Multiple sequence alignment - TraesCS1A01G393900

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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 TraesCS1A01G393900 chr1A 100.000 3127 0 0 1 3127 560247678 560250804 0.000000 5775.0
1 TraesCS1A01G393900 chr1B 88.516 3248 164 86 1 3127 645573257 645570098 0.000000 3738.0
2 TraesCS1A01G393900 chr1D 92.535 2264 67 41 1 2204 467663651 467661430 0.000000 3151.0
3 TraesCS1A01G393900 chr1D 93.268 817 26 6 2337 3127 467659703 467658890 0.000000 1177.0
4 TraesCS1A01G393900 chr5B 100.000 32 0 0 3030 3061 659588601 659588570 0.000034 60.2
5 TraesCS1A01G393900 chr5B 100.000 29 0 0 3032 3060 389153905 389153933 0.002000 54.7
6 TraesCS1A01G393900 chr4D 100.000 28 0 0 3029 3056 484411191 484411218 0.006000 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 TraesCS1A01G393900 chr1A 560247678 560250804 3126 False 5775 5775 100.0000 1 3127 1 chr1A.!!$F1 3126
1 TraesCS1A01G393900 chr1B 645570098 645573257 3159 True 3738 3738 88.5160 1 3127 1 chr1B.!!$R1 3126
2 TraesCS1A01G393900 chr1D 467658890 467663651 4761 True 2164 3151 92.9015 1 3127 2 chr1D.!!$R1 3126

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
909 954 0.035056 GTCAGCCACTGCCTGGTAAT 60.035 55.0 0.00 0.00 42.99 1.89 F
1617 1720 0.179076 TAGGTGATCCACGCATGCTG 60.179 55.0 17.13 12.61 34.83 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 1880 0.531532 CATAGCTGCTTCGTCCTGGG 60.532 60.000 7.79 0.0 0.0 4.45 R
2962 4774 3.792401 TGTTAGTTGTCTGTCCTGTGTG 58.208 45.455 0.00 0.0 0.0 3.82 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
43 44 0.761187 TCTACCTGGGCATCATCAGC 59.239 55.000 0.00 0.00 0.00 4.26
85 103 5.200368 TCAGGTTTTGAAATTCTCCTTGC 57.800 39.130 0.00 0.00 31.34 4.01
86 104 4.895297 TCAGGTTTTGAAATTCTCCTTGCT 59.105 37.500 0.00 0.00 31.34 3.91
87 105 4.986659 CAGGTTTTGAAATTCTCCTTGCTG 59.013 41.667 0.00 0.00 0.00 4.41
88 106 4.651045 AGGTTTTGAAATTCTCCTTGCTGT 59.349 37.500 0.00 0.00 0.00 4.40
89 107 4.984785 GGTTTTGAAATTCTCCTTGCTGTC 59.015 41.667 0.00 0.00 0.00 3.51
90 108 5.221322 GGTTTTGAAATTCTCCTTGCTGTCT 60.221 40.000 0.00 0.00 0.00 3.41
91 109 5.695851 TTTGAAATTCTCCTTGCTGTCTC 57.304 39.130 0.00 0.00 0.00 3.36
93 111 1.731720 AATTCTCCTTGCTGTCTCGC 58.268 50.000 0.00 0.00 0.00 5.03
94 112 0.610174 ATTCTCCTTGCTGTCTCGCA 59.390 50.000 0.00 0.00 38.31 5.10
96 114 1.181741 TCTCCTTGCTGTCTCGCAGT 61.182 55.000 0.00 0.00 46.64 4.40
101 119 1.194098 CTTGCTGTCTCGCAGTTTCTG 59.806 52.381 0.00 0.00 46.64 3.02
134 169 3.210528 GAGGAGCGTCGGGTCGAT 61.211 66.667 0.00 0.00 41.60 3.59
167 202 1.203441 AGCTGTTCCTCTGGCATGGA 61.203 55.000 5.42 5.42 0.00 3.41
258 293 4.772624 TCTAGCCCTATGTATGTGATCCAC 59.227 45.833 0.00 0.00 34.56 4.02
298 333 0.969894 AGTACACTGTCCCACTGCTC 59.030 55.000 0.00 0.00 0.00 4.26
430 465 2.124122 GTCACGACAAAAATGTTGGCC 58.876 47.619 0.00 0.00 0.00 5.36
464 499 4.270325 CGTCAAGGATCGATTTACCTTTCC 59.730 45.833 12.87 2.05 41.33 3.13
468 503 3.199946 AGGATCGATTTACCTTTCCTGCA 59.800 43.478 0.00 0.00 32.48 4.41
495 530 1.188863 GATGAATTGCCTGCTTGGGT 58.811 50.000 0.00 0.00 36.00 4.51
504 539 0.674895 CCTGCTTGGGTGTGTAGAGC 60.675 60.000 0.00 0.00 0.00 4.09
588 627 0.685097 AGGAGAAACTTGGTGCGCTA 59.315 50.000 9.73 0.00 0.00 4.26
618 657 2.880890 GCACATGGTATGCTCCTAAAGG 59.119 50.000 0.00 0.00 40.08 3.11
637 679 4.070681 AGGCCCTAGAGTTAAGTTACCA 57.929 45.455 0.00 0.00 0.00 3.25
898 943 1.174712 ATGGTGCACTTGTCAGCCAC 61.175 55.000 17.98 0.00 0.00 5.01
899 944 1.526917 GGTGCACTTGTCAGCCACT 60.527 57.895 17.98 0.00 0.00 4.00
900 945 1.650912 GTGCACTTGTCAGCCACTG 59.349 57.895 10.32 0.00 0.00 3.66
901 946 2.188829 TGCACTTGTCAGCCACTGC 61.189 57.895 0.00 0.00 37.95 4.40
902 947 2.912624 GCACTTGTCAGCCACTGCC 61.913 63.158 0.00 0.00 38.69 4.85
903 948 1.228063 CACTTGTCAGCCACTGCCT 60.228 57.895 0.00 0.00 38.69 4.75
904 949 1.228063 ACTTGTCAGCCACTGCCTG 60.228 57.895 0.00 0.00 38.69 4.85
905 950 1.970114 CTTGTCAGCCACTGCCTGG 60.970 63.158 0.00 0.00 44.08 4.45
907 952 1.414866 TTGTCAGCCACTGCCTGGTA 61.415 55.000 0.00 0.00 42.99 3.25
908 953 1.374947 GTCAGCCACTGCCTGGTAA 59.625 57.895 0.00 0.00 42.99 2.85
909 954 0.035056 GTCAGCCACTGCCTGGTAAT 60.035 55.000 0.00 0.00 42.99 1.89
910 955 1.209504 GTCAGCCACTGCCTGGTAATA 59.790 52.381 0.00 0.00 42.99 0.98
911 956 1.912731 TCAGCCACTGCCTGGTAATAA 59.087 47.619 0.00 0.00 42.99 1.40
913 958 1.064685 AGCCACTGCCTGGTAATAACC 60.065 52.381 0.00 0.00 42.99 2.85
914 959 4.641939 AGCCACTGCCTGGTAATAACCG 62.642 54.545 0.00 0.00 43.62 4.44
923 976 1.570813 GGTAATAACCGCCACCGTAC 58.429 55.000 0.00 0.00 35.62 3.67
928 981 1.184322 TAACCGCCACCGTACCAGAA 61.184 55.000 0.00 0.00 0.00 3.02
936 989 3.408634 CCACCGTACCAGAACTGAAAAT 58.591 45.455 3.19 0.00 0.00 1.82
944 997 3.005155 ACCAGAACTGAAAATGAGCAAGC 59.995 43.478 3.19 0.00 0.00 4.01
1007 1067 2.997315 GGCCCTCCACTTTTGCCC 60.997 66.667 0.00 0.00 36.07 5.36
1011 1071 1.153756 CCTCCACTTTTGCCCCAGT 59.846 57.895 0.00 0.00 0.00 4.00
1028 1088 5.299028 GCCCCAGTCAAAACAAATGAAAAAT 59.701 36.000 0.00 0.00 0.00 1.82
1268 1339 1.100510 CGTGAGTAACCCGGAGATGA 58.899 55.000 0.73 0.00 0.00 2.92
1380 1455 3.633065 GTCCTTCGTTCTAGATAGCCAGT 59.367 47.826 0.00 0.00 0.00 4.00
1421 1496 8.806634 CGAAGAATCTAAGAAGTTCTTGATCTG 58.193 37.037 25.27 11.55 41.01 2.90
1429 1508 5.312079 AGAAGTTCTTGATCTGGTTTCCTG 58.688 41.667 0.00 0.00 0.00 3.86
1500 1602 0.755698 TTCCTGCCTAGGTCCTAGCG 60.756 60.000 19.30 13.59 44.88 4.26
1524 1626 4.108699 CATGGCCACGACATGTATTTTT 57.891 40.909 8.16 0.00 43.48 1.94
1525 1627 3.567576 TGGCCACGACATGTATTTTTG 57.432 42.857 0.00 0.00 0.00 2.44
1526 1628 2.887783 TGGCCACGACATGTATTTTTGT 59.112 40.909 0.00 0.00 0.00 2.83
1529 1631 4.747605 GGCCACGACATGTATTTTTGTTTT 59.252 37.500 0.00 0.00 0.00 2.43
1568 1671 4.460382 GCATCAAGAGATTGAAGGGAACAA 59.540 41.667 0.00 0.00 34.24 2.83
1569 1672 5.392811 GCATCAAGAGATTGAAGGGAACAAG 60.393 44.000 0.00 0.00 34.24 3.16
1570 1673 4.074970 TCAAGAGATTGAAGGGAACAAGC 58.925 43.478 0.00 0.00 34.47 4.01
1571 1674 4.077822 CAAGAGATTGAAGGGAACAAGCT 58.922 43.478 0.00 0.00 44.69 3.74
1615 1718 1.597742 ATTAGGTGATCCACGCATGC 58.402 50.000 7.91 7.91 34.83 4.06
1616 1719 0.541392 TTAGGTGATCCACGCATGCT 59.459 50.000 17.13 0.00 34.83 3.79
1617 1720 0.179076 TAGGTGATCCACGCATGCTG 60.179 55.000 17.13 12.61 34.83 4.41
1618 1721 1.746615 GGTGATCCACGCATGCTGT 60.747 57.895 17.13 12.55 34.83 4.40
1619 1722 1.426621 GTGATCCACGCATGCTGTG 59.573 57.895 25.71 25.71 37.09 3.66
1672 1776 4.141482 TGCACTTTCTTCTGGGTTCTTAGT 60.141 41.667 0.00 0.00 0.00 2.24
1734 1842 2.821366 CAGCGGCCGAGCTTCATT 60.821 61.111 33.48 0.00 46.80 2.57
1744 1852 2.398498 CGAGCTTCATTGTAGATCGGG 58.602 52.381 19.25 0.00 45.02 5.14
1772 1880 0.676151 CTTGGTCAGCAAGGAGAGGC 60.676 60.000 8.86 0.00 0.00 4.70
1782 1893 2.683933 GGAGAGGCCCAGGACGAA 60.684 66.667 0.00 0.00 0.00 3.85
1783 1894 2.726351 GGAGAGGCCCAGGACGAAG 61.726 68.421 0.00 0.00 0.00 3.79
1784 1895 3.378399 GAGAGGCCCAGGACGAAGC 62.378 68.421 0.00 0.00 0.00 3.86
1903 2014 4.018960 ACTTCAAGCTCATACCCAACTGAT 60.019 41.667 0.00 0.00 0.00 2.90
1905 2016 2.868583 CAAGCTCATACCCAACTGATCG 59.131 50.000 0.00 0.00 0.00 3.69
1906 2017 2.388735 AGCTCATACCCAACTGATCGA 58.611 47.619 0.00 0.00 0.00 3.59
1969 2080 9.020731 TCTACGTCCATGTGAATGTATATGTAT 57.979 33.333 0.00 0.00 0.00 2.29
2020 2135 7.603180 AGTCTGGCTAATGTGATAACTGATA 57.397 36.000 0.00 0.00 0.00 2.15
2021 2136 8.023021 AGTCTGGCTAATGTGATAACTGATAA 57.977 34.615 0.00 0.00 0.00 1.75
2022 2137 8.147058 AGTCTGGCTAATGTGATAACTGATAAG 58.853 37.037 0.00 0.00 0.00 1.73
2023 2138 8.144478 GTCTGGCTAATGTGATAACTGATAAGA 58.856 37.037 0.00 0.00 0.00 2.10
2024 2139 8.363390 TCTGGCTAATGTGATAACTGATAAGAG 58.637 37.037 0.00 0.00 0.00 2.85
2025 2140 6.931281 TGGCTAATGTGATAACTGATAAGAGC 59.069 38.462 0.00 0.00 0.00 4.09
2040 2155 9.899226 ACTGATAAGAGCATTTGTAAGTTTTTC 57.101 29.630 0.00 0.00 0.00 2.29
2071 2190 3.383825 AGGTGAGTACGTGACAAAGAACT 59.616 43.478 0.00 0.00 0.00 3.01
2072 2191 4.117685 GGTGAGTACGTGACAAAGAACTT 58.882 43.478 0.00 0.00 0.00 2.66
2073 2192 5.068198 AGGTGAGTACGTGACAAAGAACTTA 59.932 40.000 0.00 0.00 0.00 2.24
2074 2193 5.750067 GGTGAGTACGTGACAAAGAACTTAA 59.250 40.000 0.00 0.00 0.00 1.85
2093 2212 9.989869 GAACTTAATTAGTTGCTTGACCTATTC 57.010 33.333 0.00 0.00 47.00 1.75
2275 4049 1.005569 AGTGTCCGACCTCCACATCTA 59.994 52.381 0.00 0.00 0.00 1.98
2281 4055 1.683385 CGACCTCCACATCTAGATGCA 59.317 52.381 28.86 14.35 42.39 3.96
2282 4056 2.544694 CGACCTCCACATCTAGATGCAC 60.545 54.545 28.86 13.10 42.39 4.57
2289 4063 4.340950 TCCACATCTAGATGCACACGATTA 59.659 41.667 28.86 5.36 42.39 1.75
2323 4097 8.150945 TCTGTCTATCTATGTTGGGAAATTAGC 58.849 37.037 0.00 0.00 0.00 3.09
2324 4098 6.929049 TGTCTATCTATGTTGGGAAATTAGCG 59.071 38.462 0.00 0.00 0.00 4.26
2325 4099 5.932303 TCTATCTATGTTGGGAAATTAGCGC 59.068 40.000 0.00 0.00 0.00 5.92
2326 4100 3.879998 TCTATGTTGGGAAATTAGCGCA 58.120 40.909 11.47 0.00 0.00 6.09
2327 4101 2.939460 ATGTTGGGAAATTAGCGCAC 57.061 45.000 11.47 0.00 0.00 5.34
2328 4102 1.610363 TGTTGGGAAATTAGCGCACA 58.390 45.000 11.47 0.00 0.00 4.57
2329 4103 1.957177 TGTTGGGAAATTAGCGCACAA 59.043 42.857 11.47 2.97 0.00 3.33
2330 4104 2.030363 TGTTGGGAAATTAGCGCACAAG 60.030 45.455 11.47 0.00 0.00 3.16
2335 4109 2.415893 GGAAATTAGCGCACAAGCACAT 60.416 45.455 11.47 0.00 42.27 3.21
2339 4113 2.892373 TAGCGCACAAGCACATTTAC 57.108 45.000 11.47 0.00 42.27 2.01
2356 4130 7.042051 GCACATTTACTGTTCTCTGAAACACTA 60.042 37.037 0.00 0.00 35.29 2.74
2715 4518 8.387813 TGGGTATAGTTTCTCAATTAACTGGTT 58.612 33.333 2.25 0.00 36.16 3.67
2745 4548 8.319146 TCCGTTAATCAAAGAGGACTTTAATCT 58.681 33.333 0.00 0.00 43.41 2.40
2751 4554 8.712228 ATCAAAGAGGACTTTAATCTGGTTTT 57.288 30.769 0.00 0.00 43.41 2.43
2906 4718 1.768275 TCTCTGGAACACTGCTGGAAA 59.232 47.619 0.00 0.00 0.00 3.13
2907 4719 2.172505 TCTCTGGAACACTGCTGGAAAA 59.827 45.455 0.00 0.00 0.00 2.29
2962 4774 6.546395 ACTAATTCATTGATCGTTGCTCAAC 58.454 36.000 2.80 2.80 35.57 3.18
2971 4783 0.304705 CGTTGCTCAACACACAGGAC 59.695 55.000 12.54 0.00 41.20 3.85
3086 4898 7.173735 TGAACATCTGCAACATGATATATGGAC 59.826 37.037 11.43 0.00 0.00 4.02
3095 4907 8.567104 GCAACATGATATATGGACAATTACACA 58.433 33.333 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.763073 TGATTTGAGTGGAGATAGTGCTG 58.237 43.478 0.00 0.00 0.00 4.41
86 104 1.865865 GGAACAGAAACTGCGAGACA 58.134 50.000 0.00 0.00 34.37 3.41
87 105 0.784778 CGGAACAGAAACTGCGAGAC 59.215 55.000 0.00 0.00 34.37 3.36
88 106 0.387929 ACGGAACAGAAACTGCGAGA 59.612 50.000 0.00 0.00 34.37 4.04
89 107 0.784778 GACGGAACAGAAACTGCGAG 59.215 55.000 0.00 0.00 34.37 5.03
90 108 0.103390 TGACGGAACAGAAACTGCGA 59.897 50.000 0.00 0.00 34.37 5.10
91 109 0.232303 GTGACGGAACAGAAACTGCG 59.768 55.000 0.00 0.00 34.37 5.18
93 111 0.232303 GCGTGACGGAACAGAAACTG 59.768 55.000 7.25 0.00 37.52 3.16
94 112 1.213094 CGCGTGACGGAACAGAAACT 61.213 55.000 7.25 0.00 38.44 2.66
95 113 1.200839 CGCGTGACGGAACAGAAAC 59.799 57.895 7.25 0.00 38.44 2.78
96 114 1.066093 TCGCGTGACGGAACAGAAA 59.934 52.632 7.25 0.00 43.89 2.52
129 164 4.537936 GCTGAAAGGTAAATCCATCGAC 57.462 45.455 0.00 0.00 39.02 4.20
167 202 4.588951 TCAGTCGGTTAGCATATTCCATCT 59.411 41.667 0.00 0.00 0.00 2.90
258 293 0.040157 CATTGTTCAGGGTGTGTGCG 60.040 55.000 0.00 0.00 0.00 5.34
298 333 3.571590 AGTAGGCTGAGATGAGGGTAAG 58.428 50.000 0.00 0.00 0.00 2.34
464 499 2.671396 GCAATTCATCTTTGGCTTGCAG 59.329 45.455 0.00 0.00 38.95 4.41
495 530 2.167693 CACCCTAAATCGGCTCTACACA 59.832 50.000 0.00 0.00 0.00 3.72
504 539 2.288666 CCATGACACACCCTAAATCGG 58.711 52.381 0.00 0.00 0.00 4.18
616 655 3.773667 GTGGTAACTTAACTCTAGGGCCT 59.226 47.826 12.58 12.58 37.61 5.19
617 656 3.516700 TGTGGTAACTTAACTCTAGGGCC 59.483 47.826 0.00 0.00 37.61 5.80
618 657 4.813750 TGTGGTAACTTAACTCTAGGGC 57.186 45.455 0.00 0.00 37.61 5.19
637 679 1.593196 ACATGCACGTTGCTACTTGT 58.407 45.000 6.64 6.93 45.31 3.16
898 943 0.107410 TGGCGGTTATTACCAGGCAG 60.107 55.000 14.52 0.00 45.31 4.85
899 944 0.393267 GTGGCGGTTATTACCAGGCA 60.393 55.000 14.52 14.52 45.31 4.75
900 945 1.099295 GGTGGCGGTTATTACCAGGC 61.099 60.000 1.20 6.97 45.31 4.85
901 946 0.812412 CGGTGGCGGTTATTACCAGG 60.812 60.000 1.20 0.00 45.31 4.45
902 947 0.108041 ACGGTGGCGGTTATTACCAG 60.108 55.000 1.20 0.00 45.31 4.00
903 948 1.134848 GTACGGTGGCGGTTATTACCA 60.135 52.381 1.20 0.00 45.31 3.25
904 949 1.570813 GTACGGTGGCGGTTATTACC 58.429 55.000 0.00 0.00 41.33 2.85
905 950 1.134848 TGGTACGGTGGCGGTTATTAC 60.135 52.381 0.00 0.00 0.00 1.89
907 952 0.108041 CTGGTACGGTGGCGGTTATT 60.108 55.000 0.00 0.00 0.00 1.40
908 953 0.971959 TCTGGTACGGTGGCGGTTAT 60.972 55.000 0.00 0.00 35.30 1.89
909 954 1.184322 TTCTGGTACGGTGGCGGTTA 61.184 55.000 0.00 0.00 35.30 2.85
910 955 2.509651 TTCTGGTACGGTGGCGGTT 61.510 57.895 0.00 0.00 35.30 4.44
911 956 2.918802 TTCTGGTACGGTGGCGGT 60.919 61.111 0.00 0.00 35.30 5.68
913 958 1.736645 CAGTTCTGGTACGGTGGCG 60.737 63.158 0.00 0.00 35.30 5.69
914 959 0.034337 TTCAGTTCTGGTACGGTGGC 59.966 55.000 0.00 0.00 35.30 5.01
916 961 4.062293 TCATTTTCAGTTCTGGTACGGTG 58.938 43.478 0.00 0.00 35.30 4.94
919 964 3.745975 TGCTCATTTTCAGTTCTGGTACG 59.254 43.478 0.00 0.00 0.00 3.67
920 965 5.689383 TTGCTCATTTTCAGTTCTGGTAC 57.311 39.130 0.00 0.00 0.00 3.34
923 976 3.572584 GCTTGCTCATTTTCAGTTCTGG 58.427 45.455 0.00 0.00 0.00 3.86
928 981 1.537202 GGTCGCTTGCTCATTTTCAGT 59.463 47.619 0.00 0.00 0.00 3.41
936 989 3.923864 ACCGTGGTCGCTTGCTCA 61.924 61.111 0.00 0.00 35.54 4.26
944 997 2.663852 GGTTGGTCACCGTGGTCG 60.664 66.667 0.00 0.00 35.12 4.79
1007 1067 9.190858 TCGATATTTTTCATTTGTTTTGACTGG 57.809 29.630 0.00 0.00 0.00 4.00
1028 1088 6.935240 AGGGATGATGTAGGAATTTCGATA 57.065 37.500 0.00 0.00 0.00 2.92
1041 1101 2.827921 GCAAGTTCCAAAGGGATGATGT 59.172 45.455 0.00 0.00 44.48 3.06
1268 1339 2.527875 GGATCTCCGGGGCATCCT 60.528 66.667 19.84 0.00 34.31 3.24
1421 1496 1.269778 GGTTTGAAGCAGCAGGAAACC 60.270 52.381 13.52 13.52 38.98 3.27
1429 1508 0.319405 ATGCAAGGGTTTGAAGCAGC 59.681 50.000 0.00 0.00 38.75 5.25
1500 1602 2.486504 CATGTCGTGGCCATGTGC 59.513 61.111 24.24 17.85 35.94 4.57
1524 1626 8.409371 TGATGCATTTGTAACAGTAAGAAAACA 58.591 29.630 0.00 0.00 0.00 2.83
1525 1627 8.795786 TGATGCATTTGTAACAGTAAGAAAAC 57.204 30.769 0.00 0.00 0.00 2.43
1526 1628 9.462174 CTTGATGCATTTGTAACAGTAAGAAAA 57.538 29.630 0.00 0.00 0.00 2.29
1529 1631 7.877612 TCTCTTGATGCATTTGTAACAGTAAGA 59.122 33.333 0.00 0.00 0.00 2.10
1569 1672 1.659954 CCGCAGCTCGACATCTAGC 60.660 63.158 7.07 0.00 41.67 3.42
1570 1673 1.659954 GCCGCAGCTCGACATCTAG 60.660 63.158 7.07 0.00 41.67 2.43
1571 1674 2.413351 GCCGCAGCTCGACATCTA 59.587 61.111 7.07 0.00 41.67 1.98
1615 1718 2.033141 CCAGACCCACAGGCACAG 59.967 66.667 0.00 0.00 36.11 3.66
1616 1719 3.569210 CCCAGACCCACAGGCACA 61.569 66.667 0.00 0.00 36.11 4.57
1617 1720 3.553095 GACCCAGACCCACAGGCAC 62.553 68.421 0.00 0.00 36.11 5.01
1618 1721 3.249189 GACCCAGACCCACAGGCA 61.249 66.667 0.00 0.00 36.11 4.75
1619 1722 2.606587 ATGACCCAGACCCACAGGC 61.607 63.158 0.00 0.00 36.11 4.85
1620 1723 1.200760 TCATGACCCAGACCCACAGG 61.201 60.000 0.00 0.00 40.04 4.00
1734 1842 2.128535 AGAGACTCCTCCCGATCTACA 58.871 52.381 0.00 0.00 40.30 2.74
1742 1850 1.190643 CTGACCAAGAGACTCCTCCC 58.809 60.000 0.00 0.00 40.30 4.30
1743 1851 0.534873 GCTGACCAAGAGACTCCTCC 59.465 60.000 0.00 0.00 40.30 4.30
1744 1852 1.261480 TGCTGACCAAGAGACTCCTC 58.739 55.000 0.00 0.00 39.72 3.71
1772 1880 0.531532 CATAGCTGCTTCGTCCTGGG 60.532 60.000 7.79 0.00 0.00 4.45
1799 1910 2.821366 GCATCCGGGAGTGCACAG 60.821 66.667 21.04 7.13 40.94 3.66
1800 1911 3.315142 GAGCATCCGGGAGTGCACA 62.315 63.158 21.04 0.00 43.63 4.57
1903 2014 0.742505 CGTATAGCCAGGGTGTTCGA 59.257 55.000 8.47 0.00 0.00 3.71
1905 2016 1.479323 TCACGTATAGCCAGGGTGTTC 59.521 52.381 0.00 0.00 0.00 3.18
1906 2017 1.563924 TCACGTATAGCCAGGGTGTT 58.436 50.000 0.00 0.00 0.00 3.32
2020 2135 8.283291 CGTCTAGAAAAACTTACAAATGCTCTT 58.717 33.333 0.00 0.00 0.00 2.85
2021 2136 7.441458 ACGTCTAGAAAAACTTACAAATGCTCT 59.559 33.333 0.00 0.00 0.00 4.09
2022 2137 7.530861 CACGTCTAGAAAAACTTACAAATGCTC 59.469 37.037 0.00 0.00 0.00 4.26
2023 2138 7.225931 TCACGTCTAGAAAAACTTACAAATGCT 59.774 33.333 0.00 0.00 0.00 3.79
2024 2139 7.349711 TCACGTCTAGAAAAACTTACAAATGC 58.650 34.615 0.00 0.00 0.00 3.56
2025 2140 8.009974 CCTCACGTCTAGAAAAACTTACAAATG 58.990 37.037 0.00 0.00 0.00 2.32
2037 2152 3.434641 CGTACTCACCTCACGTCTAGAAA 59.565 47.826 0.00 0.00 0.00 2.52
2040 2155 2.093941 CACGTACTCACCTCACGTCTAG 59.906 54.545 0.00 0.00 46.34 2.43
2073 2192 8.893727 GTGTATGAATAGGTCAAGCAACTAATT 58.106 33.333 0.00 0.00 40.50 1.40
2074 2193 8.267894 AGTGTATGAATAGGTCAAGCAACTAAT 58.732 33.333 0.00 0.00 40.50 1.73
2248 4022 4.179298 GTGGAGGTCGGACACTATTTAAC 58.821 47.826 10.76 0.00 32.58 2.01
2258 4032 2.054232 TCTAGATGTGGAGGTCGGAC 57.946 55.000 0.00 0.00 0.00 4.79
2275 4049 7.712639 ACAGAAAGATTATAATCGTGTGCATCT 59.287 33.333 17.69 11.64 40.35 2.90
2323 4097 2.686558 ACAGTAAATGTGCTTGTGCG 57.313 45.000 0.00 0.00 41.91 5.34
2324 4098 4.023707 AGAGAACAGTAAATGTGCTTGTGC 60.024 41.667 0.00 0.00 46.64 4.57
2325 4099 5.237127 TCAGAGAACAGTAAATGTGCTTGTG 59.763 40.000 0.00 0.00 46.64 3.33
2326 4100 5.368145 TCAGAGAACAGTAAATGTGCTTGT 58.632 37.500 0.00 0.00 46.64 3.16
2327 4101 5.929697 TCAGAGAACAGTAAATGTGCTTG 57.070 39.130 0.00 0.00 46.64 4.01
2328 4102 6.318648 TGTTTCAGAGAACAGTAAATGTGCTT 59.681 34.615 0.00 0.00 46.64 3.91
2330 4104 5.909610 GTGTTTCAGAGAACAGTAAATGTGC 59.090 40.000 0.00 0.00 43.00 4.57
2335 4109 7.171508 CAGCATAGTGTTTCAGAGAACAGTAAA 59.828 37.037 8.77 0.00 44.28 2.01
2339 4113 4.391216 CCAGCATAGTGTTTCAGAGAACAG 59.609 45.833 0.00 0.00 39.97 3.16
2356 4130 7.385267 TGCAAATTACACTTTAATTCCAGCAT 58.615 30.769 0.00 0.00 31.07 3.79
2494 4289 9.891828 TTTAGCCGTTCATATGCTTTATAAATG 57.108 29.630 0.00 0.00 36.57 2.32
2504 4299 5.682943 TGGTATTTTAGCCGTTCATATGC 57.317 39.130 0.00 0.00 0.00 3.14
2715 4518 7.447594 AAAGTCCTCTTTGATTAACGGAAGTA 58.552 34.615 0.00 0.00 42.32 2.24
2822 4627 9.123709 GATAGATTATAATAGTGCGCATCTAGC 57.876 37.037 15.91 12.29 40.87 3.42
2902 4714 8.708742 GGTGCTGAAAAATACACTTTATTTTCC 58.291 33.333 7.21 0.00 39.73 3.13
2906 4718 7.951591 AGTGGTGCTGAAAAATACACTTTATT 58.048 30.769 0.00 0.00 34.36 1.40
2907 4719 7.524717 AGTGGTGCTGAAAAATACACTTTAT 57.475 32.000 0.00 0.00 34.36 1.40
2962 4774 3.792401 TGTTAGTTGTCTGTCCTGTGTG 58.208 45.455 0.00 0.00 0.00 3.82
2971 4783 7.895975 TTCTGAATCAGATGTTAGTTGTCTG 57.104 36.000 14.31 0.00 40.39 3.51
3086 4898 9.151471 GGGCAGTATATACATAGTGTGTAATTG 57.849 37.037 15.18 1.32 45.87 2.32
3095 4907 5.537295 TGTTCGTGGGCAGTATATACATAGT 59.463 40.000 15.18 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.