Multiple sequence alignment - TraesCS5D01G517200

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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 TraesCS5D01G517200 chr5D 100.000 7381 0 0 1 7381 539216699 539224079 0.000000e+00 13631.0
1 TraesCS5D01G517200 chr5D 84.375 480 25 23 6126 6604 558059470 558059040 6.840000e-115 425.0
2 TraesCS5D01G517200 chr5D 82.051 546 42 29 6126 6670 2530208 2529718 1.480000e-111 414.0
3 TraesCS5D01G517200 chr5D 94.231 52 3 0 2494 2545 539219138 539219189 6.140000e-11 80.5
4 TraesCS5D01G517200 chr5D 94.231 52 3 0 2440 2491 539219192 539219243 6.140000e-11 80.5
5 TraesCS5D01G517200 chr5B 91.509 7549 305 128 1 7381 680917310 680924690 0.000000e+00 10080.0
6 TraesCS5D01G517200 chr5B 80.614 619 62 32 6126 6744 501484604 501484044 6.840000e-115 425.0
7 TraesCS5D01G517200 chr5B 100.000 55 0 0 2440 2494 680919820 680919874 1.310000e-17 102.0
8 TraesCS5D01G517200 chr4A 91.876 6918 297 115 120 6917 629366618 629359846 0.000000e+00 9417.0
9 TraesCS5D01G517200 chr4A 78.553 387 30 24 6996 7366 629359614 629359265 9.710000e-49 206.0
10 TraesCS5D01G517200 chr4A 92.000 50 4 0 2499 2548 629364332 629364283 3.690000e-08 71.3
11 TraesCS5D01G517200 chr3B 80.515 621 58 30 6126 6744 361841206 361841765 1.150000e-112 418.0
12 TraesCS5D01G517200 chr3B 80.354 621 54 35 6126 6744 573316232 573315678 6.890000e-110 409.0
13 TraesCS5D01G517200 chr6B 75.970 799 87 53 6126 6905 33235405 33234693 1.550000e-81 315.0
14 TraesCS5D01G517200 chr6B 85.586 111 16 0 1963 2073 393598479 393598369 4.680000e-22 117.0
15 TraesCS5D01G517200 chr6A 77.986 427 89 4 5611 6033 47902516 47902941 5.680000e-66 263.0
16 TraesCS5D01G517200 chr2D 80.000 160 24 5 1916 2073 486315629 486315476 2.180000e-20 111.0
17 TraesCS5D01G517200 chr2D 83.186 113 15 4 1963 2073 618091928 618092038 4.710000e-17 100.0


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 TraesCS5D01G517200 chr5D 539216699 539224079 7380 False 13631.000000 13631 100.000000 1 7381 1 chr5D.!!$F1 7380
1 TraesCS5D01G517200 chr5B 680917310 680924690 7380 False 10080.000000 10080 91.509000 1 7381 1 chr5B.!!$F1 7380
2 TraesCS5D01G517200 chr5B 501484044 501484604 560 True 425.000000 425 80.614000 6126 6744 1 chr5B.!!$R1 618
3 TraesCS5D01G517200 chr4A 629359265 629366618 7353 True 3231.433333 9417 87.476333 120 7366 3 chr4A.!!$R1 7246
4 TraesCS5D01G517200 chr3B 361841206 361841765 559 False 418.000000 418 80.515000 6126 6744 1 chr3B.!!$F1 618
5 TraesCS5D01G517200 chr3B 573315678 573316232 554 True 409.000000 409 80.354000 6126 6744 1 chr3B.!!$R1 618
6 TraesCS5D01G517200 chr6B 33234693 33235405 712 True 315.000000 315 75.970000 6126 6905 1 chr6B.!!$R1 779

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
462 527 0.031721 GACCGTCACCGACACTTTCT 59.968 55.000 0.00 0.00 35.63 2.52 F
470 535 0.036294 CCGACACTTTCTTCTCCCCC 60.036 60.000 0.00 0.00 0.00 5.40 F
1741 1901 0.680280 ACAGGGACGACTCGCAGTAT 60.680 55.000 0.00 0.00 28.66 2.12 F
2355 2516 0.326264 AGAAACTCGCTTGGCATCCT 59.674 50.000 0.00 0.00 0.00 3.24 F
2587 2748 1.001158 GGAAACAAACCGGCGAATTCA 60.001 47.619 9.30 0.00 0.00 2.57 F
4086 4258 3.054361 TCCCTTCTAATGGTTGGCTCTTC 60.054 47.826 0.00 0.00 0.00 2.87 F
4691 4866 0.460987 GACGAAGCAGCTGCAGGTAT 60.461 55.000 38.24 20.42 45.16 2.73 F
5885 6068 0.036010 GATATGAGTCATGGGGGCCG 60.036 60.000 16.15 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2108 0.331278 CCTACAAACAGGGGGCATCA 59.669 55.000 0.00 0.0 31.47 3.07 R
1949 2109 0.331616 ACCTACAAACAGGGGGCATC 59.668 55.000 0.00 0.0 40.29 3.91 R
3333 3503 1.202110 GCAGCACCATCATCAGAAACG 60.202 52.381 0.00 0.0 0.00 3.60 R
4086 4258 0.171455 GCAGAGACACGGACCTGTAG 59.829 60.000 0.00 0.0 0.00 2.74 R
4363 4535 7.004086 AGACAAATGTTAGGGAAACTTCATCA 58.996 34.615 0.00 0.0 38.99 3.07 R
5885 6068 0.534873 AGAAGAGCTTCCCGAAGAGC 59.465 55.000 8.65 0.0 40.79 4.09 R
6368 6560 1.069823 ACTGACTGACTGACTTGCTGG 59.930 52.381 0.00 0.0 0.00 4.85 R
7259 7663 0.030773 CGAAAGGGATCGATCGCAGA 59.969 55.000 35.12 0.0 45.48 4.26 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
24 25 6.567959 GGAGGTGAAATTTCCAATCAATCTC 58.432 40.000 15.48 10.05 0.00 2.75
27 28 5.105756 GGTGAAATTTCCAATCAATCTCCGT 60.106 40.000 15.48 0.00 0.00 4.69
38 39 2.619177 TCAATCTCCGTAGCAGAGTAGC 59.381 50.000 0.00 0.00 0.00 3.58
54 58 1.909532 GTAGCGTTAGTACTGTGTGCG 59.090 52.381 5.39 4.05 0.00 5.34
67 71 2.202783 GTGCGCATGGGCCAATTC 60.203 61.111 29.42 12.38 36.38 2.17
101 116 2.890766 GCCACTTTCCCCACGAGGA 61.891 63.158 0.00 0.00 38.24 3.71
107 122 2.092323 CTTTCCCCACGAGGATTTTCC 58.908 52.381 0.00 0.00 38.24 3.13
108 123 0.330267 TTCCCCACGAGGATTTTCCC 59.670 55.000 0.00 0.00 37.19 3.97
113 128 2.897326 CCCACGAGGATTTTCCCTTTTT 59.103 45.455 0.00 0.00 37.19 1.94
242 277 2.277756 GACGCGTACAGGCTACCG 60.278 66.667 13.97 0.00 0.00 4.02
245 280 1.065273 CGCGTACAGGCTACCGAAT 59.935 57.895 0.00 0.00 0.00 3.34
249 284 2.030091 GCGTACAGGCTACCGAATTTTC 59.970 50.000 4.13 0.00 0.00 2.29
250 285 3.255725 CGTACAGGCTACCGAATTTTCA 58.744 45.455 0.00 0.00 0.00 2.69
251 286 3.061697 CGTACAGGCTACCGAATTTTCAC 59.938 47.826 0.00 0.00 0.00 3.18
252 287 3.134574 ACAGGCTACCGAATTTTCACA 57.865 42.857 0.00 0.00 0.00 3.58
253 288 2.812011 ACAGGCTACCGAATTTTCACAC 59.188 45.455 0.00 0.00 0.00 3.82
255 290 3.125316 CAGGCTACCGAATTTTCACACTC 59.875 47.826 0.00 0.00 0.00 3.51
262 312 4.389077 ACCGAATTTTCACACTCGATCTTC 59.611 41.667 0.00 0.00 33.13 2.87
280 330 9.958234 TCGATCTTCTAAACAGAGAAATAGATG 57.042 33.333 0.00 0.00 35.06 2.90
307 362 4.301628 CCATGCTGTTTTTCCTCTCAAAC 58.698 43.478 0.00 0.00 34.09 2.93
353 410 2.571216 CGAGACGGACACCCCAACT 61.571 63.158 0.00 0.00 34.14 3.16
357 414 0.393820 GACGGACACCCCAACTAACA 59.606 55.000 0.00 0.00 34.14 2.41
366 423 0.179012 CCCAACTAACACAACCCCGT 60.179 55.000 0.00 0.00 0.00 5.28
375 432 0.037232 CACAACCCCGTTCTCTCTCC 60.037 60.000 0.00 0.00 0.00 3.71
376 433 0.471211 ACAACCCCGTTCTCTCTCCA 60.471 55.000 0.00 0.00 0.00 3.86
462 527 0.031721 GACCGTCACCGACACTTTCT 59.968 55.000 0.00 0.00 35.63 2.52
465 530 1.269621 CCGTCACCGACACTTTCTTCT 60.270 52.381 0.00 0.00 35.63 2.85
466 531 2.052157 CGTCACCGACACTTTCTTCTC 58.948 52.381 0.00 0.00 35.63 2.87
470 535 0.036294 CCGACACTTTCTTCTCCCCC 60.036 60.000 0.00 0.00 0.00 5.40
496 561 7.176690 CCTTTTTCTCTCTCTCTCTCTACAACT 59.823 40.741 0.00 0.00 0.00 3.16
601 680 4.365723 ACCGATTATTAACTCGTCGCAAT 58.634 39.130 0.00 0.00 33.11 3.56
656 750 4.004314 CCGACAGTCTAGAGAGAGAAACA 58.996 47.826 0.00 0.00 30.20 2.83
714 812 3.752167 GGGGGAGAGGAGGACCGA 61.752 72.222 0.00 0.00 41.83 4.69
715 813 2.442458 GGGGAGAGGAGGACCGAC 60.442 72.222 0.00 0.00 41.83 4.79
779 886 1.529010 GCTGTCGAAACACACACACAC 60.529 52.381 0.00 0.00 0.00 3.82
781 888 1.461512 TGTCGAAACACACACACACAC 59.538 47.619 0.00 0.00 0.00 3.82
783 890 1.461512 TCGAAACACACACACACACAC 59.538 47.619 0.00 0.00 0.00 3.82
786 893 1.164411 AACACACACACACACACAGG 58.836 50.000 0.00 0.00 0.00 4.00
787 894 1.305219 ACACACACACACACACAGGC 61.305 55.000 0.00 0.00 0.00 4.85
788 895 1.002746 ACACACACACACACAGGCA 60.003 52.632 0.00 0.00 0.00 4.75
973 1100 2.001269 CGTTCCCCATTCCCCTCCT 61.001 63.158 0.00 0.00 0.00 3.69
976 1103 2.778717 CCCCATTCCCCTCCTCCC 60.779 72.222 0.00 0.00 0.00 4.30
977 1104 2.778717 CCCATTCCCCTCCTCCCC 60.779 72.222 0.00 0.00 0.00 4.81
978 1105 2.778717 CCATTCCCCTCCTCCCCC 60.779 72.222 0.00 0.00 0.00 5.40
979 1106 3.171388 CATTCCCCTCCTCCCCCG 61.171 72.222 0.00 0.00 0.00 5.73
980 1107 3.707189 ATTCCCCTCCTCCCCCGT 61.707 66.667 0.00 0.00 0.00 5.28
981 1108 3.283467 ATTCCCCTCCTCCCCCGTT 62.283 63.158 0.00 0.00 0.00 4.44
982 1109 3.937372 TTCCCCTCCTCCCCCGTTC 62.937 68.421 0.00 0.00 0.00 3.95
986 1113 3.470888 CTCCTCCCCCGTTCGCAT 61.471 66.667 0.00 0.00 0.00 4.73
988 1115 4.547367 CCTCCCCCGTTCGCATCC 62.547 72.222 0.00 0.00 0.00 3.51
989 1116 4.891727 CTCCCCCGTTCGCATCCG 62.892 72.222 0.00 0.00 0.00 4.18
1033 1160 3.522731 CCCTCCGCCGAGAGTCTG 61.523 72.222 0.00 0.00 38.52 3.51
1034 1161 2.438614 CCTCCGCCGAGAGTCTGA 60.439 66.667 0.00 0.00 38.52 3.27
1168 1295 4.416738 GGAGCCAGGGGTGAGTGC 62.417 72.222 0.00 0.00 0.00 4.40
1169 1296 4.416738 GAGCCAGGGGTGAGTGCC 62.417 72.222 0.00 0.00 0.00 5.01
1210 1337 2.869636 GCTTCTGGTTCTGGTCTGTCTG 60.870 54.545 0.00 0.00 0.00 3.51
1293 1425 1.648467 GGCGGTGGTGCTGAGATTTC 61.648 60.000 0.00 0.00 34.52 2.17
1313 1445 1.135972 CGGTTGCCGTTTCTCAATCTG 60.136 52.381 0.00 0.00 42.73 2.90
1316 1448 3.243401 GGTTGCCGTTTCTCAATCTGTTT 60.243 43.478 0.00 0.00 0.00 2.83
1318 1450 3.963665 TGCCGTTTCTCAATCTGTTTTG 58.036 40.909 0.00 0.00 0.00 2.44
1319 1451 3.380004 TGCCGTTTCTCAATCTGTTTTGT 59.620 39.130 0.00 0.00 0.00 2.83
1321 1453 4.441087 GCCGTTTCTCAATCTGTTTTGTTC 59.559 41.667 0.00 0.00 0.00 3.18
1322 1454 4.670621 CCGTTTCTCAATCTGTTTTGTTCG 59.329 41.667 0.00 0.00 0.00 3.95
1324 1456 5.169561 CGTTTCTCAATCTGTTTTGTTCGTG 59.830 40.000 0.00 0.00 0.00 4.35
1325 1457 4.209452 TCTCAATCTGTTTTGTTCGTGC 57.791 40.909 0.00 0.00 0.00 5.34
1326 1458 2.966708 CTCAATCTGTTTTGTTCGTGCG 59.033 45.455 0.00 0.00 0.00 5.34
1327 1459 2.353269 TCAATCTGTTTTGTTCGTGCGT 59.647 40.909 0.00 0.00 0.00 5.24
1329 1461 2.445453 TCTGTTTTGTTCGTGCGTTC 57.555 45.000 0.00 0.00 0.00 3.95
1333 1468 0.858135 TTTTGTTCGTGCGTTCGTGC 60.858 50.000 1.99 0.00 0.00 5.34
1596 1738 4.176851 GACCGACCGACCGAGCTC 62.177 72.222 2.73 2.73 0.00 4.09
1608 1762 1.315257 CCGAGCTCACCCCCAATTTG 61.315 60.000 15.40 0.00 0.00 2.32
1741 1901 0.680280 ACAGGGACGACTCGCAGTAT 60.680 55.000 0.00 0.00 28.66 2.12
1862 2022 1.638070 TCACCAATGGCCAGATGGTAA 59.362 47.619 33.89 23.93 45.45 2.85
1863 2023 2.244510 TCACCAATGGCCAGATGGTAAT 59.755 45.455 33.89 17.40 45.45 1.89
1864 2024 3.033184 CACCAATGGCCAGATGGTAATT 58.967 45.455 33.89 17.10 45.45 1.40
1865 2025 4.079500 TCACCAATGGCCAGATGGTAATTA 60.080 41.667 33.89 21.45 45.45 1.40
1869 2029 7.015098 CACCAATGGCCAGATGGTAATTAATTA 59.985 37.037 33.89 3.71 45.45 1.40
1906 2066 3.037851 TCTCACACTCCTCTGCCATAT 57.962 47.619 0.00 0.00 0.00 1.78
1907 2067 2.961741 TCTCACACTCCTCTGCCATATC 59.038 50.000 0.00 0.00 0.00 1.63
1909 2069 2.697229 TCACACTCCTCTGCCATATCAG 59.303 50.000 0.00 0.00 35.46 2.90
1925 2085 3.565764 ATCAGCAGCTTATGTGCCTTA 57.434 42.857 0.00 0.00 42.24 2.69
1944 2104 2.502142 ACTGGATGCTCAATTGCTCA 57.498 45.000 0.00 1.16 0.00 4.26
1947 2107 2.089201 TGGATGCTCAATTGCTCACTG 58.911 47.619 0.00 0.00 0.00 3.66
1948 2108 2.089980 GGATGCTCAATTGCTCACTGT 58.910 47.619 0.00 0.00 0.00 3.55
1949 2109 2.159421 GGATGCTCAATTGCTCACTGTG 60.159 50.000 0.17 0.17 0.00 3.66
1950 2110 2.259266 TGCTCAATTGCTCACTGTGA 57.741 45.000 10.50 10.50 0.00 3.58
1951 2111 2.786777 TGCTCAATTGCTCACTGTGAT 58.213 42.857 11.45 0.00 0.00 3.06
1952 2112 2.486592 TGCTCAATTGCTCACTGTGATG 59.513 45.455 11.45 6.48 0.00 3.07
1953 2113 2.731341 GCTCAATTGCTCACTGTGATGC 60.731 50.000 11.45 16.12 0.00 3.91
1954 2114 1.814394 TCAATTGCTCACTGTGATGCC 59.186 47.619 21.22 11.09 0.00 4.40
1961 2121 1.075482 CACTGTGATGCCCCCTGTT 59.925 57.895 0.32 0.00 0.00 3.16
1972 2132 0.909623 CCCCCTGTTTGTAGGTCGAT 59.090 55.000 0.00 0.00 36.02 3.59
2056 2216 1.227674 CCCGCTCCCTTATGCTGAC 60.228 63.158 0.00 0.00 0.00 3.51
2096 2256 6.154445 GCGCATTTGGAAATATCATCATCTT 58.846 36.000 0.30 0.00 0.00 2.40
2148 2308 3.587061 AGGGATACTGATGGTTGTTGTGA 59.413 43.478 0.00 0.00 0.00 3.58
2197 2358 5.015603 CCCATCCAAGGATATTGGTTCCTAT 59.984 44.000 0.40 0.00 42.90 2.57
2203 2364 6.011628 CCAAGGATATTGGTTCCTATGGGTAT 60.012 42.308 0.00 0.00 42.90 2.73
2206 2367 5.340027 GGATATTGGTTCCTATGGGTATGGG 60.340 48.000 0.00 0.00 36.33 4.00
2212 2373 1.056660 CCTATGGGTATGGGAGCGTT 58.943 55.000 0.00 0.00 37.11 4.84
2290 2451 3.885297 CCAGAAATGATGGCGGTAAAGAT 59.115 43.478 0.00 0.00 0.00 2.40
2299 2460 1.445871 GCGGTAAAGATTGGAACGGT 58.554 50.000 0.00 0.00 0.00 4.83
2348 2509 2.662700 ACGACACTAGAAACTCGCTTG 58.337 47.619 0.00 0.00 0.00 4.01
2354 2515 1.936547 CTAGAAACTCGCTTGGCATCC 59.063 52.381 0.00 0.00 0.00 3.51
2355 2516 0.326264 AGAAACTCGCTTGGCATCCT 59.674 50.000 0.00 0.00 0.00 3.24
2357 2518 1.131315 GAAACTCGCTTGGCATCCTTC 59.869 52.381 0.00 0.00 0.00 3.46
2372 2533 4.762251 GCATCCTTCAGTTTGGTCTTTAGT 59.238 41.667 0.00 0.00 0.00 2.24
2375 2536 3.882888 CCTTCAGTTTGGTCTTTAGTGCA 59.117 43.478 0.00 0.00 0.00 4.57
2497 2658 7.785033 ACCTAAAATGCCAAAAGAATATCCAG 58.215 34.615 0.00 0.00 0.00 3.86
2502 2663 8.773033 AAATGCCAAAAGAATATCCAGTAGAT 57.227 30.769 0.00 0.00 39.15 1.98
2587 2748 1.001158 GGAAACAAACCGGCGAATTCA 60.001 47.619 9.30 0.00 0.00 2.57
2762 2928 6.038271 TCTGGTCTTTGCTTAGACAAAACTTC 59.962 38.462 16.89 3.02 45.07 3.01
3542 3712 6.097839 AGAGCAATGAAGGTGCATAATTTCAT 59.902 34.615 10.32 10.32 44.74 2.57
3764 3934 9.632638 ATGATTCAGGTATGCTTATTACAGTTT 57.367 29.630 0.00 0.00 0.00 2.66
3800 3970 6.932960 CCAGTCTATATGCTGACATCAAATGA 59.067 38.462 5.54 0.00 37.74 2.57
3844 4016 3.165071 CCCACTTTGCCCTAATGAAGTT 58.835 45.455 0.00 0.00 30.41 2.66
4000 4172 7.871973 TGCCATGAATGCATTGGTAATAATAAC 59.128 33.333 18.59 0.00 32.85 1.89
4086 4258 3.054361 TCCCTTCTAATGGTTGGCTCTTC 60.054 47.826 0.00 0.00 0.00 2.87
4617 4792 5.417580 GCCTAAGACAGAGAAGAAGAAGAGA 59.582 44.000 0.00 0.00 0.00 3.10
4656 4831 5.066505 GGAAGAAAATCAATCACCTGCGTAT 59.933 40.000 0.00 0.00 0.00 3.06
4691 4866 0.460987 GACGAAGCAGCTGCAGGTAT 60.461 55.000 38.24 20.42 45.16 2.73
4934 5109 4.858850 TGAAGGAAGCCATACATGTCATT 58.141 39.130 0.00 0.00 0.00 2.57
4982 5157 3.981375 ACTGGGGAAAAGAGGTAAAGTCT 59.019 43.478 0.00 0.00 0.00 3.24
5012 5190 2.099141 TGCTGTGTGCTGATTAGGTC 57.901 50.000 0.00 0.00 43.37 3.85
5041 5219 9.209175 CCAAATATCTGTTGCCTAGTAGTAATC 57.791 37.037 0.00 0.00 0.00 1.75
5089 5270 2.039480 GCAGATTGGCTGGATCTATGGA 59.961 50.000 0.00 0.00 45.03 3.41
5134 5315 2.233431 TGGGTTTAAGATGCATTGCCAC 59.767 45.455 6.12 0.09 0.00 5.01
5233 5414 2.742372 CAGGTTCTTCGGTGGGCG 60.742 66.667 0.00 0.00 0.00 6.13
5263 5444 6.991531 GGTCTATTGAGATCTTCTTCAGCAAT 59.008 38.462 0.00 2.81 33.14 3.56
5338 5519 4.819105 TTCCTACATCAACTCCATCGTT 57.181 40.909 0.00 0.00 0.00 3.85
5353 5534 4.408921 TCCATCGTTTATCCTTGGACATCT 59.591 41.667 0.00 0.00 31.67 2.90
5368 5549 3.135530 GGACATCTATTCCACTTCTGGCT 59.864 47.826 0.00 0.00 37.49 4.75
5389 5570 2.032834 TGTACGTTGCCGGCCATT 59.967 55.556 26.77 8.17 38.78 3.16
5404 5585 1.671556 GCCATTTGCTTGTTAACGGGG 60.672 52.381 0.26 0.00 36.87 5.73
5430 5611 3.445008 TCATCACTCCAGAGGTAAAGCT 58.555 45.455 0.00 0.00 0.00 3.74
5434 5615 3.514309 TCACTCCAGAGGTAAAGCTTACC 59.486 47.826 0.00 8.14 37.86 2.85
5435 5616 2.838813 ACTCCAGAGGTAAAGCTTACCC 59.161 50.000 16.70 12.14 38.33 3.69
5437 5618 3.253220 TCCAGAGGTAAAGCTTACCCAA 58.747 45.455 16.70 2.17 38.33 4.12
5451 5632 6.407202 AGCTTACCCAACTTGTAGTTCTATG 58.593 40.000 0.00 0.00 36.03 2.23
5452 5633 5.064834 GCTTACCCAACTTGTAGTTCTATGC 59.935 44.000 0.00 0.00 36.03 3.14
5462 5643 1.363744 AGTTCTATGCGCTGTGAAGC 58.636 50.000 9.73 5.40 0.00 3.86
5472 5653 3.217242 CTGTGAAGCGGCAAGTAGT 57.783 52.632 1.45 0.00 0.00 2.73
5476 5657 2.028476 TGTGAAGCGGCAAGTAGTGTAT 60.028 45.455 1.45 0.00 0.00 2.29
5496 5679 8.612145 AGTGTATGATTTAAACCTTACCCTTCT 58.388 33.333 3.76 0.00 0.00 2.85
5717 5900 1.128200 TAGCTGGTGTGGACACAAGT 58.872 50.000 14.47 5.69 46.98 3.16
5756 5939 1.205893 GCTGGAGACGATGAGGAGTTT 59.794 52.381 0.00 0.00 0.00 2.66
5771 5954 1.719780 GAGTTTTCGGAGCTGTACACG 59.280 52.381 0.00 0.00 0.00 4.49
5810 5993 1.691689 GATACCCCCGACCACCCTT 60.692 63.158 0.00 0.00 0.00 3.95
5885 6068 0.036010 GATATGAGTCATGGGGGCCG 60.036 60.000 16.15 0.00 0.00 6.13
5954 6137 1.066787 CCGTTCCTCAAGGGTCTTCTC 60.067 57.143 0.00 0.00 33.48 2.87
6107 6290 1.686052 CTGGACTGCACCTAGGAGATC 59.314 57.143 17.98 6.40 38.04 2.75
6322 6509 2.985847 GCTGCGGCAACCCTTCTT 60.986 61.111 14.08 0.00 38.54 2.52
6323 6510 2.982744 GCTGCGGCAACCCTTCTTC 61.983 63.158 14.08 0.00 38.54 2.87
6324 6511 1.600636 CTGCGGCAACCCTTCTTCA 60.601 57.895 3.44 0.00 0.00 3.02
6325 6512 1.856265 CTGCGGCAACCCTTCTTCAC 61.856 60.000 3.44 0.00 0.00 3.18
6326 6513 2.626780 GCGGCAACCCTTCTTCACC 61.627 63.158 0.00 0.00 0.00 4.02
6368 6560 4.436183 GCCACGAAGAAGAAAGAATACAGC 60.436 45.833 0.00 0.00 0.00 4.40
6696 6913 5.565259 GCACATTGTTAGTTTGTCATCTTCG 59.435 40.000 0.00 0.00 0.00 3.79
6703 6920 3.139077 AGTTTGTCATCTTCGTGTTCCC 58.861 45.455 0.00 0.00 0.00 3.97
6744 6970 2.730934 ATGCTTCATCTGCTCACCAT 57.269 45.000 0.00 0.00 0.00 3.55
6750 6976 4.820716 GCTTCATCTGCTCACCATATTTCT 59.179 41.667 0.00 0.00 0.00 2.52
6761 6987 7.560262 TGCTCACCATATTTCTAGTAGTGTAGT 59.440 37.037 0.00 0.00 0.00 2.73
6811 7050 5.131809 CCAGGATTCTTAACTCTGAAGGGAT 59.868 44.000 0.00 0.00 0.00 3.85
6820 7063 0.325933 TCTGAAGGGATGGTGCTGTG 59.674 55.000 0.00 0.00 0.00 3.66
7131 7527 0.675837 TGCTGCTTGATCCACAGAGC 60.676 55.000 10.07 3.18 35.15 4.09
7169 7569 8.804204 AGAATTAGTAGATCCTAATAACACCGG 58.196 37.037 0.00 0.00 36.79 5.28
7178 7578 6.112927 TCCTAATAACACCGGTAGTTTGTT 57.887 37.500 21.86 17.09 37.27 2.83
7192 7592 2.348605 TTTGTTTGCTGCTGCCGGAC 62.349 55.000 5.05 9.22 38.71 4.79
7255 7659 2.586079 CGCATCCGGCACTTCGAT 60.586 61.111 0.00 0.00 45.17 3.59
7256 7660 2.589492 CGCATCCGGCACTTCGATC 61.589 63.158 0.00 0.00 45.17 3.69
7257 7661 1.227380 GCATCCGGCACTTCGATCT 60.227 57.895 0.00 0.00 43.97 2.75
7258 7662 0.811616 GCATCCGGCACTTCGATCTT 60.812 55.000 0.00 0.00 43.97 2.40
7259 7663 1.656652 CATCCGGCACTTCGATCTTT 58.343 50.000 0.00 0.00 0.00 2.52
7260 7664 1.594862 CATCCGGCACTTCGATCTTTC 59.405 52.381 0.00 0.00 0.00 2.62
7261 7665 0.895530 TCCGGCACTTCGATCTTTCT 59.104 50.000 0.00 0.00 0.00 2.52
7262 7666 1.002366 CCGGCACTTCGATCTTTCTG 58.998 55.000 0.00 0.00 0.00 3.02
7263 7667 0.371645 CGGCACTTCGATCTTTCTGC 59.628 55.000 0.00 0.00 0.00 4.26
7264 7668 0.371645 GGCACTTCGATCTTTCTGCG 59.628 55.000 0.00 0.00 0.00 5.18
7265 7669 1.350193 GCACTTCGATCTTTCTGCGA 58.650 50.000 0.00 0.00 0.00 5.10
7266 7670 1.929836 GCACTTCGATCTTTCTGCGAT 59.070 47.619 0.00 0.00 33.71 4.58
7366 7783 7.256547 GCATGATGGTTAGGTTAGGTTAGGATA 60.257 40.741 0.00 0.00 0.00 2.59
7369 7786 5.470501 TGGTTAGGTTAGGTTAGGATAGGG 58.529 45.833 0.00 0.00 0.00 3.53
7377 7794 8.400317 AGGTTAGGTTAGGATAGGGTAGATTAG 58.600 40.741 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.181471 ACTCTGCTACGGAGATTGATTGG 60.181 47.826 10.33 0.00 39.05 3.16
20 21 1.231221 CGCTACTCTGCTACGGAGAT 58.769 55.000 10.33 0.00 39.05 2.75
24 25 1.669779 ACTAACGCTACTCTGCTACGG 59.330 52.381 0.00 0.00 0.00 4.02
27 28 4.331992 CACAGTACTAACGCTACTCTGCTA 59.668 45.833 0.00 0.00 0.00 3.49
38 39 1.059122 CATGCGCACACAGTACTAACG 59.941 52.381 14.90 0.00 0.00 3.18
54 58 4.225703 GCCCGAATTGGCCCATGC 62.226 66.667 0.00 0.00 46.11 4.06
62 66 4.225497 GGAGGAGTGCCCGAATTG 57.775 61.111 0.00 0.00 40.87 2.32
118 133 8.349983 GCTACTAATGTTTGTTCTTCTGGAAAA 58.650 33.333 0.00 0.00 35.51 2.29
219 254 2.507102 CCTGTACGCGTCTGCCTG 60.507 66.667 18.63 6.54 38.08 4.85
242 277 8.495949 TGTTTAGAAGATCGAGTGTGAAAATTC 58.504 33.333 0.00 0.00 0.00 2.17
245 280 7.207383 TCTGTTTAGAAGATCGAGTGTGAAAA 58.793 34.615 0.00 0.00 0.00 2.29
249 284 5.944013 TCTCTGTTTAGAAGATCGAGTGTG 58.056 41.667 0.00 0.00 31.21 3.82
250 285 6.576662 TTCTCTGTTTAGAAGATCGAGTGT 57.423 37.500 0.00 0.00 31.85 3.55
251 286 9.232082 CTATTTCTCTGTTTAGAAGATCGAGTG 57.768 37.037 0.00 0.00 36.85 3.51
252 287 9.179909 TCTATTTCTCTGTTTAGAAGATCGAGT 57.820 33.333 0.00 0.00 36.85 4.18
255 290 9.190858 CCATCTATTTCTCTGTTTAGAAGATCG 57.809 37.037 0.00 0.00 36.85 3.69
262 312 4.212214 GGCGCCATCTATTTCTCTGTTTAG 59.788 45.833 24.80 0.00 0.00 1.85
353 410 2.298163 GAGAGAGAACGGGGTTGTGTTA 59.702 50.000 0.00 0.00 0.00 2.41
357 414 0.471211 TGGAGAGAGAACGGGGTTGT 60.471 55.000 0.00 0.00 0.00 3.32
375 432 3.697045 CTGTTGACCCTAGACTCCTACTG 59.303 52.174 0.00 0.00 0.00 2.74
376 433 3.334280 ACTGTTGACCCTAGACTCCTACT 59.666 47.826 0.00 0.00 0.00 2.57
470 535 7.176690 AGTTGTAGAGAGAGAGAGAGAAAAAGG 59.823 40.741 0.00 0.00 0.00 3.11
471 536 8.110860 AGTTGTAGAGAGAGAGAGAGAAAAAG 57.889 38.462 0.00 0.00 0.00 2.27
472 537 7.942341 AGAGTTGTAGAGAGAGAGAGAGAAAAA 59.058 37.037 0.00 0.00 0.00 1.94
473 538 7.390440 CAGAGTTGTAGAGAGAGAGAGAGAAAA 59.610 40.741 0.00 0.00 0.00 2.29
474 539 6.878923 CAGAGTTGTAGAGAGAGAGAGAGAAA 59.121 42.308 0.00 0.00 0.00 2.52
475 540 6.212589 TCAGAGTTGTAGAGAGAGAGAGAGAA 59.787 42.308 0.00 0.00 0.00 2.87
476 541 5.719563 TCAGAGTTGTAGAGAGAGAGAGAGA 59.280 44.000 0.00 0.00 0.00 3.10
477 542 5.977635 TCAGAGTTGTAGAGAGAGAGAGAG 58.022 45.833 0.00 0.00 0.00 3.20
478 543 6.560003 ATCAGAGTTGTAGAGAGAGAGAGA 57.440 41.667 0.00 0.00 0.00 3.10
481 546 4.024893 GCGATCAGAGTTGTAGAGAGAGAG 60.025 50.000 0.00 0.00 0.00 3.20
620 699 2.168496 CTGTCGGTTCCCTACTTCTGA 58.832 52.381 0.00 0.00 0.00 3.27
621 700 1.893801 ACTGTCGGTTCCCTACTTCTG 59.106 52.381 0.00 0.00 0.00 3.02
622 701 2.169330 GACTGTCGGTTCCCTACTTCT 58.831 52.381 0.00 0.00 0.00 2.85
623 702 2.169330 AGACTGTCGGTTCCCTACTTC 58.831 52.381 1.52 0.00 0.00 3.01
624 703 2.305858 AGACTGTCGGTTCCCTACTT 57.694 50.000 1.52 0.00 0.00 2.24
712 810 4.592936 CTACTCGCTCGCCCGTCG 62.593 72.222 0.00 0.00 40.15 5.12
713 811 2.176273 TACTACTCGCTCGCCCGTC 61.176 63.158 0.00 0.00 0.00 4.79
714 812 2.124983 TACTACTCGCTCGCCCGT 60.125 61.111 0.00 0.00 0.00 5.28
715 813 1.985447 TTGTACTACTCGCTCGCCCG 61.985 60.000 0.00 0.00 0.00 6.13
779 886 2.111669 TGCCTCTGTGCCTGTGTG 59.888 61.111 0.00 0.00 0.00 3.82
781 888 1.964891 CTGTGCCTCTGTGCCTGTG 60.965 63.158 0.00 0.00 0.00 3.66
783 890 3.054503 GCTGTGCCTCTGTGCCTG 61.055 66.667 0.00 0.00 0.00 4.85
787 894 3.832237 AACCCGCTGTGCCTCTGTG 62.832 63.158 0.00 0.00 0.00 3.66
788 895 3.560251 AACCCGCTGTGCCTCTGT 61.560 61.111 0.00 0.00 0.00 3.41
876 1001 1.496060 TGTGGTGTGGTGTCTTCTCT 58.504 50.000 0.00 0.00 0.00 3.10
877 1002 2.417719 GATGTGGTGTGGTGTCTTCTC 58.582 52.381 0.00 0.00 0.00 2.87
878 1003 1.270305 CGATGTGGTGTGGTGTCTTCT 60.270 52.381 0.00 0.00 0.00 2.85
879 1004 1.148310 CGATGTGGTGTGGTGTCTTC 58.852 55.000 0.00 0.00 0.00 2.87
880 1005 0.884704 GCGATGTGGTGTGGTGTCTT 60.885 55.000 0.00 0.00 0.00 3.01
881 1006 1.301716 GCGATGTGGTGTGGTGTCT 60.302 57.895 0.00 0.00 0.00 3.41
882 1007 1.596752 TGCGATGTGGTGTGGTGTC 60.597 57.895 0.00 0.00 0.00 3.67
1016 1143 3.522731 CAGACTCTCGGCGGAGGG 61.523 72.222 18.92 18.92 46.80 4.30
1024 1151 4.544689 CCCGCGCTCAGACTCTCG 62.545 72.222 5.56 0.00 0.00 4.04
1025 1152 4.863925 GCCCGCGCTCAGACTCTC 62.864 72.222 5.56 0.00 0.00 3.20
1179 1306 1.423794 AACCAGAAGCGAAGGGGGAA 61.424 55.000 0.00 0.00 0.00 3.97
1180 1307 1.838073 GAACCAGAAGCGAAGGGGGA 61.838 60.000 0.00 0.00 0.00 4.81
1182 1309 0.674895 CAGAACCAGAAGCGAAGGGG 60.675 60.000 0.00 0.00 0.00 4.79
1183 1310 0.674895 CCAGAACCAGAAGCGAAGGG 60.675 60.000 0.00 0.00 0.00 3.95
1240 1367 3.623703 GAACAGCCTCCGGAACCCC 62.624 68.421 5.23 0.00 0.00 4.95
1279 1406 1.522668 CAACCGAAATCTCAGCACCA 58.477 50.000 0.00 0.00 0.00 4.17
1282 1409 2.555123 GGCAACCGAAATCTCAGCA 58.445 52.632 0.00 0.00 0.00 4.41
1313 1445 0.828959 CACGAACGCACGAACAAAAC 59.171 50.000 8.71 0.00 37.03 2.43
1316 1448 2.321740 GCACGAACGCACGAACAA 59.678 55.556 8.71 0.00 37.03 2.83
1318 1450 3.979961 ACGCACGAACGCACGAAC 61.980 61.111 14.23 0.13 36.19 3.95
1319 1451 3.978764 CACGCACGAACGCACGAA 61.979 61.111 14.23 0.00 36.19 3.85
1322 1454 4.993945 CTGCACGCACGAACGCAC 62.994 66.667 0.00 0.00 36.19 5.34
1369 1504 4.817063 CCGCAAATCTGGCACGCG 62.817 66.667 3.53 3.53 45.25 6.01
1528 1663 2.509964 AGAGTGGAACAAACCCTTGAGT 59.490 45.455 0.00 0.00 44.16 3.41
1579 1721 4.176851 GAGCTCGGTCGGTCGGTC 62.177 72.222 0.00 0.00 0.00 4.79
1589 1731 1.000896 AAATTGGGGGTGAGCTCGG 60.001 57.895 9.64 0.00 0.00 4.63
1595 1737 3.707821 CCATCCAAATTGGGGGTGA 57.292 52.632 12.67 0.00 38.32 4.02
1608 1762 0.808755 AAACGCGTCAAATCCCATCC 59.191 50.000 14.44 0.00 0.00 3.51
1663 1823 3.033773 TCCTCCTCATCCCCGGGA 61.034 66.667 26.32 9.16 35.55 5.14
1862 2022 8.700973 AGATTTGCGGGTGGTTAATTAATTAAT 58.299 29.630 20.60 4.81 35.02 1.40
1863 2023 8.068892 AGATTTGCGGGTGGTTAATTAATTAA 57.931 30.769 15.19 15.19 0.00 1.40
1864 2024 7.339721 TGAGATTTGCGGGTGGTTAATTAATTA 59.660 33.333 3.71 3.71 0.00 1.40
1865 2025 6.153680 TGAGATTTGCGGGTGGTTAATTAATT 59.846 34.615 5.89 5.89 0.00 1.40
1869 2029 3.192633 GTGAGATTTGCGGGTGGTTAATT 59.807 43.478 0.00 0.00 0.00 1.40
1880 2040 1.998315 CAGAGGAGTGTGAGATTTGCG 59.002 52.381 0.00 0.00 0.00 4.85
1906 2066 2.237143 AGTAAGGCACATAAGCTGCTGA 59.763 45.455 1.35 0.00 34.84 4.26
1907 2067 2.353889 CAGTAAGGCACATAAGCTGCTG 59.646 50.000 1.35 0.00 34.84 4.41
1909 2069 1.672881 CCAGTAAGGCACATAAGCTGC 59.327 52.381 0.00 0.00 34.17 5.25
1913 2073 3.812053 GAGCATCCAGTAAGGCACATAAG 59.188 47.826 0.00 0.00 37.29 1.73
1914 2074 3.199727 TGAGCATCCAGTAAGGCACATAA 59.800 43.478 0.00 0.00 37.29 1.90
1916 2076 1.561076 TGAGCATCCAGTAAGGCACAT 59.439 47.619 0.00 0.00 37.29 3.21
1918 2078 2.113860 TTGAGCATCCAGTAAGGCAC 57.886 50.000 0.00 0.00 37.29 5.01
1925 2085 2.089980 GTGAGCAATTGAGCATCCAGT 58.910 47.619 10.34 0.00 36.85 4.00
1944 2104 0.540365 CAAACAGGGGGCATCACAGT 60.540 55.000 0.00 0.00 0.00 3.55
1947 2107 1.463674 CTACAAACAGGGGGCATCAC 58.536 55.000 0.00 0.00 0.00 3.06
1948 2108 0.331278 CCTACAAACAGGGGGCATCA 59.669 55.000 0.00 0.00 31.47 3.07
1949 2109 0.331616 ACCTACAAACAGGGGGCATC 59.668 55.000 0.00 0.00 40.29 3.91
1950 2110 0.331616 GACCTACAAACAGGGGGCAT 59.668 55.000 0.00 0.00 40.29 4.40
1951 2111 1.765074 GACCTACAAACAGGGGGCA 59.235 57.895 0.00 0.00 40.29 5.36
1952 2112 1.376812 CGACCTACAAACAGGGGGC 60.377 63.158 0.00 0.00 40.29 5.80
1953 2113 0.909623 ATCGACCTACAAACAGGGGG 59.090 55.000 0.00 0.00 40.29 5.40
1954 2114 1.553248 TCATCGACCTACAAACAGGGG 59.447 52.381 0.00 0.00 40.29 4.79
1961 2121 1.407618 CGGGATGTCATCGACCTACAA 59.592 52.381 6.74 0.00 0.00 2.41
2148 2308 1.180029 GGATCTTGGTTGCACTGCAT 58.820 50.000 4.10 0.00 38.76 3.96
2197 2358 2.270850 GCAACGCTCCCATACCCA 59.729 61.111 0.00 0.00 0.00 4.51
2203 2364 3.551496 CTTCCAGGCAACGCTCCCA 62.551 63.158 0.00 0.00 46.39 4.37
2206 2367 1.743252 CTCCTTCCAGGCAACGCTC 60.743 63.158 0.00 0.00 46.39 5.03
2212 2373 0.984961 CCATCCTCTCCTTCCAGGCA 60.985 60.000 0.00 0.00 34.61 4.75
2290 2451 1.669760 GTCGCCATCACCGTTCCAA 60.670 57.895 0.00 0.00 0.00 3.53
2299 2460 0.598419 GATCTGCATCGTCGCCATCA 60.598 55.000 0.00 0.00 0.00 3.07
2348 2509 2.206576 AGACCAAACTGAAGGATGCC 57.793 50.000 0.00 0.00 0.00 4.40
2354 2515 5.695851 ATGCACTAAAGACCAAACTGAAG 57.304 39.130 0.00 0.00 0.00 3.02
2355 2516 6.321181 AGAAATGCACTAAAGACCAAACTGAA 59.679 34.615 0.00 0.00 0.00 3.02
2357 2518 5.916883 CAGAAATGCACTAAAGACCAAACTG 59.083 40.000 0.00 0.00 0.00 3.16
2393 2554 5.703592 TGACCGACACTAATGCTGTTAAAAT 59.296 36.000 0.00 0.00 0.00 1.82
2401 2562 3.067106 CTGTTTGACCGACACTAATGCT 58.933 45.455 0.00 0.00 0.00 3.79
2410 2571 4.705337 ATCTCTAGTCTGTTTGACCGAC 57.295 45.455 0.00 0.00 46.46 4.79
2818 2988 8.230472 AGCTTCATCCATTCTGGTAAATAAAG 57.770 34.615 0.00 0.00 39.03 1.85
3333 3503 1.202110 GCAGCACCATCATCAGAAACG 60.202 52.381 0.00 0.00 0.00 3.60
3542 3712 4.202461 ACTGAAGGAACATAGCAAAGTGGA 60.202 41.667 0.00 0.00 0.00 4.02
3764 3934 4.021104 GCATATAGACTGGATAGCACCACA 60.021 45.833 0.00 0.00 35.91 4.17
3813 3983 0.471022 GCAAAGTGGGAAAAGGGGGA 60.471 55.000 0.00 0.00 0.00 4.81
3814 3984 1.480212 GGCAAAGTGGGAAAAGGGGG 61.480 60.000 0.00 0.00 0.00 5.40
3815 3985 1.480212 GGGCAAAGTGGGAAAAGGGG 61.480 60.000 0.00 0.00 0.00 4.79
3816 3986 0.471780 AGGGCAAAGTGGGAAAAGGG 60.472 55.000 0.00 0.00 0.00 3.95
3817 3987 2.302587 TAGGGCAAAGTGGGAAAAGG 57.697 50.000 0.00 0.00 0.00 3.11
3818 3988 3.831911 TCATTAGGGCAAAGTGGGAAAAG 59.168 43.478 0.00 0.00 0.00 2.27
4000 4172 3.436015 TGGCCGAAAATGCATTCAAAATG 59.564 39.130 13.38 1.13 0.00 2.32
4007 4179 1.549203 AGACTGGCCGAAAATGCATT 58.451 45.000 5.99 5.99 0.00 3.56
4086 4258 0.171455 GCAGAGACACGGACCTGTAG 59.829 60.000 0.00 0.00 0.00 2.74
4363 4535 7.004086 AGACAAATGTTAGGGAAACTTCATCA 58.996 34.615 0.00 0.00 38.99 3.07
4617 4792 9.889128 TGATTTTCTTCCTTCTTGAAAAACAAT 57.111 25.926 0.00 0.00 41.16 2.71
4656 4831 2.832563 TCGTCAATTTCACTGAGTGCA 58.167 42.857 7.93 0.00 32.98 4.57
4691 4866 3.318839 CCAAAATGCTGGAAGTTGAGTGA 59.681 43.478 0.00 0.00 38.96 3.41
4922 5097 2.223641 GCCACAGCCAATGACATGTATG 60.224 50.000 0.00 0.00 0.00 2.39
4934 5109 0.983467 TGTCTTCATAGCCACAGCCA 59.017 50.000 0.00 0.00 41.25 4.75
4937 5112 3.930336 TGTCTTGTCTTCATAGCCACAG 58.070 45.455 0.00 0.00 0.00 3.66
4982 5157 1.102809 CACACAGCAACCAAGCTCCA 61.103 55.000 0.00 0.00 44.54 3.86
5012 5190 4.442706 ACTAGGCAACAGATATTTGGACG 58.557 43.478 0.00 0.00 41.41 4.79
5089 5270 6.493115 CAGTCAGGATATCCTCTGTAACTGAT 59.507 42.308 25.81 9.97 46.65 2.90
5110 5291 3.429410 GGCAATGCATCTTAAACCCAGTC 60.429 47.826 7.79 0.00 0.00 3.51
5134 5315 0.597637 AGTAAATCGATCGCCAGCCG 60.598 55.000 11.09 0.00 38.61 5.52
5143 5324 6.204882 GCCTTTTAGGTATGCAGTAAATCGAT 59.795 38.462 0.00 0.00 37.80 3.59
5233 5414 5.289083 AGAAGATCTCAATAGACCCAAGC 57.711 43.478 0.00 0.00 33.57 4.01
5263 5444 2.358090 CCCATACCAAAGAGGGCAATGA 60.358 50.000 0.00 0.00 43.89 2.57
5338 5519 7.348274 AGAAGTGGAATAGATGTCCAAGGATAA 59.652 37.037 0.00 0.00 46.66 1.75
5389 5570 2.351706 ACTTCCCCGTTAACAAGCAA 57.648 45.000 6.39 0.00 0.00 3.91
5404 5585 3.971245 ACCTCTGGAGTGATGAACTTC 57.029 47.619 0.00 0.00 40.07 3.01
5430 5611 5.172934 CGCATAGAACTACAAGTTGGGTAA 58.827 41.667 7.96 0.00 38.80 2.85
5434 5615 3.062639 CAGCGCATAGAACTACAAGTTGG 59.937 47.826 11.47 0.00 38.80 3.77
5435 5616 3.679980 ACAGCGCATAGAACTACAAGTTG 59.320 43.478 11.47 0.00 38.80 3.16
5437 5618 3.056821 TCACAGCGCATAGAACTACAAGT 60.057 43.478 11.47 0.00 0.00 3.16
5462 5643 6.315393 AGGTTTAAATCATACACTACTTGCCG 59.685 38.462 0.43 0.00 0.00 5.69
5470 5651 8.612145 AGAAGGGTAAGGTTTAAATCATACACT 58.388 33.333 11.87 11.87 0.00 3.55
5471 5652 8.803397 AGAAGGGTAAGGTTTAAATCATACAC 57.197 34.615 14.06 11.13 0.00 2.90
5472 5653 8.832735 AGAGAAGGGTAAGGTTTAAATCATACA 58.167 33.333 14.06 0.00 0.00 2.29
5476 5657 8.856103 CAAAAGAGAAGGGTAAGGTTTAAATCA 58.144 33.333 0.43 0.00 0.00 2.57
5549 5732 5.443693 CGTAGCAAAAATGCAGATGAAAAGC 60.444 40.000 3.41 0.00 37.25 3.51
5717 5900 1.133407 GCCTTTGTTGTGACGGTGAAA 59.867 47.619 0.00 0.00 0.00 2.69
5756 5939 0.669619 TGAACGTGTACAGCTCCGAA 59.330 50.000 10.20 0.00 0.00 4.30
5771 5954 3.383185 TCAACAGGGTTGTCCATTTGAAC 59.617 43.478 8.75 0.00 36.32 3.18
5810 5993 1.205655 CCGATGAAGTTCAGCAGGAGA 59.794 52.381 20.29 0.00 31.10 3.71
5885 6068 0.534873 AGAAGAGCTTCCCGAAGAGC 59.465 55.000 8.65 0.00 40.79 4.09
5909 6092 3.641434 AGATGGACAATCACCCAGAAG 57.359 47.619 0.00 0.00 37.81 2.85
5954 6137 1.376037 GGTCCTGTTCTGCCTTCCG 60.376 63.158 0.00 0.00 0.00 4.30
6107 6290 5.868257 TGATTTTGATCGTCGATCCTTTTG 58.132 37.500 27.83 0.00 38.20 2.44
6116 6299 5.006068 ACATGATGACTGATTTTGATCGTCG 59.994 40.000 0.00 0.00 31.02 5.12
6368 6560 1.069823 ACTGACTGACTGACTTGCTGG 59.930 52.381 0.00 0.00 0.00 4.85
6634 6850 1.365699 CATGCAGGCATTTTTCCAGC 58.634 50.000 3.57 0.00 36.74 4.85
6696 6913 5.741962 AGTAGAACTAGAAAGGGGAACAC 57.258 43.478 0.00 0.00 0.00 3.32
6774 7000 2.242882 ATCCTGGCAGGCTTTCAATT 57.757 45.000 29.02 2.77 34.61 2.32
6776 7002 1.076024 AGAATCCTGGCAGGCTTTCAA 59.924 47.619 32.41 18.37 34.61 2.69
6777 7003 0.700564 AGAATCCTGGCAGGCTTTCA 59.299 50.000 32.41 18.97 34.61 2.69
6780 7006 2.310052 AGTTAAGAATCCTGGCAGGCTT 59.690 45.455 29.02 25.35 34.61 4.35
6781 7007 1.918957 AGTTAAGAATCCTGGCAGGCT 59.081 47.619 29.02 17.40 34.61 4.58
6782 7008 2.092699 AGAGTTAAGAATCCTGGCAGGC 60.093 50.000 29.02 14.98 34.61 4.85
6783 7009 3.198635 TCAGAGTTAAGAATCCTGGCAGG 59.801 47.826 28.01 28.01 36.46 4.85
6784 7010 4.478206 TCAGAGTTAAGAATCCTGGCAG 57.522 45.455 7.75 7.75 0.00 4.85
6785 7011 4.323792 CCTTCAGAGTTAAGAATCCTGGCA 60.324 45.833 0.00 0.00 0.00 4.92
6811 7050 3.225798 GCCAAAGCCACAGCACCA 61.226 61.111 0.00 0.00 43.56 4.17
6994 7376 0.813610 GTACTATGTGGCATGGCGCA 60.814 55.000 33.86 33.86 45.17 6.09
7152 7552 6.155737 ACAAACTACCGGTGTTATTAGGATCT 59.844 38.462 19.93 0.00 0.00 2.75
7153 7553 6.343703 ACAAACTACCGGTGTTATTAGGATC 58.656 40.000 19.93 0.00 0.00 3.36
7168 7568 1.602920 GGCAGCAGCAAACAAACTACC 60.603 52.381 2.65 0.00 44.61 3.18
7169 7569 1.770957 GGCAGCAGCAAACAAACTAC 58.229 50.000 2.65 0.00 44.61 2.73
7244 7648 0.371645 GCAGAAAGATCGAAGTGCCG 59.628 55.000 0.00 0.00 0.00 5.69
7246 7650 1.350193 TCGCAGAAAGATCGAAGTGC 58.650 50.000 0.00 3.81 0.00 4.40
7253 7657 2.029470 AGGGATCGATCGCAGAAAGATC 60.029 50.000 35.12 12.55 45.78 2.75
7254 7658 1.967066 AGGGATCGATCGCAGAAAGAT 59.033 47.619 35.12 16.44 43.58 2.40
7255 7659 1.403814 AGGGATCGATCGCAGAAAGA 58.596 50.000 35.12 0.00 43.58 2.52
7256 7660 2.231215 AAGGGATCGATCGCAGAAAG 57.769 50.000 35.12 0.00 43.58 2.62
7257 7661 2.550978 GAAAGGGATCGATCGCAGAAA 58.449 47.619 35.12 0.00 43.58 2.52
7258 7662 1.536072 CGAAAGGGATCGATCGCAGAA 60.536 52.381 35.12 0.00 45.48 3.02
7259 7663 0.030773 CGAAAGGGATCGATCGCAGA 59.969 55.000 35.12 0.00 45.48 4.26
7260 7664 0.030773 TCGAAAGGGATCGATCGCAG 59.969 55.000 35.12 24.62 46.12 5.18
7261 7665 2.112029 TCGAAAGGGATCGATCGCA 58.888 52.632 35.12 17.71 46.12 5.10
7279 7683 1.682257 GACAGCAAGAAGGGAGGCT 59.318 57.895 0.00 0.00 36.99 4.58


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

AutoCloner maintained by Alex Coulton.