Multiple sequence alignment - TraesCS7A01G112900

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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 TraesCS7A01G112900 chr7A 100.000 2294 0 0 1 2294 69224137 69226430 0.000000e+00 4237.0
1 TraesCS7A01G112900 chr7A 85.204 392 35 11 995 1377 69364042 69364419 4.620000e-102 381.0
2 TraesCS7A01G112900 chr7A 77.601 567 67 35 770 1295 69526657 69527204 2.880000e-74 289.0
3 TraesCS7A01G112900 chr7A 91.935 62 5 0 1686 1747 69364873 69364934 1.130000e-13 87.9
4 TraesCS7A01G112900 chr7A 89.552 67 5 2 870 935 69363889 69363954 1.460000e-12 84.2
5 TraesCS7A01G112900 chr7B 88.536 1448 65 35 3 1408 6754398 6755786 0.000000e+00 1661.0
6 TraesCS7A01G112900 chr7B 91.521 401 20 5 1454 1843 6755782 6756179 7.210000e-150 540.0
7 TraesCS7A01G112900 chr7B 85.574 305 29 7 995 1295 6921301 6921008 2.860000e-79 305.0
8 TraesCS7A01G112900 chr7B 85.246 305 30 6 995 1295 6796995 6797288 1.330000e-77 300.0
9 TraesCS7A01G112900 chr7B 96.324 136 4 1 2159 2293 6756299 6756434 2.970000e-54 222.0
10 TraesCS7A01G112900 chr7B 84.043 94 10 3 1880 1972 6756177 6756266 4.060000e-13 86.1
11 TraesCS7A01G112900 chr7B 97.826 46 1 0 871 916 6796843 6796888 1.890000e-11 80.5
12 TraesCS7A01G112900 chr7D 85.749 828 61 26 580 1377 64893403 64894203 0.000000e+00 822.0
13 TraesCS7A01G112900 chr7D 89.711 554 25 18 3 534 64892867 64893410 0.000000e+00 678.0
14 TraesCS7A01G112900 chr7D 90.541 296 22 2 999 1294 64912482 64912771 9.940000e-104 387.0
15 TraesCS7A01G112900 chr7D 85.390 308 25 9 995 1295 65390476 65390770 3.700000e-78 302.0
16 TraesCS7A01G112900 chr7D 79.357 373 50 19 1834 2200 65010266 65010617 1.060000e-58 237.0
17 TraesCS7A01G112900 chr7D 82.022 267 35 8 1024 1290 65041473 65041726 4.960000e-52 215.0
18 TraesCS7A01G112900 chr7D 89.423 104 8 3 2194 2294 600224507 600224610 6.650000e-26 128.0
19 TraesCS7A01G112900 chr7D 97.826 46 1 0 871 916 65390327 65390372 1.890000e-11 80.5
20 TraesCS7A01G112900 chr2D 92.079 101 6 2 2196 2294 473292193 473292293 8.540000e-30 141.0
21 TraesCS7A01G112900 chr5D 91.837 98 7 1 2198 2294 282007009 282007106 3.980000e-28 135.0
22 TraesCS7A01G112900 chr5B 91.837 98 7 1 2198 2294 364132775 364132678 3.980000e-28 135.0
23 TraesCS7A01G112900 chr5B 90.099 101 8 2 2194 2292 547824035 547823935 1.850000e-26 130.0
24 TraesCS7A01G112900 chr2B 89.524 105 9 2 2191 2293 51645209 51645313 5.140000e-27 132.0
25 TraesCS7A01G112900 chr6A 91.579 95 7 1 2201 2294 222555005 222554911 1.850000e-26 130.0
26 TraesCS7A01G112900 chr5A 90.196 102 7 2 2194 2294 395300500 395300599 1.850000e-26 130.0
27 TraesCS7A01G112900 chr1D 82.258 124 21 1 1710 1833 340552948 340552826 3.120000e-19 106.0
28 TraesCS7A01G112900 chr4D 100.000 30 0 0 1417 1446 381892938 381892909 3.180000e-04 56.5
29 TraesCS7A01G112900 chr4B 100.000 29 0 0 1417 1445 181584433 181584461 1.000000e-03 54.7


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 TraesCS7A01G112900 chr7A 69224137 69226430 2293 False 4237.000 4237 100.000 1 2294 1 chr7A.!!$F1 2293
1 TraesCS7A01G112900 chr7A 69526657 69527204 547 False 289.000 289 77.601 770 1295 1 chr7A.!!$F2 525
2 TraesCS7A01G112900 chr7B 6754398 6756434 2036 False 627.275 1661 90.106 3 2293 4 chr7B.!!$F1 2290
3 TraesCS7A01G112900 chr7D 64892867 64894203 1336 False 750.000 822 87.730 3 1377 2 chr7D.!!$F5 1374

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
432 456 0.179156 CACGGATTTGGCTGTCATGC 60.179 55.0 0.0 0.0 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1908 0.179094 TATGGAACTGTTAGGCGCCG 60.179 55.0 23.2 9.03 0.0 6.46 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
150 159 0.250770 AAAGAAACGGTGCTCCTCCC 60.251 55.000 2.85 0.00 0.00 4.30
198 208 2.706890 GACTCAATTTGGTAAGGCCGA 58.293 47.619 0.00 0.00 41.21 5.54
346 365 2.515926 TGAAGCGGTGAGAGATATGC 57.484 50.000 0.00 0.00 0.00 3.14
370 394 2.203070 ATGAAGATCACGGCGGCC 60.203 61.111 13.24 9.54 0.00 6.13
432 456 0.179156 CACGGATTTGGCTGTCATGC 60.179 55.000 0.00 0.00 0.00 4.06
464 488 5.403166 TCATACTACAACGGTTTTCAACTCG 59.597 40.000 0.00 0.00 0.00 4.18
473 500 4.023783 CGGTTTTCAACTCGTACAAACAC 58.976 43.478 0.00 0.00 0.00 3.32
499 526 3.869065 TGGACCTTGATAACGATGGTTC 58.131 45.455 0.00 0.00 37.58 3.62
540 567 1.069703 CACTTCAGCACCGAACACATG 60.070 52.381 0.00 0.00 0.00 3.21
569 596 1.340399 TGCGAGATTCCTGCCCTGAT 61.340 55.000 0.00 0.00 0.00 2.90
570 597 0.883814 GCGAGATTCCTGCCCTGATG 60.884 60.000 0.00 0.00 0.00 3.07
571 598 0.755079 CGAGATTCCTGCCCTGATGA 59.245 55.000 0.00 0.00 0.00 2.92
614 641 1.475930 GGGCCAGCAGATAAAGGTCTC 60.476 57.143 4.39 0.00 0.00 3.36
620 647 4.874966 CCAGCAGATAAAGGTCTCTTTCTG 59.125 45.833 0.00 0.00 41.82 3.02
657 692 4.972514 TTTGTATTTGCGACATGGCATA 57.027 36.364 0.00 0.00 43.52 3.14
661 696 1.378531 TTTGCGACATGGCATAGGTC 58.621 50.000 0.00 3.61 43.52 3.85
742 780 5.294356 CCGTTTTATTCGGTGATGAGGATA 58.706 41.667 0.00 0.00 42.62 2.59
743 781 5.932303 CCGTTTTATTCGGTGATGAGGATAT 59.068 40.000 0.00 0.00 42.62 1.63
744 782 6.128553 CCGTTTTATTCGGTGATGAGGATATG 60.129 42.308 0.00 0.00 42.62 1.78
745 783 6.645003 CGTTTTATTCGGTGATGAGGATATGA 59.355 38.462 0.00 0.00 0.00 2.15
837 884 0.179156 CACCATCGCAATGCTTGGTC 60.179 55.000 21.61 0.00 39.49 4.02
849 896 1.880819 GCTTGGTCCCTCGTAACGGA 61.881 60.000 0.00 0.00 0.00 4.69
858 905 1.402720 CCTCGTAACGGAAAACCGCTA 60.403 52.381 8.59 0.00 36.58 4.26
861 908 1.431496 GTAACGGAAAACCGCTAGCA 58.569 50.000 16.45 0.00 36.58 3.49
912 964 1.405526 CGTGCAGCTATGTACCCAACT 60.406 52.381 0.00 0.00 38.69 3.16
913 965 2.280628 GTGCAGCTATGTACCCAACTC 58.719 52.381 0.00 0.00 36.15 3.01
914 966 1.905894 TGCAGCTATGTACCCAACTCA 59.094 47.619 0.00 0.00 0.00 3.41
915 967 2.280628 GCAGCTATGTACCCAACTCAC 58.719 52.381 0.00 0.00 0.00 3.51
916 968 2.093447 GCAGCTATGTACCCAACTCACT 60.093 50.000 0.00 0.00 0.00 3.41
917 969 3.132289 GCAGCTATGTACCCAACTCACTA 59.868 47.826 0.00 0.00 0.00 2.74
918 970 4.737946 GCAGCTATGTACCCAACTCACTAG 60.738 50.000 0.00 0.00 0.00 2.57
941 1022 1.079819 CACCACCGCCACAGTCTAG 60.080 63.158 0.00 0.00 0.00 2.43
944 1025 1.153745 CACCGCCACAGTCTAGAGC 60.154 63.158 0.00 0.00 0.00 4.09
963 1044 1.019278 CGCCTAGCATTTCACCACGT 61.019 55.000 0.00 0.00 0.00 4.49
987 1068 2.147958 ACGAATCTAGCTAGCTCCTCG 58.852 52.381 23.26 24.06 0.00 4.63
1198 1305 3.141488 CGACTGCCGGGAGTAGCT 61.141 66.667 30.03 5.96 33.91 3.32
1227 1334 4.899239 GCAGATGGGAGGGCGACG 62.899 72.222 0.00 0.00 0.00 5.12
1228 1335 4.227134 CAGATGGGAGGGCGACGG 62.227 72.222 0.00 0.00 0.00 4.79
1295 1405 1.407437 GGACCCTCAGCACCACTAATG 60.407 57.143 0.00 0.00 0.00 1.90
1298 1408 2.171448 ACCCTCAGCACCACTAATGATC 59.829 50.000 0.00 0.00 0.00 2.92
1322 1432 6.985645 TCAAGTAAACTCGCCTTGTAAAGTAA 59.014 34.615 0.00 0.00 44.25 2.24
1361 1476 2.159014 TGCGCCGTAAGTTGGAATCTAT 60.159 45.455 4.18 0.00 0.00 1.98
1362 1477 2.221055 GCGCCGTAAGTTGGAATCTATG 59.779 50.000 0.00 0.00 0.00 2.23
1382 1497 3.698678 GTCCCTCGACTTCGACTTC 57.301 57.895 0.00 0.00 44.22 3.01
1383 1498 1.166989 GTCCCTCGACTTCGACTTCT 58.833 55.000 0.00 0.00 44.22 2.85
1384 1499 2.354259 GTCCCTCGACTTCGACTTCTA 58.646 52.381 0.00 0.00 44.22 2.10
1385 1500 2.352342 GTCCCTCGACTTCGACTTCTAG 59.648 54.545 0.00 0.00 44.22 2.43
1387 1502 2.610374 CCCTCGACTTCGACTTCTAGAG 59.390 54.545 0.00 0.00 44.22 2.43
1388 1503 3.523547 CCTCGACTTCGACTTCTAGAGA 58.476 50.000 0.00 0.00 44.22 3.10
1389 1504 3.554324 CCTCGACTTCGACTTCTAGAGAG 59.446 52.174 0.00 0.00 44.22 3.20
1390 1505 4.178540 CTCGACTTCGACTTCTAGAGAGT 58.821 47.826 0.00 7.13 44.22 3.24
1391 1506 4.175516 TCGACTTCGACTTCTAGAGAGTC 58.824 47.826 17.93 17.93 44.22 3.36
1392 1507 3.927758 CGACTTCGACTTCTAGAGAGTCA 59.072 47.826 23.20 13.90 43.02 3.41
1393 1508 4.569162 CGACTTCGACTTCTAGAGAGTCAT 59.431 45.833 23.20 12.53 43.02 3.06
1394 1509 5.749588 CGACTTCGACTTCTAGAGAGTCATA 59.250 44.000 23.20 14.09 43.02 2.15
1395 1510 6.422701 CGACTTCGACTTCTAGAGAGTCATAT 59.577 42.308 23.20 12.52 43.02 1.78
1396 1511 7.595875 CGACTTCGACTTCTAGAGAGTCATATA 59.404 40.741 23.20 10.92 43.02 0.86
1397 1512 8.597662 ACTTCGACTTCTAGAGAGTCATATAC 57.402 38.462 23.20 7.16 33.20 1.47
1398 1513 8.426489 ACTTCGACTTCTAGAGAGTCATATACT 58.574 37.037 23.20 7.72 42.80 2.12
1399 1514 9.917129 CTTCGACTTCTAGAGAGTCATATACTA 57.083 37.037 23.20 8.59 39.07 1.82
1479 1597 2.695359 ACACACAAGTCTTGTTCGTGT 58.305 42.857 25.23 25.23 42.44 4.49
1493 1611 2.356793 GTGTCTCTGCAGCACGCT 60.357 61.111 9.47 0.00 43.06 5.07
1532 1650 4.096681 TCGATCATGCCATATACCCTTCT 58.903 43.478 0.00 0.00 0.00 2.85
1547 1665 7.709149 ATACCCTTCTTTTCTCCTTTTCATG 57.291 36.000 0.00 0.00 0.00 3.07
1567 1685 1.729881 GATGGCGGGTGAATTCAGC 59.270 57.895 25.92 25.92 43.14 4.26
1647 1766 2.035832 CCCAAGGCAGTCAAAATCGTTT 59.964 45.455 0.00 0.00 0.00 3.60
1659 1778 6.468000 AGTCAAAATCGTTTCAAAAAGACGAC 59.532 34.615 0.00 0.00 46.86 4.34
1709 1832 3.365364 CCCAAGTCAGTCAAAATCGCTTC 60.365 47.826 0.00 0.00 0.00 3.86
1717 1840 6.638468 GTCAGTCAAAATCGCTTCAAAAAGAT 59.362 34.615 0.00 0.00 34.14 2.40
1774 1897 1.685224 CTGCTTGGGCCTTACTCCA 59.315 57.895 4.53 0.00 37.74 3.86
1775 1898 0.257039 CTGCTTGGGCCTTACTCCAT 59.743 55.000 4.53 0.00 37.74 3.41
1776 1899 1.490490 CTGCTTGGGCCTTACTCCATA 59.510 52.381 4.53 0.00 37.74 2.74
1778 1901 2.298610 GCTTGGGCCTTACTCCATAAC 58.701 52.381 4.53 0.00 32.48 1.89
1780 1903 3.545703 CTTGGGCCTTACTCCATAACAG 58.454 50.000 4.53 0.00 32.48 3.16
1781 1904 2.840511 TGGGCCTTACTCCATAACAGA 58.159 47.619 4.53 0.00 0.00 3.41
1784 1907 3.200165 GGGCCTTACTCCATAACAGAAGT 59.800 47.826 0.84 0.00 0.00 3.01
1785 1908 4.443621 GGCCTTACTCCATAACAGAAGTC 58.556 47.826 0.00 0.00 0.00 3.01
1787 1910 4.683832 CCTTACTCCATAACAGAAGTCGG 58.316 47.826 0.00 0.00 0.00 4.79
1825 1951 2.774809 AGGCCCATTTCTCTTACTCCTC 59.225 50.000 0.00 0.00 0.00 3.71
1826 1952 2.158740 GGCCCATTTCTCTTACTCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
1827 1953 2.774809 GCCCATTTCTCTTACTCCTCCT 59.225 50.000 0.00 0.00 0.00 3.69
1840 1966 2.569404 ACTCCTCCTGCTTGAACCTAAG 59.431 50.000 0.00 0.00 0.00 2.18
1841 1967 1.909302 TCCTCCTGCTTGAACCTAAGG 59.091 52.381 0.00 0.00 0.00 2.69
1842 1968 1.065126 CCTCCTGCTTGAACCTAAGGG 60.065 57.143 0.00 0.00 38.88 3.95
1844 1970 1.351017 TCCTGCTTGAACCTAAGGGTG 59.649 52.381 0.00 0.00 46.67 4.61
1845 1971 1.614317 CCTGCTTGAACCTAAGGGTGG 60.614 57.143 0.00 0.00 46.67 4.61
1846 1972 1.351017 CTGCTTGAACCTAAGGGTGGA 59.649 52.381 0.00 0.00 46.67 4.02
1847 1973 1.777878 TGCTTGAACCTAAGGGTGGAA 59.222 47.619 0.00 0.00 46.67 3.53
1848 1974 2.175931 TGCTTGAACCTAAGGGTGGAAA 59.824 45.455 0.00 0.00 46.67 3.13
1849 1975 3.181423 TGCTTGAACCTAAGGGTGGAAAT 60.181 43.478 0.00 0.00 46.67 2.17
1850 1976 3.193479 GCTTGAACCTAAGGGTGGAAATG 59.807 47.826 0.00 0.00 46.67 2.32
1851 1977 4.407365 CTTGAACCTAAGGGTGGAAATGT 58.593 43.478 0.00 0.00 46.67 2.71
1852 1978 4.028993 TGAACCTAAGGGTGGAAATGTC 57.971 45.455 0.00 0.00 46.67 3.06
1853 1979 3.245122 TGAACCTAAGGGTGGAAATGTCC 60.245 47.826 0.00 0.00 46.67 4.02
1854 1980 1.639108 ACCTAAGGGTGGAAATGTCCC 59.361 52.381 0.00 0.00 45.43 4.46
1863 1989 6.216801 GGGTGGAAATGTCCCTAAAAATAC 57.783 41.667 0.00 0.00 44.23 1.89
1864 1990 5.128171 GGGTGGAAATGTCCCTAAAAATACC 59.872 44.000 0.00 0.00 44.23 2.73
1865 1991 5.955959 GGTGGAAATGTCCCTAAAAATACCT 59.044 40.000 0.00 0.00 44.23 3.08
1866 1992 7.120716 GGTGGAAATGTCCCTAAAAATACCTA 58.879 38.462 0.00 0.00 44.23 3.08
1867 1993 7.616542 GGTGGAAATGTCCCTAAAAATACCTAA 59.383 37.037 0.00 0.00 44.23 2.69
1868 1994 8.683615 GTGGAAATGTCCCTAAAAATACCTAAG 58.316 37.037 0.00 0.00 44.23 2.18
1869 1995 7.837187 TGGAAATGTCCCTAAAAATACCTAAGG 59.163 37.037 0.00 0.00 44.23 2.69
1871 1997 6.920695 ATGTCCCTAAAAATACCTAAGGGT 57.079 37.500 5.66 0.00 46.02 4.34
1872 1998 6.069705 TGTCCCTAAAAATACCTAAGGGTG 57.930 41.667 5.66 0.00 46.75 4.61
1873 1999 5.044698 TGTCCCTAAAAATACCTAAGGGTGG 60.045 44.000 5.66 0.00 46.75 4.61
1874 2000 5.192321 GTCCCTAAAAATACCTAAGGGTGGA 59.808 44.000 5.66 0.00 46.75 4.02
1875 2001 5.796928 TCCCTAAAAATACCTAAGGGTGGAA 59.203 40.000 5.66 0.00 46.75 3.53
1876 2002 6.277522 TCCCTAAAAATACCTAAGGGTGGAAA 59.722 38.462 5.66 0.00 46.75 3.13
1877 2003 6.605995 CCCTAAAAATACCTAAGGGTGGAAAG 59.394 42.308 0.00 0.00 46.75 2.62
1878 2004 7.179966 CCTAAAAATACCTAAGGGTGGAAAGT 58.820 38.462 0.00 0.00 46.75 2.66
1907 2033 8.529424 AGTGGTAATCCGAAATATCCGATATA 57.471 34.615 1.18 0.00 36.30 0.86
1908 2034 9.144298 AGTGGTAATCCGAAATATCCGATATAT 57.856 33.333 1.18 0.00 36.30 0.86
1978 2104 9.573166 TTAGAACTATAATGGAAATGGACATGG 57.427 33.333 0.00 0.00 0.00 3.66
2000 2126 6.862209 TGGAAATGAAAGATATTCGGGTTTG 58.138 36.000 0.00 0.00 0.00 2.93
2002 2128 7.039363 TGGAAATGAAAGATATTCGGGTTTGTT 60.039 33.333 0.00 0.00 0.00 2.83
2007 2133 8.167605 TGAAAGATATTCGGGTTTGTTTTACA 57.832 30.769 0.00 0.00 0.00 2.41
2024 2150 8.862768 TGTTTTACAAATACAAATACGCTACG 57.137 30.769 0.00 0.00 0.00 3.51
2025 2151 7.956403 TGTTTTACAAATACAAATACGCTACGG 59.044 33.333 0.00 0.00 0.00 4.02
2026 2152 6.586868 TTACAAATACAAATACGCTACGGG 57.413 37.500 0.00 0.00 0.00 5.28
2027 2153 4.757594 ACAAATACAAATACGCTACGGGA 58.242 39.130 0.00 0.00 0.00 5.14
2028 2154 4.807304 ACAAATACAAATACGCTACGGGAG 59.193 41.667 0.00 0.00 0.00 4.30
2030 2156 4.660789 ATACAAATACGCTACGGGAGTT 57.339 40.909 0.00 0.00 43.33 3.01
2031 2157 3.323751 ACAAATACGCTACGGGAGTTT 57.676 42.857 0.00 0.00 43.33 2.66
2032 2158 2.997986 ACAAATACGCTACGGGAGTTTG 59.002 45.455 0.83 0.83 43.33 2.93
2033 2159 3.255725 CAAATACGCTACGGGAGTTTGA 58.744 45.455 0.00 0.00 43.33 2.69
2034 2160 2.573941 ATACGCTACGGGAGTTTGAC 57.426 50.000 0.00 0.00 43.33 3.18
2035 2161 1.246649 TACGCTACGGGAGTTTGACA 58.753 50.000 0.00 0.00 43.33 3.58
2036 2162 0.319297 ACGCTACGGGAGTTTGACAC 60.319 55.000 0.00 0.00 43.33 3.67
2037 2163 0.319211 CGCTACGGGAGTTTGACACA 60.319 55.000 0.00 0.00 43.33 3.72
2038 2164 1.870580 CGCTACGGGAGTTTGACACAA 60.871 52.381 0.00 0.00 43.33 3.33
2039 2165 2.215196 GCTACGGGAGTTTGACACAAA 58.785 47.619 0.00 0.00 43.33 2.83
2040 2166 2.812011 GCTACGGGAGTTTGACACAAAT 59.188 45.455 0.00 0.00 43.33 2.32
2041 2167 3.998341 GCTACGGGAGTTTGACACAAATA 59.002 43.478 0.00 0.00 43.33 1.40
2042 2168 4.634443 GCTACGGGAGTTTGACACAAATAT 59.366 41.667 0.00 0.00 43.33 1.28
2043 2169 5.447279 GCTACGGGAGTTTGACACAAATATG 60.447 44.000 0.00 0.00 43.33 1.78
2044 2170 3.756434 ACGGGAGTTTGACACAAATATGG 59.244 43.478 0.00 0.00 43.33 2.74
2045 2171 4.006989 CGGGAGTTTGACACAAATATGGA 58.993 43.478 0.00 0.00 0.00 3.41
2046 2172 4.640201 CGGGAGTTTGACACAAATATGGAT 59.360 41.667 0.00 0.00 0.00 3.41
2047 2173 5.820423 CGGGAGTTTGACACAAATATGGATA 59.180 40.000 0.00 0.00 0.00 2.59
2048 2174 6.486657 CGGGAGTTTGACACAAATATGGATAT 59.513 38.462 0.00 0.00 0.00 1.63
2049 2175 7.520453 CGGGAGTTTGACACAAATATGGATATG 60.520 40.741 0.00 0.00 0.00 1.78
2050 2176 7.255590 GGGAGTTTGACACAAATATGGATATGG 60.256 40.741 0.00 0.00 0.00 2.74
2051 2177 7.255590 GGAGTTTGACACAAATATGGATATGGG 60.256 40.741 0.00 0.00 0.00 4.00
2052 2178 7.353525 AGTTTGACACAAATATGGATATGGGA 58.646 34.615 0.00 0.00 0.00 4.37
2053 2179 7.503566 AGTTTGACACAAATATGGATATGGGAG 59.496 37.037 0.00 0.00 0.00 4.30
2054 2180 6.514012 TGACACAAATATGGATATGGGAGT 57.486 37.500 0.00 0.00 0.00 3.85
2055 2181 6.298361 TGACACAAATATGGATATGGGAGTG 58.702 40.000 0.00 0.00 0.00 3.51
2056 2182 6.101005 TGACACAAATATGGATATGGGAGTGA 59.899 38.462 0.00 0.00 0.00 3.41
2057 2183 6.910191 ACACAAATATGGATATGGGAGTGAA 58.090 36.000 0.00 0.00 0.00 3.18
2058 2184 6.772716 ACACAAATATGGATATGGGAGTGAAC 59.227 38.462 0.00 0.00 0.00 3.18
2059 2185 6.772233 CACAAATATGGATATGGGAGTGAACA 59.228 38.462 0.00 0.00 0.00 3.18
2060 2186 7.285172 CACAAATATGGATATGGGAGTGAACAA 59.715 37.037 0.00 0.00 0.00 2.83
2061 2187 7.838696 ACAAATATGGATATGGGAGTGAACAAA 59.161 33.333 0.00 0.00 0.00 2.83
2062 2188 8.863086 CAAATATGGATATGGGAGTGAACAAAT 58.137 33.333 0.00 0.00 0.00 2.32
2063 2189 8.641498 AATATGGATATGGGAGTGAACAAATC 57.359 34.615 0.00 0.00 0.00 2.17
2064 2190 5.715439 TGGATATGGGAGTGAACAAATCT 57.285 39.130 0.00 0.00 0.00 2.40
2065 2191 5.439721 TGGATATGGGAGTGAACAAATCTG 58.560 41.667 0.00 0.00 0.00 2.90
2066 2192 4.276926 GGATATGGGAGTGAACAAATCTGC 59.723 45.833 0.00 0.00 0.00 4.26
2067 2193 2.655090 TGGGAGTGAACAAATCTGCA 57.345 45.000 0.00 0.00 0.00 4.41
2068 2194 3.159213 TGGGAGTGAACAAATCTGCAT 57.841 42.857 0.00 0.00 0.00 3.96
2069 2195 3.084039 TGGGAGTGAACAAATCTGCATC 58.916 45.455 0.00 0.00 0.00 3.91
2070 2196 2.424956 GGGAGTGAACAAATCTGCATCC 59.575 50.000 0.00 0.00 0.00 3.51
2071 2197 2.096496 GGAGTGAACAAATCTGCATCCG 59.904 50.000 0.00 0.00 0.00 4.18
2072 2198 3.002791 GAGTGAACAAATCTGCATCCGA 58.997 45.455 0.00 0.00 0.00 4.55
2073 2199 3.411446 AGTGAACAAATCTGCATCCGAA 58.589 40.909 0.00 0.00 0.00 4.30
2074 2200 4.012374 AGTGAACAAATCTGCATCCGAAT 58.988 39.130 0.00 0.00 0.00 3.34
2075 2201 5.185454 AGTGAACAAATCTGCATCCGAATA 58.815 37.500 0.00 0.00 0.00 1.75
2076 2202 5.647658 AGTGAACAAATCTGCATCCGAATAA 59.352 36.000 0.00 0.00 0.00 1.40
2077 2203 6.150976 AGTGAACAAATCTGCATCCGAATAAA 59.849 34.615 0.00 0.00 0.00 1.40
2078 2204 6.974622 GTGAACAAATCTGCATCCGAATAAAT 59.025 34.615 0.00 0.00 0.00 1.40
2079 2205 7.489113 GTGAACAAATCTGCATCCGAATAAATT 59.511 33.333 0.00 0.00 0.00 1.82
2080 2206 8.034215 TGAACAAATCTGCATCCGAATAAATTT 58.966 29.630 0.00 0.00 0.00 1.82
2081 2207 8.776376 AACAAATCTGCATCCGAATAAATTTT 57.224 26.923 0.00 0.00 0.00 1.82
2082 2208 8.411318 ACAAATCTGCATCCGAATAAATTTTC 57.589 30.769 0.00 0.00 0.00 2.29
2083 2209 7.220683 ACAAATCTGCATCCGAATAAATTTTCG 59.779 33.333 0.00 0.12 46.14 3.46
2084 2210 5.811399 TCTGCATCCGAATAAATTTTCGT 57.189 34.783 10.48 0.00 45.34 3.85
2085 2211 5.568482 TCTGCATCCGAATAAATTTTCGTG 58.432 37.500 10.48 5.42 45.34 4.35
2086 2212 5.352846 TCTGCATCCGAATAAATTTTCGTGA 59.647 36.000 10.48 8.11 45.34 4.35
2087 2213 5.944013 TGCATCCGAATAAATTTTCGTGAA 58.056 33.333 10.48 0.00 45.34 3.18
2088 2214 5.797934 TGCATCCGAATAAATTTTCGTGAAC 59.202 36.000 10.48 6.13 45.34 3.18
2089 2215 6.027749 GCATCCGAATAAATTTTCGTGAACT 58.972 36.000 10.48 0.00 45.34 3.01
2090 2216 7.148390 TGCATCCGAATAAATTTTCGTGAACTA 60.148 33.333 10.48 0.00 45.34 2.24
2091 2217 7.694784 GCATCCGAATAAATTTTCGTGAACTAA 59.305 33.333 10.48 0.00 45.34 2.24
2092 2218 9.716507 CATCCGAATAAATTTTCGTGAACTAAT 57.283 29.630 10.48 0.00 45.34 1.73
2105 2231 9.959749 TTTCGTGAACTAATTTTAAGCAATTCT 57.040 25.926 0.00 0.00 0.00 2.40
2108 2234 9.000018 CGTGAACTAATTTTAAGCAATTCTAGC 58.000 33.333 0.00 0.00 0.00 3.42
2109 2235 9.290483 GTGAACTAATTTTAAGCAATTCTAGCC 57.710 33.333 0.00 0.00 0.00 3.93
2110 2236 9.243105 TGAACTAATTTTAAGCAATTCTAGCCT 57.757 29.630 0.00 0.00 0.00 4.58
2111 2237 9.723447 GAACTAATTTTAAGCAATTCTAGCCTC 57.277 33.333 0.00 0.00 0.00 4.70
2112 2238 7.920738 ACTAATTTTAAGCAATTCTAGCCTCG 58.079 34.615 0.00 0.00 0.00 4.63
2113 2239 7.769044 ACTAATTTTAAGCAATTCTAGCCTCGA 59.231 33.333 0.00 0.00 0.00 4.04
2114 2240 7.573968 AATTTTAAGCAATTCTAGCCTCGAT 57.426 32.000 0.00 0.00 0.00 3.59
2115 2241 8.677148 AATTTTAAGCAATTCTAGCCTCGATA 57.323 30.769 0.00 0.00 0.00 2.92
2116 2242 8.854614 ATTTTAAGCAATTCTAGCCTCGATAT 57.145 30.769 0.00 0.00 0.00 1.63
2117 2243 7.658179 TTTAAGCAATTCTAGCCTCGATATG 57.342 36.000 0.00 0.00 0.00 1.78
2118 2244 3.594134 AGCAATTCTAGCCTCGATATGC 58.406 45.455 0.00 0.00 0.00 3.14
2119 2245 2.675348 GCAATTCTAGCCTCGATATGCC 59.325 50.000 0.00 0.00 0.00 4.40
2120 2246 3.866066 GCAATTCTAGCCTCGATATGCCA 60.866 47.826 0.00 0.00 0.00 4.92
2121 2247 4.318332 CAATTCTAGCCTCGATATGCCAA 58.682 43.478 0.00 0.00 0.00 4.52
2122 2248 4.833478 ATTCTAGCCTCGATATGCCAAT 57.167 40.909 0.00 0.00 0.00 3.16
2123 2249 4.623932 TTCTAGCCTCGATATGCCAATT 57.376 40.909 0.00 0.00 0.00 2.32
2124 2250 5.738619 TTCTAGCCTCGATATGCCAATTA 57.261 39.130 0.00 0.00 0.00 1.40
2125 2251 5.939764 TCTAGCCTCGATATGCCAATTAT 57.060 39.130 0.00 0.00 0.00 1.28
2126 2252 5.907207 TCTAGCCTCGATATGCCAATTATC 58.093 41.667 0.00 0.00 0.00 1.75
2127 2253 3.878778 AGCCTCGATATGCCAATTATCC 58.121 45.455 0.00 0.00 0.00 2.59
2128 2254 3.264193 AGCCTCGATATGCCAATTATCCA 59.736 43.478 0.00 0.00 0.00 3.41
2129 2255 4.009675 GCCTCGATATGCCAATTATCCAA 58.990 43.478 0.00 0.00 0.00 3.53
2130 2256 4.142600 GCCTCGATATGCCAATTATCCAAC 60.143 45.833 0.00 0.00 0.00 3.77
2131 2257 5.003160 CCTCGATATGCCAATTATCCAACA 58.997 41.667 0.00 0.00 0.00 3.33
2132 2258 5.473162 CCTCGATATGCCAATTATCCAACAA 59.527 40.000 0.00 0.00 0.00 2.83
2133 2259 6.016360 CCTCGATATGCCAATTATCCAACAAA 60.016 38.462 0.00 0.00 0.00 2.83
2134 2260 7.340122 TCGATATGCCAATTATCCAACAAAA 57.660 32.000 0.00 0.00 0.00 2.44
2135 2261 7.776107 TCGATATGCCAATTATCCAACAAAAA 58.224 30.769 0.00 0.00 0.00 1.94
2224 2350 6.704056 ACTCCCTCCGATCCATATTAATTT 57.296 37.500 0.00 0.00 0.00 1.82
2228 2354 5.163754 CCCTCCGATCCATATTAATTTTCGC 60.164 44.000 0.00 0.00 0.00 4.70
2251 2377 7.601508 TCGCTGAAATAGATGTATCTAGACGTA 59.398 37.037 0.00 0.00 42.20 3.57
2280 2406 2.726760 GCTAGATACATCCGTTTGAGCG 59.273 50.000 0.00 0.00 0.00 5.03
2288 2414 2.736144 TCCGTTTGAGCGACAACTAT 57.264 45.000 0.00 0.00 38.29 2.12
2289 2415 3.853831 TCCGTTTGAGCGACAACTATA 57.146 42.857 0.00 0.00 38.29 1.31
2290 2416 4.380841 TCCGTTTGAGCGACAACTATAT 57.619 40.909 0.00 0.00 38.29 0.86
2291 2417 4.109766 TCCGTTTGAGCGACAACTATATG 58.890 43.478 0.00 0.00 38.29 1.78
2293 2419 4.109766 CGTTTGAGCGACAACTATATGGA 58.890 43.478 0.00 0.00 38.29 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.632422 GCACAGTGCATGCAAATACC 58.368 50.000 24.58 9.78 44.26 2.73
72 73 2.926539 GGGGAGTAACCACCCTAGG 58.073 63.158 0.06 0.06 44.97 3.02
150 159 4.933483 GAGTCATCGAGCTAGGCG 57.067 61.111 0.00 0.00 0.00 5.52
170 179 2.271800 ACCAAATTGAGTCGAGATCGC 58.728 47.619 0.00 0.00 39.60 4.58
179 188 2.871096 TCGGCCTTACCAAATTGAGT 57.129 45.000 0.00 0.00 39.03 3.41
198 208 4.164843 ACGCACCCATTTATAACTCCAT 57.835 40.909 0.00 0.00 0.00 3.41
346 365 1.788258 CCGTGATCTTCATCCCGATG 58.212 55.000 0.00 0.00 40.09 3.84
432 456 4.250464 ACCGTTGTAGTATGACATGTTGG 58.750 43.478 0.00 0.00 0.00 3.77
464 488 2.774687 AGGTCCATTCGGTGTTTGTAC 58.225 47.619 0.00 0.00 0.00 2.90
473 500 3.173668 TCGTTATCAAGGTCCATTCGG 57.826 47.619 0.00 0.00 0.00 4.30
499 526 1.871039 ACTGATTTGTTCGTTGGACCG 59.129 47.619 0.00 0.00 0.00 4.79
569 596 4.222810 TCCAGATCGGTTCTTCTTCATTCA 59.777 41.667 3.97 0.00 35.57 2.57
570 597 4.759782 TCCAGATCGGTTCTTCTTCATTC 58.240 43.478 3.97 0.00 35.57 2.67
571 598 4.383552 CCTCCAGATCGGTTCTTCTTCATT 60.384 45.833 3.97 0.00 35.57 2.57
605 632 2.631062 TGGACGCAGAAAGAGACCTTTA 59.369 45.455 0.00 0.00 42.30 1.85
614 641 0.109597 GCCATGTTGGACGCAGAAAG 60.110 55.000 0.00 0.00 40.96 2.62
620 647 1.070038 CAAATTGCCATGTTGGACGC 58.930 50.000 0.00 0.00 40.96 5.19
647 682 2.246719 GTCCAGACCTATGCCATGTC 57.753 55.000 0.00 0.00 0.00 3.06
701 739 0.813821 GGGCCAACTTTCTGCTCATC 59.186 55.000 4.39 0.00 0.00 2.92
742 780 0.687354 GGGCGGTGACCTCATATCAT 59.313 55.000 0.00 0.00 0.00 2.45
743 781 0.398522 AGGGCGGTGACCTCATATCA 60.399 55.000 0.00 0.00 35.03 2.15
744 782 2.442056 AGGGCGGTGACCTCATATC 58.558 57.895 0.00 0.00 35.03 1.63
745 783 4.728780 AGGGCGGTGACCTCATAT 57.271 55.556 0.00 0.00 35.03 1.78
867 914 1.978580 CGAGGTGATTTATAGGGGCCT 59.021 52.381 0.84 0.00 0.00 5.19
868 915 1.003233 CCGAGGTGATTTATAGGGGCC 59.997 57.143 0.00 0.00 0.00 5.80
902 951 2.895404 GGTGACTAGTGAGTTGGGTACA 59.105 50.000 0.00 0.00 35.45 2.90
912 964 1.812686 GCGGTGGTGGTGACTAGTGA 61.813 60.000 0.00 0.00 0.00 3.41
913 965 1.374252 GCGGTGGTGGTGACTAGTG 60.374 63.158 0.00 0.00 0.00 2.74
914 966 2.580601 GGCGGTGGTGGTGACTAGT 61.581 63.158 0.00 0.00 0.00 2.57
915 967 2.264794 GGCGGTGGTGGTGACTAG 59.735 66.667 0.00 0.00 0.00 2.57
916 968 2.524640 TGGCGGTGGTGGTGACTA 60.525 61.111 0.00 0.00 0.00 2.59
917 969 4.250305 GTGGCGGTGGTGGTGACT 62.250 66.667 0.00 0.00 0.00 3.41
918 970 4.555709 TGTGGCGGTGGTGGTGAC 62.556 66.667 0.00 0.00 0.00 3.67
941 1022 0.744414 TGGTGAAATGCTAGGCGCTC 60.744 55.000 7.64 0.00 40.11 5.03
944 1025 1.019278 ACGTGGTGAAATGCTAGGCG 61.019 55.000 0.00 0.00 0.00 5.52
963 1044 5.481105 GAGGAGCTAGCTAGATTCGTAGTA 58.519 45.833 25.15 0.00 0.00 1.82
987 1068 4.671406 GCCATGAGAGGAGCGATC 57.329 61.111 0.00 0.00 0.00 3.69
1054 1152 2.745492 GGACAGCAGCAGCAGGAC 60.745 66.667 3.17 0.00 45.49 3.85
1295 1405 6.147328 ACTTTACAAGGCGAGTTTACTTGATC 59.853 38.462 10.25 0.00 43.13 2.92
1298 1408 5.668558 ACTTTACAAGGCGAGTTTACTTG 57.331 39.130 0.00 0.00 45.27 3.16
1322 1432 2.423577 GCATCCTTAACCGACACAAGT 58.576 47.619 0.00 0.00 0.00 3.16
1448 1563 6.979238 ACAAGACTTGTGTGTTAAGTACTCTC 59.021 38.462 19.96 0.00 43.48 3.20
1450 1565 7.514747 CGAACAAGACTTGTGTGTTAAGTACTC 60.515 40.741 21.24 9.38 44.59 2.59
1451 1566 6.255020 CGAACAAGACTTGTGTGTTAAGTACT 59.745 38.462 21.24 1.09 44.59 2.73
1452 1567 6.035327 ACGAACAAGACTTGTGTGTTAAGTAC 59.965 38.462 21.24 3.42 44.59 2.73
1457 1572 4.247258 ACACGAACAAGACTTGTGTGTTA 58.753 39.130 26.73 0.00 43.81 2.41
1464 1579 2.219674 GCAGAGACACGAACAAGACTTG 59.780 50.000 13.77 13.77 0.00 3.16
1465 1580 2.159099 TGCAGAGACACGAACAAGACTT 60.159 45.455 0.00 0.00 0.00 3.01
1493 1611 8.221100 GCATGATCGATACGCTTTATTTTTCTA 58.779 33.333 0.00 0.00 0.00 2.10
1512 1630 6.944862 AGAAAAGAAGGGTATATGGCATGATC 59.055 38.462 10.98 0.00 0.00 2.92
1532 1650 3.367292 GCCATCGCATGAAAAGGAGAAAA 60.367 43.478 0.00 0.00 34.03 2.29
1547 1665 2.051804 CTGAATTCACCCGCCATCGC 62.052 60.000 3.38 0.00 0.00 4.58
1567 1685 3.181501 CCATGTTGCAGGTACGGTAAATG 60.182 47.826 0.00 0.00 27.76 2.32
1659 1778 3.118738 AGCTGGTCCATTTACGAACCTAG 60.119 47.826 0.00 0.00 32.82 3.02
1675 1798 1.229658 ACTTGGGAGCCTAGCTGGT 60.230 57.895 0.00 0.00 39.88 4.00
1717 1840 5.136068 TGGCCCATTTATGAACCTAATCA 57.864 39.130 0.00 0.00 0.00 2.57
1774 1897 1.108776 TAGGCGCCGACTTCTGTTAT 58.891 50.000 23.20 0.33 0.00 1.89
1775 1898 0.889994 TTAGGCGCCGACTTCTGTTA 59.110 50.000 23.20 0.65 0.00 2.41
1776 1899 0.669625 GTTAGGCGCCGACTTCTGTT 60.670 55.000 23.20 1.83 0.00 3.16
1778 1901 1.078759 CTGTTAGGCGCCGACTTCTG 61.079 60.000 28.14 16.05 0.00 3.02
1780 1903 0.669625 AACTGTTAGGCGCCGACTTC 60.670 55.000 28.14 16.81 0.00 3.01
1781 1904 0.669625 GAACTGTTAGGCGCCGACTT 60.670 55.000 28.14 18.92 0.00 3.01
1784 1907 1.895020 ATGGAACTGTTAGGCGCCGA 61.895 55.000 23.20 14.61 0.00 5.54
1785 1908 0.179094 TATGGAACTGTTAGGCGCCG 60.179 55.000 23.20 9.03 0.00 6.46
1787 1910 1.583054 CCTATGGAACTGTTAGGCGC 58.417 55.000 0.00 0.00 0.00 6.53
1840 1966 5.128171 GGTATTTTTAGGGACATTTCCACCC 59.872 44.000 0.00 0.00 44.98 4.61
1841 1967 5.955959 AGGTATTTTTAGGGACATTTCCACC 59.044 40.000 0.00 0.00 44.98 4.61
1842 1968 8.584063 TTAGGTATTTTTAGGGACATTTCCAC 57.416 34.615 0.00 0.00 44.98 4.02
1843 1969 7.837187 CCTTAGGTATTTTTAGGGACATTTCCA 59.163 37.037 0.00 0.00 44.98 3.53
1844 1970 8.234136 CCTTAGGTATTTTTAGGGACATTTCC 57.766 38.462 0.00 0.00 41.95 3.13
1863 1989 1.282157 CTCCCACTTTCCACCCTTAGG 59.718 57.143 0.00 0.00 40.04 2.69
1864 1990 1.985895 ACTCCCACTTTCCACCCTTAG 59.014 52.381 0.00 0.00 0.00 2.18
1865 1991 1.702957 CACTCCCACTTTCCACCCTTA 59.297 52.381 0.00 0.00 0.00 2.69
1866 1992 0.478507 CACTCCCACTTTCCACCCTT 59.521 55.000 0.00 0.00 0.00 3.95
1867 1993 1.427072 CCACTCCCACTTTCCACCCT 61.427 60.000 0.00 0.00 0.00 4.34
1868 1994 1.074951 CCACTCCCACTTTCCACCC 59.925 63.158 0.00 0.00 0.00 4.61
1869 1995 1.061546 TACCACTCCCACTTTCCACC 58.938 55.000 0.00 0.00 0.00 4.61
1870 1996 2.943036 TTACCACTCCCACTTTCCAC 57.057 50.000 0.00 0.00 0.00 4.02
1871 1997 2.307686 GGATTACCACTCCCACTTTCCA 59.692 50.000 0.00 0.00 35.97 3.53
1872 1998 2.679930 CGGATTACCACTCCCACTTTCC 60.680 54.545 0.00 0.00 35.59 3.13
1873 1999 2.235402 TCGGATTACCACTCCCACTTTC 59.765 50.000 0.00 0.00 35.59 2.62
1874 2000 2.262637 TCGGATTACCACTCCCACTTT 58.737 47.619 0.00 0.00 35.59 2.66
1875 2001 1.946984 TCGGATTACCACTCCCACTT 58.053 50.000 0.00 0.00 35.59 3.16
1876 2002 1.946984 TTCGGATTACCACTCCCACT 58.053 50.000 0.00 0.00 35.59 4.00
1877 2003 2.773993 TTTCGGATTACCACTCCCAC 57.226 50.000 0.00 0.00 35.59 4.61
1878 2004 4.041198 GGATATTTCGGATTACCACTCCCA 59.959 45.833 0.00 0.00 35.59 4.37
1954 2080 7.815383 TCCATGTCCATTTCCATTATAGTTCT 58.185 34.615 0.00 0.00 0.00 3.01
1963 2089 6.441284 TCTTTCATTTCCATGTCCATTTCCAT 59.559 34.615 0.00 0.00 0.00 3.41
1968 2094 8.355169 CGAATATCTTTCATTTCCATGTCCATT 58.645 33.333 0.00 0.00 0.00 3.16
1969 2095 7.040201 CCGAATATCTTTCATTTCCATGTCCAT 60.040 37.037 0.00 0.00 0.00 3.41
1970 2096 6.262944 CCGAATATCTTTCATTTCCATGTCCA 59.737 38.462 0.00 0.00 0.00 4.02
1971 2097 6.294176 CCCGAATATCTTTCATTTCCATGTCC 60.294 42.308 0.00 0.00 0.00 4.02
1972 2098 6.263168 ACCCGAATATCTTTCATTTCCATGTC 59.737 38.462 0.00 0.00 0.00 3.06
1973 2099 6.129179 ACCCGAATATCTTTCATTTCCATGT 58.871 36.000 0.00 0.00 0.00 3.21
1974 2100 6.639632 ACCCGAATATCTTTCATTTCCATG 57.360 37.500 0.00 0.00 0.00 3.66
1975 2101 7.124147 ACAAACCCGAATATCTTTCATTTCCAT 59.876 33.333 0.00 0.00 0.00 3.41
1976 2102 6.435904 ACAAACCCGAATATCTTTCATTTCCA 59.564 34.615 0.00 0.00 0.00 3.53
1977 2103 6.863275 ACAAACCCGAATATCTTTCATTTCC 58.137 36.000 0.00 0.00 0.00 3.13
1978 2104 8.757164 AAACAAACCCGAATATCTTTCATTTC 57.243 30.769 0.00 0.00 0.00 2.17
2000 2126 7.426169 CCCGTAGCGTATTTGTATTTGTAAAAC 59.574 37.037 0.00 0.00 0.00 2.43
2002 2128 6.815641 TCCCGTAGCGTATTTGTATTTGTAAA 59.184 34.615 0.00 0.00 0.00 2.01
2007 2133 5.014808 ACTCCCGTAGCGTATTTGTATTT 57.985 39.130 0.00 0.00 0.00 1.40
2018 2144 0.319211 TGTGTCAAACTCCCGTAGCG 60.319 55.000 0.00 0.00 0.00 4.26
2019 2145 1.873698 TTGTGTCAAACTCCCGTAGC 58.126 50.000 0.00 0.00 0.00 3.58
2020 2146 5.064707 CCATATTTGTGTCAAACTCCCGTAG 59.935 44.000 0.00 0.00 0.00 3.51
2021 2147 4.938832 CCATATTTGTGTCAAACTCCCGTA 59.061 41.667 0.00 0.00 0.00 4.02
2022 2148 3.756434 CCATATTTGTGTCAAACTCCCGT 59.244 43.478 0.00 0.00 0.00 5.28
2023 2149 4.006989 TCCATATTTGTGTCAAACTCCCG 58.993 43.478 0.00 0.00 0.00 5.14
2024 2150 7.255590 CCATATCCATATTTGTGTCAAACTCCC 60.256 40.741 0.00 0.00 0.00 4.30
2025 2151 7.255590 CCCATATCCATATTTGTGTCAAACTCC 60.256 40.741 0.00 0.00 0.00 3.85
2026 2152 7.502226 TCCCATATCCATATTTGTGTCAAACTC 59.498 37.037 0.00 0.00 0.00 3.01
2027 2153 7.353525 TCCCATATCCATATTTGTGTCAAACT 58.646 34.615 0.00 0.00 0.00 2.66
2028 2154 7.285401 ACTCCCATATCCATATTTGTGTCAAAC 59.715 37.037 0.00 0.00 0.00 2.93
2029 2155 7.285172 CACTCCCATATCCATATTTGTGTCAAA 59.715 37.037 0.00 0.00 0.00 2.69
2030 2156 6.772233 CACTCCCATATCCATATTTGTGTCAA 59.228 38.462 0.00 0.00 0.00 3.18
2031 2157 6.101005 TCACTCCCATATCCATATTTGTGTCA 59.899 38.462 0.00 0.00 0.00 3.58
2032 2158 6.533730 TCACTCCCATATCCATATTTGTGTC 58.466 40.000 0.00 0.00 0.00 3.67
2033 2159 6.514012 TCACTCCCATATCCATATTTGTGT 57.486 37.500 0.00 0.00 0.00 3.72
2034 2160 6.772233 TGTTCACTCCCATATCCATATTTGTG 59.228 38.462 0.00 0.00 0.00 3.33
2035 2161 6.910191 TGTTCACTCCCATATCCATATTTGT 58.090 36.000 0.00 0.00 0.00 2.83
2036 2162 7.822161 TTGTTCACTCCCATATCCATATTTG 57.178 36.000 0.00 0.00 0.00 2.32
2037 2163 9.082313 GATTTGTTCACTCCCATATCCATATTT 57.918 33.333 0.00 0.00 0.00 1.40
2038 2164 8.451245 AGATTTGTTCACTCCCATATCCATATT 58.549 33.333 0.00 0.00 0.00 1.28
2039 2165 7.886970 CAGATTTGTTCACTCCCATATCCATAT 59.113 37.037 0.00 0.00 0.00 1.78
2040 2166 7.226441 CAGATTTGTTCACTCCCATATCCATA 58.774 38.462 0.00 0.00 0.00 2.74
2041 2167 6.066690 CAGATTTGTTCACTCCCATATCCAT 58.933 40.000 0.00 0.00 0.00 3.41
2042 2168 5.439721 CAGATTTGTTCACTCCCATATCCA 58.560 41.667 0.00 0.00 0.00 3.41
2043 2169 4.276926 GCAGATTTGTTCACTCCCATATCC 59.723 45.833 0.00 0.00 0.00 2.59
2044 2170 4.883585 TGCAGATTTGTTCACTCCCATATC 59.116 41.667 0.00 0.00 0.00 1.63
2045 2171 4.858850 TGCAGATTTGTTCACTCCCATAT 58.141 39.130 0.00 0.00 0.00 1.78
2046 2172 4.299586 TGCAGATTTGTTCACTCCCATA 57.700 40.909 0.00 0.00 0.00 2.74
2047 2173 3.159213 TGCAGATTTGTTCACTCCCAT 57.841 42.857 0.00 0.00 0.00 4.00
2048 2174 2.655090 TGCAGATTTGTTCACTCCCA 57.345 45.000 0.00 0.00 0.00 4.37
2049 2175 2.424956 GGATGCAGATTTGTTCACTCCC 59.575 50.000 0.00 0.00 0.00 4.30
2050 2176 2.096496 CGGATGCAGATTTGTTCACTCC 59.904 50.000 0.00 0.00 0.00 3.85
2051 2177 3.002791 TCGGATGCAGATTTGTTCACTC 58.997 45.455 0.00 0.00 0.00 3.51
2052 2178 3.057969 TCGGATGCAGATTTGTTCACT 57.942 42.857 0.00 0.00 0.00 3.41
2053 2179 3.829886 TTCGGATGCAGATTTGTTCAC 57.170 42.857 0.00 0.00 0.00 3.18
2054 2180 6.507958 TTTATTCGGATGCAGATTTGTTCA 57.492 33.333 0.00 0.00 0.00 3.18
2055 2181 7.992180 AATTTATTCGGATGCAGATTTGTTC 57.008 32.000 0.00 0.00 0.00 3.18
2056 2182 8.776376 AAAATTTATTCGGATGCAGATTTGTT 57.224 26.923 0.00 0.00 0.00 2.83
2057 2183 7.220683 CGAAAATTTATTCGGATGCAGATTTGT 59.779 33.333 4.66 0.00 46.32 2.83
2058 2184 7.549649 CGAAAATTTATTCGGATGCAGATTTG 58.450 34.615 4.66 0.00 46.32 2.32
2059 2185 7.684062 CGAAAATTTATTCGGATGCAGATTT 57.316 32.000 4.66 0.00 46.32 2.17
2079 2205 9.959749 AGAATTGCTTAAAATTAGTTCACGAAA 57.040 25.926 0.00 0.00 29.89 3.46
2082 2208 9.000018 GCTAGAATTGCTTAAAATTAGTTCACG 58.000 33.333 0.00 0.00 29.89 4.35
2083 2209 9.290483 GGCTAGAATTGCTTAAAATTAGTTCAC 57.710 33.333 0.00 0.00 29.89 3.18
2084 2210 9.243105 AGGCTAGAATTGCTTAAAATTAGTTCA 57.757 29.630 0.00 0.00 29.89 3.18
2085 2211 9.723447 GAGGCTAGAATTGCTTAAAATTAGTTC 57.277 33.333 0.00 0.00 29.89 3.01
2086 2212 8.398665 CGAGGCTAGAATTGCTTAAAATTAGTT 58.601 33.333 0.00 0.00 29.89 2.24
2087 2213 7.769044 TCGAGGCTAGAATTGCTTAAAATTAGT 59.231 33.333 0.00 0.00 29.89 2.24
2088 2214 8.142994 TCGAGGCTAGAATTGCTTAAAATTAG 57.857 34.615 0.00 0.00 29.89 1.73
2089 2215 8.677148 ATCGAGGCTAGAATTGCTTAAAATTA 57.323 30.769 0.25 0.00 29.89 1.40
2090 2216 7.573968 ATCGAGGCTAGAATTGCTTAAAATT 57.426 32.000 0.25 0.00 32.43 1.82
2091 2217 8.725148 CATATCGAGGCTAGAATTGCTTAAAAT 58.275 33.333 0.25 0.00 0.00 1.82
2092 2218 7.307989 GCATATCGAGGCTAGAATTGCTTAAAA 60.308 37.037 20.21 0.00 31.28 1.52
2093 2219 6.147821 GCATATCGAGGCTAGAATTGCTTAAA 59.852 38.462 20.21 0.00 31.28 1.52
2094 2220 5.639506 GCATATCGAGGCTAGAATTGCTTAA 59.360 40.000 20.21 0.00 31.28 1.85
2095 2221 5.171476 GCATATCGAGGCTAGAATTGCTTA 58.829 41.667 20.21 2.88 31.28 3.09
2096 2222 3.999663 GCATATCGAGGCTAGAATTGCTT 59.000 43.478 20.21 0.96 31.28 3.91
2097 2223 3.594134 GCATATCGAGGCTAGAATTGCT 58.406 45.455 20.21 1.56 31.28 3.91
2098 2224 2.675348 GGCATATCGAGGCTAGAATTGC 59.325 50.000 19.67 19.67 31.41 3.56
2099 2225 3.930336 TGGCATATCGAGGCTAGAATTG 58.070 45.455 0.25 3.83 31.41 2.32
2100 2226 4.623932 TTGGCATATCGAGGCTAGAATT 57.376 40.909 0.25 0.00 31.41 2.17
2101 2227 4.833478 ATTGGCATATCGAGGCTAGAAT 57.167 40.909 0.25 0.00 31.41 2.40
2102 2228 4.623932 AATTGGCATATCGAGGCTAGAA 57.376 40.909 0.25 0.00 31.41 2.10
2103 2229 5.163405 GGATAATTGGCATATCGAGGCTAGA 60.163 44.000 0.00 0.00 31.80 2.43
2104 2230 5.053145 GGATAATTGGCATATCGAGGCTAG 58.947 45.833 6.48 0.00 31.80 3.42
2105 2231 4.469586 TGGATAATTGGCATATCGAGGCTA 59.530 41.667 6.48 0.00 31.80 3.93
2106 2232 3.264193 TGGATAATTGGCATATCGAGGCT 59.736 43.478 6.48 0.00 31.80 4.58
2107 2233 3.609853 TGGATAATTGGCATATCGAGGC 58.390 45.455 0.00 0.00 31.80 4.70
2108 2234 5.003160 TGTTGGATAATTGGCATATCGAGG 58.997 41.667 0.00 0.00 31.80 4.63
2109 2235 6.558771 TTGTTGGATAATTGGCATATCGAG 57.441 37.500 0.00 0.00 31.80 4.04
2110 2236 6.951062 TTTGTTGGATAATTGGCATATCGA 57.049 33.333 0.00 0.00 31.80 3.59
2158 2284 9.523168 ACCATAAGTTTAGCCATACAAAAAGTA 57.477 29.630 0.00 0.00 37.06 2.24
2159 2285 8.417273 ACCATAAGTTTAGCCATACAAAAAGT 57.583 30.769 0.00 0.00 0.00 2.66
2224 2350 7.041303 ACGTCTAGATACATCTATTTCAGCGAA 60.041 37.037 0.00 0.00 38.60 4.70
2251 2377 6.435292 AACGGATGTATCTAGCCCTAAAAT 57.565 37.500 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.