Multiple sequence alignment - TraesCS5D01G061000

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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 TraesCS5D01G061000 chr5D 100.000 2423 0 0 1 2423 57851316 57853738 0.000000e+00 4475.0
1 TraesCS5D01G061000 chr5B 91.389 1289 48 24 417 1665 60790296 60789031 0.000000e+00 1707.0
2 TraesCS5D01G061000 chr5B 98.123 586 8 1 1 586 60790876 60790294 0.000000e+00 1018.0
3 TraesCS5D01G061000 chr5B 95.985 274 7 3 1716 1987 60789029 60788758 2.210000e-120 442.0
4 TraesCS5D01G061000 chr5B 96.133 181 7 0 1984 2164 19530922 19531102 1.820000e-76 296.0
5 TraesCS5D01G061000 chr5B 96.552 174 6 0 2164 2337 60788767 60788594 3.050000e-74 289.0
6 TraesCS5D01G061000 chr5B 88.764 178 19 1 1987 2164 435953288 435953464 1.460000e-52 217.0
7 TraesCS5D01G061000 chr5A 89.719 924 55 19 685 1580 45997625 45998536 0.000000e+00 1144.0
8 TraesCS5D01G061000 chr5A 86.185 637 44 23 58 669 45989968 45990585 0.000000e+00 649.0
9 TraesCS5D01G061000 chr5A 96.629 178 5 1 1987 2164 595688763 595688939 6.550000e-76 294.0
10 TraesCS5D01G061000 chr5A 90.000 70 4 1 1596 1665 45998665 45998731 1.190000e-13 87.9
11 TraesCS5D01G061000 chr2B 90.342 673 46 13 993 1654 698591649 698590985 0.000000e+00 865.0
12 TraesCS5D01G061000 chr3B 84.412 340 30 14 1311 1649 727504407 727504724 1.810000e-81 313.0
13 TraesCS5D01G061000 chr3B 88.268 179 21 0 1987 2165 743681763 743681941 5.250000e-52 215.0
14 TraesCS5D01G061000 chr2D 98.315 178 2 1 1987 2164 82652327 82652151 6.510000e-81 311.0
15 TraesCS5D01G061000 chr2D 82.800 250 38 4 2177 2423 358075383 358075630 4.060000e-53 219.0
16 TraesCS5D01G061000 chr1B 97.753 178 4 0 1987 2164 490725219 490725396 8.410000e-80 307.0
17 TraesCS5D01G061000 chr1B 96.045 177 7 0 1987 2163 608959794 608959618 3.050000e-74 289.0
18 TraesCS5D01G061000 chr7D 83.534 249 36 5 2175 2421 424112120 424111875 6.740000e-56 228.0
19 TraesCS5D01G061000 chr6A 88.398 181 19 2 1986 2165 591331885 591332064 1.460000e-52 217.0
20 TraesCS5D01G061000 chr6A 81.609 261 43 4 2164 2423 599707519 599707263 6.790000e-51 211.0
21 TraesCS5D01G061000 chr6A 96.491 57 0 2 1661 1715 413556941 413556997 2.570000e-15 93.5
22 TraesCS5D01G061000 chr6A 100.000 50 0 0 1666 1715 561398836 561398787 2.570000e-15 93.5
23 TraesCS5D01G061000 chrUn 88.268 179 21 0 1987 2165 377757308 377757130 5.250000e-52 215.0
24 TraesCS5D01G061000 chrUn 96.491 57 0 2 1661 1715 31315961 31316017 2.570000e-15 93.5
25 TraesCS5D01G061000 chr1D 82.400 250 39 4 2177 2423 319540373 319540620 1.890000e-51 213.0
26 TraesCS5D01G061000 chr3D 82.470 251 35 7 2175 2422 571913120 571912876 6.790000e-51 211.0
27 TraesCS5D01G061000 chr3D 95.312 64 0 3 1661 1722 572093178 572093240 5.510000e-17 99.0
28 TraesCS5D01G061000 chr6D 84.507 213 31 2 2211 2422 315978186 315977975 2.440000e-50 209.0
29 TraesCS5D01G061000 chr6D 96.491 57 0 2 1661 1715 365045017 365045073 2.570000e-15 93.5
30 TraesCS5D01G061000 chr6D 96.491 57 0 2 1661 1715 425952296 425952352 2.570000e-15 93.5
31 TraesCS5D01G061000 chr2A 80.400 250 44 4 2177 2423 480528385 480528632 4.110000e-43 185.0
32 TraesCS5D01G061000 chr7A 81.731 208 29 7 2212 2415 602989551 602989349 5.360000e-37 165.0
33 TraesCS5D01G061000 chr4D 100.000 50 0 0 1666 1715 398049245 398049196 2.570000e-15 93.5
34 TraesCS5D01G061000 chr4B 96.491 57 0 2 1661 1715 209312350 209312406 2.570000e-15 93.5
35 TraesCS5D01G061000 chr1A 96.491 57 0 2 1661 1715 94750460 94750516 2.570000e-15 93.5


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 TraesCS5D01G061000 chr5D 57851316 57853738 2422 False 4475.00 4475 100.00000 1 2423 1 chr5D.!!$F1 2422
1 TraesCS5D01G061000 chr5B 60788594 60790876 2282 True 864.00 1707 95.51225 1 2337 4 chr5B.!!$R1 2336
2 TraesCS5D01G061000 chr5A 45989968 45990585 617 False 649.00 649 86.18500 58 669 1 chr5A.!!$F1 611
3 TraesCS5D01G061000 chr5A 45997625 45998731 1106 False 615.95 1144 89.85950 685 1665 2 chr5A.!!$F3 980
4 TraesCS5D01G061000 chr2B 698590985 698591649 664 True 865.00 865 90.34200 993 1654 1 chr2B.!!$R1 661

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
977 1203 0.109342 CCAGTCTGCTTTGGTCTGGT 59.891 55.0 0.0 0.0 40.25 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 2487 0.040204 CCTGAGCCCCCACTCAAAAT 59.96 55.0 0.0 0.0 45.72 1.82 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
394 410 3.718036 CGTGAGATTTGCGACAACGTAAG 60.718 47.826 0.00 0.00 43.75 2.34
461 479 1.251251 AAGGATGCTCACTTTGCCAC 58.749 50.000 0.00 0.00 0.00 5.01
549 571 2.689471 GCATGCATGGTTATGTCCTTGA 59.311 45.455 27.34 0.00 36.65 3.02
550 572 3.243301 GCATGCATGGTTATGTCCTTGAG 60.243 47.826 27.34 0.00 36.65 3.02
551 573 3.719268 TGCATGGTTATGTCCTTGAGT 57.281 42.857 0.00 0.00 36.65 3.41
586 608 1.534163 GTACCTGAAACCGGTTGCTTC 59.466 52.381 25.82 17.62 35.98 3.86
619 817 5.065218 GGACTGCTTTTACATGATCATCGTT 59.935 40.000 4.86 0.00 0.00 3.85
621 819 6.913170 ACTGCTTTTACATGATCATCGTTTT 58.087 32.000 4.86 0.00 0.00 2.43
622 820 6.803320 ACTGCTTTTACATGATCATCGTTTTG 59.197 34.615 4.86 0.00 0.00 2.44
624 822 7.144661 TGCTTTTACATGATCATCGTTTTGTT 58.855 30.769 4.86 0.00 0.00 2.83
625 823 7.114670 TGCTTTTACATGATCATCGTTTTGTTG 59.885 33.333 4.86 0.00 0.00 3.33
626 824 6.926280 TTTACATGATCATCGTTTTGTTGC 57.074 33.333 4.86 0.00 0.00 4.17
627 825 3.491356 ACATGATCATCGTTTTGTTGCG 58.509 40.909 4.86 0.00 0.00 4.85
630 828 2.739379 TGATCATCGTTTTGTTGCGCTA 59.261 40.909 9.73 0.00 0.00 4.26
680 879 8.343366 GCTTAGCCTTAATTAATCACCACTAAC 58.657 37.037 0.00 0.00 0.00 2.34
681 880 9.391006 CTTAGCCTTAATTAATCACCACTAACA 57.609 33.333 0.00 0.00 0.00 2.41
682 881 9.914834 TTAGCCTTAATTAATCACCACTAACAT 57.085 29.630 0.00 0.00 0.00 2.71
683 882 8.225603 AGCCTTAATTAATCACCACTAACATG 57.774 34.615 0.00 0.00 0.00 3.21
702 910 9.988350 CTAACATGTAATTAGCCAACAACTTAG 57.012 33.333 0.00 0.00 0.00 2.18
776 984 6.959606 ACCTATATCTGCACTCCCATTAAT 57.040 37.500 0.00 0.00 0.00 1.40
897 1110 0.453282 CACGACCCACACGTACGTAG 60.453 60.000 22.34 17.19 42.07 3.51
899 1112 1.075542 CGACCCACACGTACGTAGTA 58.924 55.000 22.34 0.00 45.11 1.82
935 1148 3.181474 GCACCTAATTAACCTCGCTCTCT 60.181 47.826 0.00 0.00 0.00 3.10
936 1149 4.612943 CACCTAATTAACCTCGCTCTCTC 58.387 47.826 0.00 0.00 0.00 3.20
937 1150 3.315749 ACCTAATTAACCTCGCTCTCTCG 59.684 47.826 0.00 0.00 0.00 4.04
938 1151 2.873133 AATTAACCTCGCTCTCTCGG 57.127 50.000 0.00 0.00 0.00 4.63
940 1153 1.664321 TTAACCTCGCTCTCTCGGCC 61.664 60.000 0.00 0.00 0.00 6.13
941 1154 2.553765 TAACCTCGCTCTCTCGGCCT 62.554 60.000 0.00 0.00 0.00 5.19
949 1165 2.086251 CTCTCTCGGCCTGCAGATCC 62.086 65.000 17.39 14.78 0.00 3.36
966 1192 2.664081 CCTCCACCTCCCAGTCTGC 61.664 68.421 0.00 0.00 0.00 4.26
970 1196 0.607489 CCACCTCCCAGTCTGCTTTG 60.607 60.000 0.00 0.00 0.00 2.77
971 1197 0.607489 CACCTCCCAGTCTGCTTTGG 60.607 60.000 0.00 0.00 0.00 3.28
972 1198 1.062488 ACCTCCCAGTCTGCTTTGGT 61.062 55.000 0.00 0.00 32.40 3.67
974 1200 0.689623 CTCCCAGTCTGCTTTGGTCT 59.310 55.000 0.00 0.00 32.40 3.85
975 1201 0.397941 TCCCAGTCTGCTTTGGTCTG 59.602 55.000 0.00 0.00 32.40 3.51
977 1203 0.109342 CCAGTCTGCTTTGGTCTGGT 59.891 55.000 0.00 0.00 40.25 4.00
978 1204 1.477558 CCAGTCTGCTTTGGTCTGGTT 60.478 52.381 0.00 0.00 40.25 3.67
979 1205 2.301346 CAGTCTGCTTTGGTCTGGTTT 58.699 47.619 0.00 0.00 0.00 3.27
980 1206 2.291741 CAGTCTGCTTTGGTCTGGTTTC 59.708 50.000 0.00 0.00 0.00 2.78
981 1207 1.609072 GTCTGCTTTGGTCTGGTTTCC 59.391 52.381 0.00 0.00 0.00 3.13
985 1211 2.458006 CTTTGGTCTGGTTTCCGCGC 62.458 60.000 0.00 0.00 0.00 6.86
1107 1339 3.842923 CTCCGCTCCATGTCGGCT 61.843 66.667 11.89 0.00 44.91 5.52
1131 1363 2.799371 GACGTCGCCGGAGAAGAT 59.201 61.111 26.10 11.34 38.78 2.40
1140 1372 1.369321 CGGAGAAGATAGCCAGGCC 59.631 63.158 8.22 0.00 0.00 5.19
1611 1984 1.080772 CGTTCGTGTAGGCAGAGCA 60.081 57.895 0.00 0.00 0.00 4.26
1666 2039 9.906660 TGTTCTAGCTAATGGTTTTGTATTTTG 57.093 29.630 0.00 0.00 0.00 2.44
1667 2040 9.908152 GTTCTAGCTAATGGTTTTGTATTTTGT 57.092 29.630 0.00 0.00 0.00 2.83
1669 2042 9.290988 TCTAGCTAATGGTTTTGTATTTTGTCA 57.709 29.630 0.00 0.00 0.00 3.58
1670 2043 9.906660 CTAGCTAATGGTTTTGTATTTTGTCAA 57.093 29.630 0.00 0.00 0.00 3.18
1672 2045 9.777297 AGCTAATGGTTTTGTATTTTGTCAAAT 57.223 25.926 0.00 0.00 36.52 2.32
1673 2046 9.810231 GCTAATGGTTTTGTATTTTGTCAAATG 57.190 29.630 0.00 0.00 34.29 2.32
1677 2050 8.375608 TGGTTTTGTATTTTGTCAAATGATGG 57.624 30.769 0.00 0.00 34.29 3.51
1678 2051 7.443575 TGGTTTTGTATTTTGTCAAATGATGGG 59.556 33.333 0.00 0.00 34.29 4.00
1679 2052 7.659390 GGTTTTGTATTTTGTCAAATGATGGGA 59.341 33.333 0.00 0.00 34.29 4.37
1680 2053 9.050601 GTTTTGTATTTTGTCAAATGATGGGAA 57.949 29.630 0.00 0.00 34.29 3.97
1681 2054 9.618890 TTTTGTATTTTGTCAAATGATGGGAAA 57.381 25.926 0.00 0.00 34.29 3.13
1682 2055 9.618890 TTTGTATTTTGTCAAATGATGGGAAAA 57.381 25.926 0.00 0.00 34.29 2.29
1683 2056 9.618890 TTGTATTTTGTCAAATGATGGGAAAAA 57.381 25.926 0.00 0.00 34.29 1.94
1684 2057 9.270640 TGTATTTTGTCAAATGATGGGAAAAAG 57.729 29.630 0.00 0.00 34.29 2.27
1685 2058 7.748691 ATTTTGTCAAATGATGGGAAAAAGG 57.251 32.000 0.00 0.00 30.89 3.11
1686 2059 6.491714 TTTGTCAAATGATGGGAAAAAGGA 57.508 33.333 0.00 0.00 0.00 3.36
1687 2060 6.491714 TTGTCAAATGATGGGAAAAAGGAA 57.508 33.333 0.00 0.00 0.00 3.36
1688 2061 6.100404 TGTCAAATGATGGGAAAAAGGAAG 57.900 37.500 0.00 0.00 0.00 3.46
1689 2062 5.011943 TGTCAAATGATGGGAAAAAGGAAGG 59.988 40.000 0.00 0.00 0.00 3.46
1690 2063 5.245977 GTCAAATGATGGGAAAAAGGAAGGA 59.754 40.000 0.00 0.00 0.00 3.36
1691 2064 5.481473 TCAAATGATGGGAAAAAGGAAGGAG 59.519 40.000 0.00 0.00 0.00 3.69
1692 2065 4.682021 ATGATGGGAAAAAGGAAGGAGT 57.318 40.909 0.00 0.00 0.00 3.85
1693 2066 5.796502 ATGATGGGAAAAAGGAAGGAGTA 57.203 39.130 0.00 0.00 0.00 2.59
1694 2067 5.592587 TGATGGGAAAAAGGAAGGAGTAA 57.407 39.130 0.00 0.00 0.00 2.24
1695 2068 6.152638 TGATGGGAAAAAGGAAGGAGTAAT 57.847 37.500 0.00 0.00 0.00 1.89
1696 2069 6.187682 TGATGGGAAAAAGGAAGGAGTAATC 58.812 40.000 0.00 0.00 0.00 1.75
1697 2070 5.592587 TGGGAAAAAGGAAGGAGTAATCA 57.407 39.130 0.00 0.00 0.00 2.57
1698 2071 5.959512 TGGGAAAAAGGAAGGAGTAATCAA 58.040 37.500 0.00 0.00 0.00 2.57
1699 2072 6.377912 TGGGAAAAAGGAAGGAGTAATCAAA 58.622 36.000 0.00 0.00 0.00 2.69
1700 2073 6.841755 TGGGAAAAAGGAAGGAGTAATCAAAA 59.158 34.615 0.00 0.00 0.00 2.44
1701 2074 7.345914 TGGGAAAAAGGAAGGAGTAATCAAAAA 59.654 33.333 0.00 0.00 0.00 1.94
1753 2126 6.015504 CGTACAACTTGTATTGTTGAGATGC 58.984 40.000 12.64 0.00 45.27 3.91
1757 2130 6.371548 ACAACTTGTATTGTTGAGATGCGTAT 59.628 34.615 12.64 0.00 45.27 3.06
1815 2188 2.852413 CGTATGTAAAGAGGTCGTGCTG 59.148 50.000 0.00 0.00 0.00 4.41
1816 2189 3.672511 CGTATGTAAAGAGGTCGTGCTGT 60.673 47.826 0.00 0.00 0.00 4.40
1857 2232 9.620259 GTATACTTCCATTCCATTTCTTCTCTT 57.380 33.333 0.00 0.00 0.00 2.85
1865 2240 6.642733 TTCCATTTCTTCTCTTATGACCCT 57.357 37.500 0.00 0.00 0.00 4.34
1961 2336 9.229784 CAATATGTATAGCAACAAGAAGCAAAG 57.770 33.333 0.00 0.00 32.02 2.77
1986 2361 0.590195 GATCTCCATGGTTGATGCGC 59.410 55.000 21.48 0.00 0.00 6.09
1987 2362 0.107066 ATCTCCATGGTTGATGCGCA 60.107 50.000 14.96 14.96 0.00 6.09
1988 2363 0.745486 TCTCCATGGTTGATGCGCAG 60.745 55.000 18.32 0.00 0.00 5.18
1989 2364 1.002257 TCCATGGTTGATGCGCAGT 60.002 52.632 18.32 3.82 0.00 4.40
1990 2365 1.138036 CCATGGTTGATGCGCAGTG 59.862 57.895 18.32 5.64 0.00 3.66
1991 2366 1.138036 CATGGTTGATGCGCAGTGG 59.862 57.895 18.32 0.00 0.00 4.00
1992 2367 2.703798 ATGGTTGATGCGCAGTGGC 61.704 57.895 18.32 6.24 0.00 5.01
2002 2377 2.978824 GCAGTGGCGGACCTAGAA 59.021 61.111 0.00 0.00 36.63 2.10
2003 2378 1.448013 GCAGTGGCGGACCTAGAAC 60.448 63.158 0.00 0.00 36.63 3.01
2004 2379 1.153823 CAGTGGCGGACCTAGAACG 60.154 63.158 0.00 0.00 36.63 3.95
2005 2380 1.605738 AGTGGCGGACCTAGAACGT 60.606 57.895 0.00 0.00 36.63 3.99
2006 2381 0.322816 AGTGGCGGACCTAGAACGTA 60.323 55.000 0.00 0.00 36.63 3.57
2007 2382 0.743097 GTGGCGGACCTAGAACGTAT 59.257 55.000 0.00 0.00 36.63 3.06
2008 2383 1.135721 GTGGCGGACCTAGAACGTATT 59.864 52.381 0.00 0.00 36.63 1.89
2009 2384 1.826720 TGGCGGACCTAGAACGTATTT 59.173 47.619 0.00 0.00 36.63 1.40
2010 2385 2.234414 TGGCGGACCTAGAACGTATTTT 59.766 45.455 0.00 0.00 36.63 1.82
2011 2386 2.606272 GGCGGACCTAGAACGTATTTTG 59.394 50.000 0.00 0.00 0.00 2.44
2012 2387 3.514645 GCGGACCTAGAACGTATTTTGA 58.485 45.455 0.00 0.00 0.00 2.69
2013 2388 3.305361 GCGGACCTAGAACGTATTTTGAC 59.695 47.826 0.00 0.00 0.00 3.18
2014 2389 4.741342 CGGACCTAGAACGTATTTTGACT 58.259 43.478 0.00 0.00 0.00 3.41
2015 2390 4.561606 CGGACCTAGAACGTATTTTGACTG 59.438 45.833 0.00 0.00 0.00 3.51
2016 2391 4.868734 GGACCTAGAACGTATTTTGACTGG 59.131 45.833 0.00 0.00 0.00 4.00
2017 2392 4.828829 ACCTAGAACGTATTTTGACTGGG 58.171 43.478 0.00 0.00 33.40 4.45
2018 2393 4.189231 CCTAGAACGTATTTTGACTGGGG 58.811 47.826 0.00 0.00 0.00 4.96
2019 2394 3.067684 AGAACGTATTTTGACTGGGGG 57.932 47.619 0.00 0.00 0.00 5.40
2020 2395 1.471287 GAACGTATTTTGACTGGGGGC 59.529 52.381 0.00 0.00 0.00 5.80
2021 2396 0.402504 ACGTATTTTGACTGGGGGCA 59.597 50.000 0.00 0.00 0.00 5.36
2022 2397 1.202952 ACGTATTTTGACTGGGGGCAA 60.203 47.619 0.00 0.00 0.00 4.52
2023 2398 1.889829 CGTATTTTGACTGGGGGCAAA 59.110 47.619 0.00 0.00 32.63 3.68
2024 2399 2.352323 CGTATTTTGACTGGGGGCAAAC 60.352 50.000 0.00 0.00 34.09 2.93
2025 2400 2.101640 ATTTTGACTGGGGGCAAACT 57.898 45.000 0.00 0.00 34.09 2.66
2026 2401 2.757894 TTTTGACTGGGGGCAAACTA 57.242 45.000 0.00 0.00 34.09 2.24
2027 2402 1.989706 TTTGACTGGGGGCAAACTAC 58.010 50.000 0.00 0.00 0.00 2.73
2028 2403 1.145571 TTGACTGGGGGCAAACTACT 58.854 50.000 0.00 0.00 0.00 2.57
2029 2404 1.145571 TGACTGGGGGCAAACTACTT 58.854 50.000 0.00 0.00 0.00 2.24
2030 2405 1.202879 TGACTGGGGGCAAACTACTTG 60.203 52.381 0.00 0.00 38.15 3.16
2031 2406 1.073284 GACTGGGGGCAAACTACTTGA 59.927 52.381 0.00 0.00 37.17 3.02
2032 2407 1.073923 ACTGGGGGCAAACTACTTGAG 59.926 52.381 0.00 0.00 37.17 3.02
2033 2408 1.073923 CTGGGGGCAAACTACTTGAGT 59.926 52.381 0.00 0.00 41.56 3.41
2034 2409 1.202879 TGGGGGCAAACTACTTGAGTG 60.203 52.381 0.00 0.00 38.87 3.51
2035 2410 1.534729 GGGGCAAACTACTTGAGTGG 58.465 55.000 0.00 0.00 38.87 4.00
2036 2411 1.534729 GGGCAAACTACTTGAGTGGG 58.465 55.000 0.00 0.00 38.87 4.61
2037 2412 1.534729 GGCAAACTACTTGAGTGGGG 58.465 55.000 0.00 0.00 38.87 4.96
2038 2413 1.534729 GCAAACTACTTGAGTGGGGG 58.465 55.000 0.00 0.00 38.87 5.40
2039 2414 1.534729 CAAACTACTTGAGTGGGGGC 58.465 55.000 0.00 0.00 38.87 5.80
2040 2415 1.145571 AAACTACTTGAGTGGGGGCA 58.854 50.000 0.00 0.00 38.87 5.36
2041 2416 1.372501 AACTACTTGAGTGGGGGCAT 58.627 50.000 0.00 0.00 38.87 4.40
2042 2417 2.263895 ACTACTTGAGTGGGGGCATA 57.736 50.000 0.00 0.00 36.87 3.14
2043 2418 2.776665 ACTACTTGAGTGGGGGCATAT 58.223 47.619 0.00 0.00 36.87 1.78
2044 2419 3.123273 ACTACTTGAGTGGGGGCATATT 58.877 45.455 0.00 0.00 36.87 1.28
2045 2420 2.736670 ACTTGAGTGGGGGCATATTC 57.263 50.000 0.00 0.00 0.00 1.75
2046 2421 2.208872 ACTTGAGTGGGGGCATATTCT 58.791 47.619 0.00 0.00 0.00 2.40
2047 2422 3.393687 ACTTGAGTGGGGGCATATTCTA 58.606 45.455 0.00 0.00 0.00 2.10
2048 2423 3.983410 ACTTGAGTGGGGGCATATTCTAT 59.017 43.478 0.00 0.00 0.00 1.98
2049 2424 5.162637 ACTTGAGTGGGGGCATATTCTATA 58.837 41.667 0.00 0.00 0.00 1.31
2050 2425 5.610982 ACTTGAGTGGGGGCATATTCTATAA 59.389 40.000 0.00 0.00 0.00 0.98
2051 2426 6.102615 ACTTGAGTGGGGGCATATTCTATAAA 59.897 38.462 0.00 0.00 0.00 1.40
2052 2427 6.523035 TGAGTGGGGGCATATTCTATAAAA 57.477 37.500 0.00 0.00 0.00 1.52
2053 2428 6.542821 TGAGTGGGGGCATATTCTATAAAAG 58.457 40.000 0.00 0.00 0.00 2.27
2054 2429 6.102615 TGAGTGGGGGCATATTCTATAAAAGT 59.897 38.462 0.00 0.00 0.00 2.66
2055 2430 6.922540 AGTGGGGGCATATTCTATAAAAGTT 58.077 36.000 0.00 0.00 0.00 2.66
2056 2431 7.004691 AGTGGGGGCATATTCTATAAAAGTTC 58.995 38.462 0.00 0.00 0.00 3.01
2057 2432 6.775629 GTGGGGGCATATTCTATAAAAGTTCA 59.224 38.462 0.00 0.00 0.00 3.18
2058 2433 7.286775 GTGGGGGCATATTCTATAAAAGTTCAA 59.713 37.037 0.00 0.00 0.00 2.69
2059 2434 7.841729 TGGGGGCATATTCTATAAAAGTTCAAA 59.158 33.333 0.00 0.00 0.00 2.69
2060 2435 8.700973 GGGGGCATATTCTATAAAAGTTCAAAA 58.299 33.333 0.00 0.00 0.00 2.44
2092 2467 9.709495 AAGCATATTTTTCAGAAAATACAAGCA 57.291 25.926 9.19 0.00 45.50 3.91
2093 2468 9.709495 AGCATATTTTTCAGAAAATACAAGCAA 57.291 25.926 9.19 0.00 45.50 3.91
2124 2499 7.670364 AGTAGAATTTCAAATTTTGAGTGGGG 58.330 34.615 11.41 0.00 41.38 4.96
2125 2500 5.868454 AGAATTTCAAATTTTGAGTGGGGG 58.132 37.500 11.41 0.00 41.38 5.40
2126 2501 3.483808 TTTCAAATTTTGAGTGGGGGC 57.516 42.857 11.41 0.00 41.38 5.80
2127 2502 2.397044 TCAAATTTTGAGTGGGGGCT 57.603 45.000 7.74 0.00 34.08 5.19
2128 2503 2.247358 TCAAATTTTGAGTGGGGGCTC 58.753 47.619 7.74 0.00 34.08 4.70
2129 2504 1.969923 CAAATTTTGAGTGGGGGCTCA 59.030 47.619 2.88 0.00 43.03 4.26
2130 2505 1.928868 AATTTTGAGTGGGGGCTCAG 58.071 50.000 0.00 0.00 45.03 3.35
2131 2506 0.040204 ATTTTGAGTGGGGGCTCAGG 59.960 55.000 0.00 0.00 45.03 3.86
2132 2507 2.713531 TTTTGAGTGGGGGCTCAGGC 62.714 60.000 0.00 0.00 45.03 4.85
2142 2517 4.416738 GCTCAGGCCCCCACTCAC 62.417 72.222 0.00 0.00 0.00 3.51
2143 2518 3.721706 CTCAGGCCCCCACTCACC 61.722 72.222 0.00 0.00 0.00 4.02
2144 2519 4.270153 TCAGGCCCCCACTCACCT 62.270 66.667 0.00 0.00 0.00 4.00
2145 2520 3.721706 CAGGCCCCCACTCACCTC 61.722 72.222 0.00 0.00 0.00 3.85
2146 2521 4.270153 AGGCCCCCACTCACCTCA 62.270 66.667 0.00 0.00 0.00 3.86
2147 2522 3.256960 GGCCCCCACTCACCTCAA 61.257 66.667 0.00 0.00 0.00 3.02
2148 2523 2.616458 GGCCCCCACTCACCTCAAT 61.616 63.158 0.00 0.00 0.00 2.57
2149 2524 1.379044 GCCCCCACTCACCTCAATG 60.379 63.158 0.00 0.00 0.00 2.82
2150 2525 2.078452 CCCCCACTCACCTCAATGT 58.922 57.895 0.00 0.00 0.00 2.71
2151 2526 1.285280 CCCCCACTCACCTCAATGTA 58.715 55.000 0.00 0.00 0.00 2.29
2152 2527 1.210478 CCCCCACTCACCTCAATGTAG 59.790 57.143 0.00 0.00 0.00 2.74
2153 2528 1.210478 CCCCACTCACCTCAATGTAGG 59.790 57.143 0.00 0.00 42.82 3.18
2159 2534 4.857251 CCTCAATGTAGGTCCGCC 57.143 61.111 0.00 0.00 31.46 6.13
2160 2535 1.146263 CCTCAATGTAGGTCCGCCC 59.854 63.158 0.00 0.00 34.57 6.13
2161 2536 1.146263 CTCAATGTAGGTCCGCCCC 59.854 63.158 0.00 0.00 34.57 5.80
2162 2537 1.306654 TCAATGTAGGTCCGCCCCT 60.307 57.895 0.00 0.00 38.70 4.79
2163 2538 1.153168 CAATGTAGGTCCGCCCCTG 60.153 63.158 1.64 0.00 35.97 4.45
2164 2539 1.615424 AATGTAGGTCCGCCCCTGT 60.615 57.895 1.64 0.00 35.97 4.00
2165 2540 1.205460 AATGTAGGTCCGCCCCTGTT 61.205 55.000 1.64 0.00 35.97 3.16
2166 2541 1.910580 ATGTAGGTCCGCCCCTGTTG 61.911 60.000 1.64 0.00 35.97 3.33
2167 2542 2.120940 TAGGTCCGCCCCTGTTGA 59.879 61.111 1.64 0.00 35.97 3.18
2168 2543 1.306654 TAGGTCCGCCCCTGTTGAT 60.307 57.895 1.64 0.00 35.97 2.57
2169 2544 1.622607 TAGGTCCGCCCCTGTTGATG 61.623 60.000 1.64 0.00 35.97 3.07
2170 2545 3.134127 GTCCGCCCCTGTTGATGC 61.134 66.667 0.00 0.00 0.00 3.91
2171 2546 4.776322 TCCGCCCCTGTTGATGCG 62.776 66.667 0.00 0.00 46.14 4.73
2180 2555 3.249605 GTTGATGCGCGCAATGGC 61.250 61.111 39.68 25.95 0.00 4.40
2226 2601 2.730069 CGCAGCAAAACTTCATGACAA 58.270 42.857 0.00 0.00 0.00 3.18
2294 2669 4.453136 CGTTCATGGATGATGTGCATATCA 59.547 41.667 25.76 25.76 36.66 2.15
2314 2689 5.401531 TCATAAGGTGCGAAGTACTTTCT 57.598 39.130 10.02 0.69 38.04 2.52
2316 2691 2.745515 AGGTGCGAAGTACTTTCTCC 57.254 50.000 10.02 13.94 44.37 3.71
2363 2738 3.217321 AAAAAGTCGGGCCCTTGTT 57.783 47.368 22.43 5.97 0.00 2.83
2364 2739 1.037493 AAAAAGTCGGGCCCTTGTTC 58.963 50.000 22.43 5.32 0.00 3.18
2365 2740 0.106419 AAAAGTCGGGCCCTTGTTCA 60.106 50.000 22.43 0.00 0.00 3.18
2366 2741 0.112412 AAAGTCGGGCCCTTGTTCAT 59.888 50.000 22.43 0.00 0.00 2.57
2367 2742 0.609131 AAGTCGGGCCCTTGTTCATG 60.609 55.000 22.43 0.54 0.00 3.07
2368 2743 2.361104 TCGGGCCCTTGTTCATGC 60.361 61.111 22.43 0.00 0.00 4.06
2369 2744 3.451894 CGGGCCCTTGTTCATGCC 61.452 66.667 22.43 0.00 43.26 4.40
2370 2745 2.037847 GGGCCCTTGTTCATGCCT 59.962 61.111 17.04 0.00 43.50 4.75
2371 2746 1.306296 GGGCCCTTGTTCATGCCTA 59.694 57.895 17.04 0.00 43.50 3.93
2372 2747 1.037579 GGGCCCTTGTTCATGCCTAC 61.038 60.000 17.04 0.00 43.50 3.18
2373 2748 0.323360 GGCCCTTGTTCATGCCTACA 60.323 55.000 0.00 0.00 40.77 2.74
2374 2749 1.544724 GCCCTTGTTCATGCCTACAA 58.455 50.000 7.38 7.38 33.54 2.41
2375 2750 1.892474 GCCCTTGTTCATGCCTACAAA 59.108 47.619 8.52 0.00 34.17 2.83
2376 2751 2.094545 GCCCTTGTTCATGCCTACAAAG 60.095 50.000 8.52 4.14 34.17 2.77
2377 2752 3.157087 CCCTTGTTCATGCCTACAAAGT 58.843 45.455 8.52 0.00 34.17 2.66
2378 2753 3.191371 CCCTTGTTCATGCCTACAAAGTC 59.809 47.826 8.52 0.00 34.17 3.01
2379 2754 4.074970 CCTTGTTCATGCCTACAAAGTCT 58.925 43.478 8.52 0.00 34.17 3.24
2380 2755 4.083110 CCTTGTTCATGCCTACAAAGTCTG 60.083 45.833 8.52 0.00 34.17 3.51
2381 2756 2.813754 TGTTCATGCCTACAAAGTCTGC 59.186 45.455 0.00 0.00 0.00 4.26
2382 2757 2.813754 GTTCATGCCTACAAAGTCTGCA 59.186 45.455 0.00 0.00 36.23 4.41
2383 2758 2.703416 TCATGCCTACAAAGTCTGCAG 58.297 47.619 7.63 7.63 35.10 4.41
2384 2759 2.302733 TCATGCCTACAAAGTCTGCAGA 59.697 45.455 13.74 13.74 35.10 4.26
2385 2760 3.054875 TCATGCCTACAAAGTCTGCAGAT 60.055 43.478 21.47 5.78 35.10 2.90
2386 2761 4.162131 TCATGCCTACAAAGTCTGCAGATA 59.838 41.667 21.47 6.75 35.10 1.98
2387 2762 3.861840 TGCCTACAAAGTCTGCAGATAC 58.138 45.455 21.47 8.72 0.00 2.24
2388 2763 2.860735 GCCTACAAAGTCTGCAGATACG 59.139 50.000 21.47 11.40 0.00 3.06
2389 2764 3.448686 CCTACAAAGTCTGCAGATACGG 58.551 50.000 21.47 12.72 0.00 4.02
2390 2765 1.726853 ACAAAGTCTGCAGATACGGC 58.273 50.000 21.47 6.41 0.00 5.68
2391 2766 1.009829 CAAAGTCTGCAGATACGGCC 58.990 55.000 21.47 5.60 0.00 6.13
2392 2767 0.613260 AAAGTCTGCAGATACGGCCA 59.387 50.000 21.47 0.00 0.00 5.36
2393 2768 0.613260 AAGTCTGCAGATACGGCCAA 59.387 50.000 21.47 0.00 0.00 4.52
2394 2769 0.108138 AGTCTGCAGATACGGCCAAC 60.108 55.000 21.47 3.83 0.00 3.77
2395 2770 1.090052 GTCTGCAGATACGGCCAACC 61.090 60.000 21.47 0.00 0.00 3.77
2396 2771 1.078497 CTGCAGATACGGCCAACCA 60.078 57.895 8.42 0.00 34.57 3.67
2397 2772 1.369091 CTGCAGATACGGCCAACCAC 61.369 60.000 8.42 0.00 34.57 4.16
2398 2773 2.461110 GCAGATACGGCCAACCACG 61.461 63.158 2.24 0.00 34.57 4.94
2399 2774 2.125269 AGATACGGCCAACCACGC 60.125 61.111 2.24 0.00 34.57 5.34
2400 2775 2.435234 GATACGGCCAACCACGCA 60.435 61.111 2.24 0.00 34.57 5.24
2401 2776 1.817941 GATACGGCCAACCACGCAT 60.818 57.895 2.24 0.00 34.57 4.73
2402 2777 1.772063 GATACGGCCAACCACGCATC 61.772 60.000 2.24 0.00 34.57 3.91
2403 2778 2.529454 ATACGGCCAACCACGCATCA 62.529 55.000 2.24 0.00 34.57 3.07
2404 2779 4.101790 CGGCCAACCACGCATCAC 62.102 66.667 2.24 0.00 34.57 3.06
2405 2780 2.983030 GGCCAACCACGCATCACA 60.983 61.111 0.00 0.00 35.26 3.58
2406 2781 2.560119 GGCCAACCACGCATCACAA 61.560 57.895 0.00 0.00 35.26 3.33
2407 2782 1.361993 GCCAACCACGCATCACAAA 59.638 52.632 0.00 0.00 0.00 2.83
2408 2783 0.939106 GCCAACCACGCATCACAAAC 60.939 55.000 0.00 0.00 0.00 2.93
2409 2784 0.383590 CCAACCACGCATCACAAACA 59.616 50.000 0.00 0.00 0.00 2.83
2410 2785 1.202348 CCAACCACGCATCACAAACAA 60.202 47.619 0.00 0.00 0.00 2.83
2411 2786 1.851666 CAACCACGCATCACAAACAAC 59.148 47.619 0.00 0.00 0.00 3.32
2412 2787 1.388547 ACCACGCATCACAAACAACT 58.611 45.000 0.00 0.00 0.00 3.16
2413 2788 1.333619 ACCACGCATCACAAACAACTC 59.666 47.619 0.00 0.00 0.00 3.01
2414 2789 1.333308 CCACGCATCACAAACAACTCA 59.667 47.619 0.00 0.00 0.00 3.41
2415 2790 2.375110 CACGCATCACAAACAACTCAC 58.625 47.619 0.00 0.00 0.00 3.51
2416 2791 1.333619 ACGCATCACAAACAACTCACC 59.666 47.619 0.00 0.00 0.00 4.02
2417 2792 1.334960 CGCATCACAAACAACTCACCC 60.335 52.381 0.00 0.00 0.00 4.61
2418 2793 1.956477 GCATCACAAACAACTCACCCT 59.044 47.619 0.00 0.00 0.00 4.34
2419 2794 2.030805 GCATCACAAACAACTCACCCTC 60.031 50.000 0.00 0.00 0.00 4.30
2420 2795 1.948104 TCACAAACAACTCACCCTCG 58.052 50.000 0.00 0.00 0.00 4.63
2421 2796 1.483004 TCACAAACAACTCACCCTCGA 59.517 47.619 0.00 0.00 0.00 4.04
2422 2797 2.104111 TCACAAACAACTCACCCTCGAT 59.896 45.455 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
493 515 6.183360 GCATTGACATGAAAATGTTACTGCAG 60.183 38.462 13.48 13.48 42.26 4.41
596 794 5.725110 ACGATGATCATGTAAAAGCAGTC 57.275 39.130 14.30 0.00 0.00 3.51
619 817 5.414454 AGATAACCAAAGATAGCGCAACAAA 59.586 36.000 11.47 0.00 0.00 2.83
621 819 4.513442 AGATAACCAAAGATAGCGCAACA 58.487 39.130 11.47 0.00 0.00 3.33
622 820 5.485662 AAGATAACCAAAGATAGCGCAAC 57.514 39.130 11.47 0.00 0.00 4.17
624 822 4.750098 GCTAAGATAACCAAAGATAGCGCA 59.250 41.667 11.47 0.00 0.00 6.09
625 823 4.750098 TGCTAAGATAACCAAAGATAGCGC 59.250 41.667 0.00 0.00 37.64 5.92
626 824 6.292919 GGTTGCTAAGATAACCAAAGATAGCG 60.293 42.308 0.00 0.00 44.48 4.26
627 825 6.960468 GGTTGCTAAGATAACCAAAGATAGC 58.040 40.000 0.00 0.00 44.48 2.97
680 879 7.120579 TGGACTAAGTTGTTGGCTAATTACATG 59.879 37.037 0.00 0.00 0.00 3.21
681 880 7.120726 GTGGACTAAGTTGTTGGCTAATTACAT 59.879 37.037 0.00 0.00 0.00 2.29
682 881 6.428771 GTGGACTAAGTTGTTGGCTAATTACA 59.571 38.462 0.00 0.00 0.00 2.41
683 882 6.653740 AGTGGACTAAGTTGTTGGCTAATTAC 59.346 38.462 0.00 0.00 0.00 1.89
690 898 2.808543 CTGAGTGGACTAAGTTGTTGGC 59.191 50.000 0.00 0.00 0.00 4.52
702 910 2.435586 ATGCGCTGCTGAGTGGAC 60.436 61.111 9.73 0.00 32.23 4.02
733 941 0.846427 AGGGCTTGACCTGAATGGGA 60.846 55.000 0.00 0.00 40.04 4.37
776 984 0.923358 CATGGGGGTTGGCCTAGTTA 59.077 55.000 3.32 0.00 34.45 2.24
897 1110 2.824341 AGGTGCAGGTGTAGTACAGTAC 59.176 50.000 2.39 2.05 0.00 2.73
898 1111 3.165087 AGGTGCAGGTGTAGTACAGTA 57.835 47.619 2.39 0.00 0.00 2.74
899 1112 2.011122 AGGTGCAGGTGTAGTACAGT 57.989 50.000 2.39 0.00 0.00 3.55
900 1113 4.737855 ATTAGGTGCAGGTGTAGTACAG 57.262 45.455 2.39 0.00 0.00 2.74
901 1114 6.400568 GTTAATTAGGTGCAGGTGTAGTACA 58.599 40.000 0.00 0.00 0.00 2.90
902 1115 5.814188 GGTTAATTAGGTGCAGGTGTAGTAC 59.186 44.000 0.00 0.00 0.00 2.73
903 1116 5.722923 AGGTTAATTAGGTGCAGGTGTAGTA 59.277 40.000 0.00 0.00 0.00 1.82
904 1117 4.534897 AGGTTAATTAGGTGCAGGTGTAGT 59.465 41.667 0.00 0.00 0.00 2.73
910 1123 1.940613 GCGAGGTTAATTAGGTGCAGG 59.059 52.381 0.00 0.00 0.00 4.85
935 1148 3.157252 GGAGGATCTGCAGGCCGA 61.157 66.667 15.13 0.00 33.73 5.54
936 1149 3.473647 TGGAGGATCTGCAGGCCG 61.474 66.667 15.13 0.00 33.73 6.13
937 1150 2.191641 GTGGAGGATCTGCAGGCC 59.808 66.667 15.13 15.67 31.31 5.19
938 1151 2.191641 GGTGGAGGATCTGCAGGC 59.808 66.667 15.13 6.41 31.31 4.85
940 1153 1.694133 GGGAGGTGGAGGATCTGCAG 61.694 65.000 7.63 7.63 31.31 4.41
941 1154 1.690633 GGGAGGTGGAGGATCTGCA 60.691 63.158 0.00 0.00 33.73 4.41
949 1165 1.197430 AAGCAGACTGGGAGGTGGAG 61.197 60.000 4.26 0.00 0.00 3.86
966 1192 1.574428 CGCGGAAACCAGACCAAAG 59.426 57.895 0.00 0.00 0.00 2.77
1066 1292 3.138798 GTAGGAGCTGGGCGACGA 61.139 66.667 0.00 0.00 0.00 4.20
1665 2038 5.011943 CCTTCCTTTTTCCCATCATTTGACA 59.988 40.000 0.00 0.00 0.00 3.58
1666 2039 5.245977 TCCTTCCTTTTTCCCATCATTTGAC 59.754 40.000 0.00 0.00 0.00 3.18
1667 2040 5.401750 TCCTTCCTTTTTCCCATCATTTGA 58.598 37.500 0.00 0.00 0.00 2.69
1668 2041 5.246883 ACTCCTTCCTTTTTCCCATCATTTG 59.753 40.000 0.00 0.00 0.00 2.32
1669 2042 5.406163 ACTCCTTCCTTTTTCCCATCATTT 58.594 37.500 0.00 0.00 0.00 2.32
1670 2043 5.015813 ACTCCTTCCTTTTTCCCATCATT 57.984 39.130 0.00 0.00 0.00 2.57
1671 2044 4.682021 ACTCCTTCCTTTTTCCCATCAT 57.318 40.909 0.00 0.00 0.00 2.45
1672 2045 5.592587 TTACTCCTTCCTTTTTCCCATCA 57.407 39.130 0.00 0.00 0.00 3.07
1673 2046 6.187682 TGATTACTCCTTCCTTTTTCCCATC 58.812 40.000 0.00 0.00 0.00 3.51
1674 2047 6.152638 TGATTACTCCTTCCTTTTTCCCAT 57.847 37.500 0.00 0.00 0.00 4.00
1675 2048 5.592587 TGATTACTCCTTCCTTTTTCCCA 57.407 39.130 0.00 0.00 0.00 4.37
1676 2049 6.911250 TTTGATTACTCCTTCCTTTTTCCC 57.089 37.500 0.00 0.00 0.00 3.97
1706 2079 5.067413 CGGTGATTGGCTAGAAGTAGTTCTA 59.933 44.000 17.24 17.24 41.54 2.10
1707 2080 4.142138 CGGTGATTGGCTAGAAGTAGTTCT 60.142 45.833 16.83 16.83 45.48 3.01
1708 2081 4.113354 CGGTGATTGGCTAGAAGTAGTTC 58.887 47.826 1.75 1.75 0.00 3.01
1709 2082 3.514309 ACGGTGATTGGCTAGAAGTAGTT 59.486 43.478 0.00 0.00 0.00 2.24
1710 2083 3.097614 ACGGTGATTGGCTAGAAGTAGT 58.902 45.455 0.00 0.00 0.00 2.73
1711 2084 3.802948 ACGGTGATTGGCTAGAAGTAG 57.197 47.619 0.00 0.00 0.00 2.57
1712 2085 4.018490 TGTACGGTGATTGGCTAGAAGTA 58.982 43.478 0.00 0.00 0.00 2.24
1713 2086 2.829720 TGTACGGTGATTGGCTAGAAGT 59.170 45.455 0.00 0.00 0.00 3.01
1714 2087 3.520290 TGTACGGTGATTGGCTAGAAG 57.480 47.619 0.00 0.00 0.00 2.85
1780 2153 2.470821 ACATACGCTTTAGATCGCCAC 58.529 47.619 0.00 0.00 0.00 5.01
1938 2313 6.183360 GGCTTTGCTTCTTGTTGCTATACATA 60.183 38.462 0.00 0.00 0.00 2.29
1961 2336 1.412710 TCAACCATGGAGATCGTAGGC 59.587 52.381 21.47 0.00 0.00 3.93
1986 2361 1.153823 CGTTCTAGGTCCGCCACTG 60.154 63.158 0.00 0.00 37.19 3.66
1987 2362 0.322816 TACGTTCTAGGTCCGCCACT 60.323 55.000 0.00 0.00 37.19 4.00
1988 2363 0.743097 ATACGTTCTAGGTCCGCCAC 59.257 55.000 0.00 0.00 37.19 5.01
1989 2364 1.477553 AATACGTTCTAGGTCCGCCA 58.522 50.000 0.00 0.00 37.19 5.69
1990 2365 2.591571 AAATACGTTCTAGGTCCGCC 57.408 50.000 0.00 0.00 0.00 6.13
1991 2366 3.305361 GTCAAAATACGTTCTAGGTCCGC 59.695 47.826 0.00 0.00 0.00 5.54
1992 2367 4.561606 CAGTCAAAATACGTTCTAGGTCCG 59.438 45.833 0.00 0.00 0.00 4.79
1993 2368 4.868734 CCAGTCAAAATACGTTCTAGGTCC 59.131 45.833 0.00 0.00 0.00 4.46
1994 2369 4.868734 CCCAGTCAAAATACGTTCTAGGTC 59.131 45.833 0.00 0.00 0.00 3.85
1995 2370 4.323257 CCCCAGTCAAAATACGTTCTAGGT 60.323 45.833 0.00 0.00 0.00 3.08
1996 2371 4.189231 CCCCAGTCAAAATACGTTCTAGG 58.811 47.826 0.00 0.00 0.00 3.02
1997 2372 4.189231 CCCCCAGTCAAAATACGTTCTAG 58.811 47.826 0.00 0.00 0.00 2.43
1998 2373 3.620472 GCCCCCAGTCAAAATACGTTCTA 60.620 47.826 0.00 0.00 0.00 2.10
1999 2374 2.878526 GCCCCCAGTCAAAATACGTTCT 60.879 50.000 0.00 0.00 0.00 3.01
2000 2375 1.471287 GCCCCCAGTCAAAATACGTTC 59.529 52.381 0.00 0.00 0.00 3.95
2001 2376 1.202952 TGCCCCCAGTCAAAATACGTT 60.203 47.619 0.00 0.00 0.00 3.99
2002 2377 0.402504 TGCCCCCAGTCAAAATACGT 59.597 50.000 0.00 0.00 0.00 3.57
2003 2378 1.540267 TTGCCCCCAGTCAAAATACG 58.460 50.000 0.00 0.00 0.00 3.06
2004 2379 2.897326 AGTTTGCCCCCAGTCAAAATAC 59.103 45.455 0.00 0.00 34.44 1.89
2005 2380 3.252554 AGTTTGCCCCCAGTCAAAATA 57.747 42.857 0.00 0.00 34.44 1.40
2006 2381 2.101640 AGTTTGCCCCCAGTCAAAAT 57.898 45.000 0.00 0.00 34.44 1.82
2007 2382 2.091555 AGTAGTTTGCCCCCAGTCAAAA 60.092 45.455 0.00 0.00 34.44 2.44
2008 2383 1.497286 AGTAGTTTGCCCCCAGTCAAA 59.503 47.619 0.00 0.00 0.00 2.69
2009 2384 1.145571 AGTAGTTTGCCCCCAGTCAA 58.854 50.000 0.00 0.00 0.00 3.18
2010 2385 1.145571 AAGTAGTTTGCCCCCAGTCA 58.854 50.000 0.00 0.00 0.00 3.41
2011 2386 1.073284 TCAAGTAGTTTGCCCCCAGTC 59.927 52.381 0.00 0.00 36.70 3.51
2012 2387 1.073923 CTCAAGTAGTTTGCCCCCAGT 59.926 52.381 0.00 0.00 36.70 4.00
2013 2388 1.073923 ACTCAAGTAGTTTGCCCCCAG 59.926 52.381 0.00 0.00 33.35 4.45
2014 2389 1.145571 ACTCAAGTAGTTTGCCCCCA 58.854 50.000 0.00 0.00 33.35 4.96
2015 2390 1.534729 CACTCAAGTAGTTTGCCCCC 58.465 55.000 0.00 0.00 35.76 5.40
2016 2391 1.534729 CCACTCAAGTAGTTTGCCCC 58.465 55.000 0.00 0.00 35.76 5.80
2017 2392 1.534729 CCCACTCAAGTAGTTTGCCC 58.465 55.000 0.00 0.00 35.76 5.36
2018 2393 1.534729 CCCCACTCAAGTAGTTTGCC 58.465 55.000 0.00 0.00 35.76 4.52
2019 2394 1.534729 CCCCCACTCAAGTAGTTTGC 58.465 55.000 0.00 0.00 35.76 3.68
2020 2395 1.202879 TGCCCCCACTCAAGTAGTTTG 60.203 52.381 0.00 0.00 35.76 2.93
2021 2396 1.145571 TGCCCCCACTCAAGTAGTTT 58.854 50.000 0.00 0.00 35.76 2.66
2022 2397 1.372501 ATGCCCCCACTCAAGTAGTT 58.627 50.000 0.00 0.00 35.76 2.24
2023 2398 2.263895 TATGCCCCCACTCAAGTAGT 57.736 50.000 0.00 0.00 39.81 2.73
2024 2399 3.392616 AGAATATGCCCCCACTCAAGTAG 59.607 47.826 0.00 0.00 0.00 2.57
2025 2400 3.393687 AGAATATGCCCCCACTCAAGTA 58.606 45.455 0.00 0.00 0.00 2.24
2026 2401 2.208872 AGAATATGCCCCCACTCAAGT 58.791 47.619 0.00 0.00 0.00 3.16
2027 2402 4.647564 ATAGAATATGCCCCCACTCAAG 57.352 45.455 0.00 0.00 0.00 3.02
2028 2403 6.523035 TTTATAGAATATGCCCCCACTCAA 57.477 37.500 0.00 0.00 0.00 3.02
2029 2404 6.102615 ACTTTTATAGAATATGCCCCCACTCA 59.897 38.462 0.00 0.00 0.00 3.41
2030 2405 6.543735 ACTTTTATAGAATATGCCCCCACTC 58.456 40.000 0.00 0.00 0.00 3.51
2031 2406 6.530601 ACTTTTATAGAATATGCCCCCACT 57.469 37.500 0.00 0.00 0.00 4.00
2032 2407 6.775629 TGAACTTTTATAGAATATGCCCCCAC 59.224 38.462 0.00 0.00 0.00 4.61
2033 2408 6.916909 TGAACTTTTATAGAATATGCCCCCA 58.083 36.000 0.00 0.00 0.00 4.96
2034 2409 7.833285 TTGAACTTTTATAGAATATGCCCCC 57.167 36.000 0.00 0.00 0.00 5.40
2066 2441 9.709495 TGCTTGTATTTTCTGAAAAATATGCTT 57.291 25.926 18.43 4.24 44.81 3.91
2067 2442 9.709495 TTGCTTGTATTTTCTGAAAAATATGCT 57.291 25.926 18.43 4.90 44.81 3.79
2098 2473 8.802267 CCCCACTCAAAATTTGAAATTCTACTA 58.198 33.333 9.85 0.00 39.58 1.82
2099 2474 7.256296 CCCCCACTCAAAATTTGAAATTCTACT 60.256 37.037 9.85 0.00 39.58 2.57
2100 2475 6.873605 CCCCCACTCAAAATTTGAAATTCTAC 59.126 38.462 9.85 0.00 39.58 2.59
2101 2476 6.519891 GCCCCCACTCAAAATTTGAAATTCTA 60.520 38.462 9.85 0.00 39.58 2.10
2102 2477 5.745770 GCCCCCACTCAAAATTTGAAATTCT 60.746 40.000 9.85 0.00 39.58 2.40
2103 2478 4.455533 GCCCCCACTCAAAATTTGAAATTC 59.544 41.667 9.85 0.00 39.58 2.17
2104 2479 4.104579 AGCCCCCACTCAAAATTTGAAATT 59.895 37.500 9.85 0.00 39.58 1.82
2105 2480 3.652387 AGCCCCCACTCAAAATTTGAAAT 59.348 39.130 9.85 0.00 39.58 2.17
2106 2481 3.044894 AGCCCCCACTCAAAATTTGAAA 58.955 40.909 9.85 0.00 39.58 2.69
2107 2482 2.632512 GAGCCCCCACTCAAAATTTGAA 59.367 45.455 9.85 0.00 39.58 2.69
2108 2483 2.247358 GAGCCCCCACTCAAAATTTGA 58.753 47.619 8.25 8.25 36.65 2.69
2109 2484 1.969923 TGAGCCCCCACTCAAAATTTG 59.030 47.619 0.00 0.00 43.59 2.32
2110 2485 2.250924 CTGAGCCCCCACTCAAAATTT 58.749 47.619 0.00 0.00 45.72 1.82
2111 2486 1.550869 CCTGAGCCCCCACTCAAAATT 60.551 52.381 0.00 0.00 45.72 1.82
2112 2487 0.040204 CCTGAGCCCCCACTCAAAAT 59.960 55.000 0.00 0.00 45.72 1.82
2113 2488 1.460255 CCTGAGCCCCCACTCAAAA 59.540 57.895 0.00 0.00 45.72 2.44
2114 2489 3.170362 CCTGAGCCCCCACTCAAA 58.830 61.111 0.00 0.00 45.72 2.69
2115 2490 3.650950 GCCTGAGCCCCCACTCAA 61.651 66.667 0.00 0.00 45.72 3.02
2125 2500 4.416738 GTGAGTGGGGGCCTGAGC 62.417 72.222 0.84 0.00 38.76 4.26
2126 2501 3.721706 GGTGAGTGGGGGCCTGAG 61.722 72.222 0.84 0.00 0.00 3.35
2127 2502 4.270153 AGGTGAGTGGGGGCCTGA 62.270 66.667 0.84 0.00 0.00 3.86
2128 2503 3.721706 GAGGTGAGTGGGGGCCTG 61.722 72.222 0.84 0.00 0.00 4.85
2129 2504 3.810687 TTGAGGTGAGTGGGGGCCT 62.811 63.158 0.84 0.00 0.00 5.19
2130 2505 2.616458 ATTGAGGTGAGTGGGGGCC 61.616 63.158 0.00 0.00 0.00 5.80
2131 2506 1.379044 CATTGAGGTGAGTGGGGGC 60.379 63.158 0.00 0.00 0.00 5.80
2132 2507 1.210478 CTACATTGAGGTGAGTGGGGG 59.790 57.143 0.00 0.00 0.00 5.40
2133 2508 1.210478 CCTACATTGAGGTGAGTGGGG 59.790 57.143 0.00 0.00 0.00 4.96
2134 2509 2.698855 CCTACATTGAGGTGAGTGGG 57.301 55.000 0.00 0.00 0.00 4.61
2142 2517 1.146263 GGGCGGACCTACATTGAGG 59.854 63.158 0.00 0.00 42.89 3.86
2143 2518 1.146263 GGGGCGGACCTACATTGAG 59.854 63.158 0.00 0.00 40.03 3.02
2144 2519 1.306654 AGGGGCGGACCTACATTGA 60.307 57.895 0.00 0.00 39.65 2.57
2145 2520 1.153168 CAGGGGCGGACCTACATTG 60.153 63.158 0.00 0.00 39.34 2.82
2146 2521 1.205460 AACAGGGGCGGACCTACATT 61.205 55.000 0.00 0.00 39.34 2.71
2147 2522 1.615424 AACAGGGGCGGACCTACAT 60.615 57.895 0.00 0.00 39.34 2.29
2148 2523 2.203877 AACAGGGGCGGACCTACA 60.204 61.111 0.00 0.00 39.34 2.74
2149 2524 1.623542 ATCAACAGGGGCGGACCTAC 61.624 60.000 0.00 0.00 39.34 3.18
2150 2525 1.306654 ATCAACAGGGGCGGACCTA 60.307 57.895 0.00 0.00 39.34 3.08
2151 2526 2.610859 ATCAACAGGGGCGGACCT 60.611 61.111 0.00 0.00 43.08 3.85
2152 2527 2.438434 CATCAACAGGGGCGGACC 60.438 66.667 0.00 0.00 39.11 4.46
2153 2528 3.134127 GCATCAACAGGGGCGGAC 61.134 66.667 0.00 0.00 0.00 4.79
2154 2529 4.776322 CGCATCAACAGGGGCGGA 62.776 66.667 0.00 0.00 45.27 5.54
2159 2534 3.055080 ATTGCGCGCATCAACAGGG 62.055 57.895 36.83 0.00 0.00 4.45
2160 2535 1.870458 CATTGCGCGCATCAACAGG 60.870 57.895 36.83 17.98 0.00 4.00
2161 2536 1.870458 CCATTGCGCGCATCAACAG 60.870 57.895 36.83 19.50 0.00 3.16
2162 2537 2.178769 CCATTGCGCGCATCAACA 59.821 55.556 36.83 20.88 0.00 3.33
2163 2538 3.249605 GCCATTGCGCGCATCAAC 61.250 61.111 36.83 20.99 0.00 3.18
2164 2539 4.495336 GGCCATTGCGCGCATCAA 62.495 61.111 36.83 21.76 38.85 2.57
2169 2544 4.799824 AATGTGGCCATTGCGCGC 62.800 61.111 27.26 27.26 39.81 6.86
2180 2555 1.386533 GATGAGTGGAGGCAATGTGG 58.613 55.000 0.00 0.00 0.00 4.17
2226 2601 2.949177 TGGTACACCATCTGCAACTT 57.051 45.000 0.00 0.00 42.01 2.66
2284 2659 3.467374 TCGCACCTTATGATATGCACA 57.533 42.857 0.00 0.00 37.97 4.57
2294 2669 4.382793 GGGAGAAAGTACTTCGCACCTTAT 60.383 45.833 8.95 0.00 39.22 1.73
2314 2689 2.458620 TGCATGCTTCATTTCATGGGA 58.541 42.857 20.33 0.00 40.16 4.37
2316 2691 2.607635 GCTTGCATGCTTCATTTCATGG 59.392 45.455 20.33 0.00 40.16 3.66
2345 2720 1.037493 GAACAAGGGCCCGACTTTTT 58.963 50.000 18.44 4.55 0.00 1.94
2346 2721 0.106419 TGAACAAGGGCCCGACTTTT 60.106 50.000 18.44 6.49 0.00 2.27
2347 2722 0.112412 ATGAACAAGGGCCCGACTTT 59.888 50.000 18.44 8.53 0.00 2.66
2348 2723 0.609131 CATGAACAAGGGCCCGACTT 60.609 55.000 18.44 8.50 0.00 3.01
2349 2724 1.002134 CATGAACAAGGGCCCGACT 60.002 57.895 18.44 1.30 0.00 4.18
2350 2725 2.700773 GCATGAACAAGGGCCCGAC 61.701 63.158 18.44 7.93 0.00 4.79
2351 2726 2.361104 GCATGAACAAGGGCCCGA 60.361 61.111 18.44 0.00 0.00 5.14
2352 2727 3.451894 GGCATGAACAAGGGCCCG 61.452 66.667 18.44 5.44 40.55 6.13
2354 2729 0.323360 TGTAGGCATGAACAAGGGCC 60.323 55.000 0.00 0.00 46.77 5.80
2355 2730 1.544724 TTGTAGGCATGAACAAGGGC 58.455 50.000 0.00 0.00 32.11 5.19
2356 2731 3.157087 ACTTTGTAGGCATGAACAAGGG 58.843 45.455 16.75 12.27 37.10 3.95
2357 2732 4.074970 AGACTTTGTAGGCATGAACAAGG 58.925 43.478 13.13 13.13 36.96 3.61
2358 2733 4.614535 GCAGACTTTGTAGGCATGAACAAG 60.615 45.833 0.00 1.38 36.96 3.16
2359 2734 3.253188 GCAGACTTTGTAGGCATGAACAA 59.747 43.478 0.00 0.37 33.92 2.83
2360 2735 2.813754 GCAGACTTTGTAGGCATGAACA 59.186 45.455 0.00 0.00 0.00 3.18
2361 2736 2.813754 TGCAGACTTTGTAGGCATGAAC 59.186 45.455 0.00 0.00 0.00 3.18
2362 2737 3.076621 CTGCAGACTTTGTAGGCATGAA 58.923 45.455 8.42 0.00 36.04 2.57
2363 2738 2.302733 TCTGCAGACTTTGTAGGCATGA 59.697 45.455 13.74 0.00 39.69 3.07
2364 2739 2.703416 TCTGCAGACTTTGTAGGCATG 58.297 47.619 13.74 0.00 39.69 4.06
2365 2740 3.641434 ATCTGCAGACTTTGTAGGCAT 57.359 42.857 20.97 0.00 39.69 4.40
2366 2741 3.676049 CGTATCTGCAGACTTTGTAGGCA 60.676 47.826 20.97 0.00 39.69 4.75
2367 2742 2.860735 CGTATCTGCAGACTTTGTAGGC 59.139 50.000 20.97 0.84 39.69 3.93
2368 2743 3.448686 CCGTATCTGCAGACTTTGTAGG 58.551 50.000 20.97 12.28 39.69 3.18
2369 2744 2.860735 GCCGTATCTGCAGACTTTGTAG 59.139 50.000 20.97 5.58 40.50 2.74
2370 2745 2.418197 GGCCGTATCTGCAGACTTTGTA 60.418 50.000 20.97 3.96 0.00 2.41
2371 2746 1.676014 GGCCGTATCTGCAGACTTTGT 60.676 52.381 20.97 5.12 0.00 2.83
2372 2747 1.009829 GGCCGTATCTGCAGACTTTG 58.990 55.000 20.97 9.60 0.00 2.77
2373 2748 0.613260 TGGCCGTATCTGCAGACTTT 59.387 50.000 20.97 5.98 0.00 2.66
2374 2749 0.613260 TTGGCCGTATCTGCAGACTT 59.387 50.000 20.97 6.84 0.00 3.01
2375 2750 0.108138 GTTGGCCGTATCTGCAGACT 60.108 55.000 20.97 11.03 0.00 3.24
2376 2751 1.090052 GGTTGGCCGTATCTGCAGAC 61.090 60.000 20.97 7.06 0.00 3.51
2377 2752 1.220749 GGTTGGCCGTATCTGCAGA 59.779 57.895 20.79 20.79 0.00 4.26
2378 2753 1.078497 TGGTTGGCCGTATCTGCAG 60.078 57.895 7.63 7.63 37.67 4.41
2379 2754 1.376683 GTGGTTGGCCGTATCTGCA 60.377 57.895 0.00 0.00 37.67 4.41
2380 2755 2.461110 CGTGGTTGGCCGTATCTGC 61.461 63.158 0.00 0.00 37.67 4.26
2381 2756 2.461110 GCGTGGTTGGCCGTATCTG 61.461 63.158 0.00 0.00 37.67 2.90
2382 2757 2.125269 GCGTGGTTGGCCGTATCT 60.125 61.111 0.00 0.00 37.67 1.98
2383 2758 1.772063 GATGCGTGGTTGGCCGTATC 61.772 60.000 0.00 0.00 38.60 2.24
2384 2759 1.817941 GATGCGTGGTTGGCCGTAT 60.818 57.895 0.00 0.00 37.67 3.06
2385 2760 2.435234 GATGCGTGGTTGGCCGTA 60.435 61.111 0.00 0.00 37.67 4.02
2386 2761 4.634703 TGATGCGTGGTTGGCCGT 62.635 61.111 0.00 0.00 37.67 5.68
2387 2762 4.101790 GTGATGCGTGGTTGGCCG 62.102 66.667 0.00 0.00 37.67 6.13
2388 2763 2.081425 TTTGTGATGCGTGGTTGGCC 62.081 55.000 0.00 0.00 0.00 5.36
2389 2764 0.939106 GTTTGTGATGCGTGGTTGGC 60.939 55.000 0.00 0.00 0.00 4.52
2390 2765 0.383590 TGTTTGTGATGCGTGGTTGG 59.616 50.000 0.00 0.00 0.00 3.77
2391 2766 1.851666 GTTGTTTGTGATGCGTGGTTG 59.148 47.619 0.00 0.00 0.00 3.77
2392 2767 1.748493 AGTTGTTTGTGATGCGTGGTT 59.252 42.857 0.00 0.00 0.00 3.67
2393 2768 1.333619 GAGTTGTTTGTGATGCGTGGT 59.666 47.619 0.00 0.00 0.00 4.16
2394 2769 1.333308 TGAGTTGTTTGTGATGCGTGG 59.667 47.619 0.00 0.00 0.00 4.94
2395 2770 2.375110 GTGAGTTGTTTGTGATGCGTG 58.625 47.619 0.00 0.00 0.00 5.34
2396 2771 1.333619 GGTGAGTTGTTTGTGATGCGT 59.666 47.619 0.00 0.00 0.00 5.24
2397 2772 1.334960 GGGTGAGTTGTTTGTGATGCG 60.335 52.381 0.00 0.00 0.00 4.73
2398 2773 1.956477 AGGGTGAGTTGTTTGTGATGC 59.044 47.619 0.00 0.00 0.00 3.91
2399 2774 2.224079 CGAGGGTGAGTTGTTTGTGATG 59.776 50.000 0.00 0.00 0.00 3.07
2400 2775 2.104111 TCGAGGGTGAGTTGTTTGTGAT 59.896 45.455 0.00 0.00 0.00 3.06
2401 2776 1.483004 TCGAGGGTGAGTTGTTTGTGA 59.517 47.619 0.00 0.00 0.00 3.58
2402 2777 1.948104 TCGAGGGTGAGTTGTTTGTG 58.052 50.000 0.00 0.00 0.00 3.33
2403 2778 2.930826 ATCGAGGGTGAGTTGTTTGT 57.069 45.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.