Multiple sequence alignment - TraesCS4A01G115200

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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 TraesCS4A01G115200 chr4A 100.000 7673 0 0 1 7673 140286037 140278365 0.000000e+00 14170
1 TraesCS4A01G115200 chr4D 95.400 5630 180 18 2068 7673 333069369 333074943 0.000000e+00 8889
2 TraesCS4A01G115200 chr4D 88.932 1301 76 24 735 2011 333068113 333069369 0.000000e+00 1543
3 TraesCS4A01G115200 chr4D 90.566 742 35 15 15 742 333067335 333068055 0.000000e+00 950
4 TraesCS4A01G115200 chr4B 94.328 4231 154 27 1960 6168 411531234 411535400 0.000000e+00 6405
5 TraesCS4A01G115200 chr4B 97.417 968 21 3 6165 7128 411535502 411536469 0.000000e+00 1646
6 TraesCS4A01G115200 chr4B 88.345 961 62 23 735 1657 411527412 411528360 0.000000e+00 1109
7 TraesCS4A01G115200 chr4B 87.842 732 51 20 15 742 411526678 411527375 0.000000e+00 824
8 TraesCS4A01G115200 chr4B 92.072 555 39 3 7123 7673 411541501 411542054 0.000000e+00 776
9 TraesCS4A01G115200 chr4B 80.415 674 115 10 7016 7673 613351844 613351172 1.490000e-136 497
10 TraesCS4A01G115200 chr4B 91.016 256 13 6 1713 1967 411528387 411528633 3.430000e-88 337
11 TraesCS4A01G115200 chr7D 77.125 647 134 11 7034 7673 448689916 448689277 5.660000e-96 363
12 TraesCS4A01G115200 chr7B 85.116 215 25 4 6059 6272 149352757 149352549 6.030000e-51 213
13 TraesCS4A01G115200 chr3D 82.514 183 22 3 6098 6272 309674506 309674686 1.330000e-32 152
14 TraesCS4A01G115200 chr5D 79.381 194 26 7 6093 6272 269731792 269731599 2.910000e-24 124


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 TraesCS4A01G115200 chr4A 140278365 140286037 7672 True 14170.0 14170 100.000000 1 7673 1 chr4A.!!$R1 7672
1 TraesCS4A01G115200 chr4D 333067335 333074943 7608 False 3794.0 8889 91.632667 15 7673 3 chr4D.!!$F1 7658
2 TraesCS4A01G115200 chr4B 411526678 411536469 9791 False 2064.2 6405 91.789600 15 7128 5 chr4B.!!$F2 7113
3 TraesCS4A01G115200 chr4B 411541501 411542054 553 False 776.0 776 92.072000 7123 7673 1 chr4B.!!$F1 550
4 TraesCS4A01G115200 chr4B 613351172 613351844 672 True 497.0 497 80.415000 7016 7673 1 chr4B.!!$R1 657
5 TraesCS4A01G115200 chr7D 448689277 448689916 639 True 363.0 363 77.125000 7034 7673 1 chr7D.!!$R1 639

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
672 685 0.382158 CTCTCGTTGCTGCGGAGATA 59.618 55.000 8.65 0.0 33.89 1.98 F
1475 1625 0.312102 GGCAACACAGAGCAGTTTCC 59.688 55.000 0.00 0.0 0.00 3.13 F
2160 4976 0.535335 TCTTCCACGGGCTGTATGAC 59.465 55.000 0.00 0.0 0.00 3.06 F
3862 6694 1.065709 GGAATTAGCCACGGAGTCCAA 60.066 52.381 10.49 0.0 41.61 3.53 F
4922 7763 1.001406 ACTGAACCAGTAGTCAGCAGC 59.999 52.381 0.00 0.0 43.46 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 5090 0.770557 ACCCACCCCTGTTAGAAGCA 60.771 55.000 0.00 0.0 0.00 3.91 R
2674 5490 0.524862 CCTGCAGCATTCTGGAACAC 59.475 55.000 8.66 0.0 40.22 3.32 R
3891 6723 1.134401 AGCATCAACTGTACCATCGGG 60.134 52.381 0.00 0.0 41.29 5.14 R
5168 8009 0.955428 GCGGCAAATCTGTGGAGTCA 60.955 55.000 0.00 0.0 0.00 3.41 R
6681 9648 1.669999 ATCAGCCGCCAAATTGCTCC 61.670 55.000 0.00 0.0 31.77 4.70 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
45 46 4.157849 GGAAATAGTTCCCTTCCCTCTG 57.842 50.000 10.95 0.00 46.84 3.35
319 324 1.972075 TGACCGTTGTCTGGTTGGATA 59.028 47.619 0.00 0.00 40.63 2.59
354 359 6.110707 TCCTGATTCTTACGGGATTAAACAC 58.889 40.000 0.00 0.00 37.81 3.32
370 375 1.355971 ACACGCGCTTATGTAAGTGG 58.644 50.000 5.73 7.51 42.46 4.00
412 417 3.594603 GCAGGAGCTGTGTAAGTAGAA 57.405 47.619 0.00 0.00 37.91 2.10
428 433 5.532025 AGTAGAATTTACTCTGCGCAAAC 57.468 39.130 13.05 0.00 33.66 2.93
464 469 1.228124 AAGCTTGGCGTTGGCACTA 60.228 52.632 0.00 0.00 42.47 2.74
578 583 2.671396 CACGCTTAACAAGTTCCGCTAT 59.329 45.455 0.00 0.00 0.00 2.97
594 607 4.127171 CCGCTATAGTACCAAGCAACATT 58.873 43.478 11.05 0.00 35.98 2.71
605 618 4.232221 CCAAGCAACATTGACTCATTGTC 58.768 43.478 6.97 0.00 45.54 3.18
644 657 1.299926 GCACTACGCCGGAGTATGG 60.300 63.158 18.85 14.12 32.94 2.74
671 684 1.140589 CTCTCGTTGCTGCGGAGAT 59.859 57.895 8.65 0.00 33.89 2.75
672 685 0.382158 CTCTCGTTGCTGCGGAGATA 59.618 55.000 8.65 0.00 33.89 1.98
688 701 5.587289 CGGAGATAAAACCAAGAGAGAGAG 58.413 45.833 0.00 0.00 0.00 3.20
712 730 3.242248 CACCGCAATTAGCTACGAGTAAC 59.758 47.826 0.00 0.00 42.61 2.50
724 742 3.920231 ACGAGTAACCCCCTTTAATCC 57.080 47.619 0.00 0.00 0.00 3.01
762 844 2.515854 AGTACGAGAAAGAGGCACAGA 58.484 47.619 0.00 0.00 0.00 3.41
993 1114 1.815421 CCGTCCGGAGCAATCAAGG 60.815 63.158 3.06 0.00 37.50 3.61
1005 1126 2.086869 CAATCAAGGACGACAATGCCT 58.913 47.619 0.00 0.00 0.00 4.75
1167 1288 1.878522 CGCAGAGTACGTCCATGCC 60.879 63.158 0.00 0.00 33.32 4.40
1188 1315 1.761009 GCTCCCTCCCTTGCTATCTCT 60.761 57.143 0.00 0.00 0.00 3.10
1189 1316 2.688477 CTCCCTCCCTTGCTATCTCTT 58.312 52.381 0.00 0.00 0.00 2.85
1190 1317 2.632512 CTCCCTCCCTTGCTATCTCTTC 59.367 54.545 0.00 0.00 0.00 2.87
1202 1344 6.849085 TGCTATCTCTTCTGAGTTTCTCTT 57.151 37.500 0.00 0.00 40.98 2.85
1214 1361 8.214721 TCTGAGTTTCTCTTTTCTTTTCTTCC 57.785 34.615 0.00 0.00 0.00 3.46
1215 1362 7.011482 TCTGAGTTTCTCTTTTCTTTTCTTCCG 59.989 37.037 0.00 0.00 0.00 4.30
1218 1365 5.652744 TTCTCTTTTCTTTTCTTCCGTCG 57.347 39.130 0.00 0.00 0.00 5.12
1219 1366 4.056050 TCTCTTTTCTTTTCTTCCGTCGG 58.944 43.478 4.39 4.39 0.00 4.79
1221 1368 3.805971 TCTTTTCTTTTCTTCCGTCGGAC 59.194 43.478 15.07 0.00 0.00 4.79
1229 1376 2.358957 TCTTCCGTCGGACGAATTCTA 58.641 47.619 30.33 8.83 46.05 2.10
1230 1377 2.096496 TCTTCCGTCGGACGAATTCTAC 59.904 50.000 30.33 0.00 46.05 2.59
1231 1378 1.742761 TCCGTCGGACGAATTCTACT 58.257 50.000 30.33 0.00 46.05 2.57
1232 1379 2.086869 TCCGTCGGACGAATTCTACTT 58.913 47.619 30.33 0.00 46.05 2.24
1233 1380 2.096496 TCCGTCGGACGAATTCTACTTC 59.904 50.000 30.33 0.00 46.05 3.01
1234 1381 2.097142 CCGTCGGACGAATTCTACTTCT 59.903 50.000 30.33 0.00 46.05 2.85
1235 1382 3.427233 CCGTCGGACGAATTCTACTTCTT 60.427 47.826 30.33 0.00 46.05 2.52
1237 1384 3.303760 GTCGGACGAATTCTACTTCTTGC 59.696 47.826 3.52 0.00 0.00 4.01
1238 1385 2.279136 CGGACGAATTCTACTTCTTGCG 59.721 50.000 3.52 0.00 33.43 4.85
1239 1386 3.508762 GGACGAATTCTACTTCTTGCGA 58.491 45.455 3.52 0.00 0.00 5.10
1240 1387 3.924686 GGACGAATTCTACTTCTTGCGAA 59.075 43.478 3.52 0.00 0.00 4.70
1241 1388 4.201599 GGACGAATTCTACTTCTTGCGAAC 60.202 45.833 3.52 0.00 0.00 3.95
1242 1389 4.304110 ACGAATTCTACTTCTTGCGAACA 58.696 39.130 3.52 0.00 0.00 3.18
1243 1390 4.929808 ACGAATTCTACTTCTTGCGAACAT 59.070 37.500 3.52 0.00 0.00 2.71
1253 1403 5.691754 ACTTCTTGCGAACATTTTTGGATTC 59.308 36.000 0.00 0.00 0.00 2.52
1306 1456 1.498865 GGTCAGTGGTGTTGACAGCG 61.499 60.000 8.58 0.00 45.23 5.18
1307 1457 0.529773 GTCAGTGGTGTTGACAGCGA 60.530 55.000 8.58 0.00 46.53 4.93
1335 1485 8.218338 AGATCACCTAATGCTTTTGTTATGAG 57.782 34.615 0.00 0.00 0.00 2.90
1373 1523 2.623416 CAGACCCTTTTTCCAGACCAAC 59.377 50.000 0.00 0.00 0.00 3.77
1378 1528 4.647853 ACCCTTTTTCCAGACCAACTAAAC 59.352 41.667 0.00 0.00 0.00 2.01
1463 1613 1.537202 CTTGTCCTTGCTAGGCAACAC 59.463 52.381 9.60 3.15 43.99 3.32
1475 1625 0.312102 GGCAACACAGAGCAGTTTCC 59.688 55.000 0.00 0.00 0.00 3.13
1558 1708 6.720309 TCTTATGTTCCCATTCATTCACTGA 58.280 36.000 0.00 0.00 32.29 3.41
1563 1713 6.351711 TGTTCCCATTCATTCACTGATAGAG 58.648 40.000 0.00 0.00 32.72 2.43
1568 1718 7.554118 TCCCATTCATTCACTGATAGAGAAAAC 59.446 37.037 0.00 0.00 32.72 2.43
1609 1759 6.959639 ATAGAGTTTCAAGGTTGAAGCAAA 57.040 33.333 18.04 6.45 46.63 3.68
1665 1815 5.073144 AGTTTGACCCCTAGAAATCACAAGA 59.927 40.000 0.00 0.00 0.00 3.02
1666 1816 4.553330 TGACCCCTAGAAATCACAAGAC 57.447 45.455 0.00 0.00 0.00 3.01
1675 1825 4.002982 AGAAATCACAAGACGCTGCATTA 58.997 39.130 0.00 0.00 0.00 1.90
1680 1830 3.125146 TCACAAGACGCTGCATTACAATC 59.875 43.478 0.00 0.00 0.00 2.67
1683 1833 2.196749 AGACGCTGCATTACAATCGAG 58.803 47.619 0.00 0.00 0.00 4.04
1688 1838 3.685058 GCTGCATTACAATCGAGTTTCC 58.315 45.455 0.00 0.00 0.00 3.13
1690 1840 3.941483 CTGCATTACAATCGAGTTTCCCT 59.059 43.478 0.00 0.00 0.00 4.20
1691 1841 4.331968 TGCATTACAATCGAGTTTCCCTT 58.668 39.130 0.00 0.00 0.00 3.95
1694 1844 6.260050 TGCATTACAATCGAGTTTCCCTTATC 59.740 38.462 0.00 0.00 0.00 1.75
1697 1847 8.673711 CATTACAATCGAGTTTCCCTTATCAAA 58.326 33.333 0.00 0.00 0.00 2.69
1699 1849 7.703058 ACAATCGAGTTTCCCTTATCAAATT 57.297 32.000 0.00 0.00 0.00 1.82
1700 1850 8.801882 ACAATCGAGTTTCCCTTATCAAATTA 57.198 30.769 0.00 0.00 0.00 1.40
1701 1851 9.238368 ACAATCGAGTTTCCCTTATCAAATTAA 57.762 29.630 0.00 0.00 0.00 1.40
1753 1904 2.030946 GGAGACGATCATTGGCTTTTCG 59.969 50.000 0.00 0.00 35.99 3.46
1757 1908 2.556622 ACGATCATTGGCTTTTCGGTTT 59.443 40.909 0.00 0.00 34.28 3.27
1818 1969 1.079336 GCGAGGGGTCCAGTACAAC 60.079 63.158 0.00 0.00 0.00 3.32
1883 2034 3.149196 TCAGAGGTTCTTGAATTGCACC 58.851 45.455 0.00 0.00 0.00 5.01
1884 2035 3.152341 CAGAGGTTCTTGAATTGCACCT 58.848 45.455 0.00 0.00 40.75 4.00
1905 2056 5.057149 CCTAAGCCACATGTTAGGACATAC 58.943 45.833 13.93 0.00 45.77 2.39
1906 2057 4.844349 AAGCCACATGTTAGGACATACT 57.156 40.909 6.40 0.00 44.55 2.12
1907 2058 4.408182 AGCCACATGTTAGGACATACTC 57.592 45.455 6.40 0.00 44.55 2.59
1908 2059 3.134804 AGCCACATGTTAGGACATACTCC 59.865 47.826 6.40 0.00 44.55 3.85
1909 2060 3.118408 GCCACATGTTAGGACATACTCCA 60.118 47.826 6.40 0.00 44.55 3.86
1910 2061 4.444876 GCCACATGTTAGGACATACTCCAT 60.445 45.833 6.40 0.00 44.55 3.41
1911 2062 5.221641 GCCACATGTTAGGACATACTCCATA 60.222 44.000 6.40 0.00 44.55 2.74
1912 2063 6.223852 CCACATGTTAGGACATACTCCATAC 58.776 44.000 0.00 0.00 44.55 2.39
1915 2066 8.807118 CACATGTTAGGACATACTCCATACTAT 58.193 37.037 0.00 0.00 44.55 2.12
2011 4827 5.056480 TCTTCTCAGACGAAATTTCTGCAA 58.944 37.500 15.92 3.90 40.39 4.08
2012 4828 4.732285 TCTCAGACGAAATTTCTGCAAC 57.268 40.909 15.92 3.43 40.39 4.17
2015 4831 3.003275 TCAGACGAAATTTCTGCAACCAC 59.997 43.478 15.92 0.00 40.39 4.16
2016 4832 3.003689 CAGACGAAATTTCTGCAACCACT 59.996 43.478 15.92 1.80 34.41 4.00
2017 4833 3.632145 AGACGAAATTTCTGCAACCACTT 59.368 39.130 15.92 0.00 0.00 3.16
2019 4835 3.380004 ACGAAATTTCTGCAACCACTTCA 59.620 39.130 15.92 0.00 0.00 3.02
2020 4836 4.142271 ACGAAATTTCTGCAACCACTTCAA 60.142 37.500 15.92 0.00 0.00 2.69
2021 4837 4.984161 CGAAATTTCTGCAACCACTTCAAT 59.016 37.500 15.92 0.00 0.00 2.57
2022 4838 5.463061 CGAAATTTCTGCAACCACTTCAATT 59.537 36.000 15.92 0.00 0.00 2.32
2023 4839 6.018832 CGAAATTTCTGCAACCACTTCAATTT 60.019 34.615 15.92 0.00 0.00 1.82
2024 4840 7.465781 CGAAATTTCTGCAACCACTTCAATTTT 60.466 33.333 15.92 0.00 0.00 1.82
2025 4841 7.628769 AATTTCTGCAACCACTTCAATTTTT 57.371 28.000 0.00 0.00 0.00 1.94
2026 4842 6.660887 TTTCTGCAACCACTTCAATTTTTC 57.339 33.333 0.00 0.00 0.00 2.29
2027 4843 4.358851 TCTGCAACCACTTCAATTTTTCG 58.641 39.130 0.00 0.00 0.00 3.46
2028 4844 2.863137 TGCAACCACTTCAATTTTTCGC 59.137 40.909 0.00 0.00 0.00 4.70
2029 4845 3.123050 GCAACCACTTCAATTTTTCGCT 58.877 40.909 0.00 0.00 0.00 4.93
2030 4846 4.202060 TGCAACCACTTCAATTTTTCGCTA 60.202 37.500 0.00 0.00 0.00 4.26
2031 4847 4.923281 GCAACCACTTCAATTTTTCGCTAT 59.077 37.500 0.00 0.00 0.00 2.97
2032 4848 6.090129 GCAACCACTTCAATTTTTCGCTATA 58.910 36.000 0.00 0.00 0.00 1.31
2033 4849 6.584563 GCAACCACTTCAATTTTTCGCTATAA 59.415 34.615 0.00 0.00 0.00 0.98
2034 4850 7.410407 GCAACCACTTCAATTTTTCGCTATAAC 60.410 37.037 0.00 0.00 0.00 1.89
2035 4851 6.311723 ACCACTTCAATTTTTCGCTATAACG 58.688 36.000 0.00 0.00 0.00 3.18
2036 4852 6.072893 ACCACTTCAATTTTTCGCTATAACGT 60.073 34.615 0.00 0.00 0.00 3.99
2037 4853 7.118101 ACCACTTCAATTTTTCGCTATAACGTA 59.882 33.333 0.00 0.00 0.00 3.57
2038 4854 7.424452 CCACTTCAATTTTTCGCTATAACGTAC 59.576 37.037 0.00 0.00 0.00 3.67
2039 4855 8.166706 CACTTCAATTTTTCGCTATAACGTACT 58.833 33.333 0.00 0.00 0.00 2.73
2040 4856 9.357652 ACTTCAATTTTTCGCTATAACGTACTA 57.642 29.630 0.00 0.00 0.00 1.82
2041 4857 9.831054 CTTCAATTTTTCGCTATAACGTACTAG 57.169 33.333 0.00 0.00 0.00 2.57
2042 4858 8.915871 TCAATTTTTCGCTATAACGTACTAGT 57.084 30.769 0.00 0.00 0.00 2.57
2043 4859 8.800972 TCAATTTTTCGCTATAACGTACTAGTG 58.199 33.333 5.39 10.20 0.00 2.74
2044 4860 6.559042 TTTTTCGCTATAACGTACTAGTGC 57.441 37.500 5.39 2.60 0.00 4.40
2045 4861 4.880886 TTCGCTATAACGTACTAGTGCA 57.119 40.909 11.70 0.00 0.00 4.57
2046 4862 4.880886 TCGCTATAACGTACTAGTGCAA 57.119 40.909 11.70 0.00 0.00 4.08
2047 4863 5.428496 TCGCTATAACGTACTAGTGCAAT 57.572 39.130 11.70 0.00 0.00 3.56
2048 4864 5.824429 TCGCTATAACGTACTAGTGCAATT 58.176 37.500 11.70 7.16 0.00 2.32
2049 4865 6.958255 TCGCTATAACGTACTAGTGCAATTA 58.042 36.000 11.70 9.03 0.00 1.40
2050 4866 7.587629 TCGCTATAACGTACTAGTGCAATTAT 58.412 34.615 11.70 14.66 0.00 1.28
2051 4867 8.720562 TCGCTATAACGTACTAGTGCAATTATA 58.279 33.333 11.70 14.95 0.00 0.98
2052 4868 8.996933 CGCTATAACGTACTAGTGCAATTATAG 58.003 37.037 27.08 27.08 34.00 1.31
2053 4869 9.286946 GCTATAACGTACTAGTGCAATTATAGG 57.713 37.037 29.25 20.38 32.91 2.57
2056 4872 9.909644 ATAACGTACTAGTGCAATTATAGGAAG 57.090 33.333 11.70 0.00 0.00 3.46
2057 4873 7.578310 ACGTACTAGTGCAATTATAGGAAGA 57.422 36.000 11.70 0.00 0.00 2.87
2058 4874 8.179509 ACGTACTAGTGCAATTATAGGAAGAT 57.820 34.615 11.70 0.00 0.00 2.40
2059 4875 8.082852 ACGTACTAGTGCAATTATAGGAAGATG 58.917 37.037 11.70 0.00 0.00 2.90
2060 4876 7.062371 CGTACTAGTGCAATTATAGGAAGATGC 59.938 40.741 11.70 0.00 0.00 3.91
2061 4877 6.830912 ACTAGTGCAATTATAGGAAGATGCA 58.169 36.000 0.00 0.00 41.08 3.96
2062 4878 7.456725 ACTAGTGCAATTATAGGAAGATGCAT 58.543 34.615 0.00 0.00 44.51 3.96
2063 4879 6.814506 AGTGCAATTATAGGAAGATGCATC 57.185 37.500 19.37 19.37 44.51 3.91
2064 4880 6.301486 AGTGCAATTATAGGAAGATGCATCA 58.699 36.000 27.81 7.81 44.51 3.07
2065 4881 6.430308 AGTGCAATTATAGGAAGATGCATCAG 59.570 38.462 27.81 4.63 44.51 2.90
2066 4882 6.429078 GTGCAATTATAGGAAGATGCATCAGA 59.571 38.462 27.81 8.73 44.51 3.27
2067 4883 6.999871 TGCAATTATAGGAAGATGCATCAGAA 59.000 34.615 27.81 11.06 38.73 3.02
2068 4884 7.668469 TGCAATTATAGGAAGATGCATCAGAAT 59.332 33.333 27.81 12.80 38.73 2.40
2069 4885 8.521176 GCAATTATAGGAAGATGCATCAGAATT 58.479 33.333 27.81 17.42 34.10 2.17
2071 4887 9.803507 AATTATAGGAAGATGCATCAGAATTCA 57.196 29.630 27.81 8.77 0.00 2.57
2072 4888 9.976776 ATTATAGGAAGATGCATCAGAATTCAT 57.023 29.630 27.81 20.58 0.00 2.57
2075 4891 7.507733 AGGAAGATGCATCAGAATTCATAAC 57.492 36.000 27.81 9.98 0.00 1.89
2076 4892 7.288560 AGGAAGATGCATCAGAATTCATAACT 58.711 34.615 27.81 11.79 0.00 2.24
2077 4893 7.444792 AGGAAGATGCATCAGAATTCATAACTC 59.555 37.037 27.81 9.06 0.00 3.01
2078 4894 7.228108 GGAAGATGCATCAGAATTCATAACTCA 59.772 37.037 27.81 0.00 0.00 3.41
2160 4976 0.535335 TCTTCCACGGGCTGTATGAC 59.465 55.000 0.00 0.00 0.00 3.06
2256 5072 7.550746 CCTACTGGAGAAAGACGTCTGTCAC 62.551 52.000 32.16 26.66 40.93 3.67
2272 5088 4.395231 TCTGTCACAGAGATTACCTGTACG 59.605 45.833 2.36 0.00 42.44 3.67
2274 5090 4.521639 TGTCACAGAGATTACCTGTACGTT 59.478 41.667 0.00 0.00 42.44 3.99
2317 5133 1.265365 GCACAGAGCACAAACTTCCTC 59.735 52.381 0.00 0.00 44.79 3.71
2367 5183 6.531594 GCTTGTAGTTTTTCTCTTTTTGCTGT 59.468 34.615 0.00 0.00 0.00 4.40
2545 5361 9.778741 AAGTATGATGAGTTTCTGTCTTTTGTA 57.221 29.630 0.00 0.00 0.00 2.41
2557 5373 6.891388 TCTGTCTTTTGTAAGTTGGAGGTAA 58.109 36.000 0.00 0.00 32.98 2.85
2558 5374 6.764560 TCTGTCTTTTGTAAGTTGGAGGTAAC 59.235 38.462 0.00 0.00 32.98 2.50
2644 5460 3.071786 ACGTGCATGAAGAGATACTCG 57.928 47.619 14.17 0.00 35.36 4.18
2674 5490 1.996292 TCTTCAAGACAGATTCCGCG 58.004 50.000 0.00 0.00 0.00 6.46
2918 5747 2.541547 TTTGCAGGAGATCAGGCCGG 62.542 60.000 0.00 0.00 0.00 6.13
3010 5842 7.242359 TCCCCCATAAGAACAACAAAAATCTA 58.758 34.615 0.00 0.00 0.00 1.98
3011 5843 7.730784 TCCCCCATAAGAACAACAAAAATCTAA 59.269 33.333 0.00 0.00 0.00 2.10
3063 5895 9.586435 CTGTTTATTCCTTCTCAAACAAACTTT 57.414 29.630 0.00 0.00 39.60 2.66
3245 6077 2.717639 AAACCTTCTCCATGGATCGG 57.282 50.000 16.63 17.40 0.00 4.18
3392 6224 1.071857 AGGTCGACTTCCCAAGAAACC 59.928 52.381 16.46 0.00 0.00 3.27
3812 6644 2.062070 GGAGGAACTGCTCACTGGT 58.938 57.895 0.45 0.00 45.87 4.00
3833 6665 3.935828 GTGACATACTTCTTTCAGAGCCC 59.064 47.826 0.00 0.00 0.00 5.19
3851 6683 1.379527 CCGACACAAGGGAATTAGCC 58.620 55.000 0.00 0.00 0.00 3.93
3854 6686 1.737793 GACACAAGGGAATTAGCCACG 59.262 52.381 0.00 0.00 0.00 4.94
3862 6694 1.065709 GGAATTAGCCACGGAGTCCAA 60.066 52.381 10.49 0.00 41.61 3.53
3864 6696 3.181458 GGAATTAGCCACGGAGTCCAATA 60.181 47.826 10.49 0.00 41.61 1.90
3891 6723 6.851222 ATGCTATTGTCAGTAATGCTACAC 57.149 37.500 0.00 0.00 0.00 2.90
4398 7233 1.418264 TCACATCACCGAGTCCCAAAA 59.582 47.619 0.00 0.00 0.00 2.44
4422 7260 8.675705 AAAAGAAGAAGAGGAAGAAGAAGAAG 57.324 34.615 0.00 0.00 0.00 2.85
4423 7261 7.610580 AAGAAGAAGAGGAAGAAGAAGAAGA 57.389 36.000 0.00 0.00 0.00 2.87
4424 7262 7.797121 AGAAGAAGAGGAAGAAGAAGAAGAT 57.203 36.000 0.00 0.00 0.00 2.40
4425 7263 7.614494 AGAAGAAGAGGAAGAAGAAGAAGATG 58.386 38.462 0.00 0.00 0.00 2.90
4426 7264 7.454380 AGAAGAAGAGGAAGAAGAAGAAGATGA 59.546 37.037 0.00 0.00 0.00 2.92
4427 7265 7.552050 AGAAGAGGAAGAAGAAGAAGATGAA 57.448 36.000 0.00 0.00 0.00 2.57
4436 7274 9.487790 GAAGAAGAAGAAGATGAAGAAGAAGAA 57.512 33.333 0.00 0.00 0.00 2.52
4439 7277 9.143631 GAAGAAGAAGATGAAGAAGAAGAAGAG 57.856 37.037 0.00 0.00 0.00 2.85
4470 7308 3.379452 GAGGAAGAAGAGGAAGGATGGA 58.621 50.000 0.00 0.00 0.00 3.41
4478 7316 1.002624 GGAAGGATGGACGGTTGCA 60.003 57.895 0.00 0.00 0.00 4.08
4610 7448 6.581171 ATGGGTGAAGATTTGAAAGAAGTC 57.419 37.500 0.00 0.00 0.00 3.01
4671 7509 4.788679 TGGATGCAGTGAATCTGATGAAT 58.211 39.130 11.05 0.00 46.27 2.57
4736 7577 3.776417 TGGTTCCAGATGATGTGATCTCA 59.224 43.478 0.00 0.00 29.72 3.27
4805 7646 5.874895 TCACTCTCAAAGATGCAGATTTG 57.125 39.130 16.48 16.48 37.67 2.32
4848 7689 4.536090 AGGACAACTACATCCCTGAAATGA 59.464 41.667 0.00 0.00 35.38 2.57
4922 7763 1.001406 ACTGAACCAGTAGTCAGCAGC 59.999 52.381 0.00 0.00 43.46 5.25
5103 7944 3.175594 ACAGGGGAAATGCATGAATTGT 58.824 40.909 0.00 0.00 0.00 2.71
5168 8009 2.519771 TTGCAGATCAATTGGCTCCT 57.480 45.000 5.42 0.00 0.00 3.69
5268 8109 1.093159 GCTTCCTGCTCCATCAAGTG 58.907 55.000 0.00 0.00 38.95 3.16
5376 8217 0.179089 CAAGCCTCAGACAGGATCCG 60.179 60.000 5.98 3.99 41.54 4.18
5396 8237 6.645700 TCCGCATCTTTATTTGCAAAATTC 57.354 33.333 17.19 0.00 38.80 2.17
5459 8300 6.691508 AGAAAATGAAAATAACTCTGCACCC 58.308 36.000 0.00 0.00 0.00 4.61
5559 8400 3.377172 ACAGGCAACAACACTTTGTAGTC 59.623 43.478 0.00 0.00 45.69 2.59
5708 8549 1.132643 ACTTCAGTAGGCGACGACATC 59.867 52.381 2.19 0.00 38.58 3.06
5712 8553 1.585521 GTAGGCGACGACATCCACG 60.586 63.158 2.19 0.00 35.82 4.94
5774 8615 4.456222 GCTTGGTCTGAGCTCGTAGATATA 59.544 45.833 9.64 0.00 37.18 0.86
5881 8740 3.030291 TGCCAATTGAAAAGACCACTGT 58.970 40.909 7.12 0.00 0.00 3.55
5882 8741 3.181477 TGCCAATTGAAAAGACCACTGTG 60.181 43.478 7.12 0.00 0.00 3.66
5883 8742 3.799917 GCCAATTGAAAAGACCACTGTGG 60.800 47.826 24.80 24.80 45.02 4.17
5884 8743 3.636300 CCAATTGAAAAGACCACTGTGGA 59.364 43.478 32.30 8.44 40.96 4.02
5885 8744 4.261741 CCAATTGAAAAGACCACTGTGGAG 60.262 45.833 32.30 8.17 40.96 3.86
5886 8745 1.967319 TGAAAAGACCACTGTGGAGC 58.033 50.000 32.30 21.93 40.96 4.70
5887 8746 1.211703 TGAAAAGACCACTGTGGAGCA 59.788 47.619 32.30 16.30 40.96 4.26
5888 8747 2.158623 TGAAAAGACCACTGTGGAGCAT 60.159 45.455 32.30 10.75 40.96 3.79
5889 8748 1.901591 AAAGACCACTGTGGAGCATG 58.098 50.000 32.30 5.89 40.96 4.06
5890 8749 1.059098 AAGACCACTGTGGAGCATGA 58.941 50.000 32.30 0.00 40.96 3.07
5891 8750 1.059098 AGACCACTGTGGAGCATGAA 58.941 50.000 32.30 0.00 40.96 2.57
5892 8751 1.421268 AGACCACTGTGGAGCATGAAA 59.579 47.619 32.30 0.00 40.96 2.69
5893 8752 1.808945 GACCACTGTGGAGCATGAAAG 59.191 52.381 32.30 2.89 40.96 2.62
5894 8753 1.421268 ACCACTGTGGAGCATGAAAGA 59.579 47.619 32.30 0.00 40.96 2.52
5895 8754 2.040813 ACCACTGTGGAGCATGAAAGAT 59.959 45.455 32.30 3.00 40.96 2.40
5896 8755 3.087031 CCACTGTGGAGCATGAAAGATT 58.913 45.455 22.33 0.00 40.96 2.40
5897 8756 3.508793 CCACTGTGGAGCATGAAAGATTT 59.491 43.478 22.33 0.00 40.96 2.17
5898 8757 4.482386 CACTGTGGAGCATGAAAGATTTG 58.518 43.478 0.00 0.00 0.00 2.32
6053 8915 4.720649 TGACATTAGGGAGTTCTCTTCG 57.279 45.455 0.00 0.00 0.00 3.79
6314 9281 4.944619 TCAGATGAGAAGAACACAGTGT 57.055 40.909 0.00 0.00 0.00 3.55
6543 9510 2.937149 GTTAAACCCTCTCGCTTCATCC 59.063 50.000 0.00 0.00 0.00 3.51
6612 9579 0.179145 CACGGTACCGAGATGACACC 60.179 60.000 39.52 0.00 42.83 4.16
6681 9648 1.819288 TGGAGTGAGTAGCTTTCCTCG 59.181 52.381 0.00 0.00 0.00 4.63
6926 9896 1.624336 TAAGGACTGTGTGTACGCCT 58.376 50.000 3.51 0.00 33.83 5.52
7025 9996 1.627834 CTTCTGAAGCCAAGGAGACCT 59.372 52.381 4.20 0.00 33.87 3.85
7078 10049 3.181482 CGACCTACTGCAACAGATGATCT 60.181 47.826 0.78 0.00 35.18 2.75
7114 10085 3.456277 CCTTCTACATCTTAGCCACCCTT 59.544 47.826 0.00 0.00 0.00 3.95
7156 10127 1.069568 CAATTTTGCAGTACGCCGACA 60.070 47.619 0.00 0.00 41.33 4.35
7174 10145 2.926200 GACAACACTCTCATCATCACCG 59.074 50.000 0.00 0.00 0.00 4.94
7225 10198 8.150296 AGCTAAAAAGCATACTCCACAAATTTT 58.850 29.630 0.00 0.00 37.25 1.82
7265 10238 8.576442 CCTCACTATAAACTTCACAAAAACCAT 58.424 33.333 0.00 0.00 0.00 3.55
7291 10267 0.823356 AATGCACGTCTGCCCTGTTT 60.823 50.000 0.00 0.00 43.51 2.83
7349 10326 0.965439 TCCACCTTCCCGCAAATTTG 59.035 50.000 14.03 14.03 0.00 2.32
7466 10451 2.526432 ACTTCTCTCTAAGGGCGACAA 58.474 47.619 0.00 0.00 0.00 3.18
7533 10519 7.918076 ACTTTATGTCTGTCTTCCTTATTCCA 58.082 34.615 0.00 0.00 0.00 3.53
7582 10568 2.631160 TCAACGAGCCTTCTTTTGGA 57.369 45.000 0.00 0.00 0.00 3.53
7604 10590 3.840831 CAGAGGAAACCTGCATCGA 57.159 52.632 0.00 0.00 31.76 3.59
7644 10631 3.925913 CCTGGAAAAATGTATGCAAACCG 59.074 43.478 0.00 0.00 0.00 4.44
7649 10636 6.201806 TGGAAAAATGTATGCAAACCGAAAAG 59.798 34.615 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.656323 AAGGGAACTATTTCCTTTTAGAAAGTT 57.344 29.630 11.30 0.00 46.48 2.66
37 38 0.550914 AGCACAAACACCAGAGGGAA 59.449 50.000 0.00 0.00 38.05 3.97
38 39 0.108585 GAGCACAAACACCAGAGGGA 59.891 55.000 0.00 0.00 38.05 4.20
39 40 1.230635 CGAGCACAAACACCAGAGGG 61.231 60.000 0.00 0.00 41.29 4.30
41 42 0.882042 AGCGAGCACAAACACCAGAG 60.882 55.000 0.00 0.00 0.00 3.35
42 43 0.880278 GAGCGAGCACAAACACCAGA 60.880 55.000 0.00 0.00 0.00 3.86
43 44 1.571460 GAGCGAGCACAAACACCAG 59.429 57.895 0.00 0.00 0.00 4.00
44 45 2.243957 CGAGCGAGCACAAACACCA 61.244 57.895 0.00 0.00 0.00 4.17
45 46 2.551270 CGAGCGAGCACAAACACC 59.449 61.111 0.00 0.00 0.00 4.16
215 216 1.801913 CGACTCACAGGCGCAGTAC 60.802 63.158 10.83 0.00 41.27 2.73
224 225 1.187271 CGACGAAAACACGACTCACAG 59.813 52.381 0.00 0.00 37.03 3.66
252 253 4.158384 CCTTTTTACGTGTCACATGATGC 58.842 43.478 3.31 0.00 0.00 3.91
319 324 5.453903 CGTAAGAATCAGGAAGGACATCCAT 60.454 44.000 0.00 0.00 40.51 3.41
354 359 3.555956 AGATTTCCACTTACATAAGCGCG 59.444 43.478 0.00 0.00 36.79 6.86
370 375 5.294306 TGCTCCGTGTGATTATTCAGATTTC 59.706 40.000 0.00 0.00 30.85 2.17
434 439 0.609957 CCAAGCTTCCCATGAGCACA 60.610 55.000 0.00 0.00 42.56 4.57
560 565 5.461407 GGTACTATAGCGGAACTTGTTAAGC 59.539 44.000 0.00 5.08 0.00 3.09
578 583 5.222079 TGAGTCAATGTTGCTTGGTACTA 57.778 39.130 0.00 0.00 0.00 1.82
605 618 5.574055 GTGCATCATGTGAACTTGTTAATGG 59.426 40.000 0.00 0.00 33.17 3.16
656 669 1.730064 GTTTTATCTCCGCAGCAACGA 59.270 47.619 0.00 0.00 34.06 3.85
657 670 1.202031 GGTTTTATCTCCGCAGCAACG 60.202 52.381 0.00 0.00 0.00 4.10
658 671 1.810151 TGGTTTTATCTCCGCAGCAAC 59.190 47.619 0.00 0.00 0.00 4.17
659 672 2.192664 TGGTTTTATCTCCGCAGCAA 57.807 45.000 0.00 0.00 0.00 3.91
660 673 2.083774 CTTGGTTTTATCTCCGCAGCA 58.916 47.619 0.00 0.00 0.00 4.41
661 674 2.352960 CTCTTGGTTTTATCTCCGCAGC 59.647 50.000 0.00 0.00 0.00 5.25
662 675 3.861840 TCTCTTGGTTTTATCTCCGCAG 58.138 45.455 0.00 0.00 0.00 5.18
663 676 3.513912 TCTCTCTTGGTTTTATCTCCGCA 59.486 43.478 0.00 0.00 0.00 5.69
671 684 4.022242 CGGTGTCTCTCTCTCTTGGTTTTA 60.022 45.833 0.00 0.00 0.00 1.52
672 685 3.243907 CGGTGTCTCTCTCTCTTGGTTTT 60.244 47.826 0.00 0.00 0.00 2.43
712 730 1.150764 GGAGCGGGATTAAAGGGGG 59.849 63.158 0.00 0.00 0.00 5.40
724 742 3.984186 TTCTCAGGGGAGGGAGCGG 62.984 68.421 0.00 0.00 41.69 5.52
805 888 3.490439 AAATGAAGGCCCAAAAGGTTG 57.510 42.857 0.00 0.00 38.26 3.77
913 1019 0.390735 CAGCAATGGCAGCTTTTCCC 60.391 55.000 0.00 0.00 44.61 3.97
914 1020 3.132863 CAGCAATGGCAGCTTTTCC 57.867 52.632 0.00 0.00 44.61 3.13
973 1094 2.238847 CTTGATTGCTCCGGACGGGA 62.239 60.000 11.27 6.31 44.68 5.14
974 1095 1.815421 CTTGATTGCTCCGGACGGG 60.815 63.158 11.27 1.55 35.59 5.28
975 1096 1.815421 CCTTGATTGCTCCGGACGG 60.815 63.158 0.00 3.96 0.00 4.79
976 1097 1.084370 GTCCTTGATTGCTCCGGACG 61.084 60.000 0.00 0.00 33.79 4.79
977 1098 1.084370 CGTCCTTGATTGCTCCGGAC 61.084 60.000 0.00 0.00 37.50 4.79
978 1099 1.218047 CGTCCTTGATTGCTCCGGA 59.782 57.895 2.93 2.93 0.00 5.14
979 1100 1.084370 GTCGTCCTTGATTGCTCCGG 61.084 60.000 0.00 0.00 0.00 5.14
980 1101 0.389817 TGTCGTCCTTGATTGCTCCG 60.390 55.000 0.00 0.00 0.00 4.63
981 1102 1.808411 TTGTCGTCCTTGATTGCTCC 58.192 50.000 0.00 0.00 0.00 4.70
982 1103 2.476854 GCATTGTCGTCCTTGATTGCTC 60.477 50.000 0.00 0.00 0.00 4.26
983 1104 1.470098 GCATTGTCGTCCTTGATTGCT 59.530 47.619 0.00 0.00 0.00 3.91
993 1114 1.728971 CTTGACAGAGGCATTGTCGTC 59.271 52.381 14.10 4.15 46.14 4.20
1005 1126 1.227527 CACCGTGTGCCTTGACAGA 60.228 57.895 0.00 0.00 0.00 3.41
1167 1288 1.118356 AGATAGCAAGGGAGGGAGCG 61.118 60.000 0.00 0.00 0.00 5.03
1188 1315 8.678199 GGAAGAAAAGAAAAGAGAAACTCAGAA 58.322 33.333 0.00 0.00 32.06 3.02
1189 1316 7.011482 CGGAAGAAAAGAAAAGAGAAACTCAGA 59.989 37.037 0.00 0.00 32.06 3.27
1190 1317 7.128976 CGGAAGAAAAGAAAAGAGAAACTCAG 58.871 38.462 0.00 0.00 32.06 3.35
1202 1344 2.129607 CGTCCGACGGAAGAAAAGAAA 58.870 47.619 23.35 0.00 38.08 2.52
1214 1361 3.402058 AGAAGTAGAATTCGTCCGACG 57.598 47.619 14.94 14.94 44.19 5.12
1215 1362 3.303760 GCAAGAAGTAGAATTCGTCCGAC 59.696 47.826 0.00 0.00 34.27 4.79
1218 1365 3.909019 CGCAAGAAGTAGAATTCGTCC 57.091 47.619 0.00 0.00 43.02 4.79
1233 1380 7.816945 ATAAGAATCCAAAAATGTTCGCAAG 57.183 32.000 0.00 0.00 0.00 4.01
1234 1381 8.600449 AAATAAGAATCCAAAAATGTTCGCAA 57.400 26.923 0.00 0.00 0.00 4.85
1235 1382 8.600449 AAAATAAGAATCCAAAAATGTTCGCA 57.400 26.923 0.00 0.00 0.00 5.10
1237 1384 9.316859 GCAAAAATAAGAATCCAAAAATGTTCG 57.683 29.630 0.00 0.00 0.00 3.95
1238 1385 9.316859 CGCAAAAATAAGAATCCAAAAATGTTC 57.683 29.630 0.00 0.00 0.00 3.18
1239 1386 8.835439 ACGCAAAAATAAGAATCCAAAAATGTT 58.165 25.926 0.00 0.00 0.00 2.71
1240 1387 8.376889 ACGCAAAAATAAGAATCCAAAAATGT 57.623 26.923 0.00 0.00 0.00 2.71
1241 1388 8.494347 TGACGCAAAAATAAGAATCCAAAAATG 58.506 29.630 0.00 0.00 0.00 2.32
1242 1389 8.600449 TGACGCAAAAATAAGAATCCAAAAAT 57.400 26.923 0.00 0.00 0.00 1.82
1243 1390 8.494347 CATGACGCAAAAATAAGAATCCAAAAA 58.506 29.630 0.00 0.00 0.00 1.94
1253 1403 7.699391 ACTGATGATTCATGACGCAAAAATAAG 59.301 33.333 3.32 0.00 0.00 1.73
1306 1456 7.617041 AACAAAAGCATTAGGTGATCTACTC 57.383 36.000 0.00 0.00 0.00 2.59
1307 1457 9.113838 CATAACAAAAGCATTAGGTGATCTACT 57.886 33.333 0.00 0.00 0.00 2.57
1335 1485 3.049912 GTCTGAAAACCACCGAATTTGC 58.950 45.455 0.00 0.00 0.00 3.68
1373 1523 9.784531 AATCCATACATCAATCACCTAGTTTAG 57.215 33.333 0.00 0.00 0.00 1.85
1378 1528 6.533012 CGCTAATCCATACATCAATCACCTAG 59.467 42.308 0.00 0.00 0.00 3.02
1463 1613 3.633986 ACCAAGAAAAGGAAACTGCTCTG 59.366 43.478 0.00 0.00 42.68 3.35
1475 1625 4.741676 GTGCTTGATCACAACCAAGAAAAG 59.258 41.667 0.00 0.00 41.56 2.27
1552 1702 8.908786 ATCAAAGTTGTTTTCTCTATCAGTGA 57.091 30.769 0.00 0.00 0.00 3.41
1582 1732 8.718102 TGCTTCAACCTTGAAACTCTATATAC 57.282 34.615 2.25 0.00 45.61 1.47
1583 1733 9.733556 TTTGCTTCAACCTTGAAACTCTATATA 57.266 29.630 2.25 0.00 45.61 0.86
1584 1734 8.635765 TTTGCTTCAACCTTGAAACTCTATAT 57.364 30.769 2.25 0.00 45.61 0.86
1592 1742 5.398603 TTGTCTTTGCTTCAACCTTGAAA 57.601 34.783 2.25 0.00 45.61 2.69
1593 1743 5.596836 ATTGTCTTTGCTTCAACCTTGAA 57.403 34.783 0.68 0.68 44.31 2.69
1665 1815 2.010145 ACTCGATTGTAATGCAGCGT 57.990 45.000 0.00 0.00 0.00 5.07
1666 1816 3.345714 GAAACTCGATTGTAATGCAGCG 58.654 45.455 0.00 0.00 0.00 5.18
1675 1825 7.703058 AATTTGATAAGGGAAACTCGATTGT 57.297 32.000 0.00 0.00 0.00 2.71
1680 1830 7.255486 GGGGATTAATTTGATAAGGGAAACTCG 60.255 40.741 0.00 0.00 0.00 4.18
1683 1833 7.062749 GGGGGATTAATTTGATAAGGGAAAC 57.937 40.000 0.00 0.00 0.00 2.78
1753 1904 8.877808 AGAAAATCTGAAGTTGATGAAAAACC 57.122 30.769 0.00 0.00 0.00 3.27
1796 1947 1.117150 GTACTGGACCCCTCGCATTA 58.883 55.000 0.00 0.00 0.00 1.90
1818 1969 9.416794 CAAGGATATTATAGCTGAGTTGTACAG 57.583 37.037 0.00 0.00 38.27 2.74
1883 2034 5.918608 AGTATGTCCTAACATGTGGCTTAG 58.081 41.667 0.00 0.00 45.72 2.18
1884 2035 5.163343 GGAGTATGTCCTAACATGTGGCTTA 60.163 44.000 0.00 0.00 45.72 3.09
1907 2058 9.823647 ACACTGAAGATTGAACTAATAGTATGG 57.176 33.333 0.00 0.00 0.00 2.74
1915 2066 7.054124 ACCAAGAACACTGAAGATTGAACTAA 58.946 34.615 0.00 0.00 0.00 2.24
1938 2089 5.880332 TGCTACACCAAAAGATCATAAGACC 59.120 40.000 0.00 0.00 0.00 3.85
1994 4753 3.003689 AGTGGTTGCAGAAATTTCGTCTG 59.996 43.478 12.42 6.88 44.48 3.51
2011 4827 6.072893 ACGTTATAGCGAAAAATTGAAGTGGT 60.073 34.615 16.28 0.00 35.59 4.16
2012 4828 6.311723 ACGTTATAGCGAAAAATTGAAGTGG 58.688 36.000 16.28 0.00 35.59 4.00
2015 4831 9.831054 CTAGTACGTTATAGCGAAAAATTGAAG 57.169 33.333 16.28 0.00 35.59 3.02
2016 4832 9.357652 ACTAGTACGTTATAGCGAAAAATTGAA 57.642 29.630 16.28 0.00 35.59 2.69
2017 4833 8.800972 CACTAGTACGTTATAGCGAAAAATTGA 58.199 33.333 16.28 0.00 35.59 2.57
2019 4835 7.276218 TGCACTAGTACGTTATAGCGAAAAATT 59.724 33.333 16.28 0.00 35.59 1.82
2020 4836 6.753279 TGCACTAGTACGTTATAGCGAAAAAT 59.247 34.615 16.28 2.97 35.59 1.82
2021 4837 6.092092 TGCACTAGTACGTTATAGCGAAAAA 58.908 36.000 16.28 0.00 35.59 1.94
2022 4838 5.639757 TGCACTAGTACGTTATAGCGAAAA 58.360 37.500 16.28 0.00 35.59 2.29
2023 4839 5.233957 TGCACTAGTACGTTATAGCGAAA 57.766 39.130 16.28 0.48 35.59 3.46
2024 4840 4.880886 TGCACTAGTACGTTATAGCGAA 57.119 40.909 16.28 0.00 35.59 4.70
2025 4841 4.880886 TTGCACTAGTACGTTATAGCGA 57.119 40.909 16.28 0.00 35.59 4.93
2026 4842 7.792383 ATAATTGCACTAGTACGTTATAGCG 57.208 36.000 7.49 7.49 37.94 4.26
2027 4843 9.286946 CCTATAATTGCACTAGTACGTTATAGC 57.713 37.037 20.18 9.99 32.96 2.97
2030 4846 9.909644 CTTCCTATAATTGCACTAGTACGTTAT 57.090 33.333 0.00 2.33 0.00 1.89
2031 4847 9.123902 TCTTCCTATAATTGCACTAGTACGTTA 57.876 33.333 0.00 0.00 0.00 3.18
2032 4848 8.004087 TCTTCCTATAATTGCACTAGTACGTT 57.996 34.615 0.00 0.00 0.00 3.99
2033 4849 7.578310 TCTTCCTATAATTGCACTAGTACGT 57.422 36.000 0.00 0.00 0.00 3.57
2034 4850 7.062371 GCATCTTCCTATAATTGCACTAGTACG 59.938 40.741 0.00 0.00 0.00 3.67
2035 4851 7.872993 TGCATCTTCCTATAATTGCACTAGTAC 59.127 37.037 0.00 0.00 35.36 2.73
2036 4852 7.962441 TGCATCTTCCTATAATTGCACTAGTA 58.038 34.615 0.00 0.00 35.36 1.82
2037 4853 6.830912 TGCATCTTCCTATAATTGCACTAGT 58.169 36.000 0.00 0.00 35.36 2.57
2038 4854 7.605309 TGATGCATCTTCCTATAATTGCACTAG 59.395 37.037 26.32 0.00 42.23 2.57
2039 4855 7.452562 TGATGCATCTTCCTATAATTGCACTA 58.547 34.615 26.32 0.00 42.23 2.74
2040 4856 6.301486 TGATGCATCTTCCTATAATTGCACT 58.699 36.000 26.32 0.00 42.23 4.40
2041 4857 6.429078 TCTGATGCATCTTCCTATAATTGCAC 59.571 38.462 26.32 0.00 42.23 4.57
2042 4858 6.536447 TCTGATGCATCTTCCTATAATTGCA 58.464 36.000 26.32 1.71 43.42 4.08
2043 4859 7.444629 TTCTGATGCATCTTCCTATAATTGC 57.555 36.000 26.32 0.00 0.00 3.56
2045 4861 9.803507 TGAATTCTGATGCATCTTCCTATAATT 57.196 29.630 26.32 18.25 0.00 1.40
2046 4862 9.976776 ATGAATTCTGATGCATCTTCCTATAAT 57.023 29.630 26.32 12.25 23.25 1.28
2049 4865 9.228949 GTTATGAATTCTGATGCATCTTCCTAT 57.771 33.333 26.32 13.86 33.42 2.57
2050 4866 8.435187 AGTTATGAATTCTGATGCATCTTCCTA 58.565 33.333 26.32 15.21 33.42 2.94
2051 4867 7.288560 AGTTATGAATTCTGATGCATCTTCCT 58.711 34.615 26.32 16.09 33.42 3.36
2052 4868 7.228108 TGAGTTATGAATTCTGATGCATCTTCC 59.772 37.037 26.32 9.48 33.42 3.46
2053 4869 8.151141 TGAGTTATGAATTCTGATGCATCTTC 57.849 34.615 26.32 20.46 33.42 2.87
2054 4870 7.991460 TCTGAGTTATGAATTCTGATGCATCTT 59.009 33.333 26.32 13.00 33.42 2.40
2055 4871 7.441760 GTCTGAGTTATGAATTCTGATGCATCT 59.558 37.037 26.32 6.68 33.42 2.90
2056 4872 7.569043 CGTCTGAGTTATGAATTCTGATGCATC 60.569 40.741 20.14 20.14 33.42 3.91
2057 4873 6.202379 CGTCTGAGTTATGAATTCTGATGCAT 59.798 38.462 0.00 0.00 35.61 3.96
2058 4874 5.521372 CGTCTGAGTTATGAATTCTGATGCA 59.479 40.000 7.05 0.00 29.98 3.96
2059 4875 5.521735 ACGTCTGAGTTATGAATTCTGATGC 59.478 40.000 7.05 0.00 36.34 3.91
2060 4876 6.977502 AGACGTCTGAGTTATGAATTCTGATG 59.022 38.462 19.30 8.36 37.77 3.07
2061 4877 7.106439 AGACGTCTGAGTTATGAATTCTGAT 57.894 36.000 19.30 0.00 30.30 2.90
2062 4878 6.516739 AGACGTCTGAGTTATGAATTCTGA 57.483 37.500 19.30 0.00 0.00 3.27
2063 4879 6.808704 TCAAGACGTCTGAGTTATGAATTCTG 59.191 38.462 20.85 8.28 0.00 3.02
2064 4880 6.809196 GTCAAGACGTCTGAGTTATGAATTCT 59.191 38.462 20.85 0.00 0.00 2.40
2065 4881 6.035112 GGTCAAGACGTCTGAGTTATGAATTC 59.965 42.308 20.85 6.09 0.00 2.17
2066 4882 5.869888 GGTCAAGACGTCTGAGTTATGAATT 59.130 40.000 20.85 0.00 0.00 2.17
2067 4883 5.047306 TGGTCAAGACGTCTGAGTTATGAAT 60.047 40.000 20.85 0.00 0.00 2.57
2068 4884 4.279922 TGGTCAAGACGTCTGAGTTATGAA 59.720 41.667 20.85 0.94 0.00 2.57
2069 4885 3.824443 TGGTCAAGACGTCTGAGTTATGA 59.176 43.478 20.85 14.87 0.00 2.15
2070 4886 4.174411 TGGTCAAGACGTCTGAGTTATG 57.826 45.455 20.85 12.58 0.00 1.90
2071 4887 4.462834 TCATGGTCAAGACGTCTGAGTTAT 59.537 41.667 20.85 8.81 0.00 1.89
2072 4888 3.824443 TCATGGTCAAGACGTCTGAGTTA 59.176 43.478 20.85 6.69 0.00 2.24
2073 4889 2.628178 TCATGGTCAAGACGTCTGAGTT 59.372 45.455 20.85 0.00 0.00 3.01
2074 4890 2.239400 TCATGGTCAAGACGTCTGAGT 58.761 47.619 20.85 0.00 0.00 3.41
2075 4891 3.185330 CATCATGGTCAAGACGTCTGAG 58.815 50.000 20.85 15.13 0.00 3.35
2076 4892 2.675032 GCATCATGGTCAAGACGTCTGA 60.675 50.000 20.85 15.47 0.00 3.27
2077 4893 1.662629 GCATCATGGTCAAGACGTCTG 59.337 52.381 20.85 13.33 0.00 3.51
2078 4894 1.406069 GGCATCATGGTCAAGACGTCT 60.406 52.381 13.58 13.58 0.00 4.18
2133 4949 2.286523 CCCGTGGAAGACCTCTGCT 61.287 63.158 0.00 0.00 37.04 4.24
2232 5048 2.820787 ACAGACGTCTTTCTCCAGTAGG 59.179 50.000 17.26 2.24 0.00 3.18
2235 5051 2.034812 GTGACAGACGTCTTTCTCCAGT 59.965 50.000 27.06 15.98 43.06 4.00
2256 5072 4.111375 AGCAACGTACAGGTAATCTCTG 57.889 45.455 0.00 0.00 38.16 3.35
2272 5088 1.534729 CCACCCCTGTTAGAAGCAAC 58.465 55.000 0.00 0.00 0.00 4.17
2274 5090 0.770557 ACCCACCCCTGTTAGAAGCA 60.771 55.000 0.00 0.00 0.00 3.91
2317 5133 5.471456 AGTCCAAAGATGCAAGTTTACAGAG 59.529 40.000 0.00 0.00 0.00 3.35
2367 5183 3.118775 AGCATGGCAACGTTATCTCAGTA 60.119 43.478 0.00 0.00 42.51 2.74
2545 5361 1.342174 TCGCTTCGTTACCTCCAACTT 59.658 47.619 0.00 0.00 0.00 2.66
2547 5363 1.659098 CATCGCTTCGTTACCTCCAAC 59.341 52.381 0.00 0.00 0.00 3.77
2644 5460 1.377333 CTTGAAGAAGGCCGGGTCC 60.377 63.158 2.18 0.00 0.00 4.46
2674 5490 0.524862 CCTGCAGCATTCTGGAACAC 59.475 55.000 8.66 0.00 40.22 3.32
2826 5642 9.766277 GCACAAGAAACTCTTATTCTGATTTAG 57.234 33.333 0.00 0.00 37.22 1.85
2840 5656 8.012241 CAGATAAACAGTTAGCACAAGAAACTC 58.988 37.037 0.00 0.00 31.21 3.01
3032 5864 8.154649 TGTTTGAGAAGGAATAAACAGAGAAC 57.845 34.615 0.00 0.00 37.90 3.01
3137 5969 1.508632 TTAGTTGTCGGTGCTTCAGC 58.491 50.000 0.00 0.00 42.50 4.26
3245 6077 4.808364 GTGAAAGATATCTGCACCTCTGAC 59.192 45.833 20.44 2.78 0.00 3.51
3812 6644 3.368427 CGGGCTCTGAAAGAAGTATGTCA 60.368 47.826 0.00 0.00 46.34 3.58
3833 6665 1.737793 GTGGCTAATTCCCTTGTGTCG 59.262 52.381 0.00 0.00 0.00 4.35
3851 6683 1.331756 GCATTGCTATTGGACTCCGTG 59.668 52.381 0.16 0.00 0.00 4.94
3864 6696 4.885907 AGCATTACTGACAATAGCATTGCT 59.114 37.500 16.63 16.63 43.41 3.91
3891 6723 1.134401 AGCATCAACTGTACCATCGGG 60.134 52.381 0.00 0.00 41.29 5.14
3904 6736 3.730215 TGGCCCTTTTAGTAGCATCAA 57.270 42.857 0.00 0.00 0.00 2.57
4398 7233 8.028652 TCTTCTTCTTCTTCCTCTTCTTCTTT 57.971 34.615 0.00 0.00 0.00 2.52
4416 7254 7.610865 TCCTCTTCTTCTTCTTCATCTTCTTC 58.389 38.462 0.00 0.00 0.00 2.87
4417 7255 7.310609 CCTCCTCTTCTTCTTCTTCATCTTCTT 60.311 40.741 0.00 0.00 0.00 2.52
4418 7256 6.155049 CCTCCTCTTCTTCTTCTTCATCTTCT 59.845 42.308 0.00 0.00 0.00 2.85
4419 7257 6.154363 TCCTCCTCTTCTTCTTCTTCATCTTC 59.846 42.308 0.00 0.00 0.00 2.87
4420 7258 6.022315 TCCTCCTCTTCTTCTTCTTCATCTT 58.978 40.000 0.00 0.00 0.00 2.40
4421 7259 5.588845 TCCTCCTCTTCTTCTTCTTCATCT 58.411 41.667 0.00 0.00 0.00 2.90
4422 7260 5.163416 CCTCCTCCTCTTCTTCTTCTTCATC 60.163 48.000 0.00 0.00 0.00 2.92
4423 7261 4.716287 CCTCCTCCTCTTCTTCTTCTTCAT 59.284 45.833 0.00 0.00 0.00 2.57
4424 7262 4.093011 CCTCCTCCTCTTCTTCTTCTTCA 58.907 47.826 0.00 0.00 0.00 3.02
4425 7263 4.349365 TCCTCCTCCTCTTCTTCTTCTTC 58.651 47.826 0.00 0.00 0.00 2.87
4426 7264 4.352893 CTCCTCCTCCTCTTCTTCTTCTT 58.647 47.826 0.00 0.00 0.00 2.52
4427 7265 3.309848 CCTCCTCCTCCTCTTCTTCTTCT 60.310 52.174 0.00 0.00 0.00 2.85
4436 7274 0.933700 CTTCCTCCTCCTCCTCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
4439 7277 1.289530 TCTTCTTCCTCCTCCTCCTCC 59.710 57.143 0.00 0.00 0.00 4.30
4470 7308 1.968017 CATCAGGTGCTGCAACCGT 60.968 57.895 15.18 0.00 45.53 4.83
4478 7316 2.730934 ATGAATGCTCATCAGGTGCT 57.269 45.000 0.00 0.00 37.82 4.40
4610 7448 0.791983 CACGCTCTTCGCAAATGCAG 60.792 55.000 6.18 0.00 43.23 4.41
4631 7469 1.001706 CCATCAGCATCTTCCGCATTG 60.002 52.381 0.00 0.00 0.00 2.82
4671 7509 4.141733 TGTGATTTCTTCCTCCGATGCATA 60.142 41.667 0.00 0.00 0.00 3.14
4736 7577 3.379372 CAGATTGCTTGGATGAAATCGGT 59.621 43.478 0.00 0.00 46.86 4.69
4805 7646 3.066814 CCTTCCCTTGCTGCTGCC 61.067 66.667 13.47 0.00 38.71 4.85
5093 7934 4.037690 GCGGTTCTTCATACAATTCATGC 58.962 43.478 0.00 0.00 0.00 4.06
5103 7944 4.641396 CATGGATTAGGCGGTTCTTCATA 58.359 43.478 0.00 0.00 0.00 2.15
5168 8009 0.955428 GCGGCAAATCTGTGGAGTCA 60.955 55.000 0.00 0.00 0.00 3.41
5362 8203 1.039068 AGATGCGGATCCTGTCTGAG 58.961 55.000 13.85 0.00 35.02 3.35
5376 8217 5.580297 TCCCGAATTTTGCAAATAAAGATGC 59.420 36.000 13.65 0.54 42.86 3.91
5396 8237 4.410400 GGCCTTGGTGGTCTCCCG 62.410 72.222 0.00 0.00 37.49 5.14
5459 8300 3.848019 CAGATTCTTGATTTGTTTCGCCG 59.152 43.478 0.00 0.00 0.00 6.46
5559 8400 3.181495 GGTAACAGATCTGTCCGAGTCTG 60.181 52.174 28.01 0.00 44.13 3.51
5629 8470 9.624373 AAAATAGATTAGAAGACTGCACATCAT 57.376 29.630 0.00 0.00 0.00 2.45
5774 8615 3.600388 CTCCTGCTTCAGTATCGGTTTT 58.400 45.455 0.00 0.00 0.00 2.43
5881 8740 3.765381 TGGTCAAATCTTTCATGCTCCA 58.235 40.909 0.00 0.00 0.00 3.86
5882 8741 4.789012 TTGGTCAAATCTTTCATGCTCC 57.211 40.909 0.00 0.00 0.00 4.70
5883 8742 5.636543 CCTTTTGGTCAAATCTTTCATGCTC 59.363 40.000 0.00 0.00 34.07 4.26
5884 8743 5.305128 TCCTTTTGGTCAAATCTTTCATGCT 59.695 36.000 0.00 0.00 41.38 3.79
5885 8744 5.540911 TCCTTTTGGTCAAATCTTTCATGC 58.459 37.500 0.00 0.00 41.38 4.06
5886 8745 6.015180 TCCTCCTTTTGGTCAAATCTTTCATG 60.015 38.462 0.00 0.00 41.38 3.07
5887 8746 6.077322 TCCTCCTTTTGGTCAAATCTTTCAT 58.923 36.000 0.00 0.00 41.38 2.57
5888 8747 5.454062 TCCTCCTTTTGGTCAAATCTTTCA 58.546 37.500 0.00 0.00 41.38 2.69
5889 8748 6.405278 TTCCTCCTTTTGGTCAAATCTTTC 57.595 37.500 0.00 0.00 41.38 2.62
5890 8749 7.147497 ACAATTCCTCCTTTTGGTCAAATCTTT 60.147 33.333 0.00 0.00 41.38 2.52
5891 8750 6.327365 ACAATTCCTCCTTTTGGTCAAATCTT 59.673 34.615 0.00 0.00 41.38 2.40
5892 8751 5.840693 ACAATTCCTCCTTTTGGTCAAATCT 59.159 36.000 0.00 0.00 41.38 2.40
5893 8752 6.101650 ACAATTCCTCCTTTTGGTCAAATC 57.898 37.500 0.00 0.00 41.38 2.17
5894 8753 5.602145 TGACAATTCCTCCTTTTGGTCAAAT 59.398 36.000 0.00 0.00 41.38 2.32
5895 8754 4.959210 TGACAATTCCTCCTTTTGGTCAAA 59.041 37.500 0.00 0.00 41.38 2.69
5896 8755 4.541705 TGACAATTCCTCCTTTTGGTCAA 58.458 39.130 0.00 0.00 41.38 3.18
5897 8756 4.144297 CTGACAATTCCTCCTTTTGGTCA 58.856 43.478 0.00 0.00 41.38 4.02
5898 8757 3.057245 GCTGACAATTCCTCCTTTTGGTC 60.057 47.826 0.00 0.00 41.38 4.02
6053 8915 4.408182 TGCTAGTTCCTCTTCTAATGCC 57.592 45.455 0.00 0.00 0.00 4.40
6187 9154 4.324254 GGTGATGATCTTAAAGTGGTGGGA 60.324 45.833 0.00 0.00 0.00 4.37
6314 9281 7.336931 GCTTACCTTGTTCTTTATCTGATCCAA 59.663 37.037 0.00 0.00 0.00 3.53
6398 9365 7.043565 AGTTGAAAGTCTGCAAACAAATCATT 58.956 30.769 0.00 0.00 0.00 2.57
6402 9369 6.397272 TCAAGTTGAAAGTCTGCAAACAAAT 58.603 32.000 2.20 0.00 0.00 2.32
6612 9579 5.588240 ACCGCCTGTTTTTAAAAGAAGAAG 58.412 37.500 11.54 6.59 0.00 2.85
6681 9648 1.669999 ATCAGCCGCCAAATTGCTCC 61.670 55.000 0.00 0.00 31.77 4.70
7025 9996 2.176045 TGAAGAGATAGGGCGACAACA 58.824 47.619 0.00 0.00 0.00 3.33
7114 10085 0.034337 GGCGGTAGGTGTGAGAACAA 59.966 55.000 0.00 0.00 0.00 2.83
7156 10127 2.167281 CCTCGGTGATGATGAGAGTGTT 59.833 50.000 0.00 0.00 31.31 3.32
7174 10145 2.932167 GATGCGTTAATCGAAGCCTC 57.068 50.000 0.00 0.00 42.86 4.70
7184 10155 6.676943 GCTTTTTAGCTGTATGGATGCGTTAA 60.677 38.462 0.00 0.00 0.00 2.01
7186 10157 4.438744 GCTTTTTAGCTGTATGGATGCGTT 60.439 41.667 0.00 0.00 0.00 4.84
7291 10267 3.430862 GGCAATGTCGGCTGCGAA 61.431 61.111 0.00 0.00 39.55 4.70
7466 10451 7.642082 AGTACAGACGACAGTAGGATAAATT 57.358 36.000 0.00 0.00 0.00 1.82
7559 10545 3.253188 CCAAAAGAAGGCTCGTTGAATCA 59.747 43.478 0.00 0.00 0.00 2.57
7582 10568 2.032681 GCAGGTTTCCTCTGCGGT 59.967 61.111 0.21 0.00 46.33 5.68
7644 10631 2.038033 GCCTAAACCCCCAAACCTTTTC 59.962 50.000 0.00 0.00 0.00 2.29
7649 10636 0.902984 CAGGCCTAAACCCCCAAACC 60.903 60.000 3.98 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.