Multiple sequence alignment - TraesCS1A01G419000

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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 TraesCS1A01G419000 chr1A 100.000 2402 0 0 1 2402 576066888 576064487 0.000000e+00 4436.0
1 TraesCS1A01G419000 chr1A 87.197 289 31 1 980 1262 576078266 576077978 8.280000e-85 324.0
2 TraesCS1A01G419000 chr1A 85.827 254 30 3 1015 1262 576139144 576138891 5.090000e-67 265.0
3 TraesCS1A01G419000 chr1A 86.122 245 28 1 1024 1262 576203517 576203273 2.370000e-65 259.0
4 TraesCS1A01G419000 chr1D 87.479 1773 91 41 83 1767 479686765 479688494 0.000000e+00 1923.0
5 TraesCS1A01G419000 chr1D 87.413 286 33 1 980 1262 479737887 479737602 2.300000e-85 326.0
6 TraesCS1A01G419000 chr1D 93.548 217 8 4 2091 2304 479688509 479688722 3.850000e-83 318.0
7 TraesCS1A01G419000 chr1D 86.640 247 27 1 1022 1262 479750802 479750556 3.940000e-68 268.0
8 TraesCS1A01G419000 chr1D 85.827 254 30 1 1015 1262 479759374 479759121 5.090000e-67 265.0
9 TraesCS1A01G419000 chr1D 100.000 54 0 0 2289 2342 479708693 479708746 1.520000e-17 100.0
10 TraesCS1A01G419000 chr1B 92.286 350 16 4 975 1317 667918622 667918277 9.980000e-134 486.0
11 TraesCS1A01G419000 chr1B 93.231 325 15 6 551 869 667919113 667918790 2.800000e-129 472.0
12 TraesCS1A01G419000 chr1B 93.851 309 14 1 83 386 667919446 667919138 6.050000e-126 460.0
13 TraesCS1A01G419000 chr1B 92.553 282 8 6 1308 1577 667918201 667917921 2.240000e-105 392.0
14 TraesCS1A01G419000 chr1B 84.252 254 34 2 1015 1262 667997228 667996975 2.390000e-60 243.0
15 TraesCS1A01G419000 chr1B 80.597 201 29 2 135 334 668031987 668031796 1.920000e-31 147.0
16 TraesCS1A01G419000 chr1B 96.053 76 3 0 11 86 667919556 667919481 9.020000e-25 124.0
17 TraesCS1A01G419000 chr1B 95.122 41 2 0 2362 2402 667913699 667913659 5.540000e-07 65.8
18 TraesCS1A01G419000 chr1B 100.000 32 0 0 521 552 680193447 680193478 2.580000e-05 60.2
19 TraesCS1A01G419000 chr5A 91.489 47 2 1 509 553 457945652 457945606 1.990000e-06 63.9
20 TraesCS1A01G419000 chr6D 91.111 45 2 1 510 552 412190243 412190199 2.580000e-05 60.2
21 TraesCS1A01G419000 chr3D 90.909 44 2 1 510 551 40551797 40551840 9.270000e-05 58.4
22 TraesCS1A01G419000 chr3B 90.909 44 2 2 510 551 64177359 64177402 9.270000e-05 58.4


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 TraesCS1A01G419000 chr1A 576064487 576066888 2401 True 4436.0 4436 100.0000 1 2402 1 chr1A.!!$R1 2401
1 TraesCS1A01G419000 chr1D 479686765 479688722 1957 False 1120.5 1923 90.5135 83 2304 2 chr1D.!!$F2 2221
2 TraesCS1A01G419000 chr1B 667917921 667919556 1635 True 386.8 486 93.5948 11 1577 5 chr1B.!!$R4 1566

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
909 1023 0.896479 TAGCACCGCTACTCACACCA 60.896 55.0 0.0 0.0 40.44 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2410 0.106894 GAGGCCCCTTGTAGAATCCG 59.893 60.0 0.0 0.0 0.0 4.18 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
60 61 5.245075 GGTGGGACAATTTAGAATCAACCAA 59.755 40.000 0.00 0.00 44.16 3.67
110 149 8.755018 CCATCGGAATATAAAAAGACATTTTGC 58.245 33.333 0.00 0.00 41.29 3.68
111 150 8.755018 CATCGGAATATAAAAAGACATTTTGCC 58.245 33.333 0.00 0.00 41.29 4.52
152 196 6.374417 AACAGGTTGGAGCTAGATTTCTTA 57.626 37.500 0.00 0.00 0.00 2.10
389 437 7.697352 TTTCACACGAATACGAAGTTCTTTA 57.303 32.000 0.56 0.00 37.78 1.85
390 438 7.697352 TTCACACGAATACGAAGTTCTTTAA 57.303 32.000 0.56 0.00 37.78 1.52
391 439 7.878477 TCACACGAATACGAAGTTCTTTAAT 57.122 32.000 0.56 0.00 37.78 1.40
392 440 8.301730 TCACACGAATACGAAGTTCTTTAATT 57.698 30.769 0.56 0.00 37.78 1.40
393 441 8.767085 TCACACGAATACGAAGTTCTTTAATTT 58.233 29.630 0.56 0.00 37.78 1.82
394 442 8.827599 CACACGAATACGAAGTTCTTTAATTTG 58.172 33.333 0.56 2.62 37.78 2.32
395 443 8.013378 ACACGAATACGAAGTTCTTTAATTTGG 58.987 33.333 0.56 0.00 37.78 3.28
460 508 7.214467 ACAAATATATCGGCAATTTACCCAG 57.786 36.000 0.00 0.00 0.00 4.45
486 534 1.347707 TCATGCGAGGAGAGTTGGTTT 59.652 47.619 0.00 0.00 0.00 3.27
506 554 6.641176 GTTTAACCAAAACACCAACAAGAG 57.359 37.500 0.00 0.00 45.72 2.85
512 560 5.124936 ACCAAAACACCAACAAGAGTTACTC 59.875 40.000 3.85 3.85 35.85 2.59
520 568 4.263506 CCAACAAGAGTTACTCCCTCCAAT 60.264 45.833 8.96 0.00 35.85 3.16
521 569 5.045869 CCAACAAGAGTTACTCCCTCCAATA 60.046 44.000 8.96 0.00 35.85 1.90
522 570 6.353082 CCAACAAGAGTTACTCCCTCCAATAT 60.353 42.308 8.96 0.00 35.85 1.28
523 571 7.147549 CCAACAAGAGTTACTCCCTCCAATATA 60.148 40.741 8.96 0.00 35.85 0.86
526 576 9.670442 ACAAGAGTTACTCCCTCCAATATATTA 57.330 33.333 8.96 0.00 0.00 0.98
572 648 9.911788 AACTTTAGAAGATATCATTGGACACAT 57.088 29.630 5.32 0.00 0.00 3.21
655 731 5.346822 ACAATTTCGCATGCTTTGAATCTTC 59.653 36.000 17.13 0.00 0.00 2.87
844 922 3.686016 TCAGTTTTGACCTTATGCTCCC 58.314 45.455 0.00 0.00 0.00 4.30
845 923 3.073798 TCAGTTTTGACCTTATGCTCCCA 59.926 43.478 0.00 0.00 0.00 4.37
846 924 4.019174 CAGTTTTGACCTTATGCTCCCAT 58.981 43.478 0.00 0.00 35.44 4.00
847 925 5.045213 TCAGTTTTGACCTTATGCTCCCATA 60.045 40.000 0.00 0.00 32.85 2.74
848 926 5.829924 CAGTTTTGACCTTATGCTCCCATAT 59.170 40.000 0.00 0.00 34.10 1.78
849 927 5.829924 AGTTTTGACCTTATGCTCCCATATG 59.170 40.000 0.00 0.00 34.10 1.78
869 951 7.422207 CCATATGCATATTATTCCCATCTCCCT 60.422 40.741 16.71 0.00 0.00 4.20
871 953 4.851540 TGCATATTATTCCCATCTCCCTCA 59.148 41.667 0.00 0.00 0.00 3.86
872 954 5.045359 TGCATATTATTCCCATCTCCCTCAG 60.045 44.000 0.00 0.00 0.00 3.35
873 955 5.045286 GCATATTATTCCCATCTCCCTCAGT 60.045 44.000 0.00 0.00 0.00 3.41
874 956 6.523150 GCATATTATTCCCATCTCCCTCAGTT 60.523 42.308 0.00 0.00 0.00 3.16
875 957 7.465116 CATATTATTCCCATCTCCCTCAGTTT 58.535 38.462 0.00 0.00 0.00 2.66
909 1023 0.896479 TAGCACCGCTACTCACACCA 60.896 55.000 0.00 0.00 40.44 4.17
935 1049 4.227864 ACCTCATTCCTCAACAATCTCC 57.772 45.455 0.00 0.00 0.00 3.71
1158 1305 1.300971 ACGTGAGGCGCTACTACGAA 61.301 55.000 24.84 0.00 46.11 3.85
1173 1320 3.173240 GAACTGCTCGTCCGCGAC 61.173 66.667 8.23 2.72 42.81 5.19
1276 1428 4.124238 CGACAGGTTTGTACTTCCTTTGA 58.876 43.478 0.00 0.00 37.76 2.69
1281 1433 5.765182 CAGGTTTGTACTTCCTTTGACATCT 59.235 40.000 0.00 0.00 0.00 2.90
1286 1438 8.406297 GTTTGTACTTCCTTTGACATCTTCTTT 58.594 33.333 0.00 0.00 0.00 2.52
1296 1448 1.003118 ACATCTTCTTTGGGCGTGCTA 59.997 47.619 0.00 0.00 0.00 3.49
1297 1449 1.667724 CATCTTCTTTGGGCGTGCTAG 59.332 52.381 0.00 0.00 0.00 3.42
1298 1450 0.673644 TCTTCTTTGGGCGTGCTAGC 60.674 55.000 8.10 8.10 0.00 3.42
1299 1451 0.674895 CTTCTTTGGGCGTGCTAGCT 60.675 55.000 17.23 0.00 37.29 3.32
1300 1452 0.250727 TTCTTTGGGCGTGCTAGCTT 60.251 50.000 17.23 0.00 37.29 3.74
1302 1454 1.209504 TCTTTGGGCGTGCTAGCTTAT 59.790 47.619 17.23 0.00 37.29 1.73
1303 1455 1.599542 CTTTGGGCGTGCTAGCTTATC 59.400 52.381 17.23 3.36 37.29 1.75
1304 1456 0.539518 TTGGGCGTGCTAGCTTATCA 59.460 50.000 17.23 5.35 37.29 2.15
1340 1573 6.387465 AGCTTGTTGATGACATTGATTCTTG 58.613 36.000 0.00 0.00 38.26 3.02
1341 1574 6.208007 AGCTTGTTGATGACATTGATTCTTGA 59.792 34.615 0.00 0.00 38.26 3.02
1343 1576 7.574404 GCTTGTTGATGACATTGATTCTTGAGA 60.574 37.037 0.00 0.00 38.26 3.27
1344 1577 7.933215 TGTTGATGACATTGATTCTTGAGAT 57.067 32.000 0.00 0.00 32.00 2.75
1417 1652 8.487028 TGAAGATCTAGCGAGATAGATGGTATA 58.513 37.037 14.63 0.00 42.80 1.47
1471 1710 4.167502 CAGCATGGATGGGGATATCCTATT 59.832 45.833 21.18 6.18 45.59 1.73
1628 1877 8.410673 ACAGATTAGATGTTATATGACGGTCT 57.589 34.615 9.88 9.34 0.00 3.85
1630 1879 7.274468 CAGATTAGATGTTATATGACGGTCTGC 59.726 40.741 9.88 5.51 0.00 4.26
1641 1890 1.684049 CGGTCTGCCTCCTTCTCCT 60.684 63.158 0.00 0.00 0.00 3.69
1643 1892 1.220477 GTCTGCCTCCTTCTCCTGC 59.780 63.158 0.00 0.00 0.00 4.85
1650 1899 1.482593 CCTCCTTCTCCTGCGTGTAAT 59.517 52.381 0.00 0.00 0.00 1.89
1676 1925 8.812147 TCGCAGTATTCCTTATGTAAATGTAG 57.188 34.615 0.00 0.00 0.00 2.74
1677 1926 8.635328 TCGCAGTATTCCTTATGTAAATGTAGA 58.365 33.333 0.00 0.00 0.00 2.59
1698 1947 8.522178 GTAGATTATAGCGTCTACAGCAAAAT 57.478 34.615 13.10 0.00 43.89 1.82
1715 1965 4.576463 GCAAAATACAGTACTCCCTCCATG 59.424 45.833 0.00 0.00 0.00 3.66
1726 1976 1.626321 TCCCTCCATGCGAAAAGTGTA 59.374 47.619 0.00 0.00 0.00 2.90
1767 2017 6.929049 TGATGTCAATCTTCGTAAACTTGACT 59.071 34.615 13.08 1.94 43.72 3.41
1768 2018 6.525121 TGTCAATCTTCGTAAACTTGACTG 57.475 37.500 13.08 0.00 43.72 3.51
1769 2019 6.277605 TGTCAATCTTCGTAAACTTGACTGA 58.722 36.000 13.08 0.00 43.72 3.41
1770 2020 6.759356 TGTCAATCTTCGTAAACTTGACTGAA 59.241 34.615 13.08 0.00 43.72 3.02
1771 2021 7.441157 TGTCAATCTTCGTAAACTTGACTGAAT 59.559 33.333 13.08 0.00 43.72 2.57
1885 2135 8.677148 TTATTGTAGATGCAGTAAATTCCTCC 57.323 34.615 0.00 0.00 0.00 4.30
1886 2136 4.693283 TGTAGATGCAGTAAATTCCTCCG 58.307 43.478 0.00 0.00 0.00 4.63
1887 2137 3.914426 AGATGCAGTAAATTCCTCCGT 57.086 42.857 0.00 0.00 0.00 4.69
1888 2138 3.798202 AGATGCAGTAAATTCCTCCGTC 58.202 45.455 0.00 0.00 0.00 4.79
1889 2139 3.197766 AGATGCAGTAAATTCCTCCGTCA 59.802 43.478 0.00 0.00 0.00 4.35
1890 2140 2.972625 TGCAGTAAATTCCTCCGTCAG 58.027 47.619 0.00 0.00 0.00 3.51
1891 2141 2.301870 TGCAGTAAATTCCTCCGTCAGT 59.698 45.455 0.00 0.00 0.00 3.41
1892 2142 3.244422 TGCAGTAAATTCCTCCGTCAGTT 60.244 43.478 0.00 0.00 0.00 3.16
1893 2143 3.751698 GCAGTAAATTCCTCCGTCAGTTT 59.248 43.478 0.00 0.00 0.00 2.66
1894 2144 4.378459 GCAGTAAATTCCTCCGTCAGTTTG 60.378 45.833 0.00 0.00 0.00 2.93
1895 2145 4.994852 CAGTAAATTCCTCCGTCAGTTTGA 59.005 41.667 0.00 0.00 0.00 2.69
1896 2146 5.643777 CAGTAAATTCCTCCGTCAGTTTGAT 59.356 40.000 0.00 0.00 0.00 2.57
1897 2147 6.149474 CAGTAAATTCCTCCGTCAGTTTGATT 59.851 38.462 0.00 0.00 0.00 2.57
1898 2148 6.715264 AGTAAATTCCTCCGTCAGTTTGATTT 59.285 34.615 0.00 0.00 0.00 2.17
1899 2149 6.405278 AAATTCCTCCGTCAGTTTGATTTT 57.595 33.333 0.00 0.00 0.00 1.82
1900 2150 6.405278 AATTCCTCCGTCAGTTTGATTTTT 57.595 33.333 0.00 0.00 0.00 1.94
1923 2173 8.729805 TTTTTGCAGGTGAAGTTTGATTAAAT 57.270 26.923 0.00 0.00 0.00 1.40
1924 2174 8.729805 TTTTGCAGGTGAAGTTTGATTAAATT 57.270 26.923 0.00 0.00 0.00 1.82
1925 2175 8.729805 TTTGCAGGTGAAGTTTGATTAAATTT 57.270 26.923 0.00 0.00 0.00 1.82
1926 2176 8.729805 TTGCAGGTGAAGTTTGATTAAATTTT 57.270 26.923 0.00 0.00 0.00 1.82
1927 2177 9.823647 TTGCAGGTGAAGTTTGATTAAATTTTA 57.176 25.926 0.00 0.00 0.00 1.52
1928 2178 9.255304 TGCAGGTGAAGTTTGATTAAATTTTAC 57.745 29.630 0.00 5.08 33.86 2.01
1929 2179 9.255304 GCAGGTGAAGTTTGATTAAATTTTACA 57.745 29.630 12.61 0.00 35.27 2.41
1946 2196 9.643693 AAATTTTACAAAGCTTGACATCTATGG 57.356 29.630 0.00 0.00 0.00 2.74
1947 2197 7.994425 TTTTACAAAGCTTGACATCTATGGA 57.006 32.000 0.00 0.00 0.00 3.41
1948 2198 7.994425 TTTACAAAGCTTGACATCTATGGAA 57.006 32.000 0.00 0.00 0.00 3.53
1949 2199 7.994425 TTACAAAGCTTGACATCTATGGAAA 57.006 32.000 0.00 0.00 0.00 3.13
1950 2200 6.899393 ACAAAGCTTGACATCTATGGAAAA 57.101 33.333 0.00 0.00 0.00 2.29
1951 2201 7.288810 ACAAAGCTTGACATCTATGGAAAAA 57.711 32.000 0.00 0.00 0.00 1.94
1952 2202 7.899973 ACAAAGCTTGACATCTATGGAAAAAT 58.100 30.769 0.00 0.00 0.00 1.82
1953 2203 8.031277 ACAAAGCTTGACATCTATGGAAAAATC 58.969 33.333 0.00 0.00 0.00 2.17
1954 2204 7.951347 AAGCTTGACATCTATGGAAAAATCT 57.049 32.000 0.00 0.00 0.00 2.40
1955 2205 9.466497 AAAGCTTGACATCTATGGAAAAATCTA 57.534 29.630 0.00 0.00 0.00 1.98
1956 2206 9.638176 AAGCTTGACATCTATGGAAAAATCTAT 57.362 29.630 0.00 0.00 0.00 1.98
1963 2213 9.678260 ACATCTATGGAAAAATCTATATGCTCC 57.322 33.333 0.00 0.00 0.00 4.70
1964 2214 9.676861 CATCTATGGAAAAATCTATATGCTCCA 57.323 33.333 0.00 0.00 36.02 3.86
1987 2237 7.660030 CATATTTTGGACTGAAAGGGGTATT 57.340 36.000 0.00 0.00 39.30 1.89
1988 2238 8.760980 CATATTTTGGACTGAAAGGGGTATTA 57.239 34.615 0.00 0.00 39.30 0.98
1989 2239 9.196139 CATATTTTGGACTGAAAGGGGTATTAA 57.804 33.333 0.00 0.00 39.30 1.40
1990 2240 9.777008 ATATTTTGGACTGAAAGGGGTATTAAA 57.223 29.630 0.00 0.00 39.30 1.52
1991 2241 8.679344 ATTTTGGACTGAAAGGGGTATTAAAT 57.321 30.769 0.00 0.00 39.30 1.40
1992 2242 7.475137 TTTGGACTGAAAGGGGTATTAAATG 57.525 36.000 0.00 0.00 39.30 2.32
1993 2243 4.953579 TGGACTGAAAGGGGTATTAAATGC 59.046 41.667 0.00 0.00 39.30 3.56
1994 2244 5.201243 GGACTGAAAGGGGTATTAAATGCT 58.799 41.667 0.00 0.00 39.30 3.79
1995 2245 6.069323 TGGACTGAAAGGGGTATTAAATGCTA 60.069 38.462 0.00 0.00 39.30 3.49
1996 2246 6.831868 GGACTGAAAGGGGTATTAAATGCTAA 59.168 38.462 0.00 0.00 39.30 3.09
1997 2247 7.201794 GGACTGAAAGGGGTATTAAATGCTAAC 60.202 40.741 0.00 0.00 39.30 2.34
1998 2248 7.410991 ACTGAAAGGGGTATTAAATGCTAACT 58.589 34.615 0.00 0.00 39.30 2.24
1999 2249 7.893833 ACTGAAAGGGGTATTAAATGCTAACTT 59.106 33.333 0.00 0.00 39.30 2.66
2000 2250 9.403583 CTGAAAGGGGTATTAAATGCTAACTTA 57.596 33.333 0.00 0.00 0.00 2.24
2001 2251 9.403583 TGAAAGGGGTATTAAATGCTAACTTAG 57.596 33.333 0.00 0.00 0.00 2.18
2002 2252 9.623000 GAAAGGGGTATTAAATGCTAACTTAGA 57.377 33.333 0.00 0.00 0.00 2.10
2003 2253 8.975663 AAGGGGTATTAAATGCTAACTTAGAC 57.024 34.615 0.00 0.00 0.00 2.59
2004 2254 7.515586 AGGGGTATTAAATGCTAACTTAGACC 58.484 38.462 0.00 0.00 0.00 3.85
2005 2255 7.128263 AGGGGTATTAAATGCTAACTTAGACCA 59.872 37.037 0.00 0.00 0.00 4.02
2006 2256 7.228108 GGGGTATTAAATGCTAACTTAGACCAC 59.772 40.741 0.00 0.00 0.00 4.16
2007 2257 7.042254 GGGTATTAAATGCTAACTTAGACCACG 60.042 40.741 0.00 0.00 0.00 4.94
2008 2258 7.493645 GGTATTAAATGCTAACTTAGACCACGT 59.506 37.037 0.00 0.00 0.00 4.49
2009 2259 6.715344 TTAAATGCTAACTTAGACCACGTG 57.285 37.500 9.08 9.08 0.00 4.49
2010 2260 4.530710 AATGCTAACTTAGACCACGTGA 57.469 40.909 19.30 0.00 0.00 4.35
2011 2261 4.530710 ATGCTAACTTAGACCACGTGAA 57.469 40.909 19.30 1.68 0.00 3.18
2012 2262 3.909430 TGCTAACTTAGACCACGTGAAG 58.091 45.455 19.30 14.84 0.00 3.02
2013 2263 3.319972 TGCTAACTTAGACCACGTGAAGT 59.680 43.478 19.30 15.54 33.60 3.01
2014 2264 3.919197 GCTAACTTAGACCACGTGAAGTC 59.081 47.826 19.30 16.60 30.98 3.01
2015 2265 4.321082 GCTAACTTAGACCACGTGAAGTCT 60.321 45.833 24.51 24.51 45.20 3.24
2016 2266 5.106396 GCTAACTTAGACCACGTGAAGTCTA 60.106 44.000 22.87 22.87 43.09 2.59
2017 2267 5.979288 AACTTAGACCACGTGAAGTCTAT 57.021 39.130 25.51 14.88 43.30 1.98
2018 2268 5.564048 ACTTAGACCACGTGAAGTCTATC 57.436 43.478 25.51 10.24 43.30 2.08
2019 2269 4.094590 ACTTAGACCACGTGAAGTCTATCG 59.905 45.833 25.51 21.83 43.30 2.92
2020 2270 1.743958 AGACCACGTGAAGTCTATCGG 59.256 52.381 21.34 2.99 41.51 4.18
2021 2271 1.741706 GACCACGTGAAGTCTATCGGA 59.258 52.381 19.30 0.00 0.00 4.55
2022 2272 2.163010 GACCACGTGAAGTCTATCGGAA 59.837 50.000 19.30 0.00 0.00 4.30
2023 2273 2.559668 ACCACGTGAAGTCTATCGGAAA 59.440 45.455 19.30 0.00 0.00 3.13
2024 2274 3.194968 ACCACGTGAAGTCTATCGGAAAT 59.805 43.478 19.30 0.00 0.00 2.17
2025 2275 4.400251 ACCACGTGAAGTCTATCGGAAATA 59.600 41.667 19.30 0.00 0.00 1.40
2026 2276 4.976731 CCACGTGAAGTCTATCGGAAATAG 59.023 45.833 19.30 0.00 0.00 1.73
2027 2277 5.220989 CCACGTGAAGTCTATCGGAAATAGA 60.221 44.000 19.30 0.00 0.00 1.98
2028 2278 6.263344 CACGTGAAGTCTATCGGAAATAGAA 58.737 40.000 10.90 0.00 32.98 2.10
2029 2279 6.750501 CACGTGAAGTCTATCGGAAATAGAAA 59.249 38.462 10.90 0.00 32.98 2.52
2030 2280 7.435488 CACGTGAAGTCTATCGGAAATAGAAAT 59.565 37.037 10.90 0.00 32.98 2.17
2031 2281 8.627403 ACGTGAAGTCTATCGGAAATAGAAATA 58.373 33.333 0.00 0.00 32.98 1.40
2032 2282 9.119329 CGTGAAGTCTATCGGAAATAGAAATAG 57.881 37.037 0.00 0.00 32.98 1.73
2035 2285 9.628746 GAAGTCTATCGGAAATAGAAATAGACC 57.371 37.037 14.14 1.27 45.02 3.85
2036 2286 8.707796 AGTCTATCGGAAATAGAAATAGACCA 57.292 34.615 14.14 0.00 45.02 4.02
2037 2287 9.144298 AGTCTATCGGAAATAGAAATAGACCAA 57.856 33.333 14.14 0.00 45.02 3.67
2038 2288 9.413048 GTCTATCGGAAATAGAAATAGACCAAG 57.587 37.037 8.84 0.00 41.14 3.61
2039 2289 9.363401 TCTATCGGAAATAGAAATAGACCAAGA 57.637 33.333 0.00 0.00 0.00 3.02
2050 2300 8.753497 AGAAATAGACCAAGATAAATTGTCCC 57.247 34.615 0.00 0.00 0.00 4.46
2051 2301 8.560903 AGAAATAGACCAAGATAAATTGTCCCT 58.439 33.333 0.00 0.00 0.00 4.20
2052 2302 8.753497 AAATAGACCAAGATAAATTGTCCCTC 57.247 34.615 0.00 0.00 0.00 4.30
2053 2303 4.770795 AGACCAAGATAAATTGTCCCTCG 58.229 43.478 0.00 0.00 0.00 4.63
2054 2304 3.279434 ACCAAGATAAATTGTCCCTCGC 58.721 45.455 0.00 0.00 0.00 5.03
2055 2305 3.278574 CCAAGATAAATTGTCCCTCGCA 58.721 45.455 0.00 0.00 0.00 5.10
2056 2306 3.694072 CCAAGATAAATTGTCCCTCGCAA 59.306 43.478 0.00 0.00 0.00 4.85
2057 2307 4.157656 CCAAGATAAATTGTCCCTCGCAAA 59.842 41.667 0.00 0.00 0.00 3.68
2058 2308 4.965119 AGATAAATTGTCCCTCGCAAAC 57.035 40.909 0.00 0.00 0.00 2.93
2059 2309 3.694566 AGATAAATTGTCCCTCGCAAACC 59.305 43.478 0.00 0.00 0.00 3.27
2060 2310 1.698506 AAATTGTCCCTCGCAAACCA 58.301 45.000 0.00 0.00 0.00 3.67
2061 2311 1.698506 AATTGTCCCTCGCAAACCAA 58.301 45.000 0.00 0.00 0.00 3.67
2062 2312 1.923356 ATTGTCCCTCGCAAACCAAT 58.077 45.000 0.00 0.00 0.00 3.16
2063 2313 2.570415 TTGTCCCTCGCAAACCAATA 57.430 45.000 0.00 0.00 0.00 1.90
2064 2314 2.570415 TGTCCCTCGCAAACCAATAA 57.430 45.000 0.00 0.00 0.00 1.40
2065 2315 3.080300 TGTCCCTCGCAAACCAATAAT 57.920 42.857 0.00 0.00 0.00 1.28
2066 2316 2.752354 TGTCCCTCGCAAACCAATAATG 59.248 45.455 0.00 0.00 0.00 1.90
2067 2317 2.752903 GTCCCTCGCAAACCAATAATGT 59.247 45.455 0.00 0.00 0.00 2.71
2068 2318 3.192633 GTCCCTCGCAAACCAATAATGTT 59.807 43.478 0.00 0.00 0.00 2.71
2069 2319 4.396790 GTCCCTCGCAAACCAATAATGTTA 59.603 41.667 0.00 0.00 0.00 2.41
2070 2320 5.067283 GTCCCTCGCAAACCAATAATGTTAT 59.933 40.000 0.00 0.00 0.00 1.89
2071 2321 6.261381 GTCCCTCGCAAACCAATAATGTTATA 59.739 38.462 0.00 0.00 0.00 0.98
2072 2322 6.485313 TCCCTCGCAAACCAATAATGTTATAG 59.515 38.462 0.00 0.00 0.00 1.31
2073 2323 6.293955 CCCTCGCAAACCAATAATGTTATAGG 60.294 42.308 0.00 0.00 0.00 2.57
2074 2324 6.485313 CCTCGCAAACCAATAATGTTATAGGA 59.515 38.462 0.00 0.00 0.00 2.94
2075 2325 7.174946 CCTCGCAAACCAATAATGTTATAGGAT 59.825 37.037 0.00 0.00 0.00 3.24
2076 2326 8.458573 TCGCAAACCAATAATGTTATAGGATT 57.541 30.769 0.00 0.00 0.00 3.01
2077 2327 8.908903 TCGCAAACCAATAATGTTATAGGATTT 58.091 29.630 0.00 0.00 0.00 2.17
2078 2328 9.180678 CGCAAACCAATAATGTTATAGGATTTC 57.819 33.333 0.00 0.00 0.00 2.17
2079 2329 9.476202 GCAAACCAATAATGTTATAGGATTTCC 57.524 33.333 0.00 0.00 0.00 3.13
2080 2330 9.981114 CAAACCAATAATGTTATAGGATTTCCC 57.019 33.333 0.00 0.00 36.42 3.97
2081 2331 8.721133 AACCAATAATGTTATAGGATTTCCCC 57.279 34.615 0.00 0.00 36.42 4.81
2082 2332 7.246027 ACCAATAATGTTATAGGATTTCCCCC 58.754 38.462 0.00 0.00 36.42 5.40
2100 2350 2.304092 CCCCTACTATACGCACTGACA 58.696 52.381 0.00 0.00 0.00 3.58
2115 2365 4.216257 GCACTGACAATACATGGTCTGTTT 59.784 41.667 6.55 0.00 42.07 2.83
2135 2385 5.163488 TGTTTCTCACGTTCTCTTCTAACCA 60.163 40.000 0.00 0.00 0.00 3.67
2136 2386 5.723672 TTCTCACGTTCTCTTCTAACCAT 57.276 39.130 0.00 0.00 0.00 3.55
2137 2387 6.829229 TTCTCACGTTCTCTTCTAACCATA 57.171 37.500 0.00 0.00 0.00 2.74
2160 2410 6.825944 AACTGCTCCTAAAATTTTCTCCTC 57.174 37.500 6.72 0.00 0.00 3.71
2172 2422 7.617041 AAATTTTCTCCTCGGATTCTACAAG 57.383 36.000 0.00 0.00 0.00 3.16
2173 2423 4.737855 TTTCTCCTCGGATTCTACAAGG 57.262 45.455 0.00 0.00 0.00 3.61
2228 2478 9.665264 CCTTAAGCAAACTGTACTTTCTTTTAG 57.335 33.333 0.00 0.00 0.00 1.85
2234 2484 7.977293 GCAAACTGTACTTTCTTTTAGGGAAAA 59.023 33.333 0.00 0.00 33.17 2.29
2304 2557 2.734606 GCATTGTATAATAGTGCGCCGA 59.265 45.455 4.18 0.00 0.00 5.54
2305 2558 3.370978 GCATTGTATAATAGTGCGCCGAT 59.629 43.478 4.18 0.00 0.00 4.18
2306 2559 4.565166 GCATTGTATAATAGTGCGCCGATA 59.435 41.667 4.18 0.00 0.00 2.92
2307 2560 5.234329 GCATTGTATAATAGTGCGCCGATAT 59.766 40.000 4.18 0.00 0.00 1.63
2308 2561 6.238103 GCATTGTATAATAGTGCGCCGATATT 60.238 38.462 4.18 9.37 0.00 1.28
2309 2562 7.676338 GCATTGTATAATAGTGCGCCGATATTT 60.676 37.037 4.18 0.00 0.00 1.40
2310 2563 6.641176 TGTATAATAGTGCGCCGATATTTG 57.359 37.500 4.18 0.00 0.00 2.32
2311 2564 2.969443 AATAGTGCGCCGATATTTGC 57.031 45.000 4.18 0.00 0.00 3.68
2312 2565 2.169832 ATAGTGCGCCGATATTTGCT 57.830 45.000 4.18 0.00 0.00 3.91
2313 2566 1.217001 TAGTGCGCCGATATTTGCTG 58.783 50.000 4.18 0.00 0.00 4.41
2314 2567 0.461870 AGTGCGCCGATATTTGCTGA 60.462 50.000 4.18 0.00 0.00 4.26
2315 2568 0.041839 GTGCGCCGATATTTGCTGAG 60.042 55.000 4.18 0.00 0.00 3.35
2316 2569 0.461870 TGCGCCGATATTTGCTGAGT 60.462 50.000 4.18 0.00 0.00 3.41
2317 2570 0.657840 GCGCCGATATTTGCTGAGTT 59.342 50.000 0.00 0.00 0.00 3.01
2318 2571 1.064060 GCGCCGATATTTGCTGAGTTT 59.936 47.619 0.00 0.00 0.00 2.66
2319 2572 2.477863 GCGCCGATATTTGCTGAGTTTT 60.478 45.455 0.00 0.00 0.00 2.43
2320 2573 3.758300 CGCCGATATTTGCTGAGTTTTT 58.242 40.909 0.00 0.00 0.00 1.94
2346 2599 8.641499 TTTTTGAGACAACGATATTTGCTTTT 57.359 26.923 0.00 0.00 0.00 2.27
2347 2600 8.641499 TTTTGAGACAACGATATTTGCTTTTT 57.359 26.923 0.00 0.00 0.00 1.94
2370 2623 6.431198 TTTAGGGAAGACAACGATATTTGC 57.569 37.500 0.00 0.00 0.00 3.68
2371 2624 4.222124 AGGGAAGACAACGATATTTGCT 57.778 40.909 0.00 0.00 0.00 3.91
2372 2625 3.941483 AGGGAAGACAACGATATTTGCTG 59.059 43.478 0.00 0.00 0.00 4.41
2373 2626 3.938963 GGGAAGACAACGATATTTGCTGA 59.061 43.478 0.00 0.00 0.00 4.26
2374 2627 4.034510 GGGAAGACAACGATATTTGCTGAG 59.965 45.833 0.00 0.00 0.00 3.35
2375 2628 4.631813 GGAAGACAACGATATTTGCTGAGT 59.368 41.667 0.00 0.00 0.00 3.41
2376 2629 5.446473 GGAAGACAACGATATTTGCTGAGTG 60.446 44.000 0.00 0.00 0.00 3.51
2377 2630 3.935203 AGACAACGATATTTGCTGAGTGG 59.065 43.478 0.00 0.00 0.00 4.00
2378 2631 2.420022 ACAACGATATTTGCTGAGTGGC 59.580 45.455 0.00 0.00 0.00 5.01
2379 2632 2.679837 CAACGATATTTGCTGAGTGGCT 59.320 45.455 0.00 0.00 0.00 4.75
2380 2633 2.283298 ACGATATTTGCTGAGTGGCTG 58.717 47.619 0.00 0.00 0.00 4.85
2381 2634 2.093500 ACGATATTTGCTGAGTGGCTGA 60.093 45.455 0.00 0.00 0.00 4.26
2382 2635 3.136763 CGATATTTGCTGAGTGGCTGAT 58.863 45.455 0.00 0.00 0.00 2.90
2383 2636 3.186001 CGATATTTGCTGAGTGGCTGATC 59.814 47.826 0.00 0.00 0.00 2.92
2384 2637 2.803030 ATTTGCTGAGTGGCTGATCT 57.197 45.000 0.00 0.00 0.00 2.75
2385 2638 2.105006 TTTGCTGAGTGGCTGATCTC 57.895 50.000 0.00 0.00 0.00 2.75
2386 2639 0.978907 TTGCTGAGTGGCTGATCTCA 59.021 50.000 0.00 0.00 38.20 3.27
2387 2640 0.248565 TGCTGAGTGGCTGATCTCAC 59.751 55.000 0.00 0.42 36.04 3.51
2388 2641 0.248565 GCTGAGTGGCTGATCTCACA 59.751 55.000 13.78 0.00 36.04 3.58
2389 2642 1.134461 GCTGAGTGGCTGATCTCACAT 60.134 52.381 13.78 3.27 36.04 3.21
2390 2643 2.552031 CTGAGTGGCTGATCTCACATG 58.448 52.381 13.78 0.00 36.04 3.21
2391 2644 1.904537 TGAGTGGCTGATCTCACATGT 59.095 47.619 13.78 0.00 36.04 3.21
2392 2645 3.099141 TGAGTGGCTGATCTCACATGTA 58.901 45.455 0.00 0.00 36.04 2.29
2393 2646 3.708121 TGAGTGGCTGATCTCACATGTAT 59.292 43.478 0.00 0.00 36.04 2.29
2394 2647 4.895297 TGAGTGGCTGATCTCACATGTATA 59.105 41.667 0.00 0.00 36.04 1.47
2395 2648 5.541484 TGAGTGGCTGATCTCACATGTATAT 59.459 40.000 0.00 0.00 36.04 0.86
2396 2649 6.035368 AGTGGCTGATCTCACATGTATATC 57.965 41.667 0.00 2.72 36.43 1.63
2397 2650 4.861462 GTGGCTGATCTCACATGTATATCG 59.139 45.833 0.00 0.94 34.32 2.92
2398 2651 3.862267 GGCTGATCTCACATGTATATCGC 59.138 47.826 0.00 9.48 0.00 4.58
2399 2652 4.381398 GGCTGATCTCACATGTATATCGCT 60.381 45.833 0.00 0.00 0.00 4.93
2400 2653 5.163612 GGCTGATCTCACATGTATATCGCTA 60.164 44.000 0.00 0.00 0.00 4.26
2401 2654 6.460814 GGCTGATCTCACATGTATATCGCTAT 60.461 42.308 0.00 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 0.814457 TTCCTTTTGTGTGTTGCGCT 59.186 45.000 9.73 0.00 0.00 5.92
108 147 2.815158 TGTGTGACTCTACCTATGGCA 58.185 47.619 0.00 0.00 0.00 4.92
109 148 3.887621 TTGTGTGACTCTACCTATGGC 57.112 47.619 0.00 0.00 0.00 4.40
110 149 5.147330 TGTTTGTGTGACTCTACCTATGG 57.853 43.478 0.00 0.00 0.00 2.74
111 150 5.171476 CCTGTTTGTGTGACTCTACCTATG 58.829 45.833 0.00 0.00 0.00 2.23
202 246 0.538516 GGGTGTGTGTTGGCCATACA 60.539 55.000 16.84 16.84 42.17 2.29
353 401 8.380644 CGTATTCGTGTGAAATATTCAGAAAGT 58.619 33.333 0.00 0.00 41.01 2.66
389 437 4.282195 TGCCATAAAACTCGTTCCCAAATT 59.718 37.500 0.00 0.00 0.00 1.82
390 438 3.829601 TGCCATAAAACTCGTTCCCAAAT 59.170 39.130 0.00 0.00 0.00 2.32
391 439 3.004944 GTGCCATAAAACTCGTTCCCAAA 59.995 43.478 0.00 0.00 0.00 3.28
392 440 2.554893 GTGCCATAAAACTCGTTCCCAA 59.445 45.455 0.00 0.00 0.00 4.12
393 441 2.156098 GTGCCATAAAACTCGTTCCCA 58.844 47.619 0.00 0.00 0.00 4.37
394 442 2.095415 GTGTGCCATAAAACTCGTTCCC 60.095 50.000 0.00 0.00 0.00 3.97
395 443 2.812011 AGTGTGCCATAAAACTCGTTCC 59.188 45.455 0.00 0.00 0.00 3.62
460 508 1.617850 ACTCTCCTCGCATGATGATCC 59.382 52.381 0.00 0.00 0.00 3.36
486 534 5.986501 AACTCTTGTTGGTGTTTTGGTTA 57.013 34.783 0.00 0.00 34.71 2.85
512 560 6.878923 TCAGCGACAATTAATATATTGGAGGG 59.121 38.462 8.28 0.00 39.33 4.30
563 639 5.661056 TTTACACCACAAAATGTGTCCAA 57.339 34.783 9.42 0.00 46.45 3.53
565 641 6.310224 GCATATTTACACCACAAAATGTGTCC 59.690 38.462 9.42 0.00 46.45 4.02
655 731 0.317770 GCTCGATCTTCTCCTGCTCG 60.318 60.000 0.00 0.00 0.00 5.03
682 759 0.529378 CTCTTTGGCCCAGTTGCATC 59.471 55.000 0.00 0.00 0.00 3.91
822 900 4.263905 TGGGAGCATAAGGTCAAAACTGAT 60.264 41.667 0.00 0.00 43.97 2.90
844 922 7.524290 AGGGAGATGGGAATAATATGCATATG 58.476 38.462 19.77 0.00 0.00 1.78
845 923 7.351720 TGAGGGAGATGGGAATAATATGCATAT 59.648 37.037 13.63 13.63 0.00 1.78
846 924 6.677965 TGAGGGAGATGGGAATAATATGCATA 59.322 38.462 9.27 9.27 0.00 3.14
847 925 5.493613 TGAGGGAGATGGGAATAATATGCAT 59.506 40.000 3.79 3.79 0.00 3.96
848 926 4.851540 TGAGGGAGATGGGAATAATATGCA 59.148 41.667 0.00 0.00 0.00 3.96
849 927 5.045286 ACTGAGGGAGATGGGAATAATATGC 60.045 44.000 0.00 0.00 0.00 3.14
869 951 4.546829 ACTTATAGGCGGTCAAAACTGA 57.453 40.909 0.00 0.00 33.20 3.41
871 953 4.081309 TGCTACTTATAGGCGGTCAAAACT 60.081 41.667 0.00 0.00 0.00 2.66
872 954 4.033702 GTGCTACTTATAGGCGGTCAAAAC 59.966 45.833 0.00 0.00 0.00 2.43
873 955 4.186159 GTGCTACTTATAGGCGGTCAAAA 58.814 43.478 0.00 0.00 0.00 2.44
874 956 3.431207 GGTGCTACTTATAGGCGGTCAAA 60.431 47.826 0.00 0.00 0.00 2.69
875 957 2.101917 GGTGCTACTTATAGGCGGTCAA 59.898 50.000 0.00 0.00 0.00 3.18
909 1023 7.205515 AGATTGTTGAGGAATGAGGTAGAAT 57.794 36.000 0.00 0.00 0.00 2.40
935 1049 0.471617 AGCTATAGTTGGCTGCTGGG 59.528 55.000 0.84 0.00 38.40 4.45
1020 1164 3.530910 CTGTTTCGGCGTCCACCCT 62.531 63.158 6.85 0.00 0.00 4.34
1173 1320 3.554692 GCCTCGATGTTGGCGACG 61.555 66.667 0.00 0.00 39.71 5.12
1276 1428 0.250901 AGCACGCCCAAAGAAGATGT 60.251 50.000 0.00 0.00 0.00 3.06
1281 1433 0.250727 AAGCTAGCACGCCCAAAGAA 60.251 50.000 18.83 0.00 0.00 2.52
1286 1438 0.539518 TTGATAAGCTAGCACGCCCA 59.460 50.000 18.83 5.16 0.00 5.36
1296 1448 9.566432 ACAAGCTAGCTATTAATTTGATAAGCT 57.434 29.630 19.70 11.76 35.45 3.74
1302 1454 9.394767 TCATCAACAAGCTAGCTATTAATTTGA 57.605 29.630 19.70 18.30 0.00 2.69
1303 1455 9.443283 GTCATCAACAAGCTAGCTATTAATTTG 57.557 33.333 19.70 13.13 0.00 2.32
1304 1456 9.177608 TGTCATCAACAAGCTAGCTATTAATTT 57.822 29.630 19.70 0.00 34.03 1.82
1417 1652 4.393990 CGCACATGCTTCATATCCATGTAT 59.606 41.667 1.82 0.00 45.49 2.29
1583 1831 9.629878 AATCTGTACTGTACTAGCTACTATTGT 57.370 33.333 17.98 0.00 0.00 2.71
1620 1869 1.228894 AGAAGGAGGCAGACCGTCA 60.229 57.895 0.40 0.00 42.76 4.35
1623 1872 1.684049 AGGAGAAGGAGGCAGACCG 60.684 63.158 0.00 0.00 42.76 4.79
1628 1877 2.604686 ACGCAGGAGAAGGAGGCA 60.605 61.111 0.00 0.00 0.00 4.75
1630 1879 0.895530 TTACACGCAGGAGAAGGAGG 59.104 55.000 0.00 0.00 0.00 4.30
1643 1892 6.200286 ACATAAGGAATACTGCGAATTACACG 59.800 38.462 0.00 0.00 0.00 4.49
1650 1899 9.256477 CTACATTTACATAAGGAATACTGCGAA 57.744 33.333 0.00 0.00 0.00 4.70
1676 1925 8.294341 TGTATTTTGCTGTAGACGCTATAATC 57.706 34.615 0.00 0.00 0.00 1.75
1677 1926 7.926555 ACTGTATTTTGCTGTAGACGCTATAAT 59.073 33.333 0.00 0.00 0.00 1.28
1683 1932 4.863131 AGTACTGTATTTTGCTGTAGACGC 59.137 41.667 0.00 0.00 0.00 5.19
1689 1938 4.323562 GGAGGGAGTACTGTATTTTGCTGT 60.324 45.833 0.00 0.00 0.00 4.40
1698 1947 1.064240 TCGCATGGAGGGAGTACTGTA 60.064 52.381 0.00 0.00 34.74 2.74
1859 2109 9.120538 GGAGGAATTTACTGCATCTACAATAAA 57.879 33.333 0.00 0.00 0.00 1.40
1860 2110 7.441157 CGGAGGAATTTACTGCATCTACAATAA 59.559 37.037 0.78 0.00 0.00 1.40
1861 2111 6.929049 CGGAGGAATTTACTGCATCTACAATA 59.071 38.462 0.78 0.00 0.00 1.90
1862 2112 5.760253 CGGAGGAATTTACTGCATCTACAAT 59.240 40.000 0.78 0.00 0.00 2.71
1863 2113 5.116180 CGGAGGAATTTACTGCATCTACAA 58.884 41.667 0.78 0.00 0.00 2.41
1864 2114 4.161565 ACGGAGGAATTTACTGCATCTACA 59.838 41.667 0.78 0.00 0.00 2.74
1865 2115 4.694339 ACGGAGGAATTTACTGCATCTAC 58.306 43.478 0.78 0.00 0.00 2.59
1866 2116 4.404394 TGACGGAGGAATTTACTGCATCTA 59.596 41.667 0.78 0.00 0.00 1.98
1867 2117 3.197766 TGACGGAGGAATTTACTGCATCT 59.802 43.478 0.78 0.00 0.00 2.90
1868 2118 3.531538 TGACGGAGGAATTTACTGCATC 58.468 45.455 0.78 0.00 0.00 3.91
1869 2119 3.055094 ACTGACGGAGGAATTTACTGCAT 60.055 43.478 0.78 0.00 0.00 3.96
1870 2120 2.301870 ACTGACGGAGGAATTTACTGCA 59.698 45.455 0.78 0.00 0.00 4.41
1871 2121 2.973945 ACTGACGGAGGAATTTACTGC 58.026 47.619 0.00 0.00 0.00 4.40
1872 2122 4.994852 TCAAACTGACGGAGGAATTTACTG 59.005 41.667 0.00 0.00 0.00 2.74
1873 2123 5.223449 TCAAACTGACGGAGGAATTTACT 57.777 39.130 0.00 0.00 0.00 2.24
1874 2124 6.496338 AATCAAACTGACGGAGGAATTTAC 57.504 37.500 0.00 0.00 0.00 2.01
1875 2125 7.519032 AAAATCAAACTGACGGAGGAATTTA 57.481 32.000 0.00 0.00 0.00 1.40
1876 2126 6.405278 AAAATCAAACTGACGGAGGAATTT 57.595 33.333 0.00 0.00 0.00 1.82
1877 2127 6.405278 AAAAATCAAACTGACGGAGGAATT 57.595 33.333 0.00 0.00 0.00 2.17
1898 2148 8.729805 ATTTAATCAAACTTCACCTGCAAAAA 57.270 26.923 0.00 0.00 0.00 1.94
1899 2149 8.729805 AATTTAATCAAACTTCACCTGCAAAA 57.270 26.923 0.00 0.00 0.00 2.44
1900 2150 8.729805 AAATTTAATCAAACTTCACCTGCAAA 57.270 26.923 0.00 0.00 0.00 3.68
1901 2151 8.729805 AAAATTTAATCAAACTTCACCTGCAA 57.270 26.923 0.00 0.00 0.00 4.08
1902 2152 9.255304 GTAAAATTTAATCAAACTTCACCTGCA 57.745 29.630 0.00 0.00 0.00 4.41
1903 2153 9.255304 TGTAAAATTTAATCAAACTTCACCTGC 57.745 29.630 0.00 0.00 0.00 4.85
1920 2170 9.643693 CCATAGATGTCAAGCTTTGTAAAATTT 57.356 29.630 0.00 0.00 0.00 1.82
1921 2171 9.023962 TCCATAGATGTCAAGCTTTGTAAAATT 57.976 29.630 0.00 0.00 0.00 1.82
1922 2172 8.579850 TCCATAGATGTCAAGCTTTGTAAAAT 57.420 30.769 0.00 0.00 0.00 1.82
1923 2173 7.994425 TCCATAGATGTCAAGCTTTGTAAAA 57.006 32.000 0.00 0.00 0.00 1.52
1924 2174 7.994425 TTCCATAGATGTCAAGCTTTGTAAA 57.006 32.000 0.00 0.00 0.00 2.01
1925 2175 7.994425 TTTCCATAGATGTCAAGCTTTGTAA 57.006 32.000 0.00 0.00 0.00 2.41
1926 2176 7.994425 TTTTCCATAGATGTCAAGCTTTGTA 57.006 32.000 0.00 0.00 0.00 2.41
1927 2177 6.899393 TTTTCCATAGATGTCAAGCTTTGT 57.101 33.333 0.00 0.00 0.00 2.83
1928 2178 8.248945 AGATTTTTCCATAGATGTCAAGCTTTG 58.751 33.333 0.00 0.00 0.00 2.77
1929 2179 8.358582 AGATTTTTCCATAGATGTCAAGCTTT 57.641 30.769 0.00 0.00 0.00 3.51
1930 2180 7.951347 AGATTTTTCCATAGATGTCAAGCTT 57.049 32.000 0.00 0.00 0.00 3.74
1937 2187 9.678260 GGAGCATATAGATTTTTCCATAGATGT 57.322 33.333 0.00 0.00 0.00 3.06
1938 2188 9.676861 TGGAGCATATAGATTTTTCCATAGATG 57.323 33.333 0.00 0.00 0.00 2.90
1963 2213 7.660030 AATACCCCTTTCAGTCCAAAATATG 57.340 36.000 0.00 0.00 0.00 1.78
1964 2214 9.777008 TTTAATACCCCTTTCAGTCCAAAATAT 57.223 29.630 0.00 0.00 0.00 1.28
1965 2215 9.777008 ATTTAATACCCCTTTCAGTCCAAAATA 57.223 29.630 0.00 0.00 0.00 1.40
1966 2216 8.539544 CATTTAATACCCCTTTCAGTCCAAAAT 58.460 33.333 0.00 0.00 0.00 1.82
1967 2217 7.526359 GCATTTAATACCCCTTTCAGTCCAAAA 60.526 37.037 0.00 0.00 0.00 2.44
1968 2218 6.071051 GCATTTAATACCCCTTTCAGTCCAAA 60.071 38.462 0.00 0.00 0.00 3.28
1969 2219 5.420739 GCATTTAATACCCCTTTCAGTCCAA 59.579 40.000 0.00 0.00 0.00 3.53
1970 2220 4.953579 GCATTTAATACCCCTTTCAGTCCA 59.046 41.667 0.00 0.00 0.00 4.02
1971 2221 5.201243 AGCATTTAATACCCCTTTCAGTCC 58.799 41.667 0.00 0.00 0.00 3.85
1972 2222 7.556635 AGTTAGCATTTAATACCCCTTTCAGTC 59.443 37.037 0.00 0.00 0.00 3.51
1973 2223 7.410991 AGTTAGCATTTAATACCCCTTTCAGT 58.589 34.615 0.00 0.00 0.00 3.41
1974 2224 7.881775 AGTTAGCATTTAATACCCCTTTCAG 57.118 36.000 0.00 0.00 0.00 3.02
1975 2225 9.403583 CTAAGTTAGCATTTAATACCCCTTTCA 57.596 33.333 0.00 0.00 0.00 2.69
1976 2226 9.623000 TCTAAGTTAGCATTTAATACCCCTTTC 57.377 33.333 4.93 0.00 0.00 2.62
1977 2227 9.404848 GTCTAAGTTAGCATTTAATACCCCTTT 57.595 33.333 4.93 0.00 0.00 3.11
1978 2228 7.997223 GGTCTAAGTTAGCATTTAATACCCCTT 59.003 37.037 4.93 0.00 0.00 3.95
1979 2229 7.128263 TGGTCTAAGTTAGCATTTAATACCCCT 59.872 37.037 4.93 0.00 0.00 4.79
1980 2230 7.228108 GTGGTCTAAGTTAGCATTTAATACCCC 59.772 40.741 4.93 0.00 0.00 4.95
1981 2231 7.042254 CGTGGTCTAAGTTAGCATTTAATACCC 60.042 40.741 4.93 0.14 0.00 3.69
1982 2232 7.493645 ACGTGGTCTAAGTTAGCATTTAATACC 59.506 37.037 4.93 5.74 0.00 2.73
1983 2233 8.325997 CACGTGGTCTAAGTTAGCATTTAATAC 58.674 37.037 7.95 0.00 0.00 1.89
1984 2234 8.252417 TCACGTGGTCTAAGTTAGCATTTAATA 58.748 33.333 17.00 0.00 0.00 0.98
1985 2235 7.101054 TCACGTGGTCTAAGTTAGCATTTAAT 58.899 34.615 17.00 0.00 0.00 1.40
1986 2236 6.457355 TCACGTGGTCTAAGTTAGCATTTAA 58.543 36.000 17.00 0.00 0.00 1.52
1987 2237 6.028146 TCACGTGGTCTAAGTTAGCATTTA 57.972 37.500 17.00 0.00 0.00 1.40
1988 2238 4.890088 TCACGTGGTCTAAGTTAGCATTT 58.110 39.130 17.00 0.00 0.00 2.32
1989 2239 4.530710 TCACGTGGTCTAAGTTAGCATT 57.469 40.909 17.00 0.00 0.00 3.56
1990 2240 4.021368 ACTTCACGTGGTCTAAGTTAGCAT 60.021 41.667 17.00 0.00 0.00 3.79
1991 2241 3.319972 ACTTCACGTGGTCTAAGTTAGCA 59.680 43.478 17.00 0.00 0.00 3.49
1992 2242 3.910648 ACTTCACGTGGTCTAAGTTAGC 58.089 45.455 17.00 0.91 0.00 3.09
1993 2243 5.373981 AGACTTCACGTGGTCTAAGTTAG 57.626 43.478 21.34 3.29 40.49 2.34
1994 2244 6.183360 CGATAGACTTCACGTGGTCTAAGTTA 60.183 42.308 27.39 17.92 44.68 2.24
1995 2245 5.391736 CGATAGACTTCACGTGGTCTAAGTT 60.392 44.000 27.39 17.19 44.68 2.66
1996 2246 4.094590 CGATAGACTTCACGTGGTCTAAGT 59.905 45.833 27.39 22.91 44.68 2.24
1997 2247 4.496010 CCGATAGACTTCACGTGGTCTAAG 60.496 50.000 27.39 23.65 44.68 2.18
1998 2248 3.376234 CCGATAGACTTCACGTGGTCTAA 59.624 47.826 27.39 16.67 44.68 2.10
1999 2249 2.941064 CCGATAGACTTCACGTGGTCTA 59.059 50.000 26.45 26.45 45.29 2.59
2000 2250 1.743958 CCGATAGACTTCACGTGGTCT 59.256 52.381 24.51 24.51 43.93 3.85
2001 2251 1.741706 TCCGATAGACTTCACGTGGTC 59.258 52.381 17.00 15.71 39.76 4.02
2002 2252 1.830279 TCCGATAGACTTCACGTGGT 58.170 50.000 17.00 6.42 39.76 4.16
2003 2253 2.933495 TTCCGATAGACTTCACGTGG 57.067 50.000 17.00 2.57 39.76 4.94
2004 2254 5.817988 TCTATTTCCGATAGACTTCACGTG 58.182 41.667 9.94 9.94 39.76 4.49
2005 2255 6.446781 TTCTATTTCCGATAGACTTCACGT 57.553 37.500 0.00 0.00 39.76 4.49
2006 2256 7.932120 ATTTCTATTTCCGATAGACTTCACG 57.068 36.000 0.00 0.00 39.76 4.35
2009 2259 9.628746 GGTCTATTTCTATTTCCGATAGACTTC 57.371 37.037 16.70 3.43 44.17 3.01
2010 2260 9.144298 TGGTCTATTTCTATTTCCGATAGACTT 57.856 33.333 16.70 0.00 44.17 3.01
2011 2261 8.707796 TGGTCTATTTCTATTTCCGATAGACT 57.292 34.615 16.70 0.00 44.17 3.24
2012 2262 9.413048 CTTGGTCTATTTCTATTTCCGATAGAC 57.587 37.037 11.45 11.45 44.08 2.59
2013 2263 9.363401 TCTTGGTCTATTTCTATTTCCGATAGA 57.637 33.333 0.00 0.00 39.76 1.98
2024 2274 9.847224 GGGACAATTTATCTTGGTCTATTTCTA 57.153 33.333 0.00 0.00 0.00 2.10
2025 2275 8.560903 AGGGACAATTTATCTTGGTCTATTTCT 58.439 33.333 0.00 0.00 0.00 2.52
2026 2276 8.753497 AGGGACAATTTATCTTGGTCTATTTC 57.247 34.615 0.00 0.00 0.00 2.17
2027 2277 7.499232 CGAGGGACAATTTATCTTGGTCTATTT 59.501 37.037 0.00 0.00 0.00 1.40
2028 2278 6.992715 CGAGGGACAATTTATCTTGGTCTATT 59.007 38.462 0.00 0.00 0.00 1.73
2029 2279 6.525629 CGAGGGACAATTTATCTTGGTCTAT 58.474 40.000 0.00 0.00 0.00 1.98
2030 2280 5.684030 GCGAGGGACAATTTATCTTGGTCTA 60.684 44.000 0.00 0.00 0.00 2.59
2031 2281 4.770795 CGAGGGACAATTTATCTTGGTCT 58.229 43.478 0.00 0.00 0.00 3.85
2032 2282 3.312697 GCGAGGGACAATTTATCTTGGTC 59.687 47.826 0.00 0.00 0.00 4.02
2033 2283 3.279434 GCGAGGGACAATTTATCTTGGT 58.721 45.455 0.00 0.00 0.00 3.67
2034 2284 3.278574 TGCGAGGGACAATTTATCTTGG 58.721 45.455 0.00 0.00 0.00 3.61
2035 2285 4.963276 TTGCGAGGGACAATTTATCTTG 57.037 40.909 0.00 0.00 0.00 3.02
2036 2286 4.157840 GGTTTGCGAGGGACAATTTATCTT 59.842 41.667 0.00 0.00 0.00 2.40
2037 2287 3.694566 GGTTTGCGAGGGACAATTTATCT 59.305 43.478 0.00 0.00 0.00 1.98
2038 2288 3.442273 TGGTTTGCGAGGGACAATTTATC 59.558 43.478 0.00 0.00 0.00 1.75
2039 2289 3.426615 TGGTTTGCGAGGGACAATTTAT 58.573 40.909 0.00 0.00 0.00 1.40
2040 2290 2.865079 TGGTTTGCGAGGGACAATTTA 58.135 42.857 0.00 0.00 0.00 1.40
2041 2291 1.698506 TGGTTTGCGAGGGACAATTT 58.301 45.000 0.00 0.00 0.00 1.82
2042 2292 1.698506 TTGGTTTGCGAGGGACAATT 58.301 45.000 0.00 0.00 0.00 2.32
2043 2293 1.923356 ATTGGTTTGCGAGGGACAAT 58.077 45.000 0.00 0.00 0.00 2.71
2044 2294 2.570415 TATTGGTTTGCGAGGGACAA 57.430 45.000 0.00 0.00 0.00 3.18
2045 2295 2.570415 TTATTGGTTTGCGAGGGACA 57.430 45.000 0.00 0.00 0.00 4.02
2046 2296 2.752903 ACATTATTGGTTTGCGAGGGAC 59.247 45.455 0.00 0.00 0.00 4.46
2047 2297 3.080300 ACATTATTGGTTTGCGAGGGA 57.920 42.857 0.00 0.00 0.00 4.20
2048 2298 3.866883 AACATTATTGGTTTGCGAGGG 57.133 42.857 0.00 0.00 0.00 4.30
2049 2299 6.485313 TCCTATAACATTATTGGTTTGCGAGG 59.515 38.462 10.61 0.41 37.33 4.63
2050 2300 7.490962 TCCTATAACATTATTGGTTTGCGAG 57.509 36.000 10.61 0.00 37.33 5.03
2051 2301 8.458573 AATCCTATAACATTATTGGTTTGCGA 57.541 30.769 10.61 0.00 37.33 5.10
2052 2302 9.180678 GAAATCCTATAACATTATTGGTTTGCG 57.819 33.333 10.61 0.00 37.33 4.85
2053 2303 9.476202 GGAAATCCTATAACATTATTGGTTTGC 57.524 33.333 10.61 11.07 37.33 3.68
2054 2304 9.981114 GGGAAATCCTATAACATTATTGGTTTG 57.019 33.333 10.61 0.00 37.33 2.93
2055 2305 9.154632 GGGGAAATCCTATAACATTATTGGTTT 57.845 33.333 10.61 10.16 37.33 3.27
2056 2306 7.733047 GGGGGAAATCCTATAACATTATTGGTT 59.267 37.037 10.61 2.25 37.33 3.67
2057 2307 7.246027 GGGGGAAATCCTATAACATTATTGGT 58.754 38.462 10.61 0.00 37.33 3.67
2058 2308 7.718334 GGGGGAAATCCTATAACATTATTGG 57.282 40.000 5.93 5.93 37.37 3.16
2079 2329 1.612463 GTCAGTGCGTATAGTAGGGGG 59.388 57.143 0.00 0.00 0.00 5.40
2080 2330 2.304092 TGTCAGTGCGTATAGTAGGGG 58.696 52.381 0.00 0.00 0.00 4.79
2081 2331 4.585955 ATTGTCAGTGCGTATAGTAGGG 57.414 45.455 0.00 0.00 0.00 3.53
2082 2332 6.068473 TGTATTGTCAGTGCGTATAGTAGG 57.932 41.667 0.00 0.00 0.00 3.18
2083 2333 6.582672 CCATGTATTGTCAGTGCGTATAGTAG 59.417 42.308 0.00 0.00 0.00 2.57
2084 2334 6.040054 ACCATGTATTGTCAGTGCGTATAGTA 59.960 38.462 0.00 0.00 0.00 1.82
2085 2335 5.163447 ACCATGTATTGTCAGTGCGTATAGT 60.163 40.000 0.00 0.00 0.00 2.12
2086 2336 5.289595 ACCATGTATTGTCAGTGCGTATAG 58.710 41.667 0.00 0.00 0.00 1.31
2087 2337 5.068591 AGACCATGTATTGTCAGTGCGTATA 59.931 40.000 3.19 0.00 33.89 1.47
2088 2338 4.119862 GACCATGTATTGTCAGTGCGTAT 58.880 43.478 0.00 0.00 0.00 3.06
2089 2339 3.194755 AGACCATGTATTGTCAGTGCGTA 59.805 43.478 3.19 0.00 33.89 4.42
2100 2350 4.894784 ACGTGAGAAACAGACCATGTATT 58.105 39.130 0.00 0.00 43.00 1.89
2115 2365 6.433404 AGTTATGGTTAGAAGAGAACGTGAGA 59.567 38.462 0.00 0.00 0.00 3.27
2135 2385 7.281100 CGAGGAGAAAATTTTAGGAGCAGTTAT 59.719 37.037 2.75 0.00 0.00 1.89
2136 2386 6.594159 CGAGGAGAAAATTTTAGGAGCAGTTA 59.406 38.462 2.75 0.00 0.00 2.24
2137 2387 5.412904 CGAGGAGAAAATTTTAGGAGCAGTT 59.587 40.000 2.75 0.00 0.00 3.16
2160 2410 0.106894 GAGGCCCCTTGTAGAATCCG 59.893 60.000 0.00 0.00 0.00 4.18
2172 2422 4.139234 GACGTACGTGGAGGCCCC 62.139 72.222 28.16 4.50 0.00 5.80
2173 2423 3.066814 AGACGTACGTGGAGGCCC 61.067 66.667 28.16 9.39 0.00 5.80
2254 2507 8.946085 CACATAAATACAACTTTCTTGCCTCTA 58.054 33.333 0.00 0.00 0.00 2.43
2274 2527 8.921670 CGCACTATTATACAATGCTACACATAA 58.078 33.333 0.00 0.00 38.34 1.90
2321 2574 8.641499 AAAAGCAAATATCGTTGTCTCAAAAA 57.359 26.923 0.00 0.00 0.00 1.94
2322 2575 8.641499 AAAAAGCAAATATCGTTGTCTCAAAA 57.359 26.923 0.00 0.00 0.00 2.44
2345 2598 7.175990 AGCAAATATCGTTGTCTTCCCTAAAAA 59.824 33.333 0.00 0.00 0.00 1.94
2346 2599 6.657541 AGCAAATATCGTTGTCTTCCCTAAAA 59.342 34.615 0.00 0.00 0.00 1.52
2347 2600 6.093495 CAGCAAATATCGTTGTCTTCCCTAAA 59.907 38.462 0.00 0.00 0.00 1.85
2348 2601 5.584649 CAGCAAATATCGTTGTCTTCCCTAA 59.415 40.000 0.00 0.00 0.00 2.69
2349 2602 5.105106 TCAGCAAATATCGTTGTCTTCCCTA 60.105 40.000 0.00 0.00 0.00 3.53
2350 2603 3.941483 CAGCAAATATCGTTGTCTTCCCT 59.059 43.478 0.00 0.00 0.00 4.20
2351 2604 3.938963 TCAGCAAATATCGTTGTCTTCCC 59.061 43.478 0.00 0.00 0.00 3.97
2352 2605 4.631813 ACTCAGCAAATATCGTTGTCTTCC 59.368 41.667 0.00 0.00 0.00 3.46
2353 2606 5.446473 CCACTCAGCAAATATCGTTGTCTTC 60.446 44.000 0.00 0.00 0.00 2.87
2354 2607 4.393062 CCACTCAGCAAATATCGTTGTCTT 59.607 41.667 0.00 0.00 0.00 3.01
2355 2608 3.935203 CCACTCAGCAAATATCGTTGTCT 59.065 43.478 0.00 0.00 0.00 3.41
2356 2609 3.485877 GCCACTCAGCAAATATCGTTGTC 60.486 47.826 0.00 0.00 0.00 3.18
2357 2610 2.420022 GCCACTCAGCAAATATCGTTGT 59.580 45.455 0.00 0.00 0.00 3.32
2358 2611 2.679837 AGCCACTCAGCAAATATCGTTG 59.320 45.455 0.00 0.00 34.23 4.10
2359 2612 2.679837 CAGCCACTCAGCAAATATCGTT 59.320 45.455 0.00 0.00 34.23 3.85
2360 2613 2.093500 TCAGCCACTCAGCAAATATCGT 60.093 45.455 0.00 0.00 34.23 3.73
2361 2614 2.554142 TCAGCCACTCAGCAAATATCG 58.446 47.619 0.00 0.00 34.23 2.92
2362 2615 4.387598 AGATCAGCCACTCAGCAAATATC 58.612 43.478 0.00 0.00 34.23 1.63
2363 2616 4.141551 TGAGATCAGCCACTCAGCAAATAT 60.142 41.667 0.00 0.00 38.08 1.28
2364 2617 3.198417 TGAGATCAGCCACTCAGCAAATA 59.802 43.478 0.00 0.00 38.08 1.40
2365 2618 2.026542 TGAGATCAGCCACTCAGCAAAT 60.027 45.455 0.00 0.00 38.08 2.32
2366 2619 1.348696 TGAGATCAGCCACTCAGCAAA 59.651 47.619 0.00 0.00 38.08 3.68
2367 2620 0.978907 TGAGATCAGCCACTCAGCAA 59.021 50.000 0.00 0.00 38.08 3.91
2368 2621 0.248565 GTGAGATCAGCCACTCAGCA 59.751 55.000 0.00 0.00 42.56 4.41
2369 2622 0.248565 TGTGAGATCAGCCACTCAGC 59.751 55.000 12.12 0.00 42.56 4.26
2370 2623 2.093606 ACATGTGAGATCAGCCACTCAG 60.094 50.000 0.00 6.46 42.56 3.35
2371 2624 1.904537 ACATGTGAGATCAGCCACTCA 59.095 47.619 0.00 0.00 40.22 3.41
2372 2625 2.687700 ACATGTGAGATCAGCCACTC 57.312 50.000 0.00 0.00 34.57 3.51
2373 2626 5.336293 CGATATACATGTGAGATCAGCCACT 60.336 44.000 9.11 0.00 34.57 4.00
2374 2627 4.861462 CGATATACATGTGAGATCAGCCAC 59.139 45.833 9.11 0.68 0.00 5.01
2375 2628 4.619160 GCGATATACATGTGAGATCAGCCA 60.619 45.833 9.11 0.00 0.00 4.75
2376 2629 3.862267 GCGATATACATGTGAGATCAGCC 59.138 47.826 9.11 0.00 0.00 4.85
2377 2630 4.742417 AGCGATATACATGTGAGATCAGC 58.258 43.478 9.11 14.15 0.00 4.26


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

AutoCloner maintained by Alex Coulton.