Multiple sequence alignment - TraesCS1A01G218700

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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 TraesCS1A01G218700 chr1A 100.000 5432 0 0 1 5432 387358978 387364409 0.000000e+00 10032
1 TraesCS1A01G218700 chr1D 96.678 2077 60 7 2024 4097 308180397 308182467 0.000000e+00 3445
2 TraesCS1A01G218700 chr1D 94.530 1938 72 16 1 1935 308178471 308180377 0.000000e+00 2961
3 TraesCS1A01G218700 chr1D 95.362 884 29 4 4149 5022 308182466 308183347 0.000000e+00 1395
4 TraesCS1A01G218700 chr1D 82.865 356 14 11 5022 5362 308192365 308192688 5.360000e-70 276
5 TraesCS1A01G218700 chr1B 93.666 2084 110 11 2024 4099 417265861 417267930 0.000000e+00 3097
6 TraesCS1A01G218700 chr1B 96.114 1055 35 1 883 1937 417264795 417265843 0.000000e+00 1716
7 TraesCS1A01G218700 chr1B 91.371 1298 45 25 4146 5418 417267931 417269186 0.000000e+00 1714
8 TraesCS1A01G218700 chr1B 86.429 899 62 21 1 894 417263293 417264136 0.000000e+00 929
9 TraesCS1A01G218700 chr1B 90.205 633 39 11 264 894 417264164 417264775 0.000000e+00 804
10 TraesCS1A01G218700 chr2D 85.491 703 96 6 1175 1874 591020001 591020700 0.000000e+00 728
11 TraesCS1A01G218700 chr2A 84.831 712 101 7 1166 1874 726022845 726023552 0.000000e+00 710
12 TraesCS1A01G218700 chr2B 84.240 717 104 8 1164 1874 716779366 716780079 0.000000e+00 689


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 TraesCS1A01G218700 chr1A 387358978 387364409 5431 False 10032.000000 10032 100.000000 1 5432 1 chr1A.!!$F1 5431
1 TraesCS1A01G218700 chr1D 308178471 308183347 4876 False 2600.333333 3445 95.523333 1 5022 3 chr1D.!!$F2 5021
2 TraesCS1A01G218700 chr1B 417263293 417269186 5893 False 1652.000000 3097 91.557000 1 5418 5 chr1B.!!$F1 5417
3 TraesCS1A01G218700 chr2D 591020001 591020700 699 False 728.000000 728 85.491000 1175 1874 1 chr2D.!!$F1 699
4 TraesCS1A01G218700 chr2A 726022845 726023552 707 False 710.000000 710 84.831000 1166 1874 1 chr2A.!!$F1 708
5 TraesCS1A01G218700 chr2B 716779366 716780079 713 False 689.000000 689 84.240000 1164 1874 1 chr2B.!!$F1 710

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
365 984 0.040781 ACAACAACGTGCGCCATTAC 60.041 50.0 4.18 0.00 0.00 1.89 F
563 1184 0.316442 CAATAGCTTGCCACGATGCG 60.316 55.0 0.00 0.00 0.00 4.73 F
1635 2287 0.034089 CCGGGGGCAAGAAGATTTCT 60.034 55.0 0.00 0.00 43.15 2.52 F
1948 2600 0.034616 GCAAGTGTCTGACAGGAGCT 59.965 55.0 11.41 1.59 0.00 4.09 F
3239 3900 0.691078 AGTATGAGGTGGCCCGACAT 60.691 55.0 0.00 3.64 36.84 3.06 F
3412 4074 2.009681 TTTTCCAAGGGCCTTTCTCC 57.990 50.0 18.16 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 1999 1.228124 CTTGTTGGTGAGCGGGGAA 60.228 57.895 0.00 0.00 0.00 3.97 R
1955 2607 1.884579 TCTGAAGTACACCGACAGTCC 59.115 52.381 0.00 0.00 0.00 3.85 R
3105 3766 1.252904 CCAAAGCATGTGGGGACAGG 61.253 60.000 0.00 0.00 40.96 4.00 R
3852 4516 2.538449 CGGCTTAAGTACGTTATGCTGG 59.462 50.000 4.02 9.48 41.41 4.85 R
4098 4763 0.249398 ATCCGTGCACAGAAGTACCC 59.751 55.000 18.64 0.00 0.00 3.69 R
5349 6045 0.402121 AAAGGGCGCCTCTTTCTTCT 59.598 50.000 27.23 13.13 30.89 2.85 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
91 92 5.981088 TTGAGCATTTAAGGCTTTGATGA 57.019 34.783 20.17 0.00 42.78 2.92
189 190 2.867109 AGAGTTGGCATGTTAGCAGT 57.133 45.000 0.00 0.00 35.83 4.40
262 263 8.773645 TGTTTCATCATTGTCCAATATATCGTC 58.226 33.333 0.00 0.00 0.00 4.20
365 984 0.040781 ACAACAACGTGCGCCATTAC 60.041 50.000 4.18 0.00 0.00 1.89
374 993 2.350102 CGTGCGCCATTACGATCTAGTA 60.350 50.000 12.12 0.00 42.54 1.82
392 1011 9.368674 GATCTAGTAAGTTCCTCTTAAAACCAC 57.631 37.037 0.00 0.00 39.88 4.16
399 1018 2.038033 TCCTCTTAAAACCACGGACCAG 59.962 50.000 0.00 0.00 0.00 4.00
436 1055 4.252570 AGTCTTCTATTCCTCTTCCCGA 57.747 45.455 0.00 0.00 0.00 5.14
450 1069 3.583086 TCTTCCCGAAGATTCTCAAACCT 59.417 43.478 2.98 0.00 42.06 3.50
454 1073 2.668457 CCGAAGATTCTCAAACCTGTCG 59.332 50.000 0.00 0.00 0.00 4.35
512 1132 2.183478 TCCATCGCACACTTGTCATT 57.817 45.000 0.00 0.00 0.00 2.57
563 1184 0.316442 CAATAGCTTGCCACGATGCG 60.316 55.000 0.00 0.00 0.00 4.73
693 1314 5.683876 TTCAACCCCAAACTCATCAAAAA 57.316 34.783 0.00 0.00 0.00 1.94
730 1351 9.358872 GATAAACAAGGAAGACAATTCCAAATC 57.641 33.333 9.20 0.27 41.00 2.17
804 1425 7.765695 TGCTGGAATTGTCTTTTTATCTCTT 57.234 32.000 0.00 0.00 0.00 2.85
808 1429 9.403110 CTGGAATTGTCTTTTTATCTCTTTGTG 57.597 33.333 0.00 0.00 0.00 3.33
809 1430 8.912988 TGGAATTGTCTTTTTATCTCTTTGTGT 58.087 29.630 0.00 0.00 0.00 3.72
855 1476 4.023291 AGCAGAAACCCTTGTTTTCTCAA 58.977 39.130 0.00 0.00 44.57 3.02
856 1477 4.466015 AGCAGAAACCCTTGTTTTCTCAAA 59.534 37.500 0.00 0.00 44.57 2.69
857 1478 5.046663 AGCAGAAACCCTTGTTTTCTCAAAA 60.047 36.000 0.00 0.00 44.57 2.44
858 1479 5.641636 GCAGAAACCCTTGTTTTCTCAAAAA 59.358 36.000 0.00 0.00 44.57 1.94
947 1599 1.481772 CCCTACCCGATACGAACCAAA 59.518 52.381 0.00 0.00 0.00 3.28
1162 1814 2.202797 CTGTCTCCACCGATGCCG 60.203 66.667 0.00 0.00 0.00 5.69
1163 1815 4.451150 TGTCTCCACCGATGCCGC 62.451 66.667 0.00 0.00 0.00 6.53
1347 1999 4.148825 GTCATGGAGGCGCTCGGT 62.149 66.667 7.64 0.00 0.00 4.69
1509 2161 3.391382 GTGCAGCCCTACTCCGGT 61.391 66.667 0.00 0.00 0.00 5.28
1635 2287 0.034089 CCGGGGGCAAGAAGATTTCT 60.034 55.000 0.00 0.00 43.15 2.52
1647 2299 3.011032 AGAAGATTTCTGCCACCTCCATT 59.989 43.478 0.00 0.00 38.91 3.16
1848 2500 2.947652 GCTGTGTGACATGGCTCATATT 59.052 45.455 6.59 0.00 0.00 1.28
1875 2527 2.230940 CGTTGCCGCTCAGGTATCG 61.231 63.158 0.00 0.00 43.70 2.92
1879 2531 1.008309 GCCGCTCAGGTATCGACTC 60.008 63.158 0.00 0.00 43.70 3.36
1886 2538 3.488384 GCTCAGGTATCGACTCTTCTGTG 60.488 52.174 0.00 0.00 0.00 3.66
1900 2552 4.016444 TCTTCTGTGTTTCTGTGCCTTTT 58.984 39.130 0.00 0.00 0.00 2.27
1941 2593 3.532892 CATCTGTTGCAAGTGTCTGAC 57.467 47.619 0.00 0.00 0.00 3.51
1942 2594 2.689553 TCTGTTGCAAGTGTCTGACA 57.310 45.000 6.36 6.36 0.00 3.58
1943 2595 2.554142 TCTGTTGCAAGTGTCTGACAG 58.446 47.619 11.41 1.41 36.68 3.51
1944 2596 1.600957 CTGTTGCAAGTGTCTGACAGG 59.399 52.381 11.41 5.28 32.88 4.00
1945 2597 1.209261 TGTTGCAAGTGTCTGACAGGA 59.791 47.619 11.41 0.00 0.00 3.86
1946 2598 1.869767 GTTGCAAGTGTCTGACAGGAG 59.130 52.381 11.41 4.93 0.00 3.69
1947 2599 0.250038 TGCAAGTGTCTGACAGGAGC 60.250 55.000 11.41 14.72 0.00 4.70
1948 2600 0.034616 GCAAGTGTCTGACAGGAGCT 59.965 55.000 11.41 1.59 0.00 4.09
1949 2601 1.273606 GCAAGTGTCTGACAGGAGCTA 59.726 52.381 11.41 0.00 0.00 3.32
1950 2602 2.289072 GCAAGTGTCTGACAGGAGCTAA 60.289 50.000 11.41 0.00 0.00 3.09
1951 2603 3.803715 GCAAGTGTCTGACAGGAGCTAAA 60.804 47.826 11.41 0.00 0.00 1.85
1952 2604 3.669251 AGTGTCTGACAGGAGCTAAAC 57.331 47.619 11.41 0.00 0.00 2.01
1953 2605 3.235200 AGTGTCTGACAGGAGCTAAACT 58.765 45.455 11.41 0.00 0.00 2.66
1954 2606 4.408276 AGTGTCTGACAGGAGCTAAACTA 58.592 43.478 11.41 0.00 0.00 2.24
1955 2607 4.461081 AGTGTCTGACAGGAGCTAAACTAG 59.539 45.833 11.41 0.00 0.00 2.57
1956 2608 3.764434 TGTCTGACAGGAGCTAAACTAGG 59.236 47.826 6.36 0.00 0.00 3.02
1957 2609 4.017808 GTCTGACAGGAGCTAAACTAGGA 58.982 47.826 1.81 0.00 0.00 2.94
1958 2610 4.017808 TCTGACAGGAGCTAAACTAGGAC 58.982 47.826 1.81 0.00 0.00 3.85
1959 2611 4.020543 CTGACAGGAGCTAAACTAGGACT 58.979 47.826 0.00 0.00 0.00 3.85
1960 2612 3.764434 TGACAGGAGCTAAACTAGGACTG 59.236 47.826 0.00 0.00 0.00 3.51
1961 2613 3.764972 GACAGGAGCTAAACTAGGACTGT 59.235 47.826 0.00 0.00 40.28 3.55
1962 2614 3.764972 ACAGGAGCTAAACTAGGACTGTC 59.235 47.826 0.00 0.00 33.04 3.51
1963 2615 3.018149 AGGAGCTAAACTAGGACTGTCG 58.982 50.000 1.07 0.00 0.00 4.35
1964 2616 2.099427 GGAGCTAAACTAGGACTGTCGG 59.901 54.545 1.07 0.00 0.00 4.79
1965 2617 2.754002 GAGCTAAACTAGGACTGTCGGT 59.246 50.000 1.07 0.00 0.00 4.69
1966 2618 2.492484 AGCTAAACTAGGACTGTCGGTG 59.508 50.000 1.07 0.00 0.00 4.94
1967 2619 2.230750 GCTAAACTAGGACTGTCGGTGT 59.769 50.000 1.07 0.00 0.00 4.16
1968 2620 3.441572 GCTAAACTAGGACTGTCGGTGTA 59.558 47.826 1.07 0.38 0.00 2.90
1969 2621 3.930634 AAACTAGGACTGTCGGTGTAC 57.069 47.619 1.07 0.00 0.00 2.90
1970 2622 2.875094 ACTAGGACTGTCGGTGTACT 57.125 50.000 1.07 0.00 32.64 2.73
1971 2623 3.151912 ACTAGGACTGTCGGTGTACTT 57.848 47.619 1.07 0.00 30.25 2.24
1972 2624 3.080319 ACTAGGACTGTCGGTGTACTTC 58.920 50.000 1.07 0.00 30.25 3.01
1973 2625 1.991121 AGGACTGTCGGTGTACTTCA 58.009 50.000 1.07 0.00 0.00 3.02
1974 2626 1.887198 AGGACTGTCGGTGTACTTCAG 59.113 52.381 1.07 0.00 0.00 3.02
1975 2627 1.884579 GGACTGTCGGTGTACTTCAGA 59.115 52.381 1.07 0.00 0.00 3.27
1976 2628 2.295349 GGACTGTCGGTGTACTTCAGAA 59.705 50.000 1.07 0.00 0.00 3.02
1977 2629 3.243636 GGACTGTCGGTGTACTTCAGAAA 60.244 47.826 1.07 0.00 0.00 2.52
1978 2630 4.365723 GACTGTCGGTGTACTTCAGAAAA 58.634 43.478 0.00 0.00 0.00 2.29
1979 2631 4.957296 ACTGTCGGTGTACTTCAGAAAAT 58.043 39.130 0.00 0.00 0.00 1.82
1980 2632 4.750098 ACTGTCGGTGTACTTCAGAAAATG 59.250 41.667 0.00 0.00 0.00 2.32
1981 2633 3.496884 TGTCGGTGTACTTCAGAAAATGC 59.503 43.478 0.00 0.00 0.00 3.56
1982 2634 3.496884 GTCGGTGTACTTCAGAAAATGCA 59.503 43.478 0.00 0.00 0.00 3.96
1983 2635 3.745975 TCGGTGTACTTCAGAAAATGCAG 59.254 43.478 0.00 0.00 0.00 4.41
1984 2636 3.498397 CGGTGTACTTCAGAAAATGCAGT 59.502 43.478 0.00 0.00 38.95 4.40
1985 2637 4.688879 CGGTGTACTTCAGAAAATGCAGTA 59.311 41.667 0.00 0.00 36.70 2.74
1986 2638 5.178623 CGGTGTACTTCAGAAAATGCAGTAA 59.821 40.000 0.00 0.00 39.01 2.24
1987 2639 6.293190 CGGTGTACTTCAGAAAATGCAGTAAA 60.293 38.462 0.00 0.00 39.01 2.01
1988 2640 7.573096 CGGTGTACTTCAGAAAATGCAGTAAAT 60.573 37.037 0.00 0.00 39.01 1.40
1989 2641 7.750903 GGTGTACTTCAGAAAATGCAGTAAATC 59.249 37.037 0.00 0.00 39.01 2.17
1990 2642 8.289618 GTGTACTTCAGAAAATGCAGTAAATCA 58.710 33.333 0.00 0.00 39.01 2.57
1991 2643 8.289618 TGTACTTCAGAAAATGCAGTAAATCAC 58.710 33.333 0.00 0.00 39.01 3.06
1992 2644 7.516198 ACTTCAGAAAATGCAGTAAATCACT 57.484 32.000 0.00 0.00 33.27 3.41
1993 2645 7.588512 ACTTCAGAAAATGCAGTAAATCACTC 58.411 34.615 0.00 0.00 33.27 3.51
1994 2646 7.229306 ACTTCAGAAAATGCAGTAAATCACTCA 59.771 33.333 0.00 0.00 33.27 3.41
1995 2647 7.509141 TCAGAAAATGCAGTAAATCACTCAA 57.491 32.000 0.00 0.00 34.26 3.02
2039 2691 8.514330 ACAAGGTTCAACAAGTTTTAGTATGA 57.486 30.769 0.00 0.00 0.00 2.15
2124 2779 1.679559 GCAACAATGGATGCTCCCCC 61.680 60.000 6.11 0.00 39.49 5.40
2297 2954 5.460419 CAGTAAGGTAGTCGATTTCTGCATC 59.540 44.000 0.00 0.00 0.00 3.91
2372 3029 2.151502 TTTCACTGGGTTTTGGCAGA 57.848 45.000 0.00 0.00 0.00 4.26
2646 3305 4.860907 GCTCTTTACGATTACGAGGACAAA 59.139 41.667 0.00 0.00 42.66 2.83
3105 3766 4.761227 TCCCAAATACGGTTTTGTTACTCC 59.239 41.667 10.28 0.00 35.30 3.85
3239 3900 0.691078 AGTATGAGGTGGCCCGACAT 60.691 55.000 0.00 3.64 36.84 3.06
3412 4074 2.009681 TTTTCCAAGGGCCTTTCTCC 57.990 50.000 18.16 0.00 0.00 3.71
3607 4269 5.843673 TGAAAGGCAACAAAGTACAATGA 57.156 34.783 5.07 0.00 41.41 2.57
3713 4375 2.954989 TGTGGCTGTGCAAGAATACAAA 59.045 40.909 0.00 0.00 0.00 2.83
3817 4481 5.477510 TGTCAACTTTGTTTTGTGATTGCT 58.522 33.333 0.00 0.00 0.00 3.91
3852 4516 8.584600 CAACAACACGTGAACTACTATATCTTC 58.415 37.037 25.01 0.00 0.00 2.87
3915 4579 7.981225 ACATACCTGACATTTTAATCATTTGCC 59.019 33.333 0.00 0.00 0.00 4.52
3998 4662 6.944290 TGCATCATTAATCTATCCCTCTTTGG 59.056 38.462 0.00 0.00 0.00 3.28
4027 4691 3.374745 AGAAAAACGAAACATGCTGCAG 58.625 40.909 10.11 10.11 0.00 4.41
4053 4717 8.261492 AGATGAACTCACTATACAGCTTTTTG 57.739 34.615 0.00 0.00 0.00 2.44
4056 4720 8.306680 TGAACTCACTATACAGCTTTTTGTAC 57.693 34.615 0.00 0.00 36.45 2.90
4100 4765 8.752005 TTAGATTGAGAAAACTGGATATTGGG 57.248 34.615 0.00 0.00 0.00 4.12
4101 4766 6.735556 AGATTGAGAAAACTGGATATTGGGT 58.264 36.000 0.00 0.00 0.00 4.51
4102 4767 7.872138 AGATTGAGAAAACTGGATATTGGGTA 58.128 34.615 0.00 0.00 0.00 3.69
4103 4768 7.775561 AGATTGAGAAAACTGGATATTGGGTAC 59.224 37.037 0.00 0.00 0.00 3.34
4104 4769 6.636454 TGAGAAAACTGGATATTGGGTACT 57.364 37.500 0.00 0.00 0.00 2.73
4105 4770 7.027874 TGAGAAAACTGGATATTGGGTACTT 57.972 36.000 0.00 0.00 0.00 2.24
4106 4771 7.110155 TGAGAAAACTGGATATTGGGTACTTC 58.890 38.462 0.00 0.00 0.00 3.01
4107 4772 7.037586 TGAGAAAACTGGATATTGGGTACTTCT 60.038 37.037 0.00 0.00 0.00 2.85
4108 4773 7.112779 AGAAAACTGGATATTGGGTACTTCTG 58.887 38.462 0.00 0.00 0.00 3.02
4109 4774 6.388619 AAACTGGATATTGGGTACTTCTGT 57.611 37.500 0.00 0.00 0.00 3.41
4110 4775 5.359194 ACTGGATATTGGGTACTTCTGTG 57.641 43.478 0.00 0.00 0.00 3.66
4111 4776 4.130118 CTGGATATTGGGTACTTCTGTGC 58.870 47.826 0.00 0.00 0.00 4.57
4112 4777 3.521531 TGGATATTGGGTACTTCTGTGCA 59.478 43.478 0.00 0.00 0.00 4.57
4113 4778 3.877508 GGATATTGGGTACTTCTGTGCAC 59.122 47.826 10.75 10.75 32.64 4.57
4114 4779 1.808411 ATTGGGTACTTCTGTGCACG 58.192 50.000 13.13 7.36 34.84 5.34
4115 4780 0.250124 TTGGGTACTTCTGTGCACGG 60.250 55.000 20.12 20.12 34.84 4.94
4116 4781 1.116536 TGGGTACTTCTGTGCACGGA 61.117 55.000 24.54 24.54 34.84 4.69
4117 4782 0.249398 GGGTACTTCTGTGCACGGAT 59.751 55.000 28.33 17.25 0.00 4.18
4118 4783 1.479323 GGGTACTTCTGTGCACGGATA 59.521 52.381 28.33 16.19 0.00 2.59
4119 4784 2.093869 GGGTACTTCTGTGCACGGATAA 60.094 50.000 28.33 14.15 0.00 1.75
4120 4785 3.592059 GGTACTTCTGTGCACGGATAAA 58.408 45.455 28.33 13.42 0.00 1.40
4121 4786 3.370061 GGTACTTCTGTGCACGGATAAAC 59.630 47.826 28.33 22.82 0.00 2.01
4122 4787 3.402628 ACTTCTGTGCACGGATAAACT 57.597 42.857 28.33 7.16 0.00 2.66
4123 4788 3.740115 ACTTCTGTGCACGGATAAACTT 58.260 40.909 28.33 7.21 0.00 2.66
4124 4789 3.746492 ACTTCTGTGCACGGATAAACTTC 59.254 43.478 28.33 0.00 0.00 3.01
4125 4790 3.678056 TCTGTGCACGGATAAACTTCT 57.322 42.857 24.54 0.00 0.00 2.85
4126 4791 3.325870 TCTGTGCACGGATAAACTTCTG 58.674 45.455 24.54 0.00 0.00 3.02
4127 4792 3.006430 TCTGTGCACGGATAAACTTCTGA 59.994 43.478 24.54 0.00 0.00 3.27
4128 4793 3.734463 TGTGCACGGATAAACTTCTGAA 58.266 40.909 13.13 0.00 0.00 3.02
4129 4794 4.130857 TGTGCACGGATAAACTTCTGAAA 58.869 39.130 13.13 0.00 0.00 2.69
4130 4795 4.024387 TGTGCACGGATAAACTTCTGAAAC 60.024 41.667 13.13 0.00 0.00 2.78
4131 4796 4.024387 GTGCACGGATAAACTTCTGAAACA 60.024 41.667 0.00 0.00 0.00 2.83
4132 4797 4.759693 TGCACGGATAAACTTCTGAAACAT 59.240 37.500 0.00 0.00 0.00 2.71
4133 4798 5.240623 TGCACGGATAAACTTCTGAAACATT 59.759 36.000 0.00 0.00 0.00 2.71
4134 4799 6.428465 TGCACGGATAAACTTCTGAAACATTA 59.572 34.615 0.00 0.00 0.00 1.90
4135 4800 7.041030 TGCACGGATAAACTTCTGAAACATTAA 60.041 33.333 0.00 0.00 0.00 1.40
4136 4801 7.270579 GCACGGATAAACTTCTGAAACATTAAC 59.729 37.037 0.00 0.00 0.00 2.01
4137 4802 7.477422 CACGGATAAACTTCTGAAACATTAACG 59.523 37.037 0.00 4.30 0.00 3.18
4138 4803 7.385752 ACGGATAAACTTCTGAAACATTAACGA 59.614 33.333 15.36 0.00 0.00 3.85
4139 4804 8.388103 CGGATAAACTTCTGAAACATTAACGAT 58.612 33.333 0.00 0.00 0.00 3.73
4147 4812 9.638300 CTTCTGAAACATTAACGATACAATAGC 57.362 33.333 0.00 0.00 0.00 2.97
4336 5008 3.812156 TCGTTGACTTGGAGAAGAACA 57.188 42.857 0.00 0.00 32.98 3.18
4398 5070 2.219080 TTGCATTTGAGATGCCTGGA 57.781 45.000 5.44 0.00 43.94 3.86
4403 5075 3.563223 CATTTGAGATGCCTGGATTCCT 58.437 45.455 3.95 0.00 0.00 3.36
4566 5239 9.293404 ACTCATGAATAATCATTGAAGGTATGG 57.707 33.333 0.00 0.00 43.89 2.74
4570 5243 7.888424 TGAATAATCATTGAAGGTATGGCATG 58.112 34.615 10.98 0.00 0.00 4.06
4572 5245 8.481492 AATAATCATTGAAGGTATGGCATGAA 57.519 30.769 10.98 0.00 0.00 2.57
4644 5317 3.378742 TCGTTGGCAGTTTGTTTATGTGT 59.621 39.130 0.00 0.00 0.00 3.72
4797 5470 4.444536 TGCAGTACTTCAGTTTACCGTTT 58.555 39.130 0.00 0.00 0.00 3.60
4856 5529 6.449635 TCAATGGTATGCTTGGTGTATTTC 57.550 37.500 0.00 0.00 0.00 2.17
4857 5530 6.186957 TCAATGGTATGCTTGGTGTATTTCT 58.813 36.000 0.00 0.00 0.00 2.52
4858 5531 6.095300 TCAATGGTATGCTTGGTGTATTTCTG 59.905 38.462 0.00 0.00 0.00 3.02
4859 5532 5.172687 TGGTATGCTTGGTGTATTTCTGA 57.827 39.130 0.00 0.00 0.00 3.27
4981 5664 4.998033 TCTTTAATGCCGTGTGTGTATCAA 59.002 37.500 0.00 0.00 0.00 2.57
5016 5699 9.630098 TCCTATTCGTAGTTGTTTTTGTACTAG 57.370 33.333 0.00 0.00 0.00 2.57
5017 5700 9.415544 CCTATTCGTAGTTGTTTTTGTACTAGT 57.584 33.333 0.00 0.00 0.00 2.57
5101 5784 7.918562 GGTTCACATGTGTAGTTTTGTAATTGT 59.081 33.333 24.63 0.00 0.00 2.71
5139 5822 6.651225 ACTTGAAGTTTTTCTATCCTCTTCCG 59.349 38.462 0.00 0.00 34.31 4.30
5146 5829 7.125963 AGTTTTTCTATCCTCTTCCGTATCCTT 59.874 37.037 0.00 0.00 0.00 3.36
5161 5844 3.756082 ATCCTTCCTTGGCATGGTTTA 57.244 42.857 17.94 5.62 0.00 2.01
5162 5845 3.534357 TCCTTCCTTGGCATGGTTTAA 57.466 42.857 17.94 5.72 0.00 1.52
5163 5846 3.850752 TCCTTCCTTGGCATGGTTTAAA 58.149 40.909 17.94 5.40 0.00 1.52
5164 5847 3.576550 TCCTTCCTTGGCATGGTTTAAAC 59.423 43.478 17.94 9.98 0.00 2.01
5165 5848 3.578282 CCTTCCTTGGCATGGTTTAAACT 59.422 43.478 17.50 0.00 0.00 2.66
5166 5849 4.040339 CCTTCCTTGGCATGGTTTAAACTT 59.960 41.667 17.50 3.67 0.00 2.66
5167 5850 5.454613 CCTTCCTTGGCATGGTTTAAACTTT 60.455 40.000 17.50 3.33 0.00 2.66
5168 5851 5.208463 TCCTTGGCATGGTTTAAACTTTC 57.792 39.130 17.50 2.49 0.00 2.62
5216 5906 9.675464 AAATCATTCCATTTGTTTCATTATGCT 57.325 25.926 0.00 0.00 0.00 3.79
5223 5913 5.726980 TTTGTTTCATTATGCTGCCTTCT 57.273 34.783 0.00 0.00 0.00 2.85
5224 5914 4.707030 TGTTTCATTATGCTGCCTTCTG 57.293 40.909 0.00 0.00 0.00 3.02
5227 5917 4.970662 TTCATTATGCTGCCTTCTGTTC 57.029 40.909 0.00 0.00 0.00 3.18
5228 5918 3.954200 TCATTATGCTGCCTTCTGTTCA 58.046 40.909 0.00 0.00 0.00 3.18
5230 5920 4.951715 TCATTATGCTGCCTTCTGTTCATT 59.048 37.500 0.00 0.00 0.00 2.57
5231 5921 4.970662 TTATGCTGCCTTCTGTTCATTC 57.029 40.909 0.00 0.00 0.00 2.67
5232 5922 1.159285 TGCTGCCTTCTGTTCATTCG 58.841 50.000 0.00 0.00 0.00 3.34
5233 5923 1.270785 TGCTGCCTTCTGTTCATTCGA 60.271 47.619 0.00 0.00 0.00 3.71
5234 5924 1.806542 GCTGCCTTCTGTTCATTCGAA 59.193 47.619 0.00 0.00 0.00 3.71
5235 5925 2.421424 GCTGCCTTCTGTTCATTCGAAT 59.579 45.455 4.39 4.39 32.61 3.34
5236 5926 3.119708 GCTGCCTTCTGTTCATTCGAATT 60.120 43.478 8.21 0.00 32.61 2.17
5237 5927 4.094887 GCTGCCTTCTGTTCATTCGAATTA 59.905 41.667 8.21 0.00 32.61 1.40
5238 5928 5.545658 TGCCTTCTGTTCATTCGAATTAC 57.454 39.130 8.21 10.25 32.61 1.89
5239 5929 5.000591 TGCCTTCTGTTCATTCGAATTACA 58.999 37.500 8.21 14.14 32.61 2.41
5240 5930 5.106712 TGCCTTCTGTTCATTCGAATTACAC 60.107 40.000 8.21 6.07 32.61 2.90
5241 5931 5.673818 GCCTTCTGTTCATTCGAATTACACC 60.674 44.000 8.21 0.00 32.61 4.16
5242 5932 5.411361 CCTTCTGTTCATTCGAATTACACCA 59.589 40.000 8.21 0.70 32.61 4.17
5243 5933 6.072728 CCTTCTGTTCATTCGAATTACACCAA 60.073 38.462 8.21 8.26 32.61 3.67
5244 5934 6.480524 TCTGTTCATTCGAATTACACCAAG 57.519 37.500 8.21 4.72 32.61 3.61
5245 5935 5.995282 TCTGTTCATTCGAATTACACCAAGT 59.005 36.000 8.21 0.00 32.61 3.16
5246 5936 5.996219 TGTTCATTCGAATTACACCAAGTG 58.004 37.500 8.21 0.00 34.93 3.16
5247 5937 5.049060 TGTTCATTCGAATTACACCAAGTGG 60.049 40.000 8.21 0.00 33.83 4.00
5248 5938 5.048991 GTTCATTCGAATTACACCAAGTGGT 60.049 40.000 8.21 0.00 40.58 4.16
5249 5939 6.514376 GTTCATTCGAATTACACCAAGTGGTT 60.514 38.462 8.21 0.00 38.94 3.67
5250 5940 7.945822 GTTCATTCGAATTACACCAAGTGGTTT 60.946 37.037 8.21 0.00 38.94 3.27
5348 6044 7.024340 TCGCTATTCGAGTTTGATAGTTACT 57.976 36.000 3.66 0.00 43.16 2.24
5349 6045 8.146479 TCGCTATTCGAGTTTGATAGTTACTA 57.854 34.615 0.00 0.00 43.16 1.82
5350 6046 8.281194 TCGCTATTCGAGTTTGATAGTTACTAG 58.719 37.037 0.00 0.00 43.16 2.57
5362 6058 7.028926 TGATAGTTACTAGAAGAAAGAGGCG 57.971 40.000 0.00 0.00 0.00 5.52
5415 6111 8.239314 TGATCATTGTAAATCAGTTTTCTGCTC 58.761 33.333 0.00 0.00 46.59 4.26
5416 6112 7.750229 TCATTGTAAATCAGTTTTCTGCTCT 57.250 32.000 0.00 0.00 46.59 4.09
5418 6114 8.077991 TCATTGTAAATCAGTTTTCTGCTCTTG 58.922 33.333 0.00 0.00 46.59 3.02
5419 6115 6.942532 TGTAAATCAGTTTTCTGCTCTTGT 57.057 33.333 0.00 0.00 46.59 3.16
5420 6116 8.445275 TTGTAAATCAGTTTTCTGCTCTTGTA 57.555 30.769 0.00 0.00 46.59 2.41
5421 6117 8.621532 TGTAAATCAGTTTTCTGCTCTTGTAT 57.378 30.769 0.00 0.00 46.59 2.29
5422 6118 9.719355 TGTAAATCAGTTTTCTGCTCTTGTATA 57.281 29.630 0.00 0.00 46.59 1.47
5425 6121 9.453572 AAATCAGTTTTCTGCTCTTGTATATCA 57.546 29.630 0.00 0.00 46.59 2.15
5426 6122 7.834068 TCAGTTTTCTGCTCTTGTATATCAC 57.166 36.000 0.00 0.00 46.59 3.06
5427 6123 6.818644 TCAGTTTTCTGCTCTTGTATATCACC 59.181 38.462 0.00 0.00 46.59 4.02
5428 6124 6.037610 CAGTTTTCTGCTCTTGTATATCACCC 59.962 42.308 0.00 0.00 41.24 4.61
5429 6125 4.322080 TTCTGCTCTTGTATATCACCCG 57.678 45.455 0.00 0.00 0.00 5.28
5430 6126 3.296854 TCTGCTCTTGTATATCACCCGT 58.703 45.455 0.00 0.00 0.00 5.28
5431 6127 3.068165 TCTGCTCTTGTATATCACCCGTG 59.932 47.826 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
365 984 8.248945 TGGTTTTAAGAGGAACTTACTAGATCG 58.751 37.037 0.00 0.00 41.55 3.69
374 993 4.132336 GTCCGTGGTTTTAAGAGGAACTT 58.868 43.478 0.00 0.00 41.55 2.66
399 1018 9.682465 AATAGAAGACTTAAATGGTTAACCTCC 57.318 33.333 24.78 0.00 36.82 4.30
414 1033 4.611367 TCGGGAAGAGGAATAGAAGACTT 58.389 43.478 0.00 0.00 0.00 3.01
436 1055 3.071023 TGGACGACAGGTTTGAGAATCTT 59.929 43.478 0.00 0.00 34.92 2.40
450 1069 8.637196 ATGAGATAATTAGATACTGGACGACA 57.363 34.615 0.00 0.00 0.00 4.35
512 1132 7.965718 AGTTGGAATTGATGAAAAGGAATCAA 58.034 30.769 0.97 0.97 44.54 2.57
568 1189 2.255316 CACTGTTTTTCCGCGTTGTTT 58.745 42.857 4.92 0.00 0.00 2.83
804 1425 5.404366 GCGAAGTTTCTACACATCTACACAA 59.596 40.000 0.00 0.00 0.00 3.33
808 1429 6.462073 TTTGCGAAGTTTCTACACATCTAC 57.538 37.500 0.00 0.00 0.00 2.59
809 1430 7.485418 TTTTTGCGAAGTTTCTACACATCTA 57.515 32.000 0.00 0.00 0.00 1.98
811 1432 5.115622 GCTTTTTGCGAAGTTTCTACACATC 59.884 40.000 0.00 0.00 0.00 3.06
812 1433 4.976116 GCTTTTTGCGAAGTTTCTACACAT 59.024 37.500 0.00 0.00 0.00 3.21
813 1434 4.142578 TGCTTTTTGCGAAGTTTCTACACA 60.143 37.500 0.00 0.00 46.63 3.72
814 1435 4.347813 TGCTTTTTGCGAAGTTTCTACAC 58.652 39.130 0.00 0.00 46.63 2.90
866 1487 1.609208 TTGCAAGGGTTTCTGCTCTC 58.391 50.000 0.00 0.00 0.00 3.20
919 1571 2.288642 TATCGGGTAGGGCTGGTCGT 62.289 60.000 0.00 0.00 0.00 4.34
920 1572 1.529948 TATCGGGTAGGGCTGGTCG 60.530 63.158 0.00 0.00 0.00 4.79
947 1599 3.096357 CCCGGGGAAAATCTGGGT 58.904 61.111 14.71 0.00 44.04 4.51
1146 1798 4.451150 GCGGCATCGGTGGAGACA 62.451 66.667 0.00 0.00 36.79 3.41
1347 1999 1.228124 CTTGTTGGTGAGCGGGGAA 60.228 57.895 0.00 0.00 0.00 3.97
1635 2287 2.817258 CGAAAAGTAAATGGAGGTGGCA 59.183 45.455 0.00 0.00 0.00 4.92
1647 2299 2.561478 AGGGCAAGCTCGAAAAGTAA 57.439 45.000 0.00 0.00 0.00 2.24
1875 2527 2.545946 GGCACAGAAACACAGAAGAGTC 59.454 50.000 0.00 0.00 0.00 3.36
1879 2531 4.107622 CAAAAGGCACAGAAACACAGAAG 58.892 43.478 0.00 0.00 0.00 2.85
1886 2538 6.913170 TCTAATCATCAAAAGGCACAGAAAC 58.087 36.000 0.00 0.00 0.00 2.78
1921 2573 2.874086 TGTCAGACACTTGCAACAGATG 59.126 45.455 0.00 0.00 0.00 2.90
1937 2589 4.020543 AGTCCTAGTTTAGCTCCTGTCAG 58.979 47.826 0.00 0.00 0.00 3.51
1938 2590 3.764434 CAGTCCTAGTTTAGCTCCTGTCA 59.236 47.826 0.00 0.00 0.00 3.58
1939 2591 3.764972 ACAGTCCTAGTTTAGCTCCTGTC 59.235 47.826 0.00 0.00 0.00 3.51
1940 2592 3.764972 GACAGTCCTAGTTTAGCTCCTGT 59.235 47.826 0.00 0.00 0.00 4.00
1941 2593 3.181495 CGACAGTCCTAGTTTAGCTCCTG 60.181 52.174 0.00 0.00 0.00 3.86
1942 2594 3.018149 CGACAGTCCTAGTTTAGCTCCT 58.982 50.000 0.00 0.00 0.00 3.69
1943 2595 2.099427 CCGACAGTCCTAGTTTAGCTCC 59.901 54.545 0.00 0.00 0.00 4.70
1944 2596 2.754002 ACCGACAGTCCTAGTTTAGCTC 59.246 50.000 0.00 0.00 0.00 4.09
1945 2597 2.492484 CACCGACAGTCCTAGTTTAGCT 59.508 50.000 0.00 0.00 0.00 3.32
1946 2598 2.230750 ACACCGACAGTCCTAGTTTAGC 59.769 50.000 0.00 0.00 0.00 3.09
1947 2599 4.699257 AGTACACCGACAGTCCTAGTTTAG 59.301 45.833 0.00 0.00 0.00 1.85
1948 2600 4.655963 AGTACACCGACAGTCCTAGTTTA 58.344 43.478 0.00 0.00 0.00 2.01
1949 2601 3.494332 AGTACACCGACAGTCCTAGTTT 58.506 45.455 0.00 0.00 0.00 2.66
1950 2602 3.151912 AGTACACCGACAGTCCTAGTT 57.848 47.619 0.00 0.00 0.00 2.24
1951 2603 2.875094 AGTACACCGACAGTCCTAGT 57.125 50.000 0.00 0.00 0.00 2.57
1952 2604 3.079578 TGAAGTACACCGACAGTCCTAG 58.920 50.000 0.00 0.00 0.00 3.02
1953 2605 3.079578 CTGAAGTACACCGACAGTCCTA 58.920 50.000 0.00 0.00 0.00 2.94
1954 2606 1.887198 CTGAAGTACACCGACAGTCCT 59.113 52.381 0.00 0.00 0.00 3.85
1955 2607 1.884579 TCTGAAGTACACCGACAGTCC 59.115 52.381 0.00 0.00 0.00 3.85
1956 2608 3.637998 TTCTGAAGTACACCGACAGTC 57.362 47.619 0.00 0.00 0.00 3.51
1957 2609 4.395959 TTTTCTGAAGTACACCGACAGT 57.604 40.909 0.00 0.00 0.00 3.55
1958 2610 4.377431 GCATTTTCTGAAGTACACCGACAG 60.377 45.833 0.00 0.00 0.00 3.51
1959 2611 3.496884 GCATTTTCTGAAGTACACCGACA 59.503 43.478 0.00 0.00 0.00 4.35
1960 2612 3.496884 TGCATTTTCTGAAGTACACCGAC 59.503 43.478 0.00 0.00 0.00 4.79
1961 2613 3.734463 TGCATTTTCTGAAGTACACCGA 58.266 40.909 0.00 0.00 0.00 4.69
1962 2614 3.498397 ACTGCATTTTCTGAAGTACACCG 59.502 43.478 0.00 0.00 42.41 4.94
1963 2615 6.554334 TTACTGCATTTTCTGAAGTACACC 57.446 37.500 0.00 0.00 44.33 4.16
1964 2616 8.289618 TGATTTACTGCATTTTCTGAAGTACAC 58.710 33.333 0.00 0.00 44.33 2.90
1965 2617 8.289618 GTGATTTACTGCATTTTCTGAAGTACA 58.710 33.333 0.00 0.00 44.33 2.90
1966 2618 8.507249 AGTGATTTACTGCATTTTCTGAAGTAC 58.493 33.333 0.00 0.00 44.33 2.73
1967 2619 8.621532 AGTGATTTACTGCATTTTCTGAAGTA 57.378 30.769 0.00 0.00 42.41 2.24
1968 2620 7.229306 TGAGTGATTTACTGCATTTTCTGAAGT 59.771 33.333 0.00 0.00 46.24 3.01
1969 2621 7.587629 TGAGTGATTTACTGCATTTTCTGAAG 58.412 34.615 0.00 0.00 40.53 3.02
1970 2622 7.509141 TGAGTGATTTACTGCATTTTCTGAA 57.491 32.000 0.00 0.00 40.53 3.02
1971 2623 7.509141 TTGAGTGATTTACTGCATTTTCTGA 57.491 32.000 0.00 0.00 40.53 3.27
1972 2624 8.578308 TTTTGAGTGATTTACTGCATTTTCTG 57.422 30.769 0.00 0.00 40.53 3.02
2018 2670 9.916397 CGATATCATACTAAAACTTGTTGAACC 57.084 33.333 3.12 0.00 0.00 3.62
2039 2691 8.420374 ACGACAACTGACATTTAAATCGATAT 57.580 30.769 0.00 0.00 0.00 1.63
2055 2709 7.616103 TTGTTGCAATAAATAACGACAACTG 57.384 32.000 6.11 0.00 37.42 3.16
2061 2715 7.753132 GGTCTCAATTGTTGCAATAAATAACGA 59.247 33.333 12.87 8.02 0.00 3.85
2124 2779 5.942236 CCTCCATGAACATGATTATACAGGG 59.058 44.000 15.21 0.00 41.20 4.45
2297 2954 4.142730 GCAAACAGCATCTCTTGTTAGAGG 60.143 45.833 2.61 0.00 44.61 3.69
2477 3135 4.525487 TCGTAGCCTCCTGTAAGAGAAAAA 59.475 41.667 0.00 0.00 35.82 1.94
2478 3136 4.084287 TCGTAGCCTCCTGTAAGAGAAAA 58.916 43.478 0.00 0.00 35.82 2.29
2646 3305 4.734398 TGGAAACACTGCAAAGTTGATT 57.266 36.364 4.40 0.00 33.40 2.57
3032 3691 3.720193 GCCAGTGCACTGCTGTCG 61.720 66.667 36.38 24.57 42.47 4.35
3105 3766 1.252904 CCAAAGCATGTGGGGACAGG 61.253 60.000 0.00 0.00 40.96 4.00
3314 3975 4.766375 TCCTTCATAGATGAAACGGGAAC 58.234 43.478 6.42 0.00 45.26 3.62
3412 4074 3.733224 GGACGAATGATGATTCAGACTCG 59.267 47.826 5.72 8.03 38.35 4.18
3607 4269 6.127479 TGCAAGGTTAAGAACTTGAACACAAT 60.127 34.615 15.07 0.00 45.22 2.71
3713 4375 8.113462 ACCATAACTCCTAACAATAACATGGTT 58.887 33.333 0.00 0.00 39.41 3.67
3817 4481 5.583061 AGTTCACGTGTTGTTGTATTCTTCA 59.417 36.000 16.51 0.00 0.00 3.02
3852 4516 2.538449 CGGCTTAAGTACGTTATGCTGG 59.462 50.000 4.02 9.48 41.41 4.85
3928 4592 4.503741 TGAAGGTTAAACATGCAAGAGC 57.496 40.909 0.00 0.00 42.57 4.09
3998 4662 6.198966 AGCATGTTTCGTTTTTCTCAATTGTC 59.801 34.615 5.13 0.00 0.00 3.18
4027 4691 8.386606 CAAAAAGCTGTATAGTGAGTTCATCTC 58.613 37.037 0.00 0.00 43.03 2.75
4043 4707 5.123344 ACAGTTTTCTCGTACAAAAAGCTGT 59.877 36.000 19.31 19.31 35.01 4.40
4095 4760 1.610624 CCGTGCACAGAAGTACCCAAT 60.611 52.381 18.64 0.00 0.00 3.16
4096 4761 0.250124 CCGTGCACAGAAGTACCCAA 60.250 55.000 18.64 0.00 0.00 4.12
4097 4762 1.116536 TCCGTGCACAGAAGTACCCA 61.117 55.000 18.64 0.00 0.00 4.51
4098 4763 0.249398 ATCCGTGCACAGAAGTACCC 59.751 55.000 18.64 0.00 0.00 3.69
4099 4764 2.953466 TATCCGTGCACAGAAGTACC 57.047 50.000 18.64 0.00 0.00 3.34
4100 4765 4.243270 AGTTTATCCGTGCACAGAAGTAC 58.757 43.478 18.64 10.12 0.00 2.73
4101 4766 4.530710 AGTTTATCCGTGCACAGAAGTA 57.469 40.909 18.64 0.00 0.00 2.24
4102 4767 3.402628 AGTTTATCCGTGCACAGAAGT 57.597 42.857 18.64 0.00 0.00 3.01
4103 4768 3.997021 AGAAGTTTATCCGTGCACAGAAG 59.003 43.478 18.64 2.08 0.00 2.85
4104 4769 3.745975 CAGAAGTTTATCCGTGCACAGAA 59.254 43.478 18.64 0.00 0.00 3.02
4105 4770 3.006430 TCAGAAGTTTATCCGTGCACAGA 59.994 43.478 18.64 12.06 0.00 3.41
4106 4771 3.325870 TCAGAAGTTTATCCGTGCACAG 58.674 45.455 18.64 5.51 0.00 3.66
4107 4772 3.394674 TCAGAAGTTTATCCGTGCACA 57.605 42.857 18.64 0.00 0.00 4.57
4108 4773 4.024387 TGTTTCAGAAGTTTATCCGTGCAC 60.024 41.667 6.82 6.82 0.00 4.57
4109 4774 4.130857 TGTTTCAGAAGTTTATCCGTGCA 58.869 39.130 0.00 0.00 0.00 4.57
4110 4775 4.742438 TGTTTCAGAAGTTTATCCGTGC 57.258 40.909 0.00 0.00 0.00 5.34
4111 4776 7.477422 CGTTAATGTTTCAGAAGTTTATCCGTG 59.523 37.037 0.00 0.00 0.00 4.94
4112 4777 7.385752 TCGTTAATGTTTCAGAAGTTTATCCGT 59.614 33.333 0.00 0.00 0.00 4.69
4113 4778 7.735500 TCGTTAATGTTTCAGAAGTTTATCCG 58.264 34.615 0.00 0.00 0.00 4.18
4121 4786 9.638300 GCTATTGTATCGTTAATGTTTCAGAAG 57.362 33.333 0.00 0.00 0.00 2.85
4122 4787 9.157104 TGCTATTGTATCGTTAATGTTTCAGAA 57.843 29.630 0.00 0.00 0.00 3.02
4123 4788 8.710835 TGCTATTGTATCGTTAATGTTTCAGA 57.289 30.769 0.00 0.00 0.00 3.27
4126 4791 9.807386 GGTATGCTATTGTATCGTTAATGTTTC 57.193 33.333 0.00 0.00 0.00 2.78
4127 4792 9.332502 TGGTATGCTATTGTATCGTTAATGTTT 57.667 29.630 0.00 0.00 0.00 2.83
4128 4793 8.896320 TGGTATGCTATTGTATCGTTAATGTT 57.104 30.769 0.00 0.00 0.00 2.71
4129 4794 7.117812 GCTGGTATGCTATTGTATCGTTAATGT 59.882 37.037 0.00 0.00 0.00 2.71
4130 4795 7.331934 AGCTGGTATGCTATTGTATCGTTAATG 59.668 37.037 0.00 0.00 42.10 1.90
4131 4796 7.386851 AGCTGGTATGCTATTGTATCGTTAAT 58.613 34.615 0.00 0.00 42.10 1.40
4132 4797 6.755206 AGCTGGTATGCTATTGTATCGTTAA 58.245 36.000 0.00 0.00 42.10 2.01
4133 4798 6.340962 AGCTGGTATGCTATTGTATCGTTA 57.659 37.500 0.00 0.00 42.10 3.18
4134 4799 5.215252 AGCTGGTATGCTATTGTATCGTT 57.785 39.130 0.00 0.00 42.10 3.85
4135 4800 4.873746 AGCTGGTATGCTATTGTATCGT 57.126 40.909 0.00 0.00 42.10 3.73
4136 4801 6.390721 ACTTAGCTGGTATGCTATTGTATCG 58.609 40.000 0.00 0.00 43.92 2.92
4137 4802 7.872993 TGAACTTAGCTGGTATGCTATTGTATC 59.127 37.037 0.00 0.00 43.92 2.24
4138 4803 7.735917 TGAACTTAGCTGGTATGCTATTGTAT 58.264 34.615 0.00 0.00 43.92 2.29
4139 4804 7.119709 TGAACTTAGCTGGTATGCTATTGTA 57.880 36.000 0.00 0.00 43.92 2.41
4140 4805 5.989477 TGAACTTAGCTGGTATGCTATTGT 58.011 37.500 0.00 0.00 43.92 2.71
4141 4806 7.502120 AATGAACTTAGCTGGTATGCTATTG 57.498 36.000 0.00 0.00 43.92 1.90
4145 4810 8.820831 AGATATAATGAACTTAGCTGGTATGCT 58.179 33.333 0.00 0.00 46.11 3.79
4146 4811 8.877779 CAGATATAATGAACTTAGCTGGTATGC 58.122 37.037 0.00 0.00 0.00 3.14
4336 5008 2.290122 CTGAGCTCCGCGATGTCCTT 62.290 60.000 8.23 0.00 0.00 3.36
4398 5070 4.371624 TTTCATGTCTGACACCAGGAAT 57.628 40.909 13.50 0.00 40.76 3.01
4403 5075 5.003160 CCTTGTATTTCATGTCTGACACCA 58.997 41.667 13.50 0.00 0.00 4.17
4566 5239 7.463961 AGGAAATATCATCTCCATTTCATGC 57.536 36.000 8.14 0.00 39.40 4.06
4570 5243 7.401246 AGGCTAGGAAATATCATCTCCATTTC 58.599 38.462 0.00 0.00 37.75 2.17
4572 5245 6.503217 TGAGGCTAGGAAATATCATCTCCATT 59.497 38.462 0.00 0.00 0.00 3.16
4656 5329 4.142816 CCTCACTGACGCTAAAAATCCTTG 60.143 45.833 0.00 0.00 0.00 3.61
4665 5338 2.656069 GGGGCCTCACTGACGCTAA 61.656 63.158 0.84 0.00 0.00 3.09
4669 5342 4.087892 CAGGGGGCCTCACTGACG 62.088 72.222 16.17 0.00 34.21 4.35
4773 5446 3.805971 ACGGTAAACTGAAGTACTGCAAC 59.194 43.478 4.75 0.00 30.96 4.17
4797 5470 6.018588 ACGAGAAACACGATGATAAAAACACA 60.019 34.615 0.00 0.00 34.70 3.72
4940 5623 5.835113 AAAGAAACAACTAGAGCAAGCAA 57.165 34.783 0.00 0.00 0.00 3.91
4981 5664 7.166691 ACAACTACGAATAGGACAATACACT 57.833 36.000 0.00 0.00 32.08 3.55
5017 5700 9.027129 GCGACATCAAATACACTGTAAATAGTA 57.973 33.333 0.00 0.00 0.00 1.82
5018 5701 7.547722 TGCGACATCAAATACACTGTAAATAGT 59.452 33.333 0.00 0.00 0.00 2.12
5030 5713 3.698029 AGGCAATGCGACATCAAATAC 57.302 42.857 0.00 0.00 0.00 1.89
5041 5724 5.844301 AAAAGAACAAATTAGGCAATGCG 57.156 34.783 0.00 0.00 0.00 4.73
5117 5800 6.110411 ACGGAAGAGGATAGAAAAACTTCA 57.890 37.500 0.00 0.00 36.49 3.02
5118 5801 7.438757 GGATACGGAAGAGGATAGAAAAACTTC 59.561 40.741 0.00 0.00 34.80 3.01
5139 5822 2.736670 ACCATGCCAAGGAAGGATAC 57.263 50.000 0.00 0.00 0.00 2.24
5146 5829 4.651503 TGAAAGTTTAAACCATGCCAAGGA 59.348 37.500 14.72 0.00 0.00 3.36
5214 5904 1.442769 TCGAATGAACAGAAGGCAGC 58.557 50.000 0.00 0.00 0.00 5.25
5216 5906 5.000591 TGTAATTCGAATGAACAGAAGGCA 58.999 37.500 12.25 0.00 36.81 4.75
5223 5913 5.049060 CCACTTGGTGTAATTCGAATGAACA 60.049 40.000 12.25 15.79 36.81 3.18
5224 5914 5.390613 CCACTTGGTGTAATTCGAATGAAC 58.609 41.667 12.25 13.40 36.81 3.18
5240 5930 3.801594 CACCATTTCGAAAAACCACTTGG 59.198 43.478 15.66 17.31 42.17 3.61
5241 5931 4.677584 TCACCATTTCGAAAAACCACTTG 58.322 39.130 15.66 6.55 0.00 3.16
5242 5932 4.993029 TCACCATTTCGAAAAACCACTT 57.007 36.364 15.66 0.00 0.00 3.16
5243 5933 4.642885 TCTTCACCATTTCGAAAAACCACT 59.357 37.500 15.66 0.00 0.00 4.00
5244 5934 4.738252 GTCTTCACCATTTCGAAAAACCAC 59.262 41.667 15.66 0.71 0.00 4.16
5245 5935 4.642885 AGTCTTCACCATTTCGAAAAACCA 59.357 37.500 15.66 0.00 0.00 3.67
5246 5936 5.183014 AGTCTTCACCATTTCGAAAAACC 57.817 39.130 15.66 0.00 0.00 3.27
5247 5937 8.690840 CATAAAGTCTTCACCATTTCGAAAAAC 58.309 33.333 15.66 3.82 0.00 2.43
5248 5938 7.865385 CCATAAAGTCTTCACCATTTCGAAAAA 59.135 33.333 15.66 3.22 0.00 1.94
5249 5939 7.367285 CCATAAAGTCTTCACCATTTCGAAAA 58.633 34.615 15.66 0.00 0.00 2.29
5250 5940 6.569610 GCCATAAAGTCTTCACCATTTCGAAA 60.570 38.462 13.91 13.91 0.00 3.46
5251 5941 5.106317 GCCATAAAGTCTTCACCATTTCGAA 60.106 40.000 0.00 0.00 0.00 3.71
5252 5942 4.394920 GCCATAAAGTCTTCACCATTTCGA 59.605 41.667 0.00 0.00 0.00 3.71
5253 5943 4.396166 AGCCATAAAGTCTTCACCATTTCG 59.604 41.667 0.00 0.00 0.00 3.46
5254 5944 5.163612 GGAGCCATAAAGTCTTCACCATTTC 60.164 44.000 0.00 0.00 0.00 2.17
5255 5945 4.706962 GGAGCCATAAAGTCTTCACCATTT 59.293 41.667 0.00 0.00 0.00 2.32
5289 5979 5.972107 AGCAAATTCAGTGAAGCAATACT 57.028 34.783 11.91 1.42 0.00 2.12
5290 5980 7.412137 AAAAGCAAATTCAGTGAAGCAATAC 57.588 32.000 11.91 0.00 0.00 1.89
5292 5982 6.930667 AAAAAGCAAATTCAGTGAAGCAAT 57.069 29.167 11.91 0.65 0.00 3.56
5335 6031 9.089601 GCCTCTTTCTTCTAGTAACTATCAAAC 57.910 37.037 0.00 0.00 0.00 2.93
5346 6042 0.537653 GGGCGCCTCTTTCTTCTAGT 59.462 55.000 28.56 0.00 0.00 2.57
5347 6043 0.827368 AGGGCGCCTCTTTCTTCTAG 59.173 55.000 28.56 0.00 0.00 2.43
5348 6044 1.276622 AAGGGCGCCTCTTTCTTCTA 58.723 50.000 28.56 0.00 30.89 2.10
5349 6045 0.402121 AAAGGGCGCCTCTTTCTTCT 59.598 50.000 27.23 13.13 30.89 2.85
5350 6046 0.523519 CAAAGGGCGCCTCTTTCTTC 59.476 55.000 28.99 12.38 32.72 2.87
5408 6104 3.704566 ACGGGTGATATACAAGAGCAGAA 59.295 43.478 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.