00 37.90 4.52
2306 2561 7.141100 TGCCATTTTGCTAGTAAGTCTAAAC 57.859 36.000 0.00 0.00 0.00 2.01
2319 2574 7.445945 AGTAAGTCTAAACTGATGTGCTTTCT 58.554 34.615 0.00 0.00 35.36 2.52
2321 2576 4.453819 AGTCTAAACTGATGTGCTTTCTGC 59.546 41.667 0.00 0.00 36.88 4.26
2328 2583 3.511699 TGATGTGCTTTCTGCGTACTAG 58.488 45.455 0.00 0.00 46.63 2.57
2338 2593 6.579666 TTTCTGCGTACTAGTCCTAAGAAA 57.420 37.500 14.77 14.77 31.79 2.52
2340 2595 6.770746 TCTGCGTACTAGTCCTAAGAAATT 57.229 37.500 0.00 0.00 0.00 1.82
2466 2721 6.753180 TCAGAATACAGCACTAATCCATCTC 58.247 40.000 0.00 0.00 0.00 2.75
2497 2752 0.322975 AGTCAAGAGCAATCTGCCGT 59.677 50.000 0.00 0.00 46.52 5.68
2680 2935 3.084786 AGACATGAGTGACATCGACAGA 58.915 45.455 0.00 0.00 37.07 3.41
2788 3043 1.610886 GCTGACCTTGTTCACCTACCC 60.611 57.143 0.00 0.00 0.00 3.69
2878 3133 2.609459 GTGGTGGAATACAATCTCTGCG 59.391 50.000 0.00 0.00 0.00 5.18
2935 3190 1.251527 ACGTGGAGGAGCAGTACCAG 61.252 60.000 0.00 0.00 32.89 4.00
2953 3208 3.181440 ACCAGATGGAAGAACTTGAGCAA 60.181 43.478 5.72 0.00 38.94 3.91
3013 3280 2.045926 CCAGAAGGCCCAGAACCG 60.046 66.667 0.00 0.00 0.00 4.44
3029 3296 1.596752 CCGCCGGCAACATATAGCA 60.597 57.895 28.98 0.00 0.00 3.49
3166 3433 0.868406 CCGCAGAAACAACCTCTCAC 59.132 55.000 0.00 0.00 0.00 3.51
3279 3546 1.160137 CAGAAACCACCTAGCAGTGC 58.840 55.000 7.13 7.13 36.38 4.40
3579 3849 5.647589 TGATCAAAAAGATGCTGCTCATTC 58.352 37.500 0.00 0.00 37.00 2.67
3580 3850 5.184287 TGATCAAAAAGATGCTGCTCATTCA 59.816 36.000 0.00 0.00 37.00 2.57
3589 3859 1.000060 GCTGCTCATTCACCAAAGCAA 60.000 47.619 0.00 0.00 43.61 3.91
3697 3967 1.417145 GATCAGAAGAGGGCTGCATCT 59.583 52.381 0.50 0.92 33.45 2.90
3731 4001 2.281484 TGCCGCCAGGTTCTCAAC 60.281 61.111 0.00 0.00 40.50 3.18
3746 4016 2.642311 TCTCAACATACCCCTCAAGCAA 59.358 45.455 0.00 0.00 0.00 3.91
3755 4025 1.375908 CCTCAAGCAACGCCAGCTA 60.376 57.895 0.00 0.00 42.53 3.32
3778 4048 4.601621 TCTGAAAGTATCTGACTCGTCG 57.398 45.455 0.00 0.00 37.44 5.12
3820 4090 3.971245 AGTGAAGATGACCAGTTCTCC 57.029 47.619 0.00 0.00 0.00 3.71
3845 4115 6.372659 CACTAAGAGGCTCAGAAAAATGCTTA 59.627 38.462 18.26 1.58 0.00 3.09
3865 4135 1.531423 AGCAAAGTGATCCAGCAGTG 58.469 50.000 0.00 0.00 0.00 3.66
3885 4155 1.334869 GCTCAAACCACAGTCAACAGG 59.665 52.381 0.00 0.00 0.00 4.00
4133 4403 3.834489 CAGCATCTGATGGGAGTAAGT 57.166 47.619 18.60 0.00 32.44 2.24
4273 4543 4.460263 TGCAAAGTGACAAGTCCATTAGT 58.540 39.130 0.00 0.00 0.00 2.24
4287 4557 1.076332 ATTAGTTCGCCGCAAGACAC 58.924 50.000 0.00 0.00 43.02 3.67
4300 4570 3.056328 GACACGGGGAAGCAAGGC 61.056 66.667 0.00 0.00 0.00 4.35
4349 4619 1.348036 CCGAGAAACCTGGGAGAACTT 59.652 52.381 0.00 0.00 31.96 2.66
4393 4663 1.002011 GGAACAAGCCTCCCCTGAC 60.002 63.158 0.00 0.00 0.00 3.51
4504 4774 2.283173 TCACAGAGAGGCGGCTCA 60.283 61.111 36.63 15.60 37.37 4.26
4522 4792 5.133221 GGCTCATCAACCAACCTATAACAT 58.867 41.667 0.00 0.00 0.00 2.71
4523 4793 5.009010 GGCTCATCAACCAACCTATAACATG 59.991 44.000 0.00 0.00 0.00 3.21
4542 4812 5.965922 ACATGTTTCTATCACGTCATCTGA 58.034 37.500 0.00 0.00 0.00 3.27
4552 4822 2.161012 CACGTCATCTGATTGCAGCTTT 59.839 45.455 0.00 0.00 42.01 3.51
4553 4823 2.417933 ACGTCATCTGATTGCAGCTTTC 59.582 45.455 0.00 0.00 42.01 2.62
4566 4836 2.348966 GCAGCTTTCTTGTTGTCGTCTC 60.349 50.000 0.00 0.00 0.00 3.36
4595 4865 3.857052 TCCCTAGTTTAACATGCTCGTG 58.143 45.455 0.00 0.00 0.00 4.35
4862 5132 5.833131 TGTATTGAACTTCTGGGCTTCTTTT 59.167 36.000 0.00 0.00 0.00 2.27
4887 5157 3.643792 GTCATACCTGTTCTGGATAGGCT 59.356 47.826 0.00 0.00 34.93 4.58
4979 5249 9.650371 GGCAAACAAGAAAATATTGAGAAAAAC 57.350 29.630 0.00 0.00 0.00 2.43
5002 5273 3.383825 AGATACACCGGTAGGAACATGAC 59.616 47.826 6.87 0.00 41.02 3.06
5026 5297 6.209192 ACTTATGATCACAGTTGCAAATCCAA 59.791 34.615 0.00 0.00 0.00 3.53
5140 5416 3.814842 CAGGAATGAACACAACAGCACTA 59.185 43.478 0.00 0.00 0.00 2.74
5150 5426 4.021894 ACACAACAGCACTAACCAAAAACA 60.022 37.500 0.00 0.00 0.00 2.83
5161 5437 6.584563 CACTAACCAAAAACATATTCAACCCG 59.415 38.462 0.00 0.00 0.00 5.28
5162 5438 5.538849 AACCAAAAACATATTCAACCCGT 57.461 34.783 0.00 0.00 0.00 5.28
5183 5470 5.270083 CGTAGCAAAACAATCACACTCAAA 58.730 37.500 0.00 0.00 0.00 2.69
5184 5471 5.171337 CGTAGCAAAACAATCACACTCAAAC 59.829 40.000 0.00 0.00 0.00 2.93
5185 5472 5.070770 AGCAAAACAATCACACTCAAACA 57.929 34.783 0.00 0.00 0.00 2.83
5186 5473 5.663456 AGCAAAACAATCACACTCAAACAT 58.337 33.333 0.00 0.00 0.00 2.71
5187 5474 6.108015 AGCAAAACAATCACACTCAAACATT 58.892 32.000 0.00 0.00 0.00 2.71
5220 5507 3.458118 CCCCTGGATTGATGTTGTACCTA 59.542 47.826 0.00 0.00 0.00 3.08
5313 5695 6.942005 TGTCTCCTCATTTCTTGAAGCAAATA 59.058 34.615 0.00 0.00 32.78 1.40
5314 5696 7.448161 TGTCTCCTCATTTCTTGAAGCAAATAA 59.552 33.333 0.00 0.00 32.78 1.40
5316 5698 8.299570 TCTCCTCATTTCTTGAAGCAAATAAAC 58.700 33.333 0.00 0.00 32.78 2.01
5338 5720 5.857268 ACCATAAGAGCTTTGTTGCAAAAT 58.143 33.333 0.00 0.00 34.99 1.82
5347 5729 4.775664 CTTTGTTGCAAAATAAAGCAGCC 58.224 39.130 0.00 0.00 42.39 4.85
5367 5749 3.726607 CCATGAGCTATCACTTGGACTC 58.273 50.000 0.00 0.00 37.67 3.36
5391 5773 8.117813 TCATACACAGATTACTTGTACAGACA 57.882 34.615 0.00 0.00 0.00 3.41
5410 5792 4.757149 AGACATCCTGCTAAAAGAACACAC 59.243 41.667 0.00 0.00 0.00 3.82
5428 5810 2.165167 CACAGCCACATCCAATTGTCT 58.835 47.619 4.43 0.00 0.00 3.41
5468 5872 0.846015 TTGGGGTATGGAGCTCATGG 59.154 55.000 17.19 0.00 32.34 3.66
5489 5893 0.036010 GCAGGAGCTTCTTGCCTACA 60.036 55.000 0.00 0.00 42.78 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 5.371115 TGTTGCAGCTTATTTCAAGGTAC 57.629 39.130 1.17 0.00 0.00 3.34
49 50 2.793278 ATTCCTCCGTTTGTTGTTGC 57.207 45.000 0.00 0.00 0.00 4.17
113 116 8.608844 AAGTATCAAGTACTCAGAAAGTTTGG 57.391 34.615 0.00 0.00 42.83 3.28
140 143 9.528489 AGCAAAGTATCAAGTATTCCCTAAAAA 57.472 29.630 0.00 0.00 0.00 1.94
141 144 9.528489 AAGCAAAGTATCAAGTATTCCCTAAAA 57.472 29.630 0.00 0.00 0.00 1.52
145 148 8.957466 GTTTAAGCAAAGTATCAAGTATTCCCT 58.043 33.333 0.00 0.00 0.00 4.20
146 149 8.736244 TGTTTAAGCAAAGTATCAAGTATTCCC 58.264 33.333 0.00 0.00 0.00 3.97
152 155 9.683069 CATTCTTGTTTAAGCAAAGTATCAAGT 57.317 29.630 6.21 0.00 34.57 3.16
195 200 6.238402 GGAACAGAGTTGGAACTTGTTAGAAC 60.238 42.308 14.54 0.00 39.88 3.01
203 208 3.644966 TGTGGAACAGAGTTGGAACTT 57.355 42.857 0.00 0.00 45.67 2.66
217 222 7.011389 CGAGTATTATGCTTCATTTCTGTGGAA 59.989 37.037 0.00 0.00 0.00 3.53
224 229 6.147328 GGGTACCGAGTATTATGCTTCATTTC 59.853 42.308 5.65 0.00 40.86 2.17
248 253 1.039068 TGCCCAAGTGTGTGAATTGG 58.961 50.000 0.00 0.00 42.59 3.16
265 286 4.181578 ACGTAGGTAGAATCATGTGTTGC 58.818 43.478 0.00 0.00 0.00 4.17
311 332 8.077991 GGTTTCCTTTTTAAAACAGCGTATAGT 58.922 33.333 0.00 0.00 0.00 2.12
329 350 1.134037 TGTGTGCGTTAGGGTTTCCTT 60.134 47.619 0.00 0.00 41.56 3.36
344 365 1.816835 TCTAGGAAGCGTAGGTGTGTG 59.183 52.381 0.00 0.00 39.47 3.82
410 431 2.659063 CCAGCCTGACCGACATGGA 61.659 63.158 0.00 0.00 42.00 3.41
437 458 1.187567 ATCCAGGGTGCCTTTGTTGC 61.188 55.000 0.00 0.00 0.00 4.17
478 499 2.227036 AGCCTCCCAGTCAACCAGG 61.227 63.158 0.00 0.00 0.00 4.45
484 505 0.472925 TTGTACCAGCCTCCCAGTCA 60.473 55.000 0.00 0.00 0.00 3.41
485 506 0.250513 CTTGTACCAGCCTCCCAGTC 59.749 60.000 0.00 0.00 0.00 3.51
486 507 1.201429 CCTTGTACCAGCCTCCCAGT 61.201 60.000 0.00 0.00 0.00 4.00
487 508 0.909610 TCCTTGTACCAGCCTCCCAG 60.910 60.000 0.00 0.00 0.00 4.45
488 509 0.474854 TTCCTTGTACCAGCCTCCCA 60.475 55.000 0.00 0.00 0.00 4.37
489 510 0.253327 CTTCCTTGTACCAGCCTCCC 59.747 60.000 0.00 0.00 0.00 4.30
490 511 0.253327 CCTTCCTTGTACCAGCCTCC 59.747 60.000 0.00 0.00 0.00 4.30
491 512 0.253327 CCCTTCCTTGTACCAGCCTC 59.747 60.000 0.00 0.00 0.00 4.70
492 513 1.208165 CCCCTTCCTTGTACCAGCCT 61.208 60.000 0.00 0.00 0.00 4.58
493 514 1.303282 CCCCTTCCTTGTACCAGCC 59.697 63.158 0.00 0.00 0.00 4.85
494 515 1.378646 GCCCCTTCCTTGTACCAGC 60.379 63.158 0.00 0.00 0.00 4.85
495 516 1.303282 GGCCCCTTCCTTGTACCAG 59.697 63.158 0.00 0.00 0.00 4.00
496 517 0.849094 ATGGCCCCTTCCTTGTACCA 60.849 55.000 0.00 0.00 0.00 3.25
497 518 1.133884 GTATGGCCCCTTCCTTGTACC 60.134 57.143 0.00 0.00 0.00 3.34
498 519 1.562475 TGTATGGCCCCTTCCTTGTAC 59.438 52.381 0.00 0.00 0.00 2.90
499 520 1.843851 CTGTATGGCCCCTTCCTTGTA 59.156 52.381 0.00 0.00 0.00 2.41
500 521 0.625849 CTGTATGGCCCCTTCCTTGT 59.374 55.000 0.00 0.00 0.00 3.16
501 522 0.106519 CCTGTATGGCCCCTTCCTTG 60.107 60.000 0.00 0.00 0.00 3.61
502 523 0.552615 ACCTGTATGGCCCCTTCCTT 60.553 55.000 0.00 0.00 40.22 3.36
503 524 0.988678 GACCTGTATGGCCCCTTCCT 60.989 60.000 0.00 0.00 40.22 3.36
504 525 0.988678 AGACCTGTATGGCCCCTTCC 60.989 60.000 0.00 0.00 40.22 3.46
505 526 0.181350 CAGACCTGTATGGCCCCTTC 59.819 60.000 0.00 0.00 40.22 3.46
541 584 3.244249 GGAGCACAGAGGTTTTGTCTAGT 60.244 47.826 0.00 0.00 0.00 2.57
668 711 2.180159 AACCAATCGACTGACGGGGG 62.180 60.000 0.00 2.22 42.82 5.40
672 715 5.860182 TCTTTTAGTAACCAATCGACTGACG 59.140 40.000 0.00 0.00 44.09 4.35
673 716 6.310711 CCTCTTTTAGTAACCAATCGACTGAC 59.689 42.308 0.00 0.00 0.00 3.51
674 717 6.395629 CCTCTTTTAGTAACCAATCGACTGA 58.604 40.000 0.00 0.00 0.00 3.41
675 718 5.063564 GCCTCTTTTAGTAACCAATCGACTG 59.936 44.000 0.00 0.00 0.00 3.51
701 745 5.305585 AGTCGAAAGCTATTTCTTGGACAA 58.694 37.500 11.32 0.00 42.28 3.18
854 907 4.517075 GGAAAAGACAGAGAGAACAAAGGG 59.483 45.833 0.00 0.00 0.00 3.95
886 939 8.735315 CGATAGAATTAGATAAGAGGCAGAGAA 58.265 37.037 0.00 0.00 39.76 2.87
894 947 7.704472 GCATGGGACGATAGAATTAGATAAGAG 59.296 40.741 0.00 0.00 41.38 2.85
953 1006 2.641305 CTCCATGAGGAAGCAAAGAGG 58.359 52.381 0.00 0.00 45.19 3.69
965 1018 1.129917 AGGTCATCTGCCTCCATGAG 58.870 55.000 0.00 0.00 29.46 2.90
1004 1057 0.175073 CGAGTACTGTAAGCCCACCC 59.825 60.000 0.00 0.00 37.60 4.61
1023 1076 2.590007 CCGGAGCTGTATGCAGGC 60.590 66.667 13.03 5.15 45.94 4.85
1025 1078 0.811616 GAACCCGGAGCTGTATGCAG 60.812 60.000 0.73 6.42 45.94 4.41
1041 1094 4.881850 TCTCCTTTGGTTGAAGAAGTGAAC 59.118 41.667 0.00 0.00 0.00 3.18
1058 1111 0.687427 GGCCAGAGCTCTCTCTCCTT 60.687 60.000 14.96 0.00 46.32 3.36
1206 1259 6.668541 ATGTCCTTGTATGAATCTTTCACG 57.331 37.500 0.00 0.00 43.48 4.35
1218 1271 5.519808 TGGAGTCTGAGTATGTCCTTGTAT 58.480 41.667 0.00 0.00 0.00 2.29
1263 1316 4.131649 TGTACAATCTGGGTATTCCACG 57.868 45.455 0.00 0.00 41.46 4.94
1363 1416 3.395941 AGAATGGAACTGGAACACTCCTT 59.604 43.478 0.00 0.00 42.94 3.36
1387 1440 0.320073 GTCGAAATGTGGGTCCGTCA 60.320 55.000 0.00 0.00 0.00 4.35
1445 1498 8.300286 ACCAATCATAGAGTGTATATCAACGAG 58.700 37.037 0.00 0.00 0.00 4.18
1446 1499 8.178313 ACCAATCATAGAGTGTATATCAACGA 57.822 34.615 0.00 0.00 0.00 3.85
1456 1509 8.918202 TTTTCTTGTAACCAATCATAGAGTGT 57.082 30.769 0.00 0.00 0.00 3.55
1463 1516 8.776470 CAAAGCAATTTTCTTGTAACCAATCAT 58.224 29.630 0.00 0.00 0.00 2.45
1511 1581 5.883115 CAGGAGGCTATATCTCATTCGAGTA 59.117 44.000 0.00 0.00 40.44 2.59
1529 1605 3.430651 GCTGAGAATCTTGAGACAGGAGG 60.431 52.174 0.00 0.00 34.92 4.30
1639 1877 2.423185 TGTATTTTGCAGGGCTGATTCG 59.577 45.455 0.00 0.00 0.00 3.34
1715 1954 2.046292 CAACCCCCTGTCAAAACCATT 58.954 47.619 0.00 0.00 0.00 3.16
1717 1956 0.631753 TCAACCCCCTGTCAAAACCA 59.368 50.000 0.00 0.00 0.00 3.67
1735 1974 4.021719 AGCATGTTATATTGCCAAGCCATC 60.022 41.667 0.00 0.00 39.72 3.51
1741 1980 5.507817 GCAGCTAAGCATGTTATATTGCCAA 60.508 40.000 0.00 0.00 39.72 4.52
1771 2010 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
1772 2011 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
1773 2012 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
1774 2013 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
1775 2014 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
1776 2015 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
1777 2016 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
1778 2017 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
1824 2063 5.122711 CCGTCCCATATTGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
1825 2064 4.632688 CCGTCCCATATTGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
1826 2065 4.081531 TCCGTCCCATATTGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
1827 2066 3.448301 TCCGTCCCATATTGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
1828 2067 3.025978 TCCGTCCCATATTGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
1830 2069 4.583489 TCTCTCCGTCCCATATTGTAAGAC 59.417 45.833 0.00 0.00 0.00 3.01
1831 2070 4.800023 TCTCTCCGTCCCATATTGTAAGA 58.200 43.478 0.00 0.00 0.00 2.10
1832 2071 4.585162 ACTCTCTCCGTCCCATATTGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
1833 2072 4.543689 ACTCTCTCCGTCCCATATTGTAA 58.456 43.478 0.00 0.00 0.00 2.41
1834 2073 4.180377 ACTCTCTCCGTCCCATATTGTA 57.820 45.455 0.00 0.00 0.00 2.41
1835 2074 3.033659 ACTCTCTCCGTCCCATATTGT 57.966 47.619 0.00 0.00 0.00 2.71
1836 2075 5.730296 AATACTCTCTCCGTCCCATATTG 57.270 43.478 0.00 0.00 0.00 1.90
1837 2076 6.078664 AGAAATACTCTCTCCGTCCCATATT 58.921 40.000 0.00 0.00 0.00 1.28
1838 2077 5.646215 AGAAATACTCTCTCCGTCCCATAT 58.354 41.667 0.00 0.00 0.00 1.78
1839 2078 5.063017 AGAAATACTCTCTCCGTCCCATA 57.937 43.478 0.00 0.00 0.00 2.74
1840 2079 3.917300 AGAAATACTCTCTCCGTCCCAT 58.083 45.455 0.00 0.00 0.00 4.00
1841 2080 3.383698 AGAAATACTCTCTCCGTCCCA 57.616 47.619 0.00 0.00 0.00 4.37
1842 2081 4.739587 AAAGAAATACTCTCTCCGTCCC 57.260 45.455 0.00 0.00 31.02 4.46
1843 2082 5.163540 TGCTAAAGAAATACTCTCTCCGTCC 60.164 44.000 0.00 0.00 31.02 4.79
1844 2083 5.892568 TGCTAAAGAAATACTCTCTCCGTC 58.107 41.667 0.00 0.00 31.02 4.79
1845 2084 5.916661 TGCTAAAGAAATACTCTCTCCGT 57.083 39.130 0.00 0.00 31.02 4.69
1846 2085 7.168972 CAGAATGCTAAAGAAATACTCTCTCCG 59.831 40.741 0.00 0.00 31.02 4.63
1847 2086 7.440856 CCAGAATGCTAAAGAAATACTCTCTCC 59.559 40.741 0.00 0.00 30.06 3.71
1848 2087 7.984617 ACCAGAATGCTAAAGAAATACTCTCTC 59.015 37.037 0.00 0.00 30.06 3.20
1849 2088 7.856415 ACCAGAATGCTAAAGAAATACTCTCT 58.144 34.615 0.00 0.00 30.06 3.10
1850 2089 8.499403 AACCAGAATGCTAAAGAAATACTCTC 57.501 34.615 0.00 0.00 30.06 3.20
1851 2090 8.870075 AAACCAGAATGCTAAAGAAATACTCT 57.130 30.769 0.00 0.00 31.43 3.24
1852 2091 8.184848 GGAAACCAGAATGCTAAAGAAATACTC 58.815 37.037 0.00 0.00 31.97 2.59
1853 2092 7.669722 TGGAAACCAGAATGCTAAAGAAATACT 59.330 33.333 0.00 0.00 31.97 2.12
1854 2093 7.826690 TGGAAACCAGAATGCTAAAGAAATAC 58.173 34.615 0.00 0.00 31.97 1.89
1890 2134 3.375299 ACTTGCACACAGAAACAAGAGAC 59.625 43.478 8.46 0.00 41.59 3.36
1952 2197 3.242413 GCAGGAATACACTTGTATGCACG 60.242 47.826 9.21 1.54 40.78 5.34
1961 2206 7.743749 AGATATTGATGAGCAGGAATACACTT 58.256 34.615 0.00 0.00 0.00 3.16
2028 2273 0.317479 ACACACACGCTAGGAACCTC 59.683 55.000 0.00 0.00 0.00 3.85
2132 2377 6.436847 TGATGATGGAGCAATTTGAGGTTAAA 59.563 34.615 0.00 0.00 0.00 1.52
2136 2381 3.972133 TGATGATGGAGCAATTTGAGGT 58.028 40.909 0.00 0.00 0.00 3.85
2155 2400 6.988580 TGTTGCATTTCATTTACAAACCATGA 59.011 30.769 0.00 0.00 0.00 3.07
2184 2429 6.851222 AGCATGTTTACGAGATAATCCAAG 57.149 37.500 0.00 0.00 0.00 3.61
2285 2540 9.979270 CATCAGTTTAGACTTACTAGCAAAATG 57.021 33.333 0.00 0.00 32.54 2.32
2306 2561 2.341257 AGTACGCAGAAAGCACATCAG 58.659 47.619 0.00 0.00 46.13 2.90
2319 2574 9.956720 GTTATAATTTCTTAGGACTAGTACGCA 57.043 33.333 0.00 0.00 0.00 5.24
2466 2721 2.999355 GCTCTTGACTCTGCAGTTTAGG 59.001 50.000 14.67 0.00 30.63 2.69
2497 2752 6.644248 TGCTCGTAGGTTTCTGCTATATAA 57.356 37.500 0.00 0.00 0.00 0.98
2557 2812 1.339055 TGTTCAATGGAAGCCCTCTCG 60.339 52.381 0.00 0.00 32.62 4.04
2680 2935 3.182887 TCTTCCAGCTTCCTCTTCTCT 57.817 47.619 0.00 0.00 0.00 3.10
2788 3043 3.673902 TGTCACTATGTGATGGGTGTTG 58.326 45.455 3.65 0.00 44.63 3.33
2878 3133 4.704833 TGCTGCCAAGAGTCCCGC 62.705 66.667 0.00 0.00 0.00 6.13
2935 3190 3.365767 GCTGTTGCTCAAGTTCTTCCATC 60.366 47.826 0.00 0.00 36.03 3.51
3013 3280 1.576421 GCTGCTATATGTTGCCGGC 59.424 57.895 22.73 22.73 0.00 6.13
3029 3296 3.814615 CTATGCGGATGGTGCGGCT 62.815 63.158 0.00 0.00 35.42 5.52
3212 3479 1.949257 CTGGTGTTTTCTCGGTGGC 59.051 57.895 0.00 0.00 0.00 5.01
3279 3546 2.755650 AGTTACTCGTGGTGCTTTGAG 58.244 47.619 0.00 0.00 34.65 3.02
3579 3849 1.068895 TGAATGCCACTTGCTTTGGTG 59.931 47.619 1.52 0.00 42.00 4.17
3580 3850 1.342174 CTGAATGCCACTTGCTTTGGT 59.658 47.619 1.52 0.00 42.00 3.67
3589 3859 3.708403 TGAATGTCTCTGAATGCCACT 57.292 42.857 0.00 0.00 0.00 4.00
3697 3967 1.152777 CAGTTCCCTGGTTGGTGCA 60.153 57.895 0.00 0.00 34.90 4.57
3715 3985 0.392461 TATGTTGAGAACCTGGCGGC 60.392 55.000 0.00 0.00 0.00 6.53
3731 4001 1.376609 GGCGTTGCTTGAGGGGTATG 61.377 60.000 0.00 0.00 0.00 2.39
3746 4016 2.770164 ACTTTCAGATTAGCTGGCGT 57.230 45.000 0.00 0.00 44.98 5.68
3755 4025 5.574082 CGACGAGTCAGATACTTTCAGATT 58.426 41.667 4.02 0.00 39.07 2.40
3778 4048 0.899717 TGGCACCCTCTTTCATTGGC 60.900 55.000 0.00 0.00 0.00 4.52
3820 4090 4.699257 AGCATTTTTCTGAGCCTCTTAGTG 59.301 41.667 0.00 0.00 0.00 2.74
3845 4115 1.884579 CACTGCTGGATCACTTTGCTT 59.115 47.619 0.00 0.00 0.00 3.91
3865 4135 1.334869 CCTGTTGACTGTGGTTTGAGC 59.665 52.381 0.00 0.00 0.00 4.26
3885 4155 1.134189 GTACTGGAGGGGGTTGCATAC 60.134 57.143 0.00 0.00 0.00 2.39
4099 4369 4.353437 GCTGGTGCTTGCAGTGGC 62.353 66.667 0.00 0.00 37.03 5.01
4128 4398 8.113173 ACTATCCTTGGAAGATATCGACTTAC 57.887 38.462 0.00 0.00 0.00 2.34
4133 4403 6.246163 TGCTACTATCCTTGGAAGATATCGA 58.754 40.000 0.00 0.00 0.00 3.59
4287 4557 2.437359 CAGAGCCTTGCTTCCCCG 60.437 66.667 0.00 0.00 39.88 5.73
4300 4570 3.123620 GGCGGTGCAGCTTCAGAG 61.124 66.667 14.92 0.00 37.29 3.35
4349 4619 7.175797 TGAGACTCTAGTAAATCTTGTCCTGA 58.824 38.462 3.68 0.00 0.00 3.86
4495 4765 1.675641 GTTGGTTGATGAGCCGCCT 60.676 57.895 0.00 0.00 0.00 5.52
4498 4768 2.332063 ATAGGTTGGTTGATGAGCCG 57.668 50.000 0.00 0.00 0.00 5.52
4504 4774 9.920946 ATAGAAACATGTTATAGGTTGGTTGAT 57.079 29.630 12.39 0.00 32.87 2.57
4522 4792 5.291858 GCAATCAGATGACGTGATAGAAACA 59.708 40.000 0.00 0.00 33.34 2.83
4523 4793 5.291858 TGCAATCAGATGACGTGATAGAAAC 59.708 40.000 0.00 0.00 33.34 2.78
4542 4812 2.358898 ACGACAACAAGAAAGCTGCAAT 59.641 40.909 1.02 0.00 0.00 3.56
4552 4822 4.079970 AGGTAGATGAGACGACAACAAGA 58.920 43.478 0.00 0.00 0.00 3.02
4553 4823 4.416620 GAGGTAGATGAGACGACAACAAG 58.583 47.826 0.00 0.00 0.00 3.16
4566 4836 5.992217 GCATGTTAAACTAGGGAGGTAGATG 59.008 44.000 0.00 0.00 0.00 2.90
4595 4865 6.831976 AGGTGACAGATAATGGACCTTATTC 58.168 40.000 0.00 0.00 41.04 1.75
4862 5132 5.304614 GCCTATCCAGAACAGGTATGACTTA 59.695 44.000 0.00 0.00 0.00 2.24
4970 5240 4.345859 ACCGGTGTATCTGTTTTTCTCA 57.654 40.909 6.12 0.00 0.00 3.27
4979 5249 3.383505 TCATGTTCCTACCGGTGTATCTG 59.616 47.826 19.93 6.23 0.00 2.90
5002 5273 6.198650 TGGATTTGCAACTGTGATCATAAG 57.801 37.500 0.00 2.54 0.00 1.73
5026 5297 9.574516 AATTCAGATTTGTTCCTACAGTAAGTT 57.425 29.630 0.00 0.00 35.28 2.66
5110 5386 2.302733 TGTGTTCATTCCTGCTCTGCTA 59.697 45.455 0.00 0.00 0.00 3.49
5140 5416 5.538849 ACGGGTTGAATATGTTTTTGGTT 57.461 34.783 0.00 0.00 0.00 3.67
5150 5426 5.968528 TTGTTTTGCTACGGGTTGAATAT 57.031 34.783 0.00 0.00 0.00 1.28
5161 5437 6.033341 TGTTTGAGTGTGATTGTTTTGCTAC 58.967 36.000 0.00 0.00 0.00 3.58
5162 5438 6.201226 TGTTTGAGTGTGATTGTTTTGCTA 57.799 33.333 0.00 0.00 0.00 3.49
5187 5474 5.199982 TCAATCCAGGGGTAGCATAAAAA 57.800 39.130 0.00 0.00 0.00 1.94
5191 5478 3.326521 ACATCAATCCAGGGGTAGCATA 58.673 45.455 0.00 0.00 0.00 3.14
5220 5507 7.833183 GGGCCTGATTCATATGATTTATCTTCT 59.167 37.037 6.17 0.00 0.00 2.85
5313 5695 4.935352 TGCAACAAAGCTCTTATGGTTT 57.065 36.364 0.00 0.00 38.04 3.27
5314 5696 4.935352 TTGCAACAAAGCTCTTATGGTT 57.065 36.364 0.00 0.00 34.99 3.67
5316 5698 7.887996 TTATTTTGCAACAAAGCTCTTATGG 57.112 32.000 0.00 0.00 34.99 2.74
5347 5729 4.397481 TGAGTCCAAGTGATAGCTCATG 57.603 45.455 0.00 0.00 32.98 3.07
5367 5749 8.932945 ATGTCTGTACAAGTAATCTGTGTATG 57.067 34.615 0.00 0.00 39.58 2.39
5391 5773 3.503748 GCTGTGTGTTCTTTTAGCAGGAT 59.496 43.478 0.00 0.00 0.00 3.24
5410 5792 2.422479 CAGAGACAATTGGATGTGGCTG 59.578 50.000 10.83 3.78 31.51 4.85
5428 5810 7.939039 CCCCAATCTAAATATTTAGCTCACAGA 59.061 37.037 24.59 12.21 39.90 3.41
5489 5893 6.810182 GCTTGAACATAGTCTCAATGCAATTT 59.190 34.615 0.00 0.00 31.22 1.82


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

AutoCloner maintained by Alex Coulton.