Multiple sequence alignment - TraesCS5A01G336500

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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 TraesCS5A01G336500 chr5A 100.000 6301 0 0 704 7004 545217941 545211641 0.000000e+00 11636.0
1 TraesCS5A01G336500 chr5A 100.000 490 0 0 1 490 545218644 545218155 0.000000e+00 905.0
2 TraesCS5A01G336500 chr5D 94.884 5141 189 43 704 5816 429359424 429354330 0.000000e+00 7969.0
3 TraesCS5A01G336500 chr5D 95.126 636 25 5 5825 6454 429354351 429353716 0.000000e+00 998.0
4 TraesCS5A01G336500 chr5D 89.441 483 25 14 10 490 429359872 429359414 2.810000e-163 586.0
5 TraesCS5A01G336500 chr5D 89.807 363 27 8 6451 6805 429353527 429353167 2.300000e-124 457.0
6 TraesCS5A01G336500 chr5D 87.952 249 19 6 6766 7004 429353117 429352870 4.140000e-72 283.0
7 TraesCS5A01G336500 chr5D 84.255 235 19 11 6782 7004 429352526 429352298 5.500000e-51 213.0
8 TraesCS5A01G336500 chr5B 94.092 4147 190 29 704 4818 518685156 518681033 0.000000e+00 6250.0
9 TraesCS5A01G336500 chr5B 91.505 2213 90 42 4827 7004 518680962 518678813 0.000000e+00 2955.0
10 TraesCS5A01G336500 chr5B 89.095 486 21 11 11 490 518685605 518685146 6.090000e-160 575.0
11 TraesCS5A01G336500 chr5B 83.243 185 12 11 6824 7004 518672793 518672624 1.220000e-32 152.0
12 TraesCS5A01G336500 chr5B 92.857 56 3 1 6786 6840 518678472 518678417 5.820000e-11 80.5
13 TraesCS5A01G336500 chr3B 84.184 196 19 11 2276 2460 28336118 28336312 5.580000e-41 180.0
14 TraesCS5A01G336500 chr2A 88.119 101 3 5 3764 3855 615291579 615291479 2.070000e-20 111.0
15 TraesCS5A01G336500 chr2A 100.000 29 0 0 6905 6933 662740990 662741018 4.000000e-03 54.7
16 TraesCS5A01G336500 chr3A 86.207 58 6 2 6876 6932 718030484 718030540 2.110000e-05 62.1
17 TraesCS5A01G336500 chr3A 96.875 32 1 0 6906 6937 653846848 653846817 4.000000e-03 54.7
18 TraesCS5A01G336500 chr1B 91.111 45 4 0 6529 6573 120658485 120658529 2.110000e-05 62.1
19 TraesCS5A01G336500 chr7A 100.000 29 0 0 6906 6934 156270996 156271024 4.000000e-03 54.7
20 TraesCS5A01G336500 chr4D 100.000 29 0 0 6906 6934 450650726 450650754 4.000000e-03 54.7
21 TraesCS5A01G336500 chr4D 100.000 28 0 0 6905 6932 12693976 12694003 1.300000e-02 52.8
22 TraesCS5A01G336500 chr6D 100.000 28 0 0 6905 6932 443841989 443841962 1.300000e-02 52.8


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 TraesCS5A01G336500 chr5A 545211641 545218644 7003 True 6270.500 11636 100.000000 1 7004 2 chr5A.!!$R1 7003
1 TraesCS5A01G336500 chr5D 429352298 429359872 7574 True 1751.000 7969 90.244167 10 7004 6 chr5D.!!$R1 6994
2 TraesCS5A01G336500 chr5B 518678417 518685605 7188 True 2465.125 6250 91.887250 11 7004 4 chr5B.!!$R2 6993

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
978 985 0.249238 GCGATCTGCGATCTGAACCT 60.249 55.000 13.90 0.00 44.57 3.50 F
1221 1234 0.597637 CACTGGCGGATACCATCGTC 60.598 60.000 0.00 0.00 39.54 4.20 F
1291 1304 1.059098 TGCTCCTGCAGAGAAGGAAA 58.941 50.000 17.39 0.00 46.50 3.13 F
1488 1501 1.377856 GCTCAAGGGAACAGAGGGC 60.378 63.158 0.00 0.00 35.87 5.19 F
1795 1809 1.381522 ACGCGTGGGTTTTTAAGTGT 58.618 45.000 12.93 0.00 0.00 3.55 F
3341 3378 0.972883 AGCGTCTTGAGAAGGAAGCT 59.027 50.000 0.00 0.00 41.05 3.74 F
3841 3878 1.515521 GACACAAACCCAAGGAGGCG 61.516 60.000 0.00 0.00 35.39 5.52 F
4896 4998 0.884514 GAGTTTCTTTCCTGCAGGGC 59.115 55.000 32.23 13.31 35.41 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 1934 0.307760 GAACGGGCACACAACTTGAG 59.692 55.000 0.00 0.00 0.00 3.02 R
2666 2702 0.941542 TAACGACAGCTTGGTTGTGC 59.058 50.000 0.00 0.00 35.58 4.57 R
2909 2946 2.842208 TGCAGTTCACTTGGAAAACG 57.158 45.000 0.00 0.00 37.23 3.60 R
3341 3378 1.742831 AGTTGTTTCTTGAGTTGCGCA 59.257 42.857 5.66 5.66 0.00 6.09 R
3624 3661 0.032952 TCTGTTTTCGAGTGACCCCG 59.967 55.000 0.00 0.00 0.00 5.73 R
4815 4854 0.635555 TTGGGAATGGGGATGCATCA 59.364 50.000 27.25 9.05 0.00 3.07 R
5537 5639 0.258774 AAGGTGTCCTGCCAAGTGTT 59.741 50.000 0.00 0.00 32.13 3.32 R
6693 7016 0.896940 AACAAGACTAGGCCGTCCGA 60.897 55.000 7.12 0.00 37.47 4.55 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
267 271 2.108168 CGTGGGAGGAGTAGAAATCCA 58.892 52.381 0.00 0.00 39.47 3.41
399 404 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
404 409 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
802 809 3.449632 GAACCCTAGATTTCTGCTCGTC 58.550 50.000 0.00 0.00 0.00 4.20
822 829 2.028930 TCTCCTTCTTCCGTCTTTCTGC 60.029 50.000 0.00 0.00 0.00 4.26
823 830 1.691976 TCCTTCTTCCGTCTTTCTGCA 59.308 47.619 0.00 0.00 0.00 4.41
826 833 0.320771 TCTTCCGTCTTTCTGCAGCC 60.321 55.000 9.47 0.00 0.00 4.85
845 852 1.881973 CCATGAAATGCCGAATCCGAT 59.118 47.619 0.00 0.00 44.97 4.18
862 869 7.596621 CGAATCCGATCAGATCTTGATTCTTTA 59.403 37.037 28.48 4.15 46.51 1.85
877 884 2.463589 CTTTACCCAGGCCGTGCTCA 62.464 60.000 0.00 0.00 0.00 4.26
885 892 2.125512 GCCGTGCTCATCGAAGGT 60.126 61.111 0.00 0.00 0.00 3.50
890 897 2.184322 GCTCATCGAAGGTGCGGA 59.816 61.111 0.00 0.00 0.00 5.54
905 912 4.537433 GGAGCCGAGGAATGCGCT 62.537 66.667 9.73 0.00 0.00 5.92
945 952 2.680913 GCGTCTGCGGCAACTGAAT 61.681 57.895 3.44 0.00 38.78 2.57
951 958 1.298157 TGCGGCAACTGAATTCTCCG 61.298 55.000 0.00 11.85 36.83 4.63
978 985 0.249238 GCGATCTGCGATCTGAACCT 60.249 55.000 13.90 0.00 44.57 3.50
990 1000 1.006832 CTGAACCTAACCGCCAATCG 58.993 55.000 0.00 0.00 38.08 3.34
1079 1089 2.459442 GGCAGTCGCAGATGCAGTC 61.459 63.158 5.55 0.00 40.81 3.51
1207 1220 2.185350 CTCCCGCTGCTACACTGG 59.815 66.667 0.00 0.00 0.00 4.00
1212 1225 2.187946 GCTGCTACACTGGCGGAT 59.812 61.111 0.00 0.00 38.23 4.18
1216 1229 0.973496 TGCTACACTGGCGGATACCA 60.973 55.000 0.00 0.00 38.29 3.25
1218 1231 1.605712 GCTACACTGGCGGATACCATC 60.606 57.143 0.00 0.00 39.54 3.51
1221 1234 0.597637 CACTGGCGGATACCATCGTC 60.598 60.000 0.00 0.00 39.54 4.20
1254 1267 2.985456 CTGAAGCGGAAGAGGGCT 59.015 61.111 0.00 0.00 42.33 5.19
1290 1303 2.764007 TGCTCCTGCAGAGAAGGAA 58.236 52.632 17.39 0.00 46.50 3.36
1291 1304 1.059098 TGCTCCTGCAGAGAAGGAAA 58.941 50.000 17.39 0.00 46.50 3.13
1301 1314 2.483491 CAGAGAAGGAAACTCTTGCTGC 59.517 50.000 0.00 0.00 41.94 5.25
1488 1501 1.377856 GCTCAAGGGAACAGAGGGC 60.378 63.158 0.00 0.00 35.87 5.19
1558 1571 3.349488 TGATGTACGGACAATCTAGCG 57.651 47.619 3.58 0.00 39.59 4.26
1617 1630 2.175931 TCTTTGGTGCTGGGAGGTAAAA 59.824 45.455 0.00 0.00 0.00 1.52
1654 1667 6.676950 TGTTCATTTACAAGTTAGTGCCATG 58.323 36.000 0.00 0.00 0.00 3.66
1702 1716 3.646162 TCCAGAAAGAGTGGCTCTGTTTA 59.354 43.478 11.09 0.00 40.28 2.01
1737 1751 2.306847 GATGTCTTGTGGTGGGTTGTT 58.693 47.619 0.00 0.00 0.00 2.83
1755 1769 6.183360 GGGTTGTTAATTGCAGGTAAGAGATC 60.183 42.308 0.00 0.00 0.00 2.75
1795 1809 1.381522 ACGCGTGGGTTTTTAAGTGT 58.618 45.000 12.93 0.00 0.00 3.55
1853 1867 3.182967 GACTGCTCTCCATTGTAAGACG 58.817 50.000 0.00 0.00 0.00 4.18
1893 1907 6.855836 TGTTTGAACTTCCATCTATCAATGC 58.144 36.000 0.00 0.00 30.81 3.56
1917 1931 8.807667 GCTTGACAGCTAATATGCAAATTTAT 57.192 30.769 0.00 0.00 43.51 1.40
1919 1933 9.188588 CTTGACAGCTAATATGCAAATTTATGG 57.811 33.333 0.00 0.00 34.99 2.74
1920 1934 7.147312 TGACAGCTAATATGCAAATTTATGGC 58.853 34.615 0.00 0.00 34.99 4.40
1922 1936 7.373493 ACAGCTAATATGCAAATTTATGGCTC 58.627 34.615 0.00 0.00 34.99 4.70
1923 1937 7.014518 ACAGCTAATATGCAAATTTATGGCTCA 59.985 33.333 0.00 0.00 34.99 4.26
1924 1938 7.868922 CAGCTAATATGCAAATTTATGGCTCAA 59.131 33.333 0.00 0.00 34.99 3.02
1926 1940 7.869429 GCTAATATGCAAATTTATGGCTCAAGT 59.131 33.333 0.00 0.00 0.00 3.16
1928 1942 8.428186 AATATGCAAATTTATGGCTCAAGTTG 57.572 30.769 0.00 0.00 32.43 3.16
1936 1964 2.639286 GCTCAAGTTGTGTGCCCG 59.361 61.111 2.11 0.00 40.21 6.13
1949 1977 3.823873 TGTGTGCCCGTTCTTTGAATATT 59.176 39.130 0.00 0.00 0.00 1.28
1950 1978 5.004448 TGTGTGCCCGTTCTTTGAATATTA 58.996 37.500 0.00 0.00 0.00 0.98
1951 1979 5.650266 TGTGTGCCCGTTCTTTGAATATTAT 59.350 36.000 0.00 0.00 0.00 1.28
1952 1980 5.971202 GTGTGCCCGTTCTTTGAATATTATG 59.029 40.000 0.00 0.00 0.00 1.90
1953 1981 5.883115 TGTGCCCGTTCTTTGAATATTATGA 59.117 36.000 0.00 0.00 0.00 2.15
1954 1982 6.545666 TGTGCCCGTTCTTTGAATATTATGAT 59.454 34.615 0.00 0.00 0.00 2.45
1999 2027 6.751888 GTCTTGAAATGTTGTTGCAAGTTAGT 59.248 34.615 0.00 0.00 37.71 2.24
2048 2076 4.141711 TGAATTCGCCTACTCCATAGCTTT 60.142 41.667 0.00 0.00 0.00 3.51
2060 2088 6.116126 ACTCCATAGCTTTGTATTCTGTTCC 58.884 40.000 3.39 0.00 0.00 3.62
2065 2093 7.721399 CCATAGCTTTGTATTCTGTTCCCTAAT 59.279 37.037 3.39 0.00 0.00 1.73
2077 2105 7.141758 TCTGTTCCCTAATTGCATCTCTATT 57.858 36.000 0.00 0.00 0.00 1.73
2078 2106 6.994496 TCTGTTCCCTAATTGCATCTCTATTG 59.006 38.462 0.00 0.00 0.00 1.90
2079 2107 6.064060 TGTTCCCTAATTGCATCTCTATTGG 58.936 40.000 0.00 0.00 0.00 3.16
2080 2108 4.655963 TCCCTAATTGCATCTCTATTGGC 58.344 43.478 0.00 0.00 0.00 4.52
2081 2109 4.352001 TCCCTAATTGCATCTCTATTGGCT 59.648 41.667 0.00 0.00 0.00 4.75
2082 2110 5.547666 TCCCTAATTGCATCTCTATTGGCTA 59.452 40.000 0.00 0.00 0.00 3.93
2083 2111 6.216251 TCCCTAATTGCATCTCTATTGGCTAT 59.784 38.462 0.00 0.00 0.00 2.97
2250 2280 1.724582 AAGGTGTGTGCGTGCCTTTC 61.725 55.000 0.00 0.00 38.05 2.62
2251 2281 2.477176 GGTGTGTGCGTGCCTTTCA 61.477 57.895 0.00 0.00 0.00 2.69
2326 2358 5.829924 AGGATTTGAAGCCCTAATATGTGTG 59.170 40.000 0.00 0.00 34.20 3.82
2482 2517 7.713073 GCTCCTGCTAATGTTAGTATCTCTTTT 59.287 37.037 2.11 0.00 36.03 2.27
2585 2620 9.703892 ATAGATGCTATGAAGATACTGACAAAC 57.296 33.333 0.00 0.00 0.00 2.93
2615 2651 6.345096 ACATTAAGTTGCTGCACCTTATTT 57.655 33.333 18.42 8.35 0.00 1.40
2622 2658 4.503741 TGCTGCACCTTATTTGAACTTC 57.496 40.909 0.00 0.00 0.00 3.01
2909 2946 4.362279 CAACATGCCATATTACAACAGCC 58.638 43.478 0.00 0.00 0.00 4.85
2912 2949 2.717390 TGCCATATTACAACAGCCGTT 58.283 42.857 0.00 0.00 35.01 4.44
2915 2952 4.102649 GCCATATTACAACAGCCGTTTTC 58.897 43.478 0.00 0.00 31.13 2.29
2956 2993 8.862325 TCTGTTTTATCCACTAATGTCATGTT 57.138 30.769 0.00 0.00 0.00 2.71
2957 2994 8.729756 TCTGTTTTATCCACTAATGTCATGTTG 58.270 33.333 0.00 0.00 0.00 3.33
2966 3003 5.700832 CACTAATGTCATGTTGTGTACCACT 59.299 40.000 0.00 0.00 35.11 4.00
2982 3019 8.380099 TGTGTACCACTAAATTCTAGGAACAAT 58.620 33.333 0.00 0.00 35.11 2.71
2983 3020 8.880750 GTGTACCACTAAATTCTAGGAACAATC 58.119 37.037 0.00 0.00 0.00 2.67
3341 3378 0.972883 AGCGTCTTGAGAAGGAAGCT 59.027 50.000 0.00 0.00 41.05 3.74
3583 3620 5.931146 GGTGAGCAATATCTCCTAATGTCAG 59.069 44.000 0.00 0.00 31.49 3.51
3624 3661 5.048713 AGGCTAGCTTGTTAAACACATTCAC 60.049 40.000 15.72 0.00 34.43 3.18
3841 3878 1.515521 GACACAAACCCAAGGAGGCG 61.516 60.000 0.00 0.00 35.39 5.52
4036 4073 8.845413 ATGATAATTCTCTGCCAACTAGATTC 57.155 34.615 0.00 0.00 0.00 2.52
4185 4222 9.690913 ACTGCCATATCATGCTATGTTTTATAT 57.309 29.630 13.93 0.00 0.00 0.86
4425 4462 8.782144 GTTATGGATGAAGAAGATTCCAAGATC 58.218 37.037 0.00 0.00 41.36 2.75
4506 4543 8.908903 AGTGAGGTATACTCTTCTAACATTGAG 58.091 37.037 2.25 0.00 46.72 3.02
4632 4669 4.697352 AGCGCAAGACAGACAAGATTAAAT 59.303 37.500 11.47 0.00 43.02 1.40
4659 4696 5.065602 GCATTCAGATGTGATAGACAGCAAA 59.934 40.000 0.00 0.00 43.90 3.68
4677 4714 6.151648 ACAGCAAAGCATTCTCTAGCATTTAA 59.848 34.615 0.00 0.00 0.00 1.52
4715 4754 8.058847 TGCAATACTTGTTATCCCCTTTATCTT 58.941 33.333 0.00 0.00 0.00 2.40
4815 4854 8.891671 AGAAATACACATGCTTTTTGTTGATT 57.108 26.923 0.00 0.00 0.00 2.57
4835 4937 1.043022 GATGCATCCCCATTCCCAAC 58.957 55.000 16.23 0.00 0.00 3.77
4874 4976 9.491675 TGAAATATTGTTCTGCAATTCAACATT 57.508 25.926 0.00 0.00 44.82 2.71
4896 4998 0.884514 GAGTTTCTTTCCTGCAGGGC 59.115 55.000 32.23 13.31 35.41 5.19
4915 5017 4.407296 AGGGCATTCAGGTAGAAAGTCTAG 59.593 45.833 0.00 0.00 40.22 2.43
5352 5454 7.775053 TTGAATGGAGGTAGCATTTTTAAGT 57.225 32.000 0.00 0.00 0.00 2.24
5537 5639 1.409064 CGCTGGCAGGTCAGAATACTA 59.591 52.381 17.64 0.00 36.93 1.82
5549 5653 4.631813 GTCAGAATACTAACACTTGGCAGG 59.368 45.833 0.00 0.00 0.00 4.85
5735 5839 4.549668 CCACCTGGTAACTACCCTATACA 58.450 47.826 0.00 0.00 45.87 2.29
5741 5845 6.210984 CCTGGTAACTACCCTATACATCCTTC 59.789 46.154 3.45 0.00 45.87 3.46
5817 5921 0.673956 GTCCCCAGAAGACGAAAGCC 60.674 60.000 0.00 0.00 0.00 4.35
5934 6038 1.509644 CTGAGCTGCGCTTGAAACCA 61.510 55.000 9.73 0.00 39.88 3.67
6146 6250 1.455217 GGCATTGCATCCTGCTCCT 60.455 57.895 11.39 0.00 45.31 3.69
6154 6258 0.829333 CATCCTGCTCCTAGCTGTGT 59.171 55.000 0.00 0.00 42.97 3.72
6155 6259 0.829333 ATCCTGCTCCTAGCTGTGTG 59.171 55.000 0.00 0.00 42.97 3.82
6234 6338 5.801947 GTCATGTCAATTGTTCCATTGCTAC 59.198 40.000 5.13 0.00 0.00 3.58
6370 6475 7.692460 TGTCAGATTTTCTAAAGATGCATGT 57.308 32.000 2.46 0.00 0.00 3.21
6371 6476 7.755591 TGTCAGATTTTCTAAAGATGCATGTC 58.244 34.615 2.46 0.00 0.00 3.06
6555 6857 5.005094 CCCTTTGTTCGGAAATAAGTGGTA 58.995 41.667 10.41 0.00 0.00 3.25
6601 6923 4.583907 TCATCAAAGCACATGAAACCTGAA 59.416 37.500 0.00 0.00 0.00 3.02
6624 6946 9.844790 TGAACTGATTGCATAATTAAGTTCAAG 57.155 29.630 17.93 3.66 45.31 3.02
6629 6951 8.122330 TGATTGCATAATTAAGTTCAAGCTACG 58.878 33.333 0.00 0.00 0.00 3.51
6693 7016 4.031129 CTGCTGTGGGCTGCCTCT 62.031 66.667 19.68 0.00 42.39 3.69
6727 7050 0.736053 TTGTTCGTGTTGTCAAGCCC 59.264 50.000 0.00 0.00 0.00 5.19
6734 7057 2.808933 CGTGTTGTCAAGCCCCTTCTTA 60.809 50.000 0.00 0.00 0.00 2.10
6778 7101 1.167155 GCTCTGGATGCATCTGCCTG 61.167 60.000 25.28 13.94 41.18 4.85
6805 7217 1.676014 GCCATGTACTCTTCACGGCTT 60.676 52.381 0.00 0.00 40.39 4.35
6837 7249 7.326968 TCTTGTTTTCATGTACAATGTGTGA 57.673 32.000 0.00 0.00 34.10 3.58
6839 7251 7.914871 TCTTGTTTTCATGTACAATGTGTGAAG 59.085 33.333 0.00 0.00 34.10 3.02
6945 7378 7.581213 AAAGTAGACATGTCCACATCAAAAA 57.419 32.000 23.52 0.00 33.61 1.94
6989 7422 9.167311 AGATGTGTATAAAGAAATGTTCCTGAC 57.833 33.333 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.229643 GGAGTAGGGCCCTCTACGT 59.770 63.158 32.80 11.90 43.10 3.57
245 249 0.831307 ATTTCTACTCCTCCCACGCC 59.169 55.000 0.00 0.00 0.00 5.68
279 283 2.436824 GAAGGTCTGCCGCTTCCC 60.437 66.667 0.00 0.00 40.50 3.97
357 362 1.538666 GTGGGATTGGGGAGATGGG 59.461 63.158 0.00 0.00 0.00 4.00
703 708 1.818363 GACGGCCGAATTCCTTCCC 60.818 63.158 35.90 3.27 0.00 3.97
704 709 0.810426 GAGACGGCCGAATTCCTTCC 60.810 60.000 35.90 7.24 0.00 3.46
705 710 0.175989 AGAGACGGCCGAATTCCTTC 59.824 55.000 35.90 17.44 0.00 3.46
706 711 0.175989 GAGAGACGGCCGAATTCCTT 59.824 55.000 35.90 7.12 0.00 3.36
707 712 0.684805 AGAGAGACGGCCGAATTCCT 60.685 55.000 35.90 19.97 0.00 3.36
708 713 0.249114 GAGAGAGACGGCCGAATTCC 60.249 60.000 35.90 17.30 0.00 3.01
709 714 0.592754 CGAGAGAGACGGCCGAATTC 60.593 60.000 35.90 24.14 0.00 2.17
710 715 1.433879 CGAGAGAGACGGCCGAATT 59.566 57.895 35.90 16.80 0.00 2.17
711 716 3.111939 CGAGAGAGACGGCCGAAT 58.888 61.111 35.90 20.28 0.00 3.34
712 717 3.812019 GCGAGAGAGACGGCCGAA 61.812 66.667 35.90 0.00 0.00 4.30
714 719 4.116328 TTGCGAGAGAGACGGCCG 62.116 66.667 26.86 26.86 0.00 6.13
715 720 2.202676 CTTGCGAGAGAGACGGCC 60.203 66.667 0.00 0.00 0.00 6.13
716 721 2.883253 GCTTGCGAGAGAGACGGC 60.883 66.667 4.70 0.00 0.00 5.68
717 722 2.578178 CGCTTGCGAGAGAGACGG 60.578 66.667 9.60 0.00 0.00 4.79
718 723 2.578178 CCGCTTGCGAGAGAGACG 60.578 66.667 16.99 0.00 0.00 4.18
719 724 2.883253 GCCGCTTGCGAGAGAGAC 60.883 66.667 16.99 0.00 0.00 3.36
802 809 2.289072 TGCAGAAAGACGGAAGAAGGAG 60.289 50.000 0.00 0.00 0.00 3.69
826 833 2.549329 TGATCGGATTCGGCATTTCATG 59.451 45.455 0.00 0.00 36.95 3.07
845 852 5.630069 GCCTGGGTAAAGAATCAAGATCTGA 60.630 44.000 0.00 0.00 38.81 3.27
862 869 4.101448 GATGAGCACGGCCTGGGT 62.101 66.667 0.00 0.00 0.00 4.51
877 884 4.514577 CGGCTCCGCACCTTCGAT 62.515 66.667 0.00 0.00 0.00 3.59
885 892 4.838152 GCATTCCTCGGCTCCGCA 62.838 66.667 2.96 0.00 39.59 5.69
905 912 0.970427 TCTCAGATACAGGCACGGCA 60.970 55.000 0.00 0.00 0.00 5.69
918 925 4.103103 CGCAGACGCCGTCTCAGA 62.103 66.667 18.36 0.00 41.37 3.27
936 943 5.563842 CAGATTTACGGAGAATTCAGTTGC 58.436 41.667 8.44 0.00 33.65 4.17
945 952 3.706698 CAGATCGCAGATTTACGGAGAA 58.293 45.455 0.00 0.00 45.12 2.87
951 958 3.120947 CAGATCGCAGATCGCAGATTTAC 59.879 47.826 11.21 3.58 45.12 2.01
990 1000 3.455469 GCCTCCATTGTGGGCAGC 61.455 66.667 10.87 0.00 44.69 5.25
1207 1220 0.104304 ACTTGGACGATGGTATCCGC 59.896 55.000 0.00 0.00 37.87 5.54
1212 1225 1.262417 TCTGCACTTGGACGATGGTA 58.738 50.000 0.00 0.00 0.00 3.25
1216 1229 0.035317 TGCTTCTGCACTTGGACGAT 59.965 50.000 0.00 0.00 45.31 3.73
1218 1231 1.864862 CTGCTTCTGCACTTGGACG 59.135 57.895 0.00 0.00 45.31 4.79
1221 1234 0.887836 TCAGCTGCTTCTGCACTTGG 60.888 55.000 9.47 0.00 45.31 3.61
1254 1267 0.893270 CAATCACAGGGCCGTTGGAA 60.893 55.000 10.28 0.00 0.00 3.53
1290 1303 2.281761 CACCCGGCAGCAAGAGTT 60.282 61.111 0.00 0.00 0.00 3.01
1313 1326 1.846712 GAACAAGCCCTGGAGCTCCT 61.847 60.000 32.28 10.16 44.11 3.69
1488 1501 1.444553 GACCGAAGCCACAGAGACG 60.445 63.158 0.00 0.00 0.00 4.18
1558 1571 1.456296 TCCAACACATCAGCATCAGC 58.544 50.000 0.00 0.00 42.56 4.26
1617 1630 9.396022 CTTGTAAATGAACAACATAGGATAGGT 57.604 33.333 0.00 0.00 37.04 3.08
1737 1751 6.156949 ACCTTCAGATCTCTTACCTGCAATTA 59.843 38.462 0.00 0.00 0.00 1.40
1795 1809 0.603707 CTTTCTGGCAGTTCTCCGCA 60.604 55.000 15.27 0.00 0.00 5.69
1832 1846 3.182967 CGTCTTACAATGGAGAGCAGTC 58.817 50.000 0.00 0.00 0.00 3.51
1853 1867 5.627499 TCAAACATGGTGCAAGAAGATAC 57.373 39.130 0.00 0.00 0.00 2.24
1893 1907 9.188588 CCATAAATTTGCATATTAGCTGTCAAG 57.811 33.333 2.65 0.00 34.99 3.02
1901 1915 9.754382 AACTTGAGCCATAAATTTGCATATTAG 57.246 29.630 2.65 0.00 0.00 1.73
1919 1933 1.724582 AACGGGCACACAACTTGAGC 61.725 55.000 0.00 0.00 40.84 4.26
1920 1934 0.307760 GAACGGGCACACAACTTGAG 59.692 55.000 0.00 0.00 0.00 3.02
1922 1936 0.738389 AAGAACGGGCACACAACTTG 59.262 50.000 0.00 0.00 0.00 3.16
1923 1937 1.134175 CAAAGAACGGGCACACAACTT 59.866 47.619 0.00 0.00 0.00 2.66
1924 1938 0.738389 CAAAGAACGGGCACACAACT 59.262 50.000 0.00 0.00 0.00 3.16
1926 1940 1.464734 TTCAAAGAACGGGCACACAA 58.535 45.000 0.00 0.00 0.00 3.33
1928 1942 4.434713 AATATTCAAAGAACGGGCACAC 57.565 40.909 0.00 0.00 0.00 3.82
1950 1978 9.090692 GACAAAATTAACAGCAAAGCATATCAT 57.909 29.630 0.00 0.00 0.00 2.45
1951 1979 8.306038 AGACAAAATTAACAGCAAAGCATATCA 58.694 29.630 0.00 0.00 0.00 2.15
1952 1980 8.693542 AGACAAAATTAACAGCAAAGCATATC 57.306 30.769 0.00 0.00 0.00 1.63
1953 1981 8.928733 CAAGACAAAATTAACAGCAAAGCATAT 58.071 29.630 0.00 0.00 0.00 1.78
1954 1982 8.140628 TCAAGACAAAATTAACAGCAAAGCATA 58.859 29.630 0.00 0.00 0.00 3.14
1974 2002 6.751888 ACTAACTTGCAACAACATTTCAAGAC 59.248 34.615 0.00 0.00 37.96 3.01
2031 2059 2.604046 ACAAAGCTATGGAGTAGGCG 57.396 50.000 0.00 0.00 0.00 5.52
2048 2076 6.662755 AGATGCAATTAGGGAACAGAATACA 58.337 36.000 0.00 0.00 0.00 2.29
2060 2088 7.627939 GCAATAGCCAATAGAGATGCAATTAGG 60.628 40.741 0.00 0.00 33.00 2.69
2065 2093 4.463070 TGCAATAGCCAATAGAGATGCAA 58.537 39.130 0.00 0.00 39.36 4.08
2080 2108 3.057736 AGCTGACAAAGTTGCTGCAATAG 60.058 43.478 19.11 10.89 34.38 1.73
2081 2109 2.886523 AGCTGACAAAGTTGCTGCAATA 59.113 40.909 19.11 0.00 34.38 1.90
2082 2110 1.684983 AGCTGACAAAGTTGCTGCAAT 59.315 42.857 19.11 1.18 34.38 3.56
2083 2111 1.066002 GAGCTGACAAAGTTGCTGCAA 59.934 47.619 11.69 11.69 35.76 4.08
2155 2183 4.504097 GGTTCAGTGCTTTGCTTAACTTTG 59.496 41.667 0.00 0.00 0.00 2.77
2156 2184 4.402474 AGGTTCAGTGCTTTGCTTAACTTT 59.598 37.500 0.00 0.00 0.00 2.66
2250 2280 4.867047 TGCCTACAAACAAAACACAATGTG 59.133 37.500 12.40 12.40 39.75 3.21
2251 2281 5.078411 TGCCTACAAACAAAACACAATGT 57.922 34.783 0.00 0.00 0.00 2.71
2326 2358 5.872617 GGCACCCCTTTATTCACAAATAAAC 59.127 40.000 0.43 0.00 40.65 2.01
2506 2541 4.078363 TCTTTAAATACTTGCGTGCTGC 57.922 40.909 0.00 0.00 46.70 5.25
2507 2542 7.325821 TGAAATTCTTTAAATACTTGCGTGCTG 59.674 33.333 0.00 0.00 0.00 4.41
2508 2543 7.367285 TGAAATTCTTTAAATACTTGCGTGCT 58.633 30.769 0.00 0.00 0.00 4.40
2510 2545 8.948853 TCTGAAATTCTTTAAATACTTGCGTG 57.051 30.769 0.00 0.00 0.00 5.34
2511 2546 8.999431 TCTCTGAAATTCTTTAAATACTTGCGT 58.001 29.630 0.00 0.00 0.00 5.24
2512 2547 9.825972 TTCTCTGAAATTCTTTAAATACTTGCG 57.174 29.630 0.00 0.00 0.00 4.85
2585 2620 6.094048 AGGTGCAGCAACTTAATGTATACAAG 59.906 38.462 19.63 5.58 0.00 3.16
2615 2651 7.654022 AATTAAACTGGTTTCTGGAAGTTCA 57.346 32.000 5.01 0.00 31.81 3.18
2622 2658 9.981114 ACATAAGAAAATTAAACTGGTTTCTGG 57.019 29.630 1.77 0.00 39.60 3.86
2666 2702 0.941542 TAACGACAGCTTGGTTGTGC 59.058 50.000 0.00 0.00 35.58 4.57
2909 2946 2.842208 TGCAGTTCACTTGGAAAACG 57.158 45.000 0.00 0.00 37.23 3.60
2912 2949 4.402155 ACAGAAATGCAGTTCACTTGGAAA 59.598 37.500 26.87 0.00 37.23 3.13
2915 2952 3.996150 ACAGAAATGCAGTTCACTTGG 57.004 42.857 26.87 13.51 0.00 3.61
2982 3019 8.344098 GGATTGTTTTTGCATTTTCAGAATTGA 58.656 29.630 0.00 0.00 0.00 2.57
2983 3020 7.592164 GGGATTGTTTTTGCATTTTCAGAATTG 59.408 33.333 0.00 0.00 0.00 2.32
3341 3378 1.742831 AGTTGTTTCTTGAGTTGCGCA 59.257 42.857 5.66 5.66 0.00 6.09
3583 3620 8.528044 AGCTAGCCTACTATCATAAGGAATAC 57.472 38.462 12.13 0.00 31.64 1.89
3592 3629 7.711339 GTGTTTAACAAGCTAGCCTACTATCAT 59.289 37.037 12.13 0.00 0.00 2.45
3624 3661 0.032952 TCTGTTTTCGAGTGACCCCG 59.967 55.000 0.00 0.00 0.00 5.73
3732 3769 7.284944 TGTGATGCATTCCATTCAACACATATA 59.715 33.333 0.00 0.00 32.93 0.86
3738 3775 3.193903 CCTGTGATGCATTCCATTCAACA 59.806 43.478 0.00 0.00 33.29 3.33
4036 4073 7.411588 GCAAATTGCAGAAGCTTTCTCTTTATG 60.412 37.037 13.73 0.00 44.26 1.90
4185 4222 4.023279 ACGAATTACAGCACTGCAAATGAA 60.023 37.500 3.30 0.00 0.00 2.57
4425 4462 5.984926 GCTATCTTCCTCTTCTTCATCTGTG 59.015 44.000 0.00 0.00 0.00 3.66
4659 4696 5.994668 GCCTAGTTAAATGCTAGAGAATGCT 59.005 40.000 0.00 0.00 38.47 3.79
4677 4714 2.472029 AGTATTGCAGGTCAGCCTAGT 58.528 47.619 0.00 0.00 44.97 2.57
4715 4754 5.697473 TGACAGAAGTTGTTTGTTCAACA 57.303 34.783 11.22 0.00 46.78 3.33
4805 4844 3.581770 TGGGGATGCATCAATCAACAAAA 59.418 39.130 27.25 0.00 0.00 2.44
4815 4854 0.635555 TTGGGAATGGGGATGCATCA 59.364 50.000 27.25 9.05 0.00 3.07
4874 4976 2.586425 CCTGCAGGAAAGAAACTCCAA 58.414 47.619 29.88 0.00 37.39 3.53
4896 4998 6.531503 TCCACTAGACTTTCTACCTGAATG 57.468 41.667 0.00 0.00 34.24 2.67
4915 5017 3.490419 GCATCATCAGCCTTTTCATCCAC 60.490 47.826 0.00 0.00 0.00 4.02
5537 5639 0.258774 AAGGTGTCCTGCCAAGTGTT 59.741 50.000 0.00 0.00 32.13 3.32
5549 5653 7.171678 GCAGTGATAATCAGGTATTAAGGTGTC 59.828 40.741 0.00 0.00 33.76 3.67
5735 5839 7.264294 ACATTCCTACTGAGAAAAGAAGGAT 57.736 36.000 0.00 0.00 33.33 3.24
5741 5845 5.335191 GGTGCAACATTCCTACTGAGAAAAG 60.335 44.000 0.00 0.00 39.98 2.27
5817 5921 1.880271 TAGAGGGACGATCAGCTACG 58.120 55.000 0.00 5.77 0.00 3.51
5934 6038 2.057137 TGCTGCCTTGAACAGTTCTT 57.943 45.000 14.51 0.00 37.47 2.52
6234 6338 5.990386 AGCTTCACTGTCAGAATAGCATATG 59.010 40.000 19.37 0.00 0.00 1.78
6280 6384 8.971321 CATCCAATTTAAAAATTATGAGAGGCG 58.029 33.333 0.56 0.00 36.52 5.52
6332 6436 5.965033 AATCTGACAATACATCAGTCCCT 57.035 39.130 2.18 0.00 43.47 4.20
6380 6488 9.755804 CACTATAAGATCTATGCTTTTGTCAGA 57.244 33.333 0.00 0.00 0.00 3.27
6387 6495 9.061435 GGCTTTTCACTATAAGATCTATGCTTT 57.939 33.333 0.00 0.00 0.00 3.51
6391 6499 9.770097 TTCTGGCTTTTCACTATAAGATCTATG 57.230 33.333 0.00 0.00 0.00 2.23
6411 6519 6.091437 GCAGCATTCTCATATATTTTCTGGC 58.909 40.000 0.00 0.00 0.00 4.85
6555 6857 9.612066 ATGACAAACAATTTGAACTAAAACCAT 57.388 25.926 8.24 0.00 43.26 3.55
6601 6923 8.059798 AGCTTGAACTTAATTATGCAATCAGT 57.940 30.769 0.00 0.00 0.00 3.41
6624 6946 7.555639 TTAAATTTGTATTGTGCAACGTAGC 57.444 32.000 0.00 0.00 42.39 3.58
6693 7016 0.896940 AACAAGACTAGGCCGTCCGA 60.897 55.000 7.12 0.00 37.47 4.55
6734 7057 2.262915 CGAGAAGCGCCAGACCTT 59.737 61.111 2.29 0.00 0.00 3.50
6778 7101 2.027192 TGAAGAGTACATGGCCAACCTC 60.027 50.000 10.96 12.68 36.63 3.85
6805 7217 2.948979 ACATGAAAACAAGAGGCGTTCA 59.051 40.909 0.00 0.00 33.08 3.18


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

AutoCloner maintained by Alex Coulton.