Multiple sequence alignment - TraesCS3D01G074000

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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 TraesCS3D01G074000 chr3D 100.000 2276 0 0 1 2276 34051688 34053963 0.000000e+00 4204
1 TraesCS3D01G074000 chr3D 92.567 713 48 3 1563 2275 482292440 482291733 0.000000e+00 1018
2 TraesCS3D01G074000 chr3D 91.457 714 56 3 1563 2275 354661189 354661898 0.000000e+00 976
3 TraesCS3D01G074000 chr3B 90.658 1306 116 5 1 1304 97721842 97720541 0.000000e+00 1731
4 TraesCS3D01G074000 chr3B 88.718 1303 147 0 2 1304 70426609 70425307 0.000000e+00 1592
5 TraesCS3D01G074000 chr3B 76.186 1138 249 18 170 1302 485443531 485442411 4.210000e-162 580
6 TraesCS3D01G074000 chr3B 96.899 258 7 1 1305 1562 57223854 57223598 4.490000e-117 431
7 TraesCS3D01G074000 chr3B 90.310 258 7 2 1305 1562 57252977 57252738 2.820000e-84 322
8 TraesCS3D01G074000 chr7A 90.590 1254 117 1 58 1310 724151595 724150342 0.000000e+00 1661
9 TraesCS3D01G074000 chr6B 88.795 1303 143 3 2 1303 127683626 127684926 0.000000e+00 1594
10 TraesCS3D01G074000 chr4A 89.172 1256 132 3 2 1255 632212406 632211153 0.000000e+00 1563
11 TraesCS3D01G074000 chr4A 78.765 1182 239 12 128 1303 285950199 285949024 0.000000e+00 782
12 TraesCS3D01G074000 chr6D 92.857 714 48 1 1563 2276 153893923 153893213 0.000000e+00 1033
13 TraesCS3D01G074000 chr6D 91.469 715 57 2 1562 2276 65654143 65654853 0.000000e+00 979
14 TraesCS3D01G074000 chr1D 92.017 714 54 1 1563 2276 294977249 294977959 0.000000e+00 1000
15 TraesCS3D01G074000 chr2D 91.888 715 53 2 1563 2276 109398917 109399627 0.000000e+00 994
16 TraesCS3D01G074000 chr2D 91.329 715 58 2 1563 2276 327675916 327676627 0.000000e+00 974
17 TraesCS3D01G074000 chr4D 91.585 713 56 2 1563 2275 354221934 354222642 0.000000e+00 981
18 TraesCS3D01G074000 chr7D 91.457 714 57 2 1563 2276 511293606 511294315 0.000000e+00 977
19 TraesCS3D01G074000 chr1B 89.706 748 73 3 557 1302 564885629 564886374 0.000000e+00 952
20 TraesCS3D01G074000 chr1B 77.390 1318 280 18 1 1309 487940105 487941413 0.000000e+00 767
21 TraesCS3D01G074000 chr1B 89.435 549 57 1 1 549 564884406 564884953 0.000000e+00 691
22 TraesCS3D01G074000 chr3A 77.938 1319 264 26 1 1305 440509551 440510856 0.000000e+00 798
23 TraesCS3D01G074000 chr2A 77.460 559 122 4 17 573 550183947 550184503 4.690000e-87 331
24 TraesCS3D01G074000 chrUn 97.333 75 2 0 1488 1562 379858358 379858432 6.600000e-26 128


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 TraesCS3D01G074000 chr3D 34051688 34053963 2275 False 4204.0 4204 100.0000 1 2276 1 chr3D.!!$F1 2275
1 TraesCS3D01G074000 chr3D 482291733 482292440 707 True 1018.0 1018 92.5670 1563 2275 1 chr3D.!!$R1 712
2 TraesCS3D01G074000 chr3D 354661189 354661898 709 False 976.0 976 91.4570 1563 2275 1 chr3D.!!$F2 712
3 TraesCS3D01G074000 chr3B 97720541 97721842 1301 True 1731.0 1731 90.6580 1 1304 1 chr3B.!!$R4 1303
4 TraesCS3D01G074000 chr3B 70425307 70426609 1302 True 1592.0 1592 88.7180 2 1304 1 chr3B.!!$R3 1302
5 TraesCS3D01G074000 chr3B 485442411 485443531 1120 True 580.0 580 76.1860 170 1302 1 chr3B.!!$R5 1132
6 TraesCS3D01G074000 chr7A 724150342 724151595 1253 True 1661.0 1661 90.5900 58 1310 1 chr7A.!!$R1 1252
7 TraesCS3D01G074000 chr6B 127683626 127684926 1300 False 1594.0 1594 88.7950 2 1303 1 chr6B.!!$F1 1301
8 TraesCS3D01G074000 chr4A 632211153 632212406 1253 True 1563.0 1563 89.1720 2 1255 1 chr4A.!!$R2 1253
9 TraesCS3D01G074000 chr4A 285949024 285950199 1175 True 782.0 782 78.7650 128 1303 1 chr4A.!!$R1 1175
10 TraesCS3D01G074000 chr6D 153893213 153893923 710 True 1033.0 1033 92.8570 1563 2276 1 chr6D.!!$R1 713
11 TraesCS3D01G074000 chr6D 65654143 65654853 710 False 979.0 979 91.4690 1562 2276 1 chr6D.!!$F1 714
12 TraesCS3D01G074000 chr1D 294977249 294977959 710 False 1000.0 1000 92.0170 1563 2276 1 chr1D.!!$F1 713
13 TraesCS3D01G074000 chr2D 109398917 109399627 710 False 994.0 994 91.8880 1563 2276 1 chr2D.!!$F1 713
14 TraesCS3D01G074000 chr2D 327675916 327676627 711 False 974.0 974 91.3290 1563 2276 1 chr2D.!!$F2 713
15 TraesCS3D01G074000 chr4D 354221934 354222642 708 False 981.0 981 91.5850 1563 2275 1 chr4D.!!$F1 712
16 TraesCS3D01G074000 chr7D 511293606 511294315 709 False 977.0 977 91.4570 1563 2276 1 chr7D.!!$F1 713
17 TraesCS3D01G074000 chr1B 564884406 564886374 1968 False 821.5 952 89.5705 1 1302 2 chr1B.!!$F2 1301
18 TraesCS3D01G074000 chr1B 487940105 487941413 1308 False 767.0 767 77.3900 1 1309 1 chr1B.!!$F1 1308
19 TraesCS3D01G074000 chr3A 440509551 440510856 1305 False 798.0 798 77.9380 1 1305 1 chr3A.!!$F1 1304
20 TraesCS3D01G074000 chr2A 550183947 550184503 556 False 331.0 331 77.4600 17 573 1 chr2A.!!$F1 556

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
642 1313 0.24912 TGGTCTCTGTTATGTGGGCG 59.751 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 2216 0.177836 TGCGGGTCCATGTATCACTG 59.822 55.0 0.0 0.0 0.0 3.66 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
122 123 1.416401 ACTGATCCGGTCTGTGTTTGT 59.584 47.619 0.00 0.00 37.58 2.83
258 260 1.895798 TCTCTGGTGACTCGCAAAGAT 59.104 47.619 0.00 0.00 0.00 2.40
270 273 3.974912 TCGCAAAGATCATCTAGCTCTG 58.025 45.455 9.60 0.00 0.00 3.35
357 360 1.594021 GGTTTTGCCAAAGGTGCGG 60.594 57.895 0.00 0.00 37.17 5.69
484 487 3.008375 TGAGGATCTTATGCATGCCCTAC 59.992 47.826 16.68 7.19 34.92 3.18
642 1313 0.249120 TGGTCTCTGTTATGTGGGCG 59.751 55.000 0.00 0.00 0.00 6.13
649 1320 2.703536 TCTGTTATGTGGGCGATATGGT 59.296 45.455 0.00 0.00 0.00 3.55
718 1389 0.718343 GTCAGTTCAGCGCATCAGAC 59.282 55.000 11.47 6.06 0.00 3.51
753 1424 3.118629 TGCTGGATATTCCACTGTCTCAC 60.119 47.826 0.00 0.00 42.67 3.51
766 1437 1.014352 GTCTCACGCTTTGGTGTTGT 58.986 50.000 0.00 0.00 39.00 3.32
851 1522 1.285280 ATGGATTCCGACAAGGTGGA 58.715 50.000 0.00 0.00 41.99 4.02
874 1545 1.577328 GGGTGGTGTTGCACGATCTG 61.577 60.000 0.00 0.00 34.83 2.90
980 1651 7.394077 TGATGGAGTGATTTTTGCTAATCTTCA 59.606 33.333 0.00 0.00 35.89 3.02
1007 1678 7.012704 CGGTTTCTCTCATGTGATTATGGAAAT 59.987 37.037 10.46 0.00 0.00 2.17
1151 1822 5.804639 TGTTTGTAGATCAGCCAATGTACT 58.195 37.500 0.00 0.00 0.00 2.73
1318 1990 2.168201 AAAAAGTTGTCGTGTGTCGC 57.832 45.000 0.00 0.00 39.67 5.19
1319 1991 0.025770 AAAAGTTGTCGTGTGTCGCG 59.974 50.000 0.00 0.00 39.67 5.87
1320 1992 1.079875 AAAGTTGTCGTGTGTCGCGT 61.080 50.000 5.77 0.00 38.57 6.01
1321 1993 1.079875 AAGTTGTCGTGTGTCGCGTT 61.080 50.000 5.77 0.00 38.57 4.84
1322 1994 0.248580 AGTTGTCGTGTGTCGCGTTA 60.249 50.000 5.77 0.00 38.57 3.18
1323 1995 0.158096 GTTGTCGTGTGTCGCGTTAG 59.842 55.000 5.77 0.00 38.57 2.34
1324 1996 0.248580 TTGTCGTGTGTCGCGTTAGT 60.249 50.000 5.77 0.00 38.57 2.24
1325 1997 0.658244 TGTCGTGTGTCGCGTTAGTC 60.658 55.000 5.77 0.00 38.57 2.59
1326 1998 0.385223 GTCGTGTGTCGCGTTAGTCT 60.385 55.000 5.77 0.00 38.57 3.24
1327 1999 0.308684 TCGTGTGTCGCGTTAGTCTT 59.691 50.000 5.77 0.00 38.57 3.01
1328 2000 1.530720 TCGTGTGTCGCGTTAGTCTTA 59.469 47.619 5.77 0.00 38.57 2.10
1329 2001 1.640915 CGTGTGTCGCGTTAGTCTTAC 59.359 52.381 5.77 0.00 32.40 2.34
1330 2002 2.663879 CGTGTGTCGCGTTAGTCTTACT 60.664 50.000 5.77 0.00 32.40 2.24
1331 2003 2.907392 GTGTGTCGCGTTAGTCTTACTC 59.093 50.000 5.77 0.00 0.00 2.59
1332 2004 2.164427 GTGTCGCGTTAGTCTTACTCG 58.836 52.381 5.77 0.00 0.00 4.18
1333 2005 1.129251 TGTCGCGTTAGTCTTACTCGG 59.871 52.381 5.77 0.00 0.00 4.63
1334 2006 1.129437 GTCGCGTTAGTCTTACTCGGT 59.871 52.381 5.77 0.00 0.00 4.69
1335 2007 1.806542 TCGCGTTAGTCTTACTCGGTT 59.193 47.619 5.77 0.00 0.00 4.44
1336 2008 2.226437 TCGCGTTAGTCTTACTCGGTTT 59.774 45.455 5.77 0.00 0.00 3.27
1337 2009 3.435327 TCGCGTTAGTCTTACTCGGTTTA 59.565 43.478 5.77 0.00 0.00 2.01
1338 2010 3.539954 CGCGTTAGTCTTACTCGGTTTAC 59.460 47.826 0.00 0.00 0.00 2.01
1339 2011 3.539954 GCGTTAGTCTTACTCGGTTTACG 59.460 47.826 0.00 0.00 46.11 3.18
1340 2012 4.712763 CGTTAGTCTTACTCGGTTTACGT 58.287 43.478 0.00 0.00 44.69 3.57
1341 2013 4.551126 CGTTAGTCTTACTCGGTTTACGTG 59.449 45.833 0.00 0.00 44.69 4.49
1343 2015 4.574599 AGTCTTACTCGGTTTACGTGTT 57.425 40.909 0.00 0.00 45.96 3.32
1344 2016 5.689383 AGTCTTACTCGGTTTACGTGTTA 57.311 39.130 0.00 0.00 45.96 2.41
1345 2017 6.072112 AGTCTTACTCGGTTTACGTGTTAA 57.928 37.500 0.00 0.00 45.96 2.01
1346 2018 6.681777 AGTCTTACTCGGTTTACGTGTTAAT 58.318 36.000 0.00 0.00 45.96 1.40
1347 2019 7.816640 AGTCTTACTCGGTTTACGTGTTAATA 58.183 34.615 0.00 0.00 45.96 0.98
1348 2020 8.296713 AGTCTTACTCGGTTTACGTGTTAATAA 58.703 33.333 0.00 0.00 45.96 1.40
1349 2021 8.578769 GTCTTACTCGGTTTACGTGTTAATAAG 58.421 37.037 0.00 0.00 45.96 1.73
1350 2022 5.768333 ACTCGGTTTACGTGTTAATAAGC 57.232 39.130 0.00 0.00 45.96 3.09
1351 2023 4.627035 ACTCGGTTTACGTGTTAATAAGCC 59.373 41.667 0.00 0.00 45.96 4.35
1352 2024 3.915067 CGGTTTACGTGTTAATAAGCCG 58.085 45.455 7.26 7.26 44.86 5.52
1353 2025 3.367630 CGGTTTACGTGTTAATAAGCCGT 59.632 43.478 12.03 3.52 45.03 5.68
1354 2026 4.640956 GGTTTACGTGTTAATAAGCCGTG 58.359 43.478 0.00 0.00 33.32 4.94
1355 2027 4.388469 GGTTTACGTGTTAATAAGCCGTGA 59.612 41.667 0.00 0.00 33.32 4.35
1356 2028 5.107143 GGTTTACGTGTTAATAAGCCGTGAA 60.107 40.000 0.00 3.40 33.32 3.18
1357 2029 5.514059 TTACGTGTTAATAAGCCGTGAAC 57.486 39.130 0.00 0.00 33.32 3.18
1358 2030 2.738314 ACGTGTTAATAAGCCGTGAACC 59.262 45.455 0.00 0.00 0.00 3.62
1359 2031 2.094734 CGTGTTAATAAGCCGTGAACCC 59.905 50.000 0.00 0.00 0.00 4.11
1360 2032 2.094734 GTGTTAATAAGCCGTGAACCCG 59.905 50.000 0.00 0.00 0.00 5.28
1361 2033 2.289569 TGTTAATAAGCCGTGAACCCGT 60.290 45.455 0.00 0.00 0.00 5.28
1362 2034 2.012937 TAATAAGCCGTGAACCCGTG 57.987 50.000 0.00 0.00 0.00 4.94
1363 2035 0.035739 AATAAGCCGTGAACCCGTGT 59.964 50.000 0.00 0.00 0.00 4.49
1364 2036 0.035739 ATAAGCCGTGAACCCGTGTT 59.964 50.000 0.00 0.00 37.42 3.32
1365 2037 0.179051 TAAGCCGTGAACCCGTGTTT 60.179 50.000 0.00 0.00 33.97 2.83
1366 2038 1.033202 AAGCCGTGAACCCGTGTTTT 61.033 50.000 0.00 0.00 33.97 2.43
1367 2039 1.298788 GCCGTGAACCCGTGTTTTG 60.299 57.895 0.00 0.00 33.97 2.44
1368 2040 1.716826 GCCGTGAACCCGTGTTTTGA 61.717 55.000 0.00 0.00 33.97 2.69
1369 2041 0.948678 CCGTGAACCCGTGTTTTGAT 59.051 50.000 0.00 0.00 33.97 2.57
1370 2042 2.144730 CCGTGAACCCGTGTTTTGATA 58.855 47.619 0.00 0.00 33.97 2.15
1371 2043 2.096119 CCGTGAACCCGTGTTTTGATAC 60.096 50.000 0.00 0.00 33.97 2.24
1372 2044 2.803956 CGTGAACCCGTGTTTTGATACT 59.196 45.455 0.00 0.00 33.97 2.12
1373 2045 3.120786 CGTGAACCCGTGTTTTGATACTC 60.121 47.826 0.00 0.00 33.97 2.59
1374 2046 3.061322 TGAACCCGTGTTTTGATACTCG 58.939 45.455 0.00 0.00 33.97 4.18
1378 2050 2.409975 CCGTGTTTTGATACTCGGTGT 58.590 47.619 8.59 0.00 45.32 4.16
1379 2051 3.577667 CCGTGTTTTGATACTCGGTGTA 58.422 45.455 8.59 0.00 45.32 2.90
1380 2052 4.178540 CCGTGTTTTGATACTCGGTGTAT 58.821 43.478 8.59 2.57 45.32 2.29
1381 2053 4.032445 CCGTGTTTTGATACTCGGTGTATG 59.968 45.833 7.39 0.00 45.32 2.39
1382 2054 4.860352 CGTGTTTTGATACTCGGTGTATGA 59.140 41.667 7.39 0.00 41.55 2.15
1383 2055 5.220154 CGTGTTTTGATACTCGGTGTATGAC 60.220 44.000 7.39 2.87 41.55 3.06
1384 2056 5.867716 GTGTTTTGATACTCGGTGTATGACT 59.132 40.000 7.39 0.00 41.55 3.41
1385 2057 6.367969 GTGTTTTGATACTCGGTGTATGACTT 59.632 38.462 7.39 0.00 41.55 3.01
1386 2058 6.367695 TGTTTTGATACTCGGTGTATGACTTG 59.632 38.462 7.39 0.00 41.55 3.16
1387 2059 5.907866 TTGATACTCGGTGTATGACTTGA 57.092 39.130 7.39 0.00 41.55 3.02
1388 2060 6.465439 TTGATACTCGGTGTATGACTTGAT 57.535 37.500 7.39 0.00 41.55 2.57
1389 2061 7.576861 TTGATACTCGGTGTATGACTTGATA 57.423 36.000 7.39 0.00 41.55 2.15
1390 2062 6.967135 TGATACTCGGTGTATGACTTGATAC 58.033 40.000 7.39 0.00 41.55 2.24
1391 2063 6.771267 TGATACTCGGTGTATGACTTGATACT 59.229 38.462 7.39 0.00 41.55 2.12
1392 2064 7.935210 TGATACTCGGTGTATGACTTGATACTA 59.065 37.037 7.39 0.00 41.55 1.82
1393 2065 8.865420 ATACTCGGTGTATGACTTGATACTAT 57.135 34.615 2.15 0.00 40.12 2.12
1394 2066 6.971602 ACTCGGTGTATGACTTGATACTATG 58.028 40.000 0.00 0.00 31.15 2.23
1395 2067 6.546403 ACTCGGTGTATGACTTGATACTATGT 59.454 38.462 0.00 0.00 31.15 2.29
1396 2068 6.735130 TCGGTGTATGACTTGATACTATGTG 58.265 40.000 0.00 0.00 31.15 3.21
1397 2069 6.544564 TCGGTGTATGACTTGATACTATGTGA 59.455 38.462 0.00 0.00 31.15 3.58
1398 2070 6.637254 CGGTGTATGACTTGATACTATGTGAC 59.363 42.308 0.00 0.00 31.15 3.67
1399 2071 6.637254 GGTGTATGACTTGATACTATGTGACG 59.363 42.308 0.00 0.00 31.15 4.35
1400 2072 7.194278 GTGTATGACTTGATACTATGTGACGT 58.806 38.462 0.00 0.00 31.15 4.34
1401 2073 8.340443 GTGTATGACTTGATACTATGTGACGTA 58.660 37.037 0.00 0.00 31.15 3.57
1402 2074 9.063615 TGTATGACTTGATACTATGTGACGTAT 57.936 33.333 0.00 0.00 31.15 3.06
1403 2075 9.331106 GTATGACTTGATACTATGTGACGTATG 57.669 37.037 0.00 0.00 0.00 2.39
1404 2076 7.329588 TGACTTGATACTATGTGACGTATGT 57.670 36.000 0.00 0.00 0.00 2.29
1405 2077 7.768240 TGACTTGATACTATGTGACGTATGTT 58.232 34.615 0.00 0.00 0.00 2.71
1406 2078 8.248253 TGACTTGATACTATGTGACGTATGTTT 58.752 33.333 0.00 0.00 0.00 2.83
1407 2079 8.997621 ACTTGATACTATGTGACGTATGTTTT 57.002 30.769 0.00 0.00 0.00 2.43
1408 2080 9.431887 ACTTGATACTATGTGACGTATGTTTTT 57.568 29.630 0.00 0.00 0.00 1.94
1409 2081 9.901724 CTTGATACTATGTGACGTATGTTTTTC 57.098 33.333 0.00 0.00 0.00 2.29
1410 2082 9.647797 TTGATACTATGTGACGTATGTTTTTCT 57.352 29.630 0.00 0.00 0.00 2.52
1411 2083 9.647797 TGATACTATGTGACGTATGTTTTTCTT 57.352 29.630 0.00 0.00 0.00 2.52
1416 2088 9.702726 CTATGTGACGTATGTTTTTCTTAATGG 57.297 33.333 0.00 0.00 0.00 3.16
1417 2089 6.904498 TGTGACGTATGTTTTTCTTAATGGG 58.096 36.000 0.00 0.00 0.00 4.00
1418 2090 6.487331 TGTGACGTATGTTTTTCTTAATGGGT 59.513 34.615 0.00 0.00 0.00 4.51
1419 2091 6.799925 GTGACGTATGTTTTTCTTAATGGGTG 59.200 38.462 0.00 0.00 0.00 4.61
1420 2092 6.487331 TGACGTATGTTTTTCTTAATGGGTGT 59.513 34.615 0.00 0.00 0.00 4.16
1421 2093 7.660617 TGACGTATGTTTTTCTTAATGGGTGTA 59.339 33.333 0.00 0.00 0.00 2.90
1422 2094 8.036273 ACGTATGTTTTTCTTAATGGGTGTAG 57.964 34.615 0.00 0.00 0.00 2.74
1423 2095 7.879160 ACGTATGTTTTTCTTAATGGGTGTAGA 59.121 33.333 0.00 0.00 0.00 2.59
1424 2096 8.723311 CGTATGTTTTTCTTAATGGGTGTAGAA 58.277 33.333 0.00 0.00 0.00 2.10
1427 2099 9.758651 ATGTTTTTCTTAATGGGTGTAGAAAAC 57.241 29.630 0.00 0.00 42.82 2.43
1428 2100 8.750298 TGTTTTTCTTAATGGGTGTAGAAAACA 58.250 29.630 0.00 0.00 42.82 2.83
1429 2101 9.758651 GTTTTTCTTAATGGGTGTAGAAAACAT 57.241 29.630 0.00 0.00 42.82 2.71
1430 2102 9.757227 TTTTTCTTAATGGGTGTAGAAAACATG 57.243 29.630 0.00 0.00 42.82 3.21
1431 2103 8.698973 TTTCTTAATGGGTGTAGAAAACATGA 57.301 30.769 0.00 0.00 41.10 3.07
1432 2104 8.698973 TTCTTAATGGGTGTAGAAAACATGAA 57.301 30.769 0.00 0.00 41.10 2.57
1433 2105 8.335532 TCTTAATGGGTGTAGAAAACATGAAG 57.664 34.615 0.00 0.00 41.10 3.02
1434 2106 5.982890 AATGGGTGTAGAAAACATGAAGG 57.017 39.130 0.00 0.00 41.10 3.46
1435 2107 3.153919 TGGGTGTAGAAAACATGAAGGC 58.846 45.455 0.00 0.00 41.10 4.35
1436 2108 3.181434 TGGGTGTAGAAAACATGAAGGCT 60.181 43.478 0.00 0.00 41.10 4.58
1437 2109 4.042311 TGGGTGTAGAAAACATGAAGGCTA 59.958 41.667 0.00 0.00 41.10 3.93
1438 2110 4.636206 GGGTGTAGAAAACATGAAGGCTAG 59.364 45.833 0.00 0.00 41.10 3.42
1439 2111 5.488341 GGTGTAGAAAACATGAAGGCTAGA 58.512 41.667 0.00 0.00 41.10 2.43
1440 2112 6.116126 GGTGTAGAAAACATGAAGGCTAGAT 58.884 40.000 0.00 0.00 41.10 1.98
1441 2113 6.599638 GGTGTAGAAAACATGAAGGCTAGATT 59.400 38.462 0.00 0.00 41.10 2.40
1442 2114 7.121315 GGTGTAGAAAACATGAAGGCTAGATTT 59.879 37.037 0.00 0.00 41.10 2.17
1443 2115 8.515414 GTGTAGAAAACATGAAGGCTAGATTTT 58.485 33.333 0.00 0.00 41.10 1.82
1444 2116 8.730680 TGTAGAAAACATGAAGGCTAGATTTTC 58.269 33.333 0.00 2.05 35.69 2.29
1445 2117 8.951243 GTAGAAAACATGAAGGCTAGATTTTCT 58.049 33.333 19.63 19.63 43.59 2.52
1447 2119 8.951243 AGAAAACATGAAGGCTAGATTTTCTAC 58.049 33.333 16.65 0.54 41.00 2.59
1448 2120 7.631717 AAACATGAAGGCTAGATTTTCTACC 57.368 36.000 0.00 0.00 0.00 3.18
1449 2121 6.313519 ACATGAAGGCTAGATTTTCTACCA 57.686 37.500 0.00 0.00 0.00 3.25
1450 2122 6.904626 ACATGAAGGCTAGATTTTCTACCAT 58.095 36.000 0.00 0.00 0.00 3.55
1451 2123 6.769822 ACATGAAGGCTAGATTTTCTACCATG 59.230 38.462 0.00 0.00 0.00 3.66
1452 2124 5.126067 TGAAGGCTAGATTTTCTACCATGC 58.874 41.667 0.00 0.00 0.00 4.06
1453 2125 4.778213 AGGCTAGATTTTCTACCATGCA 57.222 40.909 0.00 0.00 0.00 3.96
1454 2126 4.455606 AGGCTAGATTTTCTACCATGCAC 58.544 43.478 0.00 0.00 0.00 4.57
1455 2127 4.080356 AGGCTAGATTTTCTACCATGCACA 60.080 41.667 0.00 0.00 0.00 4.57
1456 2128 4.274459 GGCTAGATTTTCTACCATGCACAG 59.726 45.833 0.00 0.00 0.00 3.66
1457 2129 4.274459 GCTAGATTTTCTACCATGCACAGG 59.726 45.833 5.50 5.50 0.00 4.00
1458 2130 4.574674 AGATTTTCTACCATGCACAGGA 57.425 40.909 13.62 0.00 0.00 3.86
1459 2131 4.521146 AGATTTTCTACCATGCACAGGAG 58.479 43.478 13.62 2.31 0.00 3.69
1460 2132 2.787473 TTTCTACCATGCACAGGAGG 57.213 50.000 13.62 2.05 0.00 4.30
1461 2133 1.656587 TTCTACCATGCACAGGAGGT 58.343 50.000 13.62 7.76 38.14 3.85
1462 2134 1.195115 TCTACCATGCACAGGAGGTC 58.805 55.000 13.62 0.00 35.62 3.85
1463 2135 0.179000 CTACCATGCACAGGAGGTCC 59.821 60.000 13.62 0.00 35.62 4.46
1464 2136 1.271840 TACCATGCACAGGAGGTCCC 61.272 60.000 13.62 0.00 35.62 4.46
1465 2137 2.124983 CATGCACAGGAGGTCCCG 60.125 66.667 0.00 0.00 40.87 5.14
1466 2138 2.607750 ATGCACAGGAGGTCCCGT 60.608 61.111 0.00 0.00 40.87 5.28
1467 2139 2.959484 ATGCACAGGAGGTCCCGTG 61.959 63.158 7.88 7.88 40.19 4.94
1469 2141 3.625897 CACAGGAGGTCCCGTGCA 61.626 66.667 0.00 0.00 40.87 4.57
1470 2142 2.607750 ACAGGAGGTCCCGTGCAT 60.608 61.111 0.00 0.00 40.87 3.96
1471 2143 2.124983 CAGGAGGTCCCGTGCATG 60.125 66.667 0.00 0.00 40.87 4.06
1472 2144 3.402681 AGGAGGTCCCGTGCATGG 61.403 66.667 18.73 18.73 40.87 3.66
1473 2145 3.717294 GGAGGTCCCGTGCATGGT 61.717 66.667 23.39 4.73 0.00 3.55
1474 2146 2.125106 GAGGTCCCGTGCATGGTC 60.125 66.667 23.39 15.16 0.00 4.02
1475 2147 3.682292 GAGGTCCCGTGCATGGTCC 62.682 68.421 23.39 22.42 0.00 4.46
1476 2148 4.028490 GGTCCCGTGCATGGTCCA 62.028 66.667 23.39 4.32 0.00 4.02
1477 2149 2.436646 GTCCCGTGCATGGTCCAG 60.437 66.667 23.39 8.35 0.00 3.86
1478 2150 2.927856 TCCCGTGCATGGTCCAGT 60.928 61.111 23.39 0.00 0.00 4.00
1479 2151 2.034066 CCCGTGCATGGTCCAGTT 59.966 61.111 23.39 0.00 0.00 3.16
1480 2152 1.195442 TCCCGTGCATGGTCCAGTTA 61.195 55.000 23.39 0.00 0.00 2.24
1481 2153 0.744414 CCCGTGCATGGTCCAGTTAG 60.744 60.000 23.39 1.68 0.00 2.34
1482 2154 1.369091 CCGTGCATGGTCCAGTTAGC 61.369 60.000 17.42 0.00 0.00 3.09
1483 2155 0.673333 CGTGCATGGTCCAGTTAGCA 60.673 55.000 0.00 2.34 0.00 3.49
1484 2156 0.804989 GTGCATGGTCCAGTTAGCAC 59.195 55.000 19.30 19.30 44.31 4.40
1485 2157 0.692476 TGCATGGTCCAGTTAGCACT 59.308 50.000 0.00 0.00 0.00 4.40
1486 2158 1.339055 TGCATGGTCCAGTTAGCACTC 60.339 52.381 0.00 0.00 0.00 3.51
1487 2159 1.065854 GCATGGTCCAGTTAGCACTCT 60.066 52.381 0.00 0.00 0.00 3.24
1488 2160 2.616510 GCATGGTCCAGTTAGCACTCTT 60.617 50.000 0.00 0.00 0.00 2.85
1489 2161 3.679389 CATGGTCCAGTTAGCACTCTTT 58.321 45.455 0.00 0.00 0.00 2.52
1490 2162 3.126001 TGGTCCAGTTAGCACTCTTTG 57.874 47.619 0.00 0.00 0.00 2.77
1491 2163 2.438021 TGGTCCAGTTAGCACTCTTTGT 59.562 45.455 0.00 0.00 0.00 2.83
1492 2164 3.644265 TGGTCCAGTTAGCACTCTTTGTA 59.356 43.478 0.00 0.00 0.00 2.41
1493 2165 3.995048 GGTCCAGTTAGCACTCTTTGTAC 59.005 47.826 0.00 0.00 0.00 2.90
1494 2166 4.502604 GGTCCAGTTAGCACTCTTTGTACA 60.503 45.833 0.00 0.00 0.00 2.90
1495 2167 5.054477 GTCCAGTTAGCACTCTTTGTACAA 58.946 41.667 3.59 3.59 0.00 2.41
1496 2168 5.701290 GTCCAGTTAGCACTCTTTGTACAAT 59.299 40.000 9.56 0.00 0.00 2.71
1497 2169 6.872020 GTCCAGTTAGCACTCTTTGTACAATA 59.128 38.462 9.56 0.00 0.00 1.90
1498 2170 7.549488 GTCCAGTTAGCACTCTTTGTACAATAT 59.451 37.037 9.56 0.00 0.00 1.28
1499 2171 7.764443 TCCAGTTAGCACTCTTTGTACAATATC 59.236 37.037 9.56 0.00 0.00 1.63
1500 2172 7.011482 CCAGTTAGCACTCTTTGTACAATATCC 59.989 40.741 9.56 0.00 0.00 2.59
1501 2173 7.549134 CAGTTAGCACTCTTTGTACAATATCCA 59.451 37.037 9.56 0.00 0.00 3.41
1502 2174 8.100791 AGTTAGCACTCTTTGTACAATATCCAA 58.899 33.333 9.56 0.00 0.00 3.53
1503 2175 8.893727 GTTAGCACTCTTTGTACAATATCCAAT 58.106 33.333 9.56 0.00 0.00 3.16
1504 2176 7.559590 AGCACTCTTTGTACAATATCCAATC 57.440 36.000 9.56 0.00 0.00 2.67
1505 2177 6.543831 AGCACTCTTTGTACAATATCCAATCC 59.456 38.462 9.56 0.00 0.00 3.01
1506 2178 6.318648 GCACTCTTTGTACAATATCCAATCCA 59.681 38.462 9.56 0.00 0.00 3.41
1507 2179 7.013655 GCACTCTTTGTACAATATCCAATCCAT 59.986 37.037 9.56 0.00 0.00 3.41
1508 2180 9.559732 CACTCTTTGTACAATATCCAATCCATA 57.440 33.333 9.56 0.00 0.00 2.74
1509 2181 9.561069 ACTCTTTGTACAATATCCAATCCATAC 57.439 33.333 9.56 0.00 0.00 2.39
1510 2182 8.601845 TCTTTGTACAATATCCAATCCATACG 57.398 34.615 9.56 0.00 0.00 3.06
1511 2183 8.208224 TCTTTGTACAATATCCAATCCATACGT 58.792 33.333 9.56 0.00 0.00 3.57
1512 2184 7.956420 TTGTACAATATCCAATCCATACGTC 57.044 36.000 3.59 0.00 0.00 4.34
1513 2185 7.297936 TGTACAATATCCAATCCATACGTCT 57.702 36.000 0.00 0.00 0.00 4.18
1514 2186 8.411991 TGTACAATATCCAATCCATACGTCTA 57.588 34.615 0.00 0.00 0.00 2.59
1515 2187 8.520351 TGTACAATATCCAATCCATACGTCTAG 58.480 37.037 0.00 0.00 0.00 2.43
1516 2188 7.776618 ACAATATCCAATCCATACGTCTAGA 57.223 36.000 0.00 0.00 0.00 2.43
1517 2189 7.831753 ACAATATCCAATCCATACGTCTAGAG 58.168 38.462 0.00 0.00 0.00 2.43
1518 2190 7.670140 ACAATATCCAATCCATACGTCTAGAGA 59.330 37.037 0.00 0.00 0.00 3.10
1519 2191 8.523658 CAATATCCAATCCATACGTCTAGAGAA 58.476 37.037 0.00 0.00 0.00 2.87
1520 2192 8.830915 ATATCCAATCCATACGTCTAGAGAAT 57.169 34.615 0.00 0.00 0.00 2.40
1521 2193 9.922477 ATATCCAATCCATACGTCTAGAGAATA 57.078 33.333 0.00 0.00 0.00 1.75
1522 2194 8.830915 ATCCAATCCATACGTCTAGAGAATAT 57.169 34.615 0.00 0.00 0.00 1.28
1523 2195 8.651589 TCCAATCCATACGTCTAGAGAATATT 57.348 34.615 0.00 0.00 0.00 1.28
1524 2196 8.740906 TCCAATCCATACGTCTAGAGAATATTC 58.259 37.037 7.41 7.41 0.00 1.75
1525 2197 8.523658 CCAATCCATACGTCTAGAGAATATTCA 58.476 37.037 17.56 0.00 0.00 2.57
1528 2200 8.863872 TCCATACGTCTAGAGAATATTCATCA 57.136 34.615 17.56 1.07 0.00 3.07
1529 2201 9.297037 TCCATACGTCTAGAGAATATTCATCAA 57.703 33.333 17.56 0.00 0.00 2.57
1530 2202 9.347934 CCATACGTCTAGAGAATATTCATCAAC 57.652 37.037 17.56 7.79 0.00 3.18
1531 2203 9.899226 CATACGTCTAGAGAATATTCATCAACA 57.101 33.333 17.56 0.00 0.00 3.33
1559 2231 4.832248 TGAGAAACAGTGATACATGGACC 58.168 43.478 0.00 0.00 0.00 4.46
1560 2232 4.192317 GAGAAACAGTGATACATGGACCC 58.808 47.826 0.00 0.00 0.00 4.46
1591 2263 1.156736 GGTTGCTGCTAACACGACAT 58.843 50.000 13.95 0.00 32.22 3.06
1600 2272 5.390461 GCTGCTAACACGACATTACAATCAA 60.390 40.000 0.00 0.00 0.00 2.57
1604 2276 6.955963 GCTAACACGACATTACAATCAAAGAG 59.044 38.462 0.00 0.00 0.00 2.85
1637 2309 3.009026 ACTGTGTGCGATGCATTAATCA 58.991 40.909 0.00 0.00 41.91 2.57
1688 2361 3.304613 GCAAAACGTTTGCGGTGG 58.695 55.556 15.46 1.90 43.45 4.61
1689 2362 1.226717 GCAAAACGTTTGCGGTGGA 60.227 52.632 15.46 0.00 43.45 4.02
1731 2404 4.034048 GGTTCAGATTATAGTTGCGTGTGG 59.966 45.833 0.00 0.00 0.00 4.17
1777 2450 4.517075 TCAATTAACTGTTTGCGATGTGGA 59.483 37.500 0.00 0.00 0.00 4.02
1782 2455 5.446143 AACTGTTTGCGATGTGGAAATAA 57.554 34.783 0.00 0.00 40.21 1.40
1807 2480 2.151202 GAAACGGACAGCCAGATGAAA 58.849 47.619 0.00 0.00 0.00 2.69
1831 2504 2.092211 GTGTGCGATATATGGCTTACGC 59.908 50.000 18.91 12.91 44.95 4.42
1835 2508 2.279136 GCGATATATGGCTTACGCTTCG 59.721 50.000 12.05 0.00 42.19 3.79
1840 2513 2.506438 GGCTTACGCTTCGCTCGT 60.506 61.111 0.00 0.00 43.20 4.18
1852 2525 3.611113 GCTTCGCTCGTATGAACTGTTTA 59.389 43.478 0.00 0.00 0.00 2.01
1858 2531 6.019881 TCGCTCGTATGAACTGTTTATGATTG 60.020 38.462 7.94 0.00 0.00 2.67
1860 2533 6.257849 GCTCGTATGAACTGTTTATGATTGGA 59.742 38.462 7.94 0.00 0.00 3.53
1870 2543 7.551585 ACTGTTTATGATTGGACAACACAAAA 58.448 30.769 0.00 0.00 0.00 2.44
1871 2544 7.706179 ACTGTTTATGATTGGACAACACAAAAG 59.294 33.333 0.00 0.00 0.00 2.27
1881 2556 5.128499 TGGACAACACAAAAGAAATGGTCAT 59.872 36.000 0.00 0.00 0.00 3.06
1906 2581 5.049828 CAGATCAAGGTGTGTGCGATATAA 58.950 41.667 0.00 0.00 0.00 0.98
1943 2618 2.650608 GGATGAACTGTTTGCGTTGAC 58.349 47.619 0.00 0.00 0.00 3.18
2085 2761 7.980062 ACGTATGTGATATGCTCTATCTACAG 58.020 38.462 0.00 3.91 0.00 2.74
2162 2838 3.766591 CGAAGAGGGCATCCTATATCAGT 59.233 47.826 0.00 0.00 45.05 3.41
2176 2852 8.921353 TCCTATATCAGTAAGGACTAGTTGTC 57.079 38.462 0.00 0.00 44.63 3.18
2263 2939 2.092323 GGTAACTGGATGGGAAGTTGC 58.908 52.381 0.00 0.00 37.23 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
258 260 2.425538 CCCTTCCTCCAGAGCTAGATGA 60.426 54.545 0.00 0.00 0.00 2.92
270 273 3.268330 GTTTGTAATCGTCCCTTCCTCC 58.732 50.000 0.00 0.00 0.00 4.30
357 360 3.133183 GGATAACTCTCCACCAGAAGACC 59.867 52.174 0.00 0.00 35.24 3.85
484 487 0.592637 TTGGCGTGAGAACAATGCAG 59.407 50.000 0.00 0.00 33.28 4.41
559 1230 0.464036 TCCCGTGACCATGTATCTGC 59.536 55.000 0.00 0.00 0.00 4.26
753 1424 2.637025 CCCGACAACACCAAAGCG 59.363 61.111 0.00 0.00 0.00 4.68
787 1458 2.642171 TTGACCACCCCTATCTCTGT 57.358 50.000 0.00 0.00 0.00 3.41
980 1651 5.104941 TCCATAATCACATGAGAGAAACCGT 60.105 40.000 0.00 0.00 0.00 4.83
1007 1678 0.396435 AACAATCTCCACGCAGTCCA 59.604 50.000 0.00 0.00 41.61 4.02
1036 1707 6.256539 ACAGATAAGCTATTGTGACGATGTTG 59.743 38.462 0.00 0.00 0.00 3.33
1131 1802 4.769688 CCAGTACATTGGCTGATCTACAA 58.230 43.478 10.73 0.00 34.87 2.41
1309 1981 1.640915 GTAAGACTAACGCGACACACG 59.359 52.381 15.93 0.00 45.66 4.49
1310 1982 2.907392 GAGTAAGACTAACGCGACACAC 59.093 50.000 15.93 0.66 0.00 3.82
1311 1983 2.411935 CGAGTAAGACTAACGCGACACA 60.412 50.000 15.93 0.00 41.80 3.72
1312 1984 2.164427 CGAGTAAGACTAACGCGACAC 58.836 52.381 15.93 0.00 41.80 3.67
1313 1985 1.129251 CCGAGTAAGACTAACGCGACA 59.871 52.381 15.93 0.00 41.80 4.35
1314 1986 1.129437 ACCGAGTAAGACTAACGCGAC 59.871 52.381 15.93 0.00 41.80 5.19
1315 1987 1.442769 ACCGAGTAAGACTAACGCGA 58.557 50.000 15.93 0.00 41.80 5.87
1316 1988 2.253392 AACCGAGTAAGACTAACGCG 57.747 50.000 3.53 3.53 39.44 6.01
1317 1989 3.539954 CGTAAACCGAGTAAGACTAACGC 59.460 47.826 0.00 0.00 39.56 4.84
1318 1990 4.551126 CACGTAAACCGAGTAAGACTAACG 59.449 45.833 0.00 0.00 40.70 3.18
1319 1991 5.452777 ACACGTAAACCGAGTAAGACTAAC 58.547 41.667 0.00 0.00 38.64 2.34
1320 1992 5.689383 ACACGTAAACCGAGTAAGACTAA 57.311 39.130 0.00 0.00 38.64 2.24
1321 1993 5.689383 AACACGTAAACCGAGTAAGACTA 57.311 39.130 0.00 0.00 39.53 2.59
1322 1994 4.574599 AACACGTAAACCGAGTAAGACT 57.425 40.909 0.00 0.00 39.53 3.24
1323 1995 6.934561 ATTAACACGTAAACCGAGTAAGAC 57.065 37.500 0.00 0.00 39.53 3.01
1324 1996 7.273381 GCTTATTAACACGTAAACCGAGTAAGA 59.727 37.037 0.00 0.00 39.53 2.10
1325 1997 7.386414 GCTTATTAACACGTAAACCGAGTAAG 58.614 38.462 0.00 0.00 39.53 2.34
1326 1998 6.310224 GGCTTATTAACACGTAAACCGAGTAA 59.690 38.462 0.00 0.00 39.53 2.24
1327 1999 5.804979 GGCTTATTAACACGTAAACCGAGTA 59.195 40.000 0.00 0.00 39.53 2.59
1328 2000 4.627035 GGCTTATTAACACGTAAACCGAGT 59.373 41.667 0.00 0.00 42.34 4.18
1329 2001 4.259530 CGGCTTATTAACACGTAAACCGAG 60.260 45.833 2.90 0.00 39.22 4.63
1330 2002 3.611986 CGGCTTATTAACACGTAAACCGA 59.388 43.478 2.90 0.00 39.22 4.69
1331 2003 3.367630 ACGGCTTATTAACACGTAAACCG 59.632 43.478 6.75 6.75 42.42 4.44
1332 2004 4.388469 TCACGGCTTATTAACACGTAAACC 59.612 41.667 0.00 0.00 35.85 3.27
1333 2005 5.514059 TCACGGCTTATTAACACGTAAAC 57.486 39.130 0.00 0.00 35.85 2.01
1334 2006 5.107143 GGTTCACGGCTTATTAACACGTAAA 60.107 40.000 0.00 0.00 35.85 2.01
1335 2007 4.388469 GGTTCACGGCTTATTAACACGTAA 59.612 41.667 0.00 0.00 35.85 3.18
1336 2008 3.925913 GGTTCACGGCTTATTAACACGTA 59.074 43.478 0.00 0.00 35.85 3.57
1337 2009 2.738314 GGTTCACGGCTTATTAACACGT 59.262 45.455 0.00 0.00 38.43 4.49
1338 2010 2.094734 GGGTTCACGGCTTATTAACACG 59.905 50.000 0.00 0.00 0.00 4.49
1339 2011 2.094734 CGGGTTCACGGCTTATTAACAC 59.905 50.000 0.00 0.00 0.00 3.32
1340 2012 2.289569 ACGGGTTCACGGCTTATTAACA 60.290 45.455 0.00 0.00 38.39 2.41
1341 2013 2.094734 CACGGGTTCACGGCTTATTAAC 59.905 50.000 0.00 0.00 38.39 2.01
1342 2014 2.289569 ACACGGGTTCACGGCTTATTAA 60.290 45.455 0.00 0.00 38.39 1.40
1343 2015 1.275856 ACACGGGTTCACGGCTTATTA 59.724 47.619 0.00 0.00 38.39 0.98
1344 2016 0.035739 ACACGGGTTCACGGCTTATT 59.964 50.000 0.00 0.00 38.39 1.40
1345 2017 0.035739 AACACGGGTTCACGGCTTAT 59.964 50.000 0.00 0.00 38.39 1.73
1346 2018 0.179051 AAACACGGGTTCACGGCTTA 60.179 50.000 2.08 0.00 35.82 3.09
1347 2019 1.033202 AAAACACGGGTTCACGGCTT 61.033 50.000 2.08 0.00 35.82 4.35
1348 2020 1.452470 AAAACACGGGTTCACGGCT 60.452 52.632 2.08 0.00 35.82 5.52
1349 2021 1.298788 CAAAACACGGGTTCACGGC 60.299 57.895 2.08 0.00 35.82 5.68
1350 2022 0.948678 ATCAAAACACGGGTTCACGG 59.051 50.000 2.08 0.00 35.82 4.94
1351 2023 2.803956 AGTATCAAAACACGGGTTCACG 59.196 45.455 2.08 0.00 35.82 4.35
1352 2024 3.120786 CGAGTATCAAAACACGGGTTCAC 60.121 47.826 2.08 0.00 32.66 3.18
1353 2025 3.061322 CGAGTATCAAAACACGGGTTCA 58.939 45.455 2.08 0.00 32.66 3.18
1354 2026 2.414138 CCGAGTATCAAAACACGGGTTC 59.586 50.000 2.08 0.00 46.02 3.62
1355 2027 2.419667 CCGAGTATCAAAACACGGGTT 58.580 47.619 0.00 0.00 46.02 4.11
1356 2028 2.088950 CCGAGTATCAAAACACGGGT 57.911 50.000 5.16 0.00 46.02 5.28
1359 2031 4.860352 TCATACACCGAGTATCAAAACACG 59.140 41.667 0.00 0.00 41.47 4.49
1360 2032 5.867716 AGTCATACACCGAGTATCAAAACAC 59.132 40.000 0.00 0.00 41.47 3.32
1361 2033 6.032956 AGTCATACACCGAGTATCAAAACA 57.967 37.500 0.00 0.00 41.47 2.83
1362 2034 6.588756 TCAAGTCATACACCGAGTATCAAAAC 59.411 38.462 0.00 0.00 41.47 2.43
1363 2035 6.693466 TCAAGTCATACACCGAGTATCAAAA 58.307 36.000 0.00 0.00 41.47 2.44
1364 2036 6.275494 TCAAGTCATACACCGAGTATCAAA 57.725 37.500 0.00 0.00 41.47 2.69
1365 2037 5.907866 TCAAGTCATACACCGAGTATCAA 57.092 39.130 0.00 0.00 41.47 2.57
1366 2038 6.771267 AGTATCAAGTCATACACCGAGTATCA 59.229 38.462 0.00 0.00 41.47 2.15
1367 2039 7.204496 AGTATCAAGTCATACACCGAGTATC 57.796 40.000 0.00 0.00 41.47 2.24
1368 2040 8.731605 CATAGTATCAAGTCATACACCGAGTAT 58.268 37.037 0.00 0.00 44.20 2.12
1369 2041 7.718314 ACATAGTATCAAGTCATACACCGAGTA 59.282 37.037 0.00 0.00 37.06 2.59
1370 2042 6.546403 ACATAGTATCAAGTCATACACCGAGT 59.454 38.462 0.00 0.00 32.39 4.18
1371 2043 6.858478 CACATAGTATCAAGTCATACACCGAG 59.142 42.308 0.00 0.00 32.39 4.63
1372 2044 6.544564 TCACATAGTATCAAGTCATACACCGA 59.455 38.462 0.00 0.00 32.39 4.69
1373 2045 6.637254 GTCACATAGTATCAAGTCATACACCG 59.363 42.308 0.00 0.00 32.39 4.94
1374 2046 6.637254 CGTCACATAGTATCAAGTCATACACC 59.363 42.308 0.00 0.00 32.39 4.16
1375 2047 7.194278 ACGTCACATAGTATCAAGTCATACAC 58.806 38.462 0.00 0.00 32.39 2.90
1376 2048 7.329588 ACGTCACATAGTATCAAGTCATACA 57.670 36.000 0.00 0.00 32.39 2.29
1377 2049 9.331106 CATACGTCACATAGTATCAAGTCATAC 57.669 37.037 0.00 0.00 31.81 2.39
1378 2050 9.063615 ACATACGTCACATAGTATCAAGTCATA 57.936 33.333 0.00 0.00 31.81 2.15
1379 2051 7.941919 ACATACGTCACATAGTATCAAGTCAT 58.058 34.615 0.00 0.00 31.81 3.06
1380 2052 7.329588 ACATACGTCACATAGTATCAAGTCA 57.670 36.000 0.00 0.00 31.81 3.41
1381 2053 8.630278 AAACATACGTCACATAGTATCAAGTC 57.370 34.615 0.00 0.00 31.81 3.01
1382 2054 8.997621 AAAACATACGTCACATAGTATCAAGT 57.002 30.769 0.00 0.00 31.81 3.16
1383 2055 9.901724 GAAAAACATACGTCACATAGTATCAAG 57.098 33.333 0.00 0.00 31.81 3.02
1384 2056 9.647797 AGAAAAACATACGTCACATAGTATCAA 57.352 29.630 0.00 0.00 31.81 2.57
1385 2057 9.647797 AAGAAAAACATACGTCACATAGTATCA 57.352 29.630 0.00 0.00 31.81 2.15
1390 2062 9.702726 CCATTAAGAAAAACATACGTCACATAG 57.297 33.333 0.00 0.00 0.00 2.23
1391 2063 8.670135 CCCATTAAGAAAAACATACGTCACATA 58.330 33.333 0.00 0.00 0.00 2.29
1392 2064 7.175990 ACCCATTAAGAAAAACATACGTCACAT 59.824 33.333 0.00 0.00 0.00 3.21
1393 2065 6.487331 ACCCATTAAGAAAAACATACGTCACA 59.513 34.615 0.00 0.00 0.00 3.58
1394 2066 6.799925 CACCCATTAAGAAAAACATACGTCAC 59.200 38.462 0.00 0.00 0.00 3.67
1395 2067 6.487331 ACACCCATTAAGAAAAACATACGTCA 59.513 34.615 0.00 0.00 0.00 4.35
1396 2068 6.905578 ACACCCATTAAGAAAAACATACGTC 58.094 36.000 0.00 0.00 0.00 4.34
1397 2069 6.887626 ACACCCATTAAGAAAAACATACGT 57.112 33.333 0.00 0.00 0.00 3.57
1398 2070 8.259049 TCTACACCCATTAAGAAAAACATACG 57.741 34.615 0.00 0.00 0.00 3.06
1401 2073 9.758651 GTTTTCTACACCCATTAAGAAAAACAT 57.241 29.630 9.85 0.00 44.86 2.71
1402 2074 8.750298 TGTTTTCTACACCCATTAAGAAAAACA 58.250 29.630 9.85 6.71 44.86 2.83
1403 2075 9.758651 ATGTTTTCTACACCCATTAAGAAAAAC 57.241 29.630 9.85 4.48 44.86 2.43
1404 2076 9.757227 CATGTTTTCTACACCCATTAAGAAAAA 57.243 29.630 9.85 3.50 44.86 1.94
1405 2077 9.137459 TCATGTTTTCTACACCCATTAAGAAAA 57.863 29.630 5.28 5.28 42.57 2.29
1406 2078 8.698973 TCATGTTTTCTACACCCATTAAGAAA 57.301 30.769 0.00 0.00 40.19 2.52
1407 2079 8.698973 TTCATGTTTTCTACACCCATTAAGAA 57.301 30.769 0.00 0.00 40.19 2.52
1408 2080 7.393234 CCTTCATGTTTTCTACACCCATTAAGA 59.607 37.037 0.00 0.00 40.19 2.10
1409 2081 7.538575 CCTTCATGTTTTCTACACCCATTAAG 58.461 38.462 0.00 0.00 40.19 1.85
1410 2082 6.071616 GCCTTCATGTTTTCTACACCCATTAA 60.072 38.462 0.00 0.00 40.19 1.40
1411 2083 5.417580 GCCTTCATGTTTTCTACACCCATTA 59.582 40.000 0.00 0.00 40.19 1.90
1412 2084 4.220602 GCCTTCATGTTTTCTACACCCATT 59.779 41.667 0.00 0.00 40.19 3.16
1413 2085 3.763897 GCCTTCATGTTTTCTACACCCAT 59.236 43.478 0.00 0.00 40.19 4.00
1414 2086 3.153919 GCCTTCATGTTTTCTACACCCA 58.846 45.455 0.00 0.00 40.19 4.51
1415 2087 3.421844 AGCCTTCATGTTTTCTACACCC 58.578 45.455 0.00 0.00 40.19 4.61
1416 2088 5.488341 TCTAGCCTTCATGTTTTCTACACC 58.512 41.667 0.00 0.00 40.19 4.16
1417 2089 7.617041 AATCTAGCCTTCATGTTTTCTACAC 57.383 36.000 0.00 0.00 40.19 2.90
1418 2090 8.635765 AAAATCTAGCCTTCATGTTTTCTACA 57.364 30.769 0.00 0.00 41.97 2.74
1419 2091 8.951243 AGAAAATCTAGCCTTCATGTTTTCTAC 58.049 33.333 11.15 0.00 40.55 2.59
1421 2093 8.951243 GTAGAAAATCTAGCCTTCATGTTTTCT 58.049 33.333 15.10 15.10 43.10 2.52
1422 2094 8.184848 GGTAGAAAATCTAGCCTTCATGTTTTC 58.815 37.037 5.49 0.00 40.54 2.29
1423 2095 7.669722 TGGTAGAAAATCTAGCCTTCATGTTTT 59.330 33.333 12.53 0.00 44.47 2.43
1424 2096 7.175104 TGGTAGAAAATCTAGCCTTCATGTTT 58.825 34.615 12.53 0.00 44.47 2.83
1425 2097 6.721318 TGGTAGAAAATCTAGCCTTCATGTT 58.279 36.000 12.53 0.00 44.47 2.71
1426 2098 6.313519 TGGTAGAAAATCTAGCCTTCATGT 57.686 37.500 12.53 0.00 44.47 3.21
1427 2099 6.293845 GCATGGTAGAAAATCTAGCCTTCATG 60.294 42.308 12.53 10.48 44.47 3.07
1428 2100 5.767168 GCATGGTAGAAAATCTAGCCTTCAT 59.233 40.000 12.53 0.00 44.47 2.57
1429 2101 5.126067 GCATGGTAGAAAATCTAGCCTTCA 58.874 41.667 12.53 0.00 44.47 3.02
1430 2102 5.008118 GTGCATGGTAGAAAATCTAGCCTTC 59.992 44.000 12.53 0.86 44.47 3.46
1431 2103 4.884164 GTGCATGGTAGAAAATCTAGCCTT 59.116 41.667 12.53 0.36 44.47 4.35
1432 2104 4.080356 TGTGCATGGTAGAAAATCTAGCCT 60.080 41.667 12.53 2.21 44.47 4.58
1433 2105 4.199310 TGTGCATGGTAGAAAATCTAGCC 58.801 43.478 12.53 6.60 44.47 3.93
1434 2106 4.274459 CCTGTGCATGGTAGAAAATCTAGC 59.726 45.833 9.12 9.12 45.10 3.42
1435 2107 5.674525 TCCTGTGCATGGTAGAAAATCTAG 58.325 41.667 8.29 0.00 28.01 2.43
1436 2108 5.396772 CCTCCTGTGCATGGTAGAAAATCTA 60.397 44.000 8.29 0.00 0.00 1.98
1437 2109 4.521146 CTCCTGTGCATGGTAGAAAATCT 58.479 43.478 8.29 0.00 0.00 2.40
1438 2110 3.629398 CCTCCTGTGCATGGTAGAAAATC 59.371 47.826 8.29 0.00 0.00 2.17
1439 2111 3.010584 ACCTCCTGTGCATGGTAGAAAAT 59.989 43.478 8.29 0.00 0.00 1.82
1440 2112 2.375174 ACCTCCTGTGCATGGTAGAAAA 59.625 45.455 8.29 0.00 0.00 2.29
1441 2113 1.985159 ACCTCCTGTGCATGGTAGAAA 59.015 47.619 8.29 0.00 0.00 2.52
1442 2114 1.555075 GACCTCCTGTGCATGGTAGAA 59.445 52.381 8.29 0.00 32.30 2.10
1443 2115 1.195115 GACCTCCTGTGCATGGTAGA 58.805 55.000 8.29 0.00 32.30 2.59
1444 2116 0.179000 GGACCTCCTGTGCATGGTAG 59.821 60.000 8.29 5.36 34.99 3.18
1445 2117 1.271840 GGGACCTCCTGTGCATGGTA 61.272 60.000 8.29 0.00 36.96 3.25
1446 2118 2.606587 GGGACCTCCTGTGCATGGT 61.607 63.158 8.29 3.82 36.96 3.55
1447 2119 2.273449 GGGACCTCCTGTGCATGG 59.727 66.667 0.00 0.00 36.96 3.66
1448 2120 2.124983 CGGGACCTCCTGTGCATG 60.125 66.667 0.00 0.00 36.96 4.06
1455 2127 3.402681 CCATGCACGGGACCTCCT 61.403 66.667 0.00 0.00 35.95 3.69
1456 2128 3.682292 GACCATGCACGGGACCTCC 62.682 68.421 12.94 0.00 0.00 4.30
1457 2129 2.125106 GACCATGCACGGGACCTC 60.125 66.667 12.94 0.00 0.00 3.85
1458 2130 3.717294 GGACCATGCACGGGACCT 61.717 66.667 16.94 0.00 37.29 3.85
1459 2131 3.976701 CTGGACCATGCACGGGACC 62.977 68.421 17.25 17.25 40.15 4.46
1460 2132 2.436646 CTGGACCATGCACGGGAC 60.437 66.667 12.94 6.70 0.00 4.46
1461 2133 1.195442 TAACTGGACCATGCACGGGA 61.195 55.000 12.94 0.00 0.00 5.14
1462 2134 0.744414 CTAACTGGACCATGCACGGG 60.744 60.000 2.80 3.91 0.00 5.28
1463 2135 1.369091 GCTAACTGGACCATGCACGG 61.369 60.000 0.00 0.00 0.00 4.94
1464 2136 0.673333 TGCTAACTGGACCATGCACG 60.673 55.000 0.00 0.00 0.00 5.34
1465 2137 0.804989 GTGCTAACTGGACCATGCAC 59.195 55.000 19.09 19.09 42.69 4.57
1466 2138 0.692476 AGTGCTAACTGGACCATGCA 59.308 50.000 0.00 0.94 37.77 3.96
1467 2139 1.065854 AGAGTGCTAACTGGACCATGC 60.066 52.381 0.00 0.00 36.52 4.06
1468 2140 3.340814 AAGAGTGCTAACTGGACCATG 57.659 47.619 0.00 0.00 36.52 3.66
1469 2141 3.073062 ACAAAGAGTGCTAACTGGACCAT 59.927 43.478 0.00 0.00 36.52 3.55
1470 2142 2.438021 ACAAAGAGTGCTAACTGGACCA 59.562 45.455 0.00 0.00 36.52 4.02
1471 2143 3.127425 ACAAAGAGTGCTAACTGGACC 57.873 47.619 0.00 0.00 36.52 4.46
1472 2144 4.628074 TGTACAAAGAGTGCTAACTGGAC 58.372 43.478 0.00 0.00 36.52 4.02
1473 2145 4.948341 TGTACAAAGAGTGCTAACTGGA 57.052 40.909 0.00 0.00 36.52 3.86
1474 2146 7.011482 GGATATTGTACAAAGAGTGCTAACTGG 59.989 40.741 13.23 0.00 36.52 4.00
1475 2147 7.549134 TGGATATTGTACAAAGAGTGCTAACTG 59.451 37.037 13.23 0.00 36.52 3.16
1476 2148 7.620880 TGGATATTGTACAAAGAGTGCTAACT 58.379 34.615 13.23 0.00 40.21 2.24
1477 2149 7.843490 TGGATATTGTACAAAGAGTGCTAAC 57.157 36.000 13.23 0.00 33.54 2.34
1478 2150 9.109393 GATTGGATATTGTACAAAGAGTGCTAA 57.891 33.333 13.23 4.34 33.40 3.09
1479 2151 7.715249 GGATTGGATATTGTACAAAGAGTGCTA 59.285 37.037 13.23 0.00 33.40 3.49
1480 2152 6.543831 GGATTGGATATTGTACAAAGAGTGCT 59.456 38.462 13.23 0.00 33.40 4.40
1481 2153 6.318648 TGGATTGGATATTGTACAAAGAGTGC 59.681 38.462 13.23 5.10 33.40 4.40
1482 2154 7.864108 TGGATTGGATATTGTACAAAGAGTG 57.136 36.000 13.23 0.00 33.40 3.51
1483 2155 9.561069 GTATGGATTGGATATTGTACAAAGAGT 57.439 33.333 13.23 0.00 33.40 3.24
1484 2156 8.712363 CGTATGGATTGGATATTGTACAAAGAG 58.288 37.037 13.23 0.00 33.40 2.85
1485 2157 8.208224 ACGTATGGATTGGATATTGTACAAAGA 58.792 33.333 13.23 4.14 33.40 2.52
1486 2158 8.378172 ACGTATGGATTGGATATTGTACAAAG 57.622 34.615 13.23 0.00 33.40 2.77
1487 2159 8.208224 AGACGTATGGATTGGATATTGTACAAA 58.792 33.333 13.23 2.74 33.40 2.83
1488 2160 7.732025 AGACGTATGGATTGGATATTGTACAA 58.268 34.615 11.41 11.41 34.44 2.41
1489 2161 7.297936 AGACGTATGGATTGGATATTGTACA 57.702 36.000 0.00 0.00 0.00 2.90
1490 2162 8.737175 TCTAGACGTATGGATTGGATATTGTAC 58.263 37.037 0.00 0.00 0.00 2.90
1491 2163 8.873186 TCTAGACGTATGGATTGGATATTGTA 57.127 34.615 0.00 0.00 0.00 2.41
1492 2164 7.670140 TCTCTAGACGTATGGATTGGATATTGT 59.330 37.037 0.00 0.00 0.00 2.71
1493 2165 8.056407 TCTCTAGACGTATGGATTGGATATTG 57.944 38.462 0.00 0.00 0.00 1.90
1494 2166 8.651589 TTCTCTAGACGTATGGATTGGATATT 57.348 34.615 0.00 0.00 0.00 1.28
1495 2167 8.830915 ATTCTCTAGACGTATGGATTGGATAT 57.169 34.615 0.00 0.00 0.00 1.63
1496 2168 9.922477 ATATTCTCTAGACGTATGGATTGGATA 57.078 33.333 0.00 0.00 0.00 2.59
1497 2169 8.830915 ATATTCTCTAGACGTATGGATTGGAT 57.169 34.615 0.00 0.00 0.00 3.41
1498 2170 8.651589 AATATTCTCTAGACGTATGGATTGGA 57.348 34.615 0.00 0.00 0.00 3.53
1499 2171 8.523658 TGAATATTCTCTAGACGTATGGATTGG 58.476 37.037 16.24 0.00 0.00 3.16
1502 2174 9.467796 TGATGAATATTCTCTAGACGTATGGAT 57.532 33.333 16.24 0.00 0.00 3.41
1503 2175 8.863872 TGATGAATATTCTCTAGACGTATGGA 57.136 34.615 16.24 0.00 0.00 3.41
1504 2176 9.347934 GTTGATGAATATTCTCTAGACGTATGG 57.652 37.037 16.24 0.00 0.00 2.74
1505 2177 9.899226 TGTTGATGAATATTCTCTAGACGTATG 57.101 33.333 16.24 0.00 0.00 2.39
1537 2209 4.323485 GGGTCCATGTATCACTGTTTCTCA 60.323 45.833 0.00 0.00 0.00 3.27
1538 2210 4.192317 GGGTCCATGTATCACTGTTTCTC 58.808 47.826 0.00 0.00 0.00 2.87
1539 2211 3.369471 CGGGTCCATGTATCACTGTTTCT 60.369 47.826 0.00 0.00 0.00 2.52
1540 2212 2.936498 CGGGTCCATGTATCACTGTTTC 59.064 50.000 0.00 0.00 0.00 2.78
1541 2213 2.939640 GCGGGTCCATGTATCACTGTTT 60.940 50.000 0.00 0.00 0.00 2.83
1542 2214 1.406887 GCGGGTCCATGTATCACTGTT 60.407 52.381 0.00 0.00 0.00 3.16
1543 2215 0.178068 GCGGGTCCATGTATCACTGT 59.822 55.000 0.00 0.00 0.00 3.55
1544 2216 0.177836 TGCGGGTCCATGTATCACTG 59.822 55.000 0.00 0.00 0.00 3.66
1545 2217 0.178068 GTGCGGGTCCATGTATCACT 59.822 55.000 0.00 0.00 0.00 3.41
1546 2218 0.178068 AGTGCGGGTCCATGTATCAC 59.822 55.000 0.00 0.00 0.00 3.06
1547 2219 1.411246 GTAGTGCGGGTCCATGTATCA 59.589 52.381 0.00 0.00 0.00 2.15
1548 2220 1.687123 AGTAGTGCGGGTCCATGTATC 59.313 52.381 0.00 0.00 0.00 2.24
1549 2221 1.412710 CAGTAGTGCGGGTCCATGTAT 59.587 52.381 0.00 0.00 0.00 2.29
1550 2222 0.821517 CAGTAGTGCGGGTCCATGTA 59.178 55.000 0.00 0.00 0.00 2.29
1551 2223 1.596934 CAGTAGTGCGGGTCCATGT 59.403 57.895 0.00 0.00 0.00 3.21
1552 2224 1.815421 GCAGTAGTGCGGGTCCATG 60.815 63.158 6.82 0.00 40.71 3.66
1553 2225 2.584608 GCAGTAGTGCGGGTCCAT 59.415 61.111 6.82 0.00 40.71 3.41
1591 2263 3.678072 CGTCGAAGGCTCTTTGATTGTAA 59.322 43.478 7.79 0.00 0.00 2.41
1600 2272 1.068741 ACAGTTTCGTCGAAGGCTCTT 59.931 47.619 7.86 0.00 0.00 2.85
1604 2276 0.232303 CACACAGTTTCGTCGAAGGC 59.768 55.000 7.86 5.73 0.00 4.35
1669 2342 0.873743 CCACCGCAAACGTTTTGCAT 60.874 50.000 24.71 14.97 45.14 3.96
1685 2358 2.019984 GTTTGATGCATCCTCCTCCAC 58.980 52.381 23.67 6.28 0.00 4.02
1687 2360 2.019984 GTGTTTGATGCATCCTCCTCC 58.980 52.381 23.67 6.59 0.00 4.30
1688 2361 1.667724 CGTGTTTGATGCATCCTCCTC 59.332 52.381 23.67 10.50 0.00 3.71
1689 2362 1.679944 CCGTGTTTGATGCATCCTCCT 60.680 52.381 23.67 0.00 0.00 3.69
1782 2455 2.650322 TCTGGCTGTCCGTTTCTTTTT 58.350 42.857 0.00 0.00 34.14 1.94
1794 2467 0.250467 ACACGCTTTCATCTGGCTGT 60.250 50.000 0.00 0.00 0.00 4.40
1807 2480 0.318441 AGCCATATATCGCACACGCT 59.682 50.000 5.09 0.00 39.84 5.07
1831 2504 5.515270 TCATAAACAGTTCATACGAGCGAAG 59.485 40.000 0.00 0.00 0.00 3.79
1835 2508 6.257849 TCCAATCATAAACAGTTCATACGAGC 59.742 38.462 0.00 0.00 0.00 5.03
1840 2513 8.511321 GTGTTGTCCAATCATAAACAGTTCATA 58.489 33.333 0.00 0.00 31.80 2.15
1852 2525 6.707161 CCATTTCTTTTGTGTTGTCCAATCAT 59.293 34.615 0.00 0.00 0.00 2.45
1858 2531 5.004922 TGACCATTTCTTTTGTGTTGTCC 57.995 39.130 0.00 0.00 0.00 4.02
1860 2533 5.128499 TGGATGACCATTTCTTTTGTGTTGT 59.872 36.000 0.00 0.00 41.77 3.32
1870 2543 4.229123 ACCTTGATCTGGATGACCATTTCT 59.771 41.667 11.38 0.00 45.87 2.52
1871 2544 4.337555 CACCTTGATCTGGATGACCATTTC 59.662 45.833 11.38 0.00 45.87 2.17
1881 2556 0.320683 CGCACACACCTTGATCTGGA 60.321 55.000 11.38 0.00 0.00 3.86
1906 2581 2.434884 CGAGTGAACCGCATGCCT 60.435 61.111 13.15 1.20 0.00 4.75
1943 2618 3.621268 TGAACCGTTTCTGTTCTCTTGTG 59.379 43.478 4.94 0.00 42.04 3.33
1991 2667 4.623932 TCTGATTACAGACCTGTTTGCT 57.376 40.909 8.06 0.00 46.55 3.91
2022 2698 5.957798 TCGTCTGTGTTATTATCGGTCTTT 58.042 37.500 0.00 0.00 0.00 2.52
2176 2852 4.590647 TCTCTTAGATGAGCTATTGGTGGG 59.409 45.833 0.00 0.00 34.29 4.61
2246 2922 3.363787 GGCAACTTCCCATCCAGTT 57.636 52.632 0.00 0.00 33.29 3.16


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

AutoCloner maintained by Alex Coulton.