Multiple sequence alignment - TraesCS5B01G196600

Loading Multiple Alignment...

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 TraesCS5B01G196600 chr5B 100.000 4015 0 0 1 4015 354242512 354238498 0.000000e+00 7415.0
1 TraesCS5B01G196600 chr5D 93.183 1599 70 11 1876 3470 309005667 309004104 0.000000e+00 2313.0
2 TraesCS5B01G196600 chr5D 89.460 1518 79 36 356 1819 309007151 309005661 0.000000e+00 1842.0
3 TraesCS5B01G196600 chr5D 93.375 317 9 3 1 317 309007459 309007155 3.660000e-125 459.0
4 TraesCS5B01G196600 chr5D 84.282 439 65 4 3468 3905 309004052 309003617 3.710000e-115 425.0
5 TraesCS5B01G196600 chr5A 90.447 1612 96 18 1876 3470 389071521 389073091 0.000000e+00 2071.0
6 TraesCS5B01G196600 chr5A 89.377 1092 57 27 355 1414 389070073 389071137 0.000000e+00 1319.0
7 TraesCS5B01G196600 chr5A 85.009 547 63 8 3470 4015 389073244 389073772 4.570000e-149 538.0
8 TraesCS5B01G196600 chr5A 92.722 316 13 4 2 316 389069763 389070069 7.920000e-122 448.0
9 TraesCS5B01G196600 chr5A 89.456 294 12 9 1544 1819 389071235 389071527 1.780000e-93 353.0
10 TraesCS5B01G196600 chr6B 91.165 249 12 2 1166 1414 255097119 255096881 2.990000e-86 329.0
11 TraesCS5B01G196600 chr6B 85.000 140 18 2 1037 1173 255097282 255097143 5.410000e-29 139.0
12 TraesCS5B01G196600 chr6B 88.000 75 5 4 2568 2640 460209798 460209870 7.150000e-13 86.1
13 TraesCS5B01G196600 chr4A 91.165 249 12 2 1166 1414 198002173 198001935 2.990000e-86 329.0
14 TraesCS5B01G196600 chr4A 88.889 72 8 0 1036 1107 198002371 198002300 5.530000e-14 89.8
15 TraesCS5B01G196600 chr2D 91.165 249 12 2 1166 1414 118801130 118800892 2.990000e-86 329.0
16 TraesCS5B01G196600 chr7B 90.196 255 15 2 1160 1414 374717236 374717480 1.390000e-84 324.0
17 TraesCS5B01G196600 chr7B 90.361 249 14 2 1166 1414 705711814 705711576 6.480000e-83 318.0
18 TraesCS5B01G196600 chr7B 87.778 180 11 3 1160 1338 244641594 244641763 2.450000e-47 200.0
19 TraesCS5B01G196600 chr7B 85.135 148 18 3 1036 1180 705711977 705711831 8.990000e-32 148.0
20 TraesCS5B01G196600 chr7B 85.106 141 18 2 1036 1173 244641435 244641575 1.500000e-29 141.0
21 TraesCS5B01G196600 chr3B 90.234 256 14 3 1160 1414 169825949 169826194 1.390000e-84 324.0
22 TraesCS5B01G196600 chr3B 84.397 141 19 2 1036 1173 169825791 169825931 7.000000e-28 135.0
23 TraesCS5B01G196600 chr2B 85.106 141 18 2 1036 1173 178772511 178772371 1.500000e-29 141.0
24 TraesCS5B01G196600 chr7A 88.889 72 8 0 1036 1107 133316885 133316956 5.530000e-14 89.8
25 TraesCS5B01G196600 chr6D 88.000 75 5 4 2568 2640 296824533 296824461 7.150000e-13 86.1
26 TraesCS5B01G196600 chr6A 88.000 75 5 4 2568 2640 423533558 423533486 7.150000e-13 86.1


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 TraesCS5B01G196600 chr5B 354238498 354242512 4014 True 7415.00 7415 100.0000 1 4015 1 chr5B.!!$R1 4014
1 TraesCS5B01G196600 chr5D 309003617 309007459 3842 True 1259.75 2313 90.0750 1 3905 4 chr5D.!!$R1 3904
2 TraesCS5B01G196600 chr5A 389069763 389073772 4009 False 945.80 2071 89.4022 2 4015 5 chr5A.!!$F1 4013

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
326 332 0.037046 TGATCACTGATGCACACGCT 60.037 50.0 0.0 0.0 39.64 5.07 F
1092 1143 0.034059 AGTGCAGTCCTCTGTTTCCG 59.966 55.0 0.0 0.0 43.05 4.30 F
2459 2557 0.179108 GCACCTTCGGCTACTTCGAT 60.179 55.0 0.0 0.0 36.49 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1920 1.340114 GCTAGTCAAACTGGAAGGGGG 60.340 57.143 0.00 0.0 39.3 5.40 R
2462 2560 0.179121 CCATTACCAGCGCGTACTCA 60.179 55.000 8.43 0.0 0.0 3.41 R
3916 4188 0.038166 TTCCCCTGCACCAGTGATTC 59.962 55.000 0.99 0.0 0.0 2.52 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
59 60 2.893398 CCACCTCTACCACCGCTC 59.107 66.667 0.00 0.00 0.00 5.03
60 61 2.490217 CACCTCTACCACCGCTCG 59.510 66.667 0.00 0.00 0.00 5.03
61 62 3.450115 ACCTCTACCACCGCTCGC 61.450 66.667 0.00 0.00 0.00 5.03
62 63 3.141488 CCTCTACCACCGCTCGCT 61.141 66.667 0.00 0.00 0.00 4.93
63 64 2.409651 CTCTACCACCGCTCGCTC 59.590 66.667 0.00 0.00 0.00 5.03
64 65 3.127352 CTCTACCACCGCTCGCTCC 62.127 68.421 0.00 0.00 0.00 4.70
65 66 3.141488 CTACCACCGCTCGCTCCT 61.141 66.667 0.00 0.00 0.00 3.69
105 106 0.811616 CAGGCCCTTCCGATTCTTCG 60.812 60.000 0.00 0.00 45.08 3.79
159 160 3.515602 AGTTCTGCTCAACCATTTCCT 57.484 42.857 0.00 0.00 0.00 3.36
241 243 0.321122 CAACTGACACCCAGCTCTCC 60.321 60.000 0.00 0.00 46.81 3.71
242 244 1.484444 AACTGACACCCAGCTCTCCC 61.484 60.000 0.00 0.00 46.81 4.30
243 245 1.611851 CTGACACCCAGCTCTCCCT 60.612 63.158 0.00 0.00 35.89 4.20
244 246 1.610673 TGACACCCAGCTCTCCCTC 60.611 63.158 0.00 0.00 0.00 4.30
245 247 2.284995 ACACCCAGCTCTCCCTCC 60.285 66.667 0.00 0.00 0.00 4.30
324 330 1.718396 AGTGATCACTGATGCACACG 58.282 50.000 27.37 0.00 40.75 4.49
325 331 0.095935 GTGATCACTGATGCACACGC 59.904 55.000 18.83 0.00 39.24 5.34
326 332 0.037046 TGATCACTGATGCACACGCT 60.037 50.000 0.00 0.00 39.64 5.07
327 333 0.372679 GATCACTGATGCACACGCTG 59.627 55.000 0.00 0.00 39.64 5.18
336 342 4.385093 CACACGCTGCTGCTGCTG 62.385 66.667 25.43 22.59 40.48 4.41
358 364 0.524414 GCTGCTGCATCAACACATCA 59.476 50.000 11.11 0.00 39.41 3.07
420 426 0.037326 TCCTCCACACGCTTTGCTAG 60.037 55.000 0.00 0.00 0.00 3.42
526 532 1.630126 GCTCCCAAGAGATCAGCCCA 61.630 60.000 0.00 0.00 43.39 5.36
528 534 1.072015 CTCCCAAGAGATCAGCCCATC 59.928 57.143 0.00 0.00 43.39 3.51
535 546 0.839853 AGATCAGCCCATCCCCTAGC 60.840 60.000 0.00 0.00 0.00 3.42
570 594 2.815211 CGCCTGTACTGCACGCAT 60.815 61.111 8.36 0.00 0.00 4.73
576 600 2.616960 CTGTACTGCACGCATTCCTTA 58.383 47.619 0.00 0.00 0.00 2.69
590 614 4.081420 GCATTCCTTAGTCTTGTCCTCTCA 60.081 45.833 0.00 0.00 0.00 3.27
591 615 5.415221 CATTCCTTAGTCTTGTCCTCTCAC 58.585 45.833 0.00 0.00 0.00 3.51
592 616 3.432378 TCCTTAGTCTTGTCCTCTCACC 58.568 50.000 0.00 0.00 0.00 4.02
593 617 2.498078 CCTTAGTCTTGTCCTCTCACCC 59.502 54.545 0.00 0.00 0.00 4.61
594 618 3.436243 CTTAGTCTTGTCCTCTCACCCT 58.564 50.000 0.00 0.00 0.00 4.34
595 619 2.407340 AGTCTTGTCCTCTCACCCTT 57.593 50.000 0.00 0.00 0.00 3.95
596 620 2.252714 AGTCTTGTCCTCTCACCCTTC 58.747 52.381 0.00 0.00 0.00 3.46
597 621 2.158234 AGTCTTGTCCTCTCACCCTTCT 60.158 50.000 0.00 0.00 0.00 2.85
598 622 2.028567 GTCTTGTCCTCTCACCCTTCTG 60.029 54.545 0.00 0.00 0.00 3.02
599 623 1.974236 CTTGTCCTCTCACCCTTCTGT 59.026 52.381 0.00 0.00 0.00 3.41
600 624 1.633774 TGTCCTCTCACCCTTCTGTC 58.366 55.000 0.00 0.00 0.00 3.51
601 625 0.899019 GTCCTCTCACCCTTCTGTCC 59.101 60.000 0.00 0.00 0.00 4.02
602 626 0.787084 TCCTCTCACCCTTCTGTCCT 59.213 55.000 0.00 0.00 0.00 3.85
603 627 1.190643 CCTCTCACCCTTCTGTCCTC 58.809 60.000 0.00 0.00 0.00 3.71
604 628 1.272985 CCTCTCACCCTTCTGTCCTCT 60.273 57.143 0.00 0.00 0.00 3.69
605 629 2.534990 CTCTCACCCTTCTGTCCTCTT 58.465 52.381 0.00 0.00 0.00 2.85
606 630 2.495669 CTCTCACCCTTCTGTCCTCTTC 59.504 54.545 0.00 0.00 0.00 2.87
607 631 2.158310 TCTCACCCTTCTGTCCTCTTCA 60.158 50.000 0.00 0.00 0.00 3.02
618 642 3.948473 CTGTCCTCTTCATCTCTTCCGTA 59.052 47.826 0.00 0.00 0.00 4.02
626 658 0.107508 ATCTCTTCCGTACCGTCCGA 60.108 55.000 0.00 0.00 0.00 4.55
660 692 3.425713 CACCGCGCAGTGCATTCT 61.426 61.111 16.83 0.00 46.97 2.40
661 693 3.121030 ACCGCGCAGTGCATTCTC 61.121 61.111 16.83 0.00 46.97 2.87
664 696 2.863153 GCGCAGTGCATTCTCGTT 59.137 55.556 16.83 0.00 45.45 3.85
667 699 0.792640 CGCAGTGCATTCTCGTTTCT 59.207 50.000 16.83 0.00 0.00 2.52
669 701 1.800586 GCAGTGCATTCTCGTTTCTCA 59.199 47.619 11.09 0.00 0.00 3.27
670 702 2.159734 GCAGTGCATTCTCGTTTCTCAG 60.160 50.000 11.09 0.00 0.00 3.35
671 703 2.072298 AGTGCATTCTCGTTTCTCAGC 58.928 47.619 0.00 0.00 0.00 4.26
682 714 0.472471 TTTCTCAGCCGGTTCAGGTT 59.528 50.000 1.90 0.00 0.00 3.50
761 794 2.358957 CGCTGGGATTGATTTGTCTGA 58.641 47.619 0.00 0.00 0.00 3.27
771 805 3.743521 TGATTTGTCTGACTGGTTCTGG 58.256 45.455 9.51 0.00 0.00 3.86
1080 1126 2.880890 GTTGAATCCTTGTGAGTGCAGT 59.119 45.455 0.00 0.00 0.00 4.40
1092 1143 0.034059 AGTGCAGTCCTCTGTTTCCG 59.966 55.000 0.00 0.00 43.05 4.30
1095 1146 0.318762 GCAGTCCTCTGTTTCCGTCT 59.681 55.000 0.00 0.00 43.05 4.18
1100 1151 1.887198 TCCTCTGTTTCCGTCTCACTC 59.113 52.381 0.00 0.00 0.00 3.51
1121 1175 2.549754 CTGTTGTCGGCAGAGTCATTTT 59.450 45.455 0.00 0.00 36.12 1.82
1132 1186 5.091431 GCAGAGTCATTTTTCACTGTATGC 58.909 41.667 0.00 0.00 0.00 3.14
1134 1188 6.569226 GCAGAGTCATTTTTCACTGTATGCTT 60.569 38.462 0.00 0.00 0.00 3.91
1153 1209 4.821260 TGCTTATCTGTTTCTTCAGTGCAA 59.179 37.500 0.00 0.00 36.85 4.08
1154 1210 5.474532 TGCTTATCTGTTTCTTCAGTGCAAT 59.525 36.000 0.00 0.00 36.85 3.56
1163 1219 8.177119 TGTTTCTTCAGTGCAATATTTAAGGT 57.823 30.769 0.00 0.00 0.00 3.50
1218 1279 0.396435 CTGCAGGGGTGTACAAGACA 59.604 55.000 5.57 0.00 34.94 3.41
1244 1305 2.401699 CTGTGGCAGGTGAAGGAGCA 62.402 60.000 0.00 0.00 0.00 4.26
1245 1306 1.228245 GTGGCAGGTGAAGGAGCAA 60.228 57.895 0.00 0.00 0.00 3.91
1246 1307 1.073722 TGGCAGGTGAAGGAGCAAG 59.926 57.895 0.00 0.00 0.00 4.01
1247 1308 1.676967 GGCAGGTGAAGGAGCAAGG 60.677 63.158 0.00 0.00 0.00 3.61
1248 1309 2.338785 GCAGGTGAAGGAGCAAGGC 61.339 63.158 0.00 0.00 0.00 4.35
1249 1310 2.037136 CAGGTGAAGGAGCAAGGCG 61.037 63.158 0.00 0.00 0.00 5.52
1250 1311 3.435186 GGTGAAGGAGCAAGGCGC 61.435 66.667 0.00 0.00 42.91 6.53
1446 1507 4.795278 CGAAATACGTACGGCTCTTACTTT 59.205 41.667 21.06 6.75 37.22 2.66
1541 1602 4.949856 GCAGGGTCTGAATATTTCCAAAGA 59.050 41.667 0.00 0.00 32.44 2.52
1542 1603 5.595952 GCAGGGTCTGAATATTTCCAAAGAT 59.404 40.000 0.00 0.00 32.44 2.40
1581 1657 8.325282 GTGGTGTTTTGTCATTTAGCTTTTTAC 58.675 33.333 0.00 0.00 0.00 2.01
1582 1658 8.035394 TGGTGTTTTGTCATTTAGCTTTTTACA 58.965 29.630 0.00 0.00 0.00 2.41
1665 1741 5.183713 CCTCTTTGGTTCTATGCATTTGTCA 59.816 40.000 3.54 0.00 0.00 3.58
1666 1742 6.258230 TCTTTGGTTCTATGCATTTGTCAG 57.742 37.500 3.54 0.00 0.00 3.51
1667 1743 5.769662 TCTTTGGTTCTATGCATTTGTCAGT 59.230 36.000 3.54 0.00 0.00 3.41
1668 1744 6.939730 TCTTTGGTTCTATGCATTTGTCAGTA 59.060 34.615 3.54 0.00 0.00 2.74
1669 1745 6.741992 TTGGTTCTATGCATTTGTCAGTAG 57.258 37.500 3.54 0.00 0.00 2.57
1679 1772 4.148230 GTCAGTAGGACACACGCG 57.852 61.111 3.53 3.53 46.19 6.01
1745 1838 1.537202 GAGTGGTGTGACATTTGCTCC 59.463 52.381 0.00 0.00 0.00 4.70
1818 1911 9.603921 GATCAAACACCAATAAATTCCAATGAT 57.396 29.630 0.00 0.00 0.00 2.45
1819 1912 8.774890 TCAAACACCAATAAATTCCAATGATG 57.225 30.769 0.00 0.00 0.00 3.07
1820 1913 8.373981 TCAAACACCAATAAATTCCAATGATGT 58.626 29.630 0.00 0.00 0.00 3.06
1821 1914 9.001542 CAAACACCAATAAATTCCAATGATGTT 57.998 29.630 0.00 0.00 0.00 2.71
1822 1915 9.571816 AAACACCAATAAATTCCAATGATGTTT 57.428 25.926 0.00 0.00 0.00 2.83
1823 1916 9.571816 AACACCAATAAATTCCAATGATGTTTT 57.428 25.926 0.00 0.00 0.00 2.43
1831 1924 5.948742 TTCCAATGATGTTTTATTCCCCC 57.051 39.130 0.00 0.00 0.00 5.40
1832 1925 5.219468 TCCAATGATGTTTTATTCCCCCT 57.781 39.130 0.00 0.00 0.00 4.79
1833 1926 5.598754 TCCAATGATGTTTTATTCCCCCTT 58.401 37.500 0.00 0.00 0.00 3.95
1834 1927 5.660864 TCCAATGATGTTTTATTCCCCCTTC 59.339 40.000 0.00 0.00 0.00 3.46
1835 1928 5.163311 CCAATGATGTTTTATTCCCCCTTCC 60.163 44.000 0.00 0.00 0.00 3.46
1836 1929 4.683766 TGATGTTTTATTCCCCCTTCCA 57.316 40.909 0.00 0.00 0.00 3.53
1837 1930 4.609301 TGATGTTTTATTCCCCCTTCCAG 58.391 43.478 0.00 0.00 0.00 3.86
1838 1931 4.045334 TGATGTTTTATTCCCCCTTCCAGT 59.955 41.667 0.00 0.00 0.00 4.00
1839 1932 4.479156 TGTTTTATTCCCCCTTCCAGTT 57.521 40.909 0.00 0.00 0.00 3.16
1840 1933 4.821940 TGTTTTATTCCCCCTTCCAGTTT 58.178 39.130 0.00 0.00 0.00 2.66
1841 1934 4.591072 TGTTTTATTCCCCCTTCCAGTTTG 59.409 41.667 0.00 0.00 0.00 2.93
1842 1935 4.750833 TTTATTCCCCCTTCCAGTTTGA 57.249 40.909 0.00 0.00 0.00 2.69
1843 1936 2.604912 ATTCCCCCTTCCAGTTTGAC 57.395 50.000 0.00 0.00 0.00 3.18
1844 1937 1.529744 TTCCCCCTTCCAGTTTGACT 58.470 50.000 0.00 0.00 0.00 3.41
1845 1938 2.426431 TCCCCCTTCCAGTTTGACTA 57.574 50.000 0.00 0.00 0.00 2.59
1846 1939 2.266279 TCCCCCTTCCAGTTTGACTAG 58.734 52.381 0.00 0.00 0.00 2.57
1847 1940 1.340114 CCCCCTTCCAGTTTGACTAGC 60.340 57.143 0.00 0.00 0.00 3.42
1848 1941 1.351017 CCCCTTCCAGTTTGACTAGCA 59.649 52.381 0.00 0.00 0.00 3.49
1849 1942 2.025887 CCCCTTCCAGTTTGACTAGCAT 60.026 50.000 0.00 0.00 0.00 3.79
1850 1943 3.199946 CCCCTTCCAGTTTGACTAGCATA 59.800 47.826 0.00 0.00 0.00 3.14
1851 1944 4.446371 CCCTTCCAGTTTGACTAGCATAG 58.554 47.826 0.00 0.00 46.50 2.23
1852 1945 4.162320 CCCTTCCAGTTTGACTAGCATAGA 59.838 45.833 0.00 0.00 42.77 1.98
1853 1946 5.163258 CCCTTCCAGTTTGACTAGCATAGAT 60.163 44.000 0.00 0.00 42.77 1.98
1854 1947 6.042093 CCCTTCCAGTTTGACTAGCATAGATA 59.958 42.308 0.00 0.00 42.77 1.98
1855 1948 6.926272 CCTTCCAGTTTGACTAGCATAGATAC 59.074 42.308 0.00 0.00 42.77 2.24
1856 1949 7.417911 CCTTCCAGTTTGACTAGCATAGATACA 60.418 40.741 0.00 0.00 42.77 2.29
1857 1950 6.806751 TCCAGTTTGACTAGCATAGATACAC 58.193 40.000 0.00 0.00 42.77 2.90
1858 1951 5.986135 CCAGTTTGACTAGCATAGATACACC 59.014 44.000 0.00 0.00 42.77 4.16
1859 1952 6.406961 CCAGTTTGACTAGCATAGATACACCA 60.407 42.308 0.00 0.00 42.77 4.17
1860 1953 7.041721 CAGTTTGACTAGCATAGATACACCAA 58.958 38.462 0.00 0.00 42.77 3.67
1861 1954 7.712639 CAGTTTGACTAGCATAGATACACCAAT 59.287 37.037 0.00 0.00 42.77 3.16
1862 1955 8.924303 AGTTTGACTAGCATAGATACACCAATA 58.076 33.333 0.00 0.00 42.77 1.90
1863 1956 9.542462 GTTTGACTAGCATAGATACACCAATAA 57.458 33.333 0.00 0.00 42.77 1.40
1896 1989 8.768501 TGATCAAGGAGTATGTCATTAGTAGT 57.231 34.615 0.00 0.00 0.00 2.73
1913 2006 8.604035 CATTAGTAGTACTGAATGCGATGTTTT 58.396 33.333 13.29 0.00 0.00 2.43
1918 2011 7.016361 AGTACTGAATGCGATGTTTTATTCC 57.984 36.000 0.00 0.00 0.00 3.01
1988 2086 5.680619 TCAGTCCAACTAATGTCTTGTTGT 58.319 37.500 0.00 0.00 39.30 3.32
2006 2104 6.653526 TGTTGTTGTGAATGGATGAAGATT 57.346 33.333 0.00 0.00 0.00 2.40
2333 2431 1.374252 CCACCGGGACTTCAAGTCG 60.374 63.158 11.52 1.49 45.96 4.18
2459 2557 0.179108 GCACCTTCGGCTACTTCGAT 60.179 55.000 0.00 0.00 36.49 3.59
2462 2560 1.033574 CCTTCGGCTACTTCGATCCT 58.966 55.000 0.00 0.00 36.49 3.24
2487 2585 3.202001 CGCTGGTAATGGCCACGG 61.202 66.667 8.16 0.34 34.36 4.94
2502 2600 3.508840 CGGCCCTCGCACCATTTC 61.509 66.667 0.00 0.00 36.38 2.17
2510 2608 1.741706 CTCGCACCATTTCTGCAGAAT 59.258 47.619 28.89 16.19 34.00 2.40
2511 2609 1.739466 TCGCACCATTTCTGCAGAATC 59.261 47.619 28.89 12.91 34.00 2.52
2531 2629 4.003788 CCGTGCTGGTCGGGTTCT 62.004 66.667 0.00 0.00 43.68 3.01
2535 2633 2.430367 GCTGGTCGGGTTCTTGGT 59.570 61.111 0.00 0.00 0.00 3.67
2548 2646 3.821033 GGTTCTTGGTTGCACTAATGAGT 59.179 43.478 0.00 0.00 35.80 3.41
2550 2648 5.472137 GGTTCTTGGTTGCACTAATGAGTAA 59.528 40.000 0.00 0.00 33.32 2.24
2552 2650 6.741992 TCTTGGTTGCACTAATGAGTAATG 57.258 37.500 0.00 0.00 33.32 1.90
2553 2651 6.472016 TCTTGGTTGCACTAATGAGTAATGA 58.528 36.000 0.00 0.00 33.32 2.57
2554 2652 6.595326 TCTTGGTTGCACTAATGAGTAATGAG 59.405 38.462 0.00 0.00 33.32 2.90
2555 2653 5.185454 TGGTTGCACTAATGAGTAATGAGG 58.815 41.667 0.00 0.00 33.32 3.86
2556 2654 5.045942 TGGTTGCACTAATGAGTAATGAGGA 60.046 40.000 0.00 0.00 33.32 3.71
2717 2815 2.242708 GGTACTTCCTCTCTCCCTCTCA 59.757 54.545 0.00 0.00 0.00 3.27
2870 2983 4.109675 GTGGACCGGGACATGGGG 62.110 72.222 6.32 0.00 0.00 4.96
2886 2999 2.278330 GGGAAGGGGTCGTACACGT 61.278 63.158 1.19 0.00 40.80 4.49
2912 3025 2.358247 GTGTCCATGTTCGCGGGT 60.358 61.111 6.13 0.00 0.00 5.28
3038 3151 3.811118 TTTTGAGAACGGCCGCGGA 62.811 57.895 33.48 0.69 0.00 5.54
3065 3178 3.318839 TGCTTGGTTCAGTCTTGGAATTG 59.681 43.478 0.00 0.00 0.00 2.32
3069 3182 6.294731 GCTTGGTTCAGTCTTGGAATTGTTAT 60.295 38.462 0.00 0.00 0.00 1.89
3086 3202 5.584253 TGTTATTCGAGGAAGAGGAAGAG 57.416 43.478 0.00 0.00 0.00 2.85
3139 3255 4.082245 CCCCGTTCCATCCATATTAATTGC 60.082 45.833 0.00 0.00 0.00 3.56
3189 3305 7.757097 ATATCAGCGACAATTAATACGGATC 57.243 36.000 10.14 0.00 0.00 3.36
3193 3309 5.045215 AGCGACAATTAATACGGATCGAAA 58.955 37.500 0.00 0.00 0.00 3.46
3194 3310 5.521010 AGCGACAATTAATACGGATCGAAAA 59.479 36.000 0.00 0.00 0.00 2.29
3204 3320 7.752557 AATACGGATCGAAAAGAGTAACTTC 57.247 36.000 0.00 0.00 37.93 3.01
3207 3323 5.048224 ACGGATCGAAAAGAGTAACTTCTCA 60.048 40.000 0.00 0.00 37.93 3.27
3209 3325 6.197468 CGGATCGAAAAGAGTAACTTCTCATC 59.803 42.308 0.00 0.00 37.93 2.92
3215 3331 0.525668 AGTAACTTCTCATCGCGCCG 60.526 55.000 0.00 0.00 0.00 6.46
3216 3332 0.801067 GTAACTTCTCATCGCGCCGT 60.801 55.000 0.00 0.00 0.00 5.68
3270 3387 3.683802 AGTCTTGAAATGAGAGGGCTTG 58.316 45.455 0.00 0.00 0.00 4.01
3306 3425 5.180868 CCAAGAAATGGTGTCTCAAGAAGAG 59.819 44.000 0.00 0.00 44.85 2.85
3346 3465 0.614697 TCGATGGAGGGAGCAAGTGA 60.615 55.000 0.00 0.00 0.00 3.41
3514 3786 5.324784 TGTCTTAGTGCTATCGTTGTCAT 57.675 39.130 0.00 0.00 0.00 3.06
3531 3803 4.894784 TGTCATAGTCTGGACAAAGGTTC 58.105 43.478 6.69 0.00 40.80 3.62
3586 3858 4.217767 TCGACACAATAGCAAGTAGACACT 59.782 41.667 0.00 0.00 36.19 3.55
3589 3861 5.611374 ACACAATAGCAAGTAGACACTGTT 58.389 37.500 0.00 0.00 34.36 3.16
3618 3890 2.096614 AGGTAACAACGCAAATTCGTCG 60.097 45.455 0.00 0.00 42.46 5.12
3627 3899 0.511221 CAAATTCGTCGCGGTTGAGT 59.489 50.000 6.13 0.00 0.00 3.41
3687 3959 6.560253 AACTTGAAGCGTGTTCTAATCAAT 57.440 33.333 0.00 0.00 0.00 2.57
3693 3965 9.541143 TTGAAGCGTGTTCTAATCAATATATCA 57.459 29.630 2.04 0.00 0.00 2.15
3755 4027 3.131400 TGCCAAAACAGAAGGGTACAAAC 59.869 43.478 0.00 0.00 0.00 2.93
3808 4080 1.076727 GCCACTGGCTTTAGGGGTT 59.923 57.895 13.28 0.00 46.69 4.11
3809 4081 0.965866 GCCACTGGCTTTAGGGGTTC 60.966 60.000 13.28 0.00 46.69 3.62
3810 4082 0.404040 CCACTGGCTTTAGGGGTTCA 59.596 55.000 0.00 0.00 36.46 3.18
3812 4084 2.557452 CCACTGGCTTTAGGGGTTCATT 60.557 50.000 0.00 0.00 36.46 2.57
3826 4098 3.369052 GGGTTCATTCATGTCTCGGTGTA 60.369 47.826 0.00 0.00 0.00 2.90
3827 4099 4.250464 GGTTCATTCATGTCTCGGTGTAA 58.750 43.478 0.00 0.00 0.00 2.41
3831 4103 5.547465 TCATTCATGTCTCGGTGTAAAACT 58.453 37.500 0.00 0.00 0.00 2.66
3870 4142 2.719376 GGCACGGGTCATATTGCAT 58.281 52.632 0.00 0.00 36.66 3.96
3897 4169 8.656849 CATTCACCATATTATTAGAACCGCTAC 58.343 37.037 0.00 0.00 0.00 3.58
3899 4171 7.728148 TCACCATATTATTAGAACCGCTACAA 58.272 34.615 0.00 0.00 0.00 2.41
3907 4179 3.444703 AGAACCGCTACAATGCTAGAG 57.555 47.619 0.00 0.00 0.00 2.43
3908 4180 1.861575 GAACCGCTACAATGCTAGAGC 59.138 52.381 0.00 0.00 42.50 4.09
3910 4182 0.390860 CCGCTACAATGCTAGAGCCT 59.609 55.000 0.00 0.00 41.18 4.58
3911 4183 1.495878 CGCTACAATGCTAGAGCCTG 58.504 55.000 0.00 0.00 41.18 4.85
3912 4184 1.224965 GCTACAATGCTAGAGCCTGC 58.775 55.000 0.00 0.00 41.18 4.85
3913 4185 1.495878 CTACAATGCTAGAGCCTGCG 58.504 55.000 0.00 0.00 41.18 5.18
3915 4187 1.890979 CAATGCTAGAGCCTGCGGG 60.891 63.158 7.41 7.41 41.18 6.13
3916 4188 3.112205 AATGCTAGAGCCTGCGGGG 62.112 63.158 15.02 1.86 41.18 5.73
3917 4189 4.777854 TGCTAGAGCCTGCGGGGA 62.778 66.667 15.02 0.00 41.18 4.81
3919 4191 2.812619 GCTAGAGCCTGCGGGGAAT 61.813 63.158 15.02 0.00 37.23 3.01
3921 4193 1.382557 TAGAGCCTGCGGGGAATCA 60.383 57.895 15.02 0.00 37.23 2.57
3922 4194 1.686325 TAGAGCCTGCGGGGAATCAC 61.686 60.000 15.02 0.00 37.23 3.06
3923 4195 3.011517 AGCCTGCGGGGAATCACT 61.012 61.111 15.02 0.00 37.23 3.41
3924 4196 2.825836 GCCTGCGGGGAATCACTG 60.826 66.667 15.02 0.00 37.23 3.66
3925 4197 2.124570 CCTGCGGGGAATCACTGG 60.125 66.667 2.57 0.00 37.23 4.00
3926 4198 2.671070 CTGCGGGGAATCACTGGT 59.329 61.111 0.00 0.00 0.00 4.00
3927 4199 1.746615 CTGCGGGGAATCACTGGTG 60.747 63.158 0.00 0.00 0.00 4.17
3928 4200 3.134127 GCGGGGAATCACTGGTGC 61.134 66.667 0.00 0.00 0.00 5.01
3929 4201 2.350895 CGGGGAATCACTGGTGCA 59.649 61.111 0.00 0.00 0.00 4.57
3930 4202 1.746615 CGGGGAATCACTGGTGCAG 60.747 63.158 0.00 0.00 37.52 4.41
3931 4203 1.379044 GGGGAATCACTGGTGCAGG 60.379 63.158 0.00 0.00 35.51 4.85
3932 4204 1.379044 GGGAATCACTGGTGCAGGG 60.379 63.158 0.00 0.00 36.00 4.45
3933 4205 1.379044 GGAATCACTGGTGCAGGGG 60.379 63.158 0.00 0.00 35.28 4.79
3934 4206 1.685224 GAATCACTGGTGCAGGGGA 59.315 57.895 0.00 0.00 35.28 4.81
3935 4207 0.038166 GAATCACTGGTGCAGGGGAA 59.962 55.000 0.00 0.00 35.28 3.97
3936 4208 0.706433 AATCACTGGTGCAGGGGAAT 59.294 50.000 0.00 0.00 35.28 3.01
3945 4217 2.048603 GCAGGGGAATCACTGGTGC 61.049 63.158 6.38 0.00 35.30 5.01
3966 4238 3.198068 CACCCCTTACTCATCAATGTCG 58.802 50.000 0.00 0.00 0.00 4.35
3969 4241 4.654262 ACCCCTTACTCATCAATGTCGTAT 59.346 41.667 0.00 0.00 0.00 3.06
3971 4243 5.453339 CCCCTTACTCATCAATGTCGTATGT 60.453 44.000 0.00 0.00 0.00 2.29
3976 4248 4.330894 ACTCATCAATGTCGTATGTTGCTG 59.669 41.667 0.00 0.00 0.00 4.41
3994 4266 1.004918 GCTAGCACCACGAACACCT 60.005 57.895 10.63 0.00 0.00 4.00
3999 4271 1.414919 AGCACCACGAACACCTTCTTA 59.585 47.619 0.00 0.00 0.00 2.10
4005 4277 4.525487 ACCACGAACACCTTCTTACTATGA 59.475 41.667 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.296056 GGTTGCGATGTAGCCGTTGT 61.296 55.000 0.00 0.00 36.02 3.32
59 60 2.043450 AGGGACTGAGGAGGAGCG 60.043 66.667 0.00 0.00 37.18 5.03
105 106 0.463833 GTGATTGGGACATCGGGGAC 60.464 60.000 0.00 0.00 39.30 4.46
159 160 1.117994 TGGTTGGTGCATTGCAAAGA 58.882 45.000 13.94 0.00 41.47 2.52
241 243 3.798511 GAAAGCCGGGGAGGGAGG 61.799 72.222 2.18 0.00 41.48 4.30
242 244 4.162690 CGAAAGCCGGGGAGGGAG 62.163 72.222 2.18 0.00 41.48 4.30
339 345 0.524414 TGATGTGTTGATGCAGCAGC 59.476 50.000 12.24 12.24 42.57 5.25
340 346 2.223502 GGATGATGTGTTGATGCAGCAG 60.224 50.000 4.20 0.00 34.42 4.24
341 347 1.746787 GGATGATGTGTTGATGCAGCA 59.253 47.619 0.00 0.00 35.43 4.41
342 348 1.746787 TGGATGATGTGTTGATGCAGC 59.253 47.619 0.00 0.00 0.00 5.25
343 349 4.649088 AATGGATGATGTGTTGATGCAG 57.351 40.909 0.00 0.00 0.00 4.41
344 350 4.382147 CCAAATGGATGATGTGTTGATGCA 60.382 41.667 0.00 0.00 37.39 3.96
345 351 4.116961 CCAAATGGATGATGTGTTGATGC 58.883 43.478 0.00 0.00 37.39 3.91
346 352 5.585820 TCCAAATGGATGATGTGTTGATG 57.414 39.130 0.00 0.00 39.78 3.07
526 532 5.346782 TCAGAGATAAGAAGCTAGGGGAT 57.653 43.478 0.00 0.00 0.00 3.85
528 534 5.046663 GGATTCAGAGATAAGAAGCTAGGGG 60.047 48.000 0.00 0.00 31.29 4.79
535 546 3.323403 AGGCGGGATTCAGAGATAAGAAG 59.677 47.826 0.00 0.00 0.00 2.85
570 594 3.833070 GGTGAGAGGACAAGACTAAGGAA 59.167 47.826 0.00 0.00 0.00 3.36
576 600 2.158234 AGAAGGGTGAGAGGACAAGACT 60.158 50.000 0.00 0.00 0.00 3.24
590 614 3.103742 GAGATGAAGAGGACAGAAGGGT 58.896 50.000 0.00 0.00 0.00 4.34
591 615 3.373830 AGAGATGAAGAGGACAGAAGGG 58.626 50.000 0.00 0.00 0.00 3.95
592 616 4.141959 GGAAGAGATGAAGAGGACAGAAGG 60.142 50.000 0.00 0.00 0.00 3.46
593 617 4.439974 CGGAAGAGATGAAGAGGACAGAAG 60.440 50.000 0.00 0.00 0.00 2.85
594 618 3.445450 CGGAAGAGATGAAGAGGACAGAA 59.555 47.826 0.00 0.00 0.00 3.02
595 619 3.020274 CGGAAGAGATGAAGAGGACAGA 58.980 50.000 0.00 0.00 0.00 3.41
596 620 2.757868 ACGGAAGAGATGAAGAGGACAG 59.242 50.000 0.00 0.00 0.00 3.51
597 621 2.808919 ACGGAAGAGATGAAGAGGACA 58.191 47.619 0.00 0.00 0.00 4.02
598 622 3.067040 GGTACGGAAGAGATGAAGAGGAC 59.933 52.174 0.00 0.00 0.00 3.85
599 623 3.288964 GGTACGGAAGAGATGAAGAGGA 58.711 50.000 0.00 0.00 0.00 3.71
600 624 3.719173 GGTACGGAAGAGATGAAGAGG 57.281 52.381 0.00 0.00 0.00 3.69
618 642 3.745803 GAGGCTTCGTCGGACGGT 61.746 66.667 28.07 9.82 42.81 4.83
644 676 3.121030 GAGAATGCACTGCGCGGT 61.121 61.111 18.16 18.16 46.97 5.68
645 677 4.214383 CGAGAATGCACTGCGCGG 62.214 66.667 16.39 16.39 46.97 6.46
646 678 2.498761 AAACGAGAATGCACTGCGCG 62.499 55.000 0.00 0.00 46.97 6.86
647 679 0.790866 GAAACGAGAATGCACTGCGC 60.791 55.000 0.00 0.00 42.89 6.09
648 680 0.792640 AGAAACGAGAATGCACTGCG 59.207 50.000 0.00 0.00 0.00 5.18
649 681 1.800586 TGAGAAACGAGAATGCACTGC 59.199 47.619 0.00 0.00 0.00 4.40
650 682 2.159734 GCTGAGAAACGAGAATGCACTG 60.160 50.000 0.00 0.00 0.00 3.66
651 683 2.072298 GCTGAGAAACGAGAATGCACT 58.928 47.619 0.00 0.00 0.00 4.40
660 692 0.319555 CTGAACCGGCTGAGAAACGA 60.320 55.000 0.00 0.00 0.00 3.85
661 693 1.291877 CCTGAACCGGCTGAGAAACG 61.292 60.000 0.00 0.00 0.00 3.60
664 696 0.034896 GAACCTGAACCGGCTGAGAA 59.965 55.000 0.00 0.00 0.00 2.87
667 699 1.371183 CTGAACCTGAACCGGCTGA 59.629 57.895 0.00 0.00 0.00 4.26
669 701 2.032681 GCTGAACCTGAACCGGCT 59.967 61.111 0.00 0.00 0.00 5.52
670 702 3.056328 GGCTGAACCTGAACCGGC 61.056 66.667 0.00 0.00 34.51 6.13
682 714 1.352622 AACACTGGGGACAAGGCTGA 61.353 55.000 0.00 0.00 42.06 4.26
693 725 1.067516 CAGGACAAGCAAAACACTGGG 59.932 52.381 0.00 0.00 0.00 4.45
761 794 6.176183 CAAGTATCAGAAATCCAGAACCAGT 58.824 40.000 0.00 0.00 0.00 4.00
1017 1063 2.240667 CCTCCTCTTGTTCCATGTGGAT 59.759 50.000 1.98 0.00 44.98 3.41
1080 1126 1.887198 GAGTGAGACGGAAACAGAGGA 59.113 52.381 0.00 0.00 0.00 3.71
1092 1143 0.032130 TGCCGACAACAGAGTGAGAC 59.968 55.000 0.00 0.00 0.00 3.36
1095 1146 2.425562 TCTGCCGACAACAGAGTGA 58.574 52.632 0.00 0.00 39.21 3.41
1100 1151 1.800805 AATGACTCTGCCGACAACAG 58.199 50.000 0.00 0.00 36.44 3.16
1121 1175 7.877612 TGAAGAAACAGATAAGCATACAGTGAA 59.122 33.333 0.00 0.00 0.00 3.18
1153 1209 7.919385 ATTCCTCATGGCAAACCTTAAATAT 57.081 32.000 0.00 0.00 36.63 1.28
1154 1210 7.732222 AATTCCTCATGGCAAACCTTAAATA 57.268 32.000 0.00 0.00 36.63 1.40
1163 1219 5.659525 AGATGATCAAATTCCTCATGGCAAA 59.340 36.000 0.00 0.00 30.00 3.68
1283 1344 1.878775 GTGAACACCATGGAGCAGC 59.121 57.895 21.47 4.13 0.00 5.25
1446 1507 5.233083 ACAACACCATCTTCTGAATCTGA 57.767 39.130 0.00 0.00 0.00 3.27
1541 1602 7.330262 ACAAAACACCACAATCTTCTGAAAAT 58.670 30.769 0.00 0.00 0.00 1.82
1542 1603 6.696411 ACAAAACACCACAATCTTCTGAAAA 58.304 32.000 0.00 0.00 0.00 2.29
1606 1682 5.105228 CCCAACAGAATCATTGGTGCTAAAT 60.105 40.000 13.15 0.00 43.36 1.40
1607 1683 4.220382 CCCAACAGAATCATTGGTGCTAAA 59.780 41.667 13.15 0.00 43.36 1.85
1665 1741 2.989824 AGGCGCGTGTGTCCTACT 60.990 61.111 8.43 0.00 0.00 2.57
1666 1742 2.809601 CAGGCGCGTGTGTCCTAC 60.810 66.667 21.45 0.00 0.00 3.18
1667 1743 2.986979 TCAGGCGCGTGTGTCCTA 60.987 61.111 27.39 6.40 0.00 2.94
1668 1744 4.664677 GTCAGGCGCGTGTGTCCT 62.665 66.667 27.39 1.30 0.00 3.85
1677 1770 3.414700 CACGTTCAGGTCAGGCGC 61.415 66.667 0.00 0.00 0.00 6.53
1679 1772 2.380084 TTATCACGTTCAGGTCAGGC 57.620 50.000 0.00 0.00 0.00 4.85
1718 1811 3.606595 ATGTCACACCACTCTGATCTG 57.393 47.619 0.00 0.00 0.00 2.90
1745 1838 3.675228 GCTTTTCTTGACATGGATGCCAG 60.675 47.826 0.00 0.00 36.75 4.85
1818 1911 4.479156 AACTGGAAGGGGGAATAAAACA 57.521 40.909 0.00 0.00 39.30 2.83
1819 1912 4.836175 TCAAACTGGAAGGGGGAATAAAAC 59.164 41.667 0.00 0.00 39.30 2.43
1820 1913 4.836175 GTCAAACTGGAAGGGGGAATAAAA 59.164 41.667 0.00 0.00 39.30 1.52
1821 1914 4.107311 AGTCAAACTGGAAGGGGGAATAAA 59.893 41.667 0.00 0.00 39.30 1.40
1822 1915 3.660669 AGTCAAACTGGAAGGGGGAATAA 59.339 43.478 0.00 0.00 39.30 1.40
1823 1916 3.265489 AGTCAAACTGGAAGGGGGAATA 58.735 45.455 0.00 0.00 39.30 1.75
1824 1917 2.073776 AGTCAAACTGGAAGGGGGAAT 58.926 47.619 0.00 0.00 39.30 3.01
1825 1918 1.529744 AGTCAAACTGGAAGGGGGAA 58.470 50.000 0.00 0.00 39.30 3.97
1826 1919 2.266279 CTAGTCAAACTGGAAGGGGGA 58.734 52.381 0.00 0.00 39.30 4.81
1827 1920 1.340114 GCTAGTCAAACTGGAAGGGGG 60.340 57.143 0.00 0.00 39.30 5.40
1828 1921 1.351017 TGCTAGTCAAACTGGAAGGGG 59.649 52.381 0.00 0.00 39.30 4.79
1829 1922 2.859165 TGCTAGTCAAACTGGAAGGG 57.141 50.000 0.00 0.00 39.30 3.95
1830 1923 5.344743 TCTATGCTAGTCAAACTGGAAGG 57.655 43.478 0.00 0.00 39.30 3.46
1831 1924 7.436673 GTGTATCTATGCTAGTCAAACTGGAAG 59.563 40.741 0.00 0.00 42.29 3.46
1832 1925 7.265673 GTGTATCTATGCTAGTCAAACTGGAA 58.734 38.462 0.00 0.00 0.00 3.53
1833 1926 6.183360 GGTGTATCTATGCTAGTCAAACTGGA 60.183 42.308 0.00 0.00 0.00 3.86
1834 1927 5.986135 GGTGTATCTATGCTAGTCAAACTGG 59.014 44.000 0.00 0.00 0.00 4.00
1835 1928 6.573434 TGGTGTATCTATGCTAGTCAAACTG 58.427 40.000 0.00 0.00 0.00 3.16
1836 1929 6.791867 TGGTGTATCTATGCTAGTCAAACT 57.208 37.500 0.00 0.00 0.00 2.66
1837 1930 9.542462 TTATTGGTGTATCTATGCTAGTCAAAC 57.458 33.333 0.00 0.00 0.00 2.93
1868 1961 8.954950 ACTAATGACATACTCCTTGATCAAAG 57.045 34.615 9.88 7.57 35.47 2.77
1870 1963 9.201989 ACTACTAATGACATACTCCTTGATCAA 57.798 33.333 8.12 8.12 0.00 2.57
1871 1964 8.768501 ACTACTAATGACATACTCCTTGATCA 57.231 34.615 0.00 0.00 0.00 2.92
1873 1966 9.869667 AGTACTACTAATGACATACTCCTTGAT 57.130 33.333 0.00 0.00 0.00 2.57
1874 1967 9.121658 CAGTACTACTAATGACATACTCCTTGA 57.878 37.037 0.00 0.00 0.00 3.02
1875 1968 9.121658 TCAGTACTACTAATGACATACTCCTTG 57.878 37.037 0.00 0.00 0.00 3.61
1876 1969 9.696572 TTCAGTACTACTAATGACATACTCCTT 57.303 33.333 0.00 0.00 26.69 3.36
1877 1970 9.869667 ATTCAGTACTACTAATGACATACTCCT 57.130 33.333 0.00 0.00 26.69 3.69
1878 1971 9.900710 CATTCAGTACTACTAATGACATACTCC 57.099 37.037 14.95 0.00 32.29 3.85
1879 1972 9.400638 GCATTCAGTACTACTAATGACATACTC 57.599 37.037 20.62 5.43 32.29 2.59
1880 1973 8.076781 CGCATTCAGTACTACTAATGACATACT 58.923 37.037 20.62 0.00 32.29 2.12
1881 1974 8.074370 TCGCATTCAGTACTACTAATGACATAC 58.926 37.037 20.62 8.16 32.29 2.39
1896 1989 5.298276 GGGGAATAAAACATCGCATTCAGTA 59.702 40.000 0.00 0.00 0.00 2.74
1913 2006 5.602291 TTTACAAACTGGAAGGGGGAATA 57.398 39.130 0.00 0.00 39.30 1.75
1918 2011 4.407365 ACAGATTTACAAACTGGAAGGGG 58.593 43.478 0.00 0.00 39.30 4.79
1988 2086 4.082081 GCCACAATCTTCATCCATTCACAA 60.082 41.667 0.00 0.00 0.00 3.33
2333 2431 3.657956 CGAGAGGAGGATGTTGCTC 57.342 57.895 0.00 0.00 35.95 4.26
2459 2557 0.961857 TTACCAGCGCGTACTCAGGA 60.962 55.000 8.43 0.00 0.00 3.86
2462 2560 0.179121 CCATTACCAGCGCGTACTCA 60.179 55.000 8.43 0.00 0.00 3.41
2487 2585 3.056313 GCAGAAATGGTGCGAGGGC 62.056 63.158 0.00 0.00 40.52 5.19
2492 2590 1.202222 GGATTCTGCAGAAATGGTGCG 60.202 52.381 31.55 0.00 44.35 5.34
2502 2600 3.869272 GCACGGCGGATTCTGCAG 61.869 66.667 18.80 16.84 0.00 4.41
2531 2629 5.647658 CCTCATTACTCATTAGTGCAACCAA 59.352 40.000 0.00 0.00 37.80 3.67
2535 2633 6.767902 GGAATCCTCATTACTCATTAGTGCAA 59.232 38.462 0.00 0.00 36.36 4.08
2555 2653 1.530293 GTCTGCATGCGAGATGGAATC 59.470 52.381 14.09 1.10 46.04 2.52
2556 2654 1.590932 GTCTGCATGCGAGATGGAAT 58.409 50.000 14.09 0.00 0.00 3.01
2702 2800 1.618030 GGCTGAGAGGGAGAGAGGA 59.382 63.158 0.00 0.00 0.00 3.71
2703 2801 1.827789 CGGCTGAGAGGGAGAGAGG 60.828 68.421 0.00 0.00 0.00 3.69
2704 2802 1.827789 CCGGCTGAGAGGGAGAGAG 60.828 68.421 0.00 0.00 0.00 3.20
2705 2803 2.277072 CCGGCTGAGAGGGAGAGA 59.723 66.667 0.00 0.00 0.00 3.10
2706 2804 3.535962 GCCGGCTGAGAGGGAGAG 61.536 72.222 22.15 0.00 0.00 3.20
2707 2805 4.067512 AGCCGGCTGAGAGGGAGA 62.068 66.667 32.33 0.00 0.00 3.71
2708 2806 3.847602 CAGCCGGCTGAGAGGGAG 61.848 72.222 46.72 21.06 46.30 4.30
2762 2875 3.386237 GCCGAGGGTCAGCAGAGT 61.386 66.667 0.00 0.00 0.00 3.24
2764 2877 3.385384 CAGCCGAGGGTCAGCAGA 61.385 66.667 0.00 0.00 0.00 4.26
2870 2983 0.668401 CCAACGTGTACGACCCCTTC 60.668 60.000 11.79 0.00 43.02 3.46
2886 2999 0.762418 AACATGGACACCGACTCCAA 59.238 50.000 0.00 0.00 41.27 3.53
3038 3151 3.571401 CCAAGACTGAACCAAGCAAAGAT 59.429 43.478 0.00 0.00 0.00 2.40
3065 3178 4.645588 TCCTCTTCCTCTTCCTCGAATAAC 59.354 45.833 0.00 0.00 0.00 1.89
3069 3182 2.901338 TCCTCTTCCTCTTCCTCGAA 57.099 50.000 0.00 0.00 0.00 3.71
3086 3202 2.695359 TCTGTACAAGTTTCGCCATCC 58.305 47.619 0.00 0.00 0.00 3.51
3139 3255 7.649973 AGTATAAAGTTGTACTAGATCAGCCG 58.350 38.462 0.00 0.00 34.01 5.52
3184 3300 5.399858 TGAGAAGTTACTCTTTTCGATCCG 58.600 41.667 0.00 0.00 39.29 4.18
3189 3305 4.259056 CGCGATGAGAAGTTACTCTTTTCG 60.259 45.833 0.00 0.00 39.29 3.46
3193 3309 2.531206 GCGCGATGAGAAGTTACTCTT 58.469 47.619 12.10 0.00 39.32 2.85
3194 3310 1.202313 GGCGCGATGAGAAGTTACTCT 60.202 52.381 12.10 0.00 37.73 3.24
3204 3320 2.565394 GAACGTACGGCGCGATGAG 61.565 63.158 21.06 0.00 46.11 2.90
3207 3323 2.156446 CAAGAACGTACGGCGCGAT 61.156 57.895 21.06 0.00 46.11 4.58
3209 3325 3.101428 ACAAGAACGTACGGCGCG 61.101 61.111 21.06 0.00 46.11 6.86
3215 3331 2.762745 ACCACCATCACAAGAACGTAC 58.237 47.619 0.00 0.00 0.00 3.67
3216 3332 3.056393 CCTACCACCATCACAAGAACGTA 60.056 47.826 0.00 0.00 0.00 3.57
3306 3425 1.078759 CGTTGACGACAGGGCAGATC 61.079 60.000 0.00 0.00 43.02 2.75
3492 3764 4.776795 TGACAACGATAGCACTAAGACA 57.223 40.909 0.00 0.00 42.67 3.41
3500 3772 3.951680 TCCAGACTATGACAACGATAGCA 59.048 43.478 0.00 0.00 42.67 3.49
3514 3786 4.223032 GGATGAGAACCTTTGTCCAGACTA 59.777 45.833 0.00 0.00 0.00 2.59
3528 3800 4.396790 AGTCTCGACAACTAGGATGAGAAC 59.603 45.833 4.95 5.62 34.57 3.01
3531 3803 4.024387 GCTAGTCTCGACAACTAGGATGAG 60.024 50.000 22.55 7.70 44.17 2.90
3589 3861 4.436242 TTGCGTTGTTACCTTGTTGAAA 57.564 36.364 0.00 0.00 0.00 2.69
3622 3894 3.934068 GACCTTTATTGGTCGGACTCAA 58.066 45.455 8.23 10.69 45.69 3.02
3646 3918 5.183713 TCAAGTTCGGACGGAAACTCTTATA 59.816 40.000 0.00 0.00 36.14 0.98
3659 3931 0.935196 AACACGCTTCAAGTTCGGAC 59.065 50.000 0.00 0.00 0.00 4.79
3711 3983 0.173481 GAGTGCTAGCGGATGTGACA 59.827 55.000 10.77 0.00 0.00 3.58
3715 3987 0.105593 CATGGAGTGCTAGCGGATGT 59.894 55.000 10.77 0.00 0.00 3.06
3743 4015 3.506067 CCACCAATCTGTTTGTACCCTTC 59.494 47.826 0.00 0.00 33.15 3.46
3755 4027 3.019564 GGAAAGATGTCCCACCAATCTG 58.980 50.000 0.00 0.00 0.00 2.90
3808 4080 5.408299 CAGTTTTACACCGAGACATGAATGA 59.592 40.000 0.00 0.00 0.00 2.57
3809 4081 5.408299 TCAGTTTTACACCGAGACATGAATG 59.592 40.000 0.00 0.00 0.00 2.67
3810 4082 5.408604 GTCAGTTTTACACCGAGACATGAAT 59.591 40.000 0.00 0.00 0.00 2.57
3812 4084 4.304110 GTCAGTTTTACACCGAGACATGA 58.696 43.478 0.00 0.00 0.00 3.07
3826 4098 1.963515 GGAATGGCAGTGGTCAGTTTT 59.036 47.619 0.00 0.00 28.09 2.43
3827 4099 1.133513 TGGAATGGCAGTGGTCAGTTT 60.134 47.619 0.00 0.00 28.09 2.66
3831 4103 0.537143 GTGTGGAATGGCAGTGGTCA 60.537 55.000 0.00 0.00 0.00 4.02
3858 4130 5.717078 ATGGTGAATGATGCAATATGACC 57.283 39.130 0.00 0.00 0.00 4.02
3870 4142 7.450074 AGCGGTTCTAATAATATGGTGAATGA 58.550 34.615 0.00 0.00 0.00 2.57
3887 4159 2.482142 GCTCTAGCATTGTAGCGGTTCT 60.482 50.000 0.00 0.00 41.59 3.01
3890 4162 0.105039 GGCTCTAGCATTGTAGCGGT 59.895 55.000 4.07 0.00 44.36 5.68
3897 4169 3.728474 CCGCAGGCTCTAGCATTG 58.272 61.111 4.07 3.10 46.14 2.82
3910 4182 2.350895 CACCAGTGATTCCCCGCA 59.649 61.111 0.00 0.00 0.00 5.69
3911 4183 3.134127 GCACCAGTGATTCCCCGC 61.134 66.667 0.99 0.00 0.00 6.13
3912 4184 1.746615 CTGCACCAGTGATTCCCCG 60.747 63.158 0.99 0.00 0.00 5.73
3913 4185 1.379044 CCTGCACCAGTGATTCCCC 60.379 63.158 0.99 0.00 0.00 4.81
3915 4187 1.379044 CCCCTGCACCAGTGATTCC 60.379 63.158 0.99 0.00 0.00 3.01
3916 4188 0.038166 TTCCCCTGCACCAGTGATTC 59.962 55.000 0.99 0.00 0.00 2.52
3917 4189 0.706433 ATTCCCCTGCACCAGTGATT 59.294 50.000 0.99 0.00 0.00 2.57
3919 4191 1.133181 TGATTCCCCTGCACCAGTGA 61.133 55.000 0.99 0.00 0.00 3.41
3921 4193 1.136329 AGTGATTCCCCTGCACCAGT 61.136 55.000 0.00 0.00 33.14 4.00
3922 4194 0.679002 CAGTGATTCCCCTGCACCAG 60.679 60.000 0.00 0.00 33.14 4.00
3923 4195 1.379916 CAGTGATTCCCCTGCACCA 59.620 57.895 0.00 0.00 33.14 4.17
3924 4196 1.379044 CCAGTGATTCCCCTGCACC 60.379 63.158 0.00 0.00 33.14 5.01
3925 4197 0.962356 CACCAGTGATTCCCCTGCAC 60.962 60.000 0.00 0.00 0.00 4.57
3926 4198 1.379916 CACCAGTGATTCCCCTGCA 59.620 57.895 0.00 0.00 0.00 4.41
3927 4199 2.048603 GCACCAGTGATTCCCCTGC 61.049 63.158 0.99 0.00 0.00 4.85
3928 4200 0.962356 GTGCACCAGTGATTCCCCTG 60.962 60.000 5.22 0.00 0.00 4.45
3929 4201 1.380302 GTGCACCAGTGATTCCCCT 59.620 57.895 5.22 0.00 0.00 4.79
3930 4202 1.678970 GGTGCACCAGTGATTCCCC 60.679 63.158 31.23 0.00 35.64 4.81
3931 4203 1.678970 GGGTGCACCAGTGATTCCC 60.679 63.158 35.78 12.94 39.85 3.97
3932 4204 1.678970 GGGGTGCACCAGTGATTCC 60.679 63.158 35.78 22.10 42.91 3.01
3933 4205 0.251341 AAGGGGTGCACCAGTGATTC 60.251 55.000 35.78 17.15 42.91 2.52
3934 4206 1.072266 TAAGGGGTGCACCAGTGATT 58.928 50.000 35.78 22.64 42.91 2.57
3935 4207 0.328258 GTAAGGGGTGCACCAGTGAT 59.672 55.000 35.78 19.02 42.91 3.06
3936 4208 0.766674 AGTAAGGGGTGCACCAGTGA 60.767 55.000 35.78 16.30 42.91 3.41
3945 4217 3.198068 CGACATTGATGAGTAAGGGGTG 58.802 50.000 0.00 0.00 0.00 4.61
3976 4248 0.602905 AAGGTGTTCGTGGTGCTAGC 60.603 55.000 8.10 8.10 0.00 3.42


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

AutoCloner maintained by Alex Coulton.