Multiple sequence alignment - TraesCS4A01G095000

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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 TraesCS4A01G095000 chr4A 100.000 4122 0 0 720 4841 103386612 103390733 0.000000e+00 7613.0
1 TraesCS4A01G095000 chr4A 100.000 330 0 0 1 330 103385893 103386222 1.150000e-170 610.0
2 TraesCS4A01G095000 chr4A 96.364 55 1 1 3870 3924 569482990 569482937 6.670000e-14 89.8
3 TraesCS4A01G095000 chr4D 94.643 3192 125 27 720 3877 361599841 361596662 0.000000e+00 4905.0
4 TraesCS4A01G095000 chr4D 92.090 885 39 15 3958 4841 361596618 361595764 0.000000e+00 1218.0
5 TraesCS4A01G095000 chr4D 92.236 322 18 3 16 330 361600270 361599949 2.660000e-122 449.0
6 TraesCS4A01G095000 chr4B 93.111 2874 151 25 720 3564 446857797 446854942 0.000000e+00 4167.0
7 TraesCS4A01G095000 chr4B 93.296 895 39 10 3958 4841 446854670 446853786 0.000000e+00 1301.0
8 TraesCS4A01G095000 chr4B 94.603 315 10 2 16 330 446858211 446857904 9.420000e-132 481.0
9 TraesCS4A01G095000 chr4B 96.386 249 9 0 3610 3858 446854946 446854698 1.250000e-110 411.0
10 TraesCS4A01G095000 chr4B 90.625 96 6 2 1666 1760 446856897 446856804 1.830000e-24 124.0
11 TraesCS4A01G095000 chr5A 82.751 1287 155 25 2086 3338 9324614 9325867 0.000000e+00 1085.0
12 TraesCS4A01G095000 chr5A 93.220 59 2 2 3870 3926 665078723 665078665 8.630000e-13 86.1
13 TraesCS4A01G095000 chr5D 83.638 1149 143 13 2087 3222 10898609 10899725 0.000000e+00 1038.0
14 TraesCS4A01G095000 chr5B 81.966 1292 161 19 2087 3338 11456010 11457269 0.000000e+00 1029.0
15 TraesCS4A01G095000 chr7A 96.491 57 1 1 3869 3924 116615960 116616016 5.160000e-15 93.5
16 TraesCS4A01G095000 chr3D 93.333 60 1 1 3870 3926 435451258 435451317 8.630000e-13 86.1
17 TraesCS4A01G095000 chr2D 93.220 59 3 1 3870 3927 311556772 311556714 8.630000e-13 86.1
18 TraesCS4A01G095000 chr2D 92.857 56 2 2 3870 3925 29227486 29227433 4.020000e-11 80.5
19 TraesCS4A01G095000 chr1B 94.643 56 1 1 3870 3925 579608120 579608067 8.630000e-13 86.1
20 TraesCS4A01G095000 chr7D 90.625 64 4 1 3865 3928 8879526 8879465 3.100000e-12 84.2
21 TraesCS4A01G095000 chr1D 92.857 56 2 1 3870 3925 62888700 62888753 4.020000e-11 80.5


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 TraesCS4A01G095000 chr4A 103385893 103390733 4840 False 4111.500000 7613 100.000000 1 4841 2 chr4A.!!$F1 4840
1 TraesCS4A01G095000 chr4D 361595764 361600270 4506 True 2190.666667 4905 92.989667 16 4841 3 chr4D.!!$R1 4825
2 TraesCS4A01G095000 chr4B 446853786 446858211 4425 True 1296.800000 4167 93.604200 16 4841 5 chr4B.!!$R1 4825
3 TraesCS4A01G095000 chr5A 9324614 9325867 1253 False 1085.000000 1085 82.751000 2086 3338 1 chr5A.!!$F1 1252
4 TraesCS4A01G095000 chr5D 10898609 10899725 1116 False 1038.000000 1038 83.638000 2087 3222 1 chr5D.!!$F1 1135
5 TraesCS4A01G095000 chr5B 11456010 11457269 1259 False 1029.000000 1029 81.966000 2087 3338 1 chr5B.!!$F1 1251

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
280 288 0.030705 CTCCCCCTCTCCTGAATCCA 60.031 60.000 0.0 0.00 0.00 3.41 F
1021 1030 2.033141 CCACACCAGGGAGCAGTG 59.967 66.667 0.0 0.00 37.53 3.66 F
1358 1388 2.897271 TGGTGTTGGTCCATGCTAAT 57.103 45.000 0.0 0.00 0.00 1.73 F
1434 1466 2.996249 ACAGCATCACCTGGAGTATG 57.004 50.000 0.0 2.04 37.16 2.39 F
2548 2591 1.537776 CCTCCTGAACTAGCTCATGCG 60.538 57.143 0.0 0.00 45.42 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 2017 0.676151 CTCCACAGCTGAAGGAAGGC 60.676 60.000 23.35 0.00 0.0 4.35 R
1976 2018 0.689623 ACTCCACAGCTGAAGGAAGG 59.310 55.000 23.35 16.97 0.0 3.46 R
2308 2351 1.430632 CGATGATGGTGGTGCAAGC 59.569 57.895 0.00 0.00 0.0 4.01 R
3396 3478 0.109723 CTGGGGTGAAAAGTCGGGAA 59.890 55.000 0.00 0.00 0.0 3.97 R
4230 4337 0.179043 TGCCTAACCAGTCGTTGCAA 60.179 50.000 0.00 0.00 32.2 4.08 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
55 56 1.000019 ACCGACCTCTCCCATTCGA 60.000 57.895 0.00 0.00 33.20 3.71
276 284 1.460839 TTCCCTCCCCCTCTCCTGAA 61.461 60.000 0.00 0.00 0.00 3.02
277 285 1.238896 TCCCTCCCCCTCTCCTGAAT 61.239 60.000 0.00 0.00 0.00 2.57
280 288 0.030705 CTCCCCCTCTCCTGAATCCA 60.031 60.000 0.00 0.00 0.00 3.41
294 302 2.705658 TGAATCCATCTTATGCTCGGGT 59.294 45.455 0.00 0.00 0.00 5.28
1021 1030 2.033141 CCACACCAGGGAGCAGTG 59.967 66.667 0.00 0.00 37.53 3.66
1191 1201 3.879932 AGCTAGTCGTTTGTGCTTTTC 57.120 42.857 0.00 0.00 0.00 2.29
1203 1214 5.431420 TTGTGCTTTTCGCTTTAGATGAA 57.569 34.783 0.00 0.00 40.11 2.57
1222 1233 4.587891 TGAACACATCCATCACTGCATAA 58.412 39.130 0.00 0.00 0.00 1.90
1358 1388 2.897271 TGGTGTTGGTCCATGCTAAT 57.103 45.000 0.00 0.00 0.00 1.73
1390 1420 7.290118 GCATTTTGCACTAGTTTGGTAATTTG 58.710 34.615 0.00 0.00 44.26 2.32
1391 1421 6.836577 TTTTGCACTAGTTTGGTAATTTGC 57.163 33.333 0.00 0.00 0.00 3.68
1392 1422 5.521906 TTGCACTAGTTTGGTAATTTGCA 57.478 34.783 0.00 0.00 36.97 4.08
1394 1424 5.907207 TGCACTAGTTTGGTAATTTGCAAA 58.093 33.333 15.44 15.44 35.87 3.68
1410 1442 3.291584 TGCAAAACCACATACCTTGTCA 58.708 40.909 0.00 0.00 36.00 3.58
1434 1466 2.996249 ACAGCATCACCTGGAGTATG 57.004 50.000 0.00 2.04 37.16 2.39
1460 1492 7.563888 TGCTCTTTCATTCCTTTCATAGATG 57.436 36.000 0.00 0.00 0.00 2.90
1494 1526 6.955364 TCAGTATATAGGTATAGCTGGTCGT 58.045 40.000 14.72 0.00 30.85 4.34
1575 1612 5.048713 ACTTTGGAAAGCACTTACTGTATGC 60.049 40.000 5.48 5.48 39.63 3.14
1825 1864 8.432110 ACACAATTTATATGTTCTATGTGCGA 57.568 30.769 0.00 0.00 40.29 5.10
1852 1891 5.981174 CATTTTGTGCTTGTGAATTTCTGG 58.019 37.500 0.00 0.00 0.00 3.86
1867 1906 7.062255 GTGAATTTCTGGCTAATTTACTTGCAC 59.938 37.037 0.00 0.00 32.11 4.57
1875 1914 6.071840 TGGCTAATTTACTTGCACGGTTATTT 60.072 34.615 0.00 0.00 0.00 1.40
1885 1924 5.316327 TGCACGGTTATTTATGATGCAAA 57.684 34.783 0.00 0.00 38.56 3.68
1975 2017 7.706179 ACATTGTGTTGTCAATTCTAAACTTGG 59.294 33.333 0.00 0.00 36.10 3.61
1976 2018 5.587289 TGTGTTGTCAATTCTAAACTTGGC 58.413 37.500 0.00 0.00 0.00 4.52
1981 2023 4.522789 TGTCAATTCTAAACTTGGCCTTCC 59.477 41.667 3.32 0.00 0.00 3.46
2000 2042 3.173151 TCCTTCAGCTGTGGAGTCAATA 58.827 45.455 21.27 4.20 0.00 1.90
2276 2319 6.939132 ATGCTCTTCAATCTGGTAGAAATG 57.061 37.500 0.00 0.00 0.00 2.32
2308 2351 9.894783 CAAAATGGAGCTATGAATTTATCTCTG 57.105 33.333 0.00 0.00 0.00 3.35
2440 2483 3.245284 CGTCTAATATGTTCGCTGTTGGG 59.755 47.826 0.00 0.00 0.00 4.12
2548 2591 1.537776 CCTCCTGAACTAGCTCATGCG 60.538 57.143 0.00 0.00 45.42 4.73
2725 2771 3.172339 CCCTTCTAGCAGCCTCATATCT 58.828 50.000 0.00 0.00 0.00 1.98
2784 2830 2.322355 ATCCCTGAGCAAGATGTTCG 57.678 50.000 0.00 0.00 29.60 3.95
2979 3031 5.010213 CCCCTAGAAACTGTCTGCTAGATAC 59.990 48.000 0.00 0.00 37.12 2.24
3244 3314 3.434940 ACTGAGGTGTCCCCATTTAAC 57.565 47.619 0.00 0.00 34.66 2.01
3260 3336 5.760253 CCATTTAACGATCTGCCTAATGAGT 59.240 40.000 0.00 0.00 0.00 3.41
3370 3452 3.668447 CAGTCCACAGAAAGTACTGCAT 58.332 45.455 0.00 0.00 41.06 3.96
3371 3453 4.067896 CAGTCCACAGAAAGTACTGCATT 58.932 43.478 0.00 0.00 41.06 3.56
3418 3500 1.971695 CGACTTTTCACCCCAGCCC 60.972 63.158 0.00 0.00 0.00 5.19
3419 3501 1.971695 GACTTTTCACCCCAGCCCG 60.972 63.158 0.00 0.00 0.00 6.13
3422 3504 1.524008 CTTTTCACCCCAGCCCGTTC 61.524 60.000 0.00 0.00 0.00 3.95
3427 3509 1.844289 ACCCCAGCCCGTTCTGTTA 60.844 57.895 1.35 0.00 32.32 2.41
3432 3514 2.368875 CCCAGCCCGTTCTGTTATATCT 59.631 50.000 1.35 0.00 32.32 1.98
3474 3556 2.328819 AGATCTCCATGAACTGCTGC 57.671 50.000 0.00 0.00 0.00 5.25
3498 3585 5.920273 CGCAGACCAATTGTTCAGTAATTTT 59.080 36.000 5.73 0.00 0.00 1.82
3499 3586 6.420604 CGCAGACCAATTGTTCAGTAATTTTT 59.579 34.615 5.73 0.00 0.00 1.94
3500 3587 7.593273 CGCAGACCAATTGTTCAGTAATTTTTA 59.407 33.333 5.73 0.00 0.00 1.52
3501 3588 9.423061 GCAGACCAATTGTTCAGTAATTTTTAT 57.577 29.630 5.73 0.00 0.00 1.40
3551 3638 7.041635 ACACAAATGTCTTTCATCAACATCA 57.958 32.000 0.00 0.00 31.55 3.07
3581 3668 4.998672 ACCCAGATTTTGATTTGCACAATG 59.001 37.500 0.00 0.00 27.44 2.82
3601 3688 6.840705 ACAATGCCCTAATGATGTCCTTAATT 59.159 34.615 0.00 0.00 0.00 1.40
3602 3689 6.906157 ATGCCCTAATGATGTCCTTAATTG 57.094 37.500 0.00 0.00 0.00 2.32
3617 3704 7.038017 TGTCCTTAATTGACTTCTCTCAGGAAT 60.038 37.037 6.78 0.00 33.83 3.01
3652 3739 0.037326 GTCTGAGGATGACGCAACCA 60.037 55.000 8.40 0.00 0.00 3.67
3660 3747 0.865769 ATGACGCAACCACGAAAGAC 59.134 50.000 0.00 0.00 36.70 3.01
3816 3905 1.071299 TGTTCTGTCATGGCGCAGT 59.929 52.632 10.83 0.00 34.57 4.40
3867 3956 3.005554 CTCTGGTATGCAGGACAAGTTG 58.994 50.000 0.00 0.00 0.00 3.16
3868 3957 2.637382 TCTGGTATGCAGGACAAGTTGA 59.363 45.455 10.54 0.00 0.00 3.18
3869 3958 3.264193 TCTGGTATGCAGGACAAGTTGAT 59.736 43.478 10.54 0.00 0.00 2.57
3870 3959 4.469586 TCTGGTATGCAGGACAAGTTGATA 59.530 41.667 10.54 0.00 0.00 2.15
3871 3960 4.513442 TGGTATGCAGGACAAGTTGATAC 58.487 43.478 10.54 5.80 0.00 2.24
3872 3961 4.225042 TGGTATGCAGGACAAGTTGATACT 59.775 41.667 10.54 1.43 35.68 2.12
3873 3962 4.811557 GGTATGCAGGACAAGTTGATACTC 59.188 45.833 10.54 0.00 31.99 2.59
3874 3963 3.334583 TGCAGGACAAGTTGATACTCC 57.665 47.619 10.54 5.99 31.99 3.85
3875 3964 2.027192 TGCAGGACAAGTTGATACTCCC 60.027 50.000 10.54 1.08 31.99 4.30
3876 3965 2.237392 GCAGGACAAGTTGATACTCCCT 59.763 50.000 10.54 3.30 31.99 4.20
3877 3966 3.680196 GCAGGACAAGTTGATACTCCCTC 60.680 52.174 10.54 0.00 31.99 4.30
3878 3967 3.772025 CAGGACAAGTTGATACTCCCTCT 59.228 47.826 10.54 0.00 31.99 3.69
3879 3968 3.772025 AGGACAAGTTGATACTCCCTCTG 59.228 47.826 10.54 0.00 31.99 3.35
3880 3969 3.515901 GGACAAGTTGATACTCCCTCTGT 59.484 47.826 10.54 0.00 31.99 3.41
3881 3970 4.710375 GGACAAGTTGATACTCCCTCTGTA 59.290 45.833 10.54 0.00 31.99 2.74
3882 3971 5.364157 GGACAAGTTGATACTCCCTCTGTAT 59.636 44.000 10.54 0.00 31.99 2.29
3883 3972 6.550108 GGACAAGTTGATACTCCCTCTGTATA 59.450 42.308 10.54 0.00 31.99 1.47
3884 3973 7.255660 GGACAAGTTGATACTCCCTCTGTATAG 60.256 44.444 10.54 0.00 31.99 1.31
3885 3974 7.126733 ACAAGTTGATACTCCCTCTGTATAGT 58.873 38.462 10.54 0.00 31.99 2.12
3886 3975 7.068839 ACAAGTTGATACTCCCTCTGTATAGTG 59.931 40.741 10.54 0.00 31.99 2.74
3887 3976 6.912426 AGTTGATACTCCCTCTGTATAGTGA 58.088 40.000 0.00 0.00 31.55 3.41
3888 3977 7.531317 AGTTGATACTCCCTCTGTATAGTGAT 58.469 38.462 0.00 0.00 31.55 3.06
3889 3978 7.668052 AGTTGATACTCCCTCTGTATAGTGATC 59.332 40.741 0.00 0.00 31.55 2.92
3890 3979 7.336475 TGATACTCCCTCTGTATAGTGATCT 57.664 40.000 0.00 0.00 31.55 2.75
3891 3980 8.450780 TGATACTCCCTCTGTATAGTGATCTA 57.549 38.462 0.00 0.00 31.55 1.98
3892 3981 8.891501 TGATACTCCCTCTGTATAGTGATCTAA 58.108 37.037 0.00 0.00 31.55 2.10
3893 3982 9.742144 GATACTCCCTCTGTATAGTGATCTAAA 57.258 37.037 0.00 0.00 31.55 1.85
3894 3983 7.826918 ACTCCCTCTGTATAGTGATCTAAAC 57.173 40.000 0.00 0.00 0.00 2.01
3895 3984 7.355101 ACTCCCTCTGTATAGTGATCTAAACA 58.645 38.462 0.00 0.00 0.00 2.83
3896 3985 7.285858 ACTCCCTCTGTATAGTGATCTAAACAC 59.714 40.741 0.00 0.00 38.38 3.32
3898 3987 7.502895 TCCCTCTGTATAGTGATCTAAACACTC 59.497 40.741 0.00 0.00 45.58 3.51
3899 3988 7.504238 CCCTCTGTATAGTGATCTAAACACTCT 59.496 40.741 0.00 0.00 45.58 3.24
3900 3989 8.908903 CCTCTGTATAGTGATCTAAACACTCTT 58.091 37.037 0.00 0.00 45.58 2.85
3917 4006 8.943909 AACACTCTTATATTTCTTTACGGAGG 57.056 34.615 0.00 0.00 0.00 4.30
3918 4007 7.498443 ACACTCTTATATTTCTTTACGGAGGG 58.502 38.462 0.00 0.00 0.00 4.30
3919 4008 7.343833 ACACTCTTATATTTCTTTACGGAGGGA 59.656 37.037 0.00 0.00 0.00 4.20
3920 4009 7.868415 CACTCTTATATTTCTTTACGGAGGGAG 59.132 40.741 0.00 0.00 0.00 4.30
4084 4191 8.531982 TGATGAACAGCTTGTATTCTACTACTT 58.468 33.333 0.00 0.00 0.00 2.24
4157 4264 2.533266 CGGAGCAATGAAATGAAAGGC 58.467 47.619 0.00 0.00 0.00 4.35
4219 4326 7.739825 TCATGTTTCTCCCCTGAAATATCTAG 58.260 38.462 0.00 0.00 36.23 2.43
4230 4337 7.016072 CCCCTGAAATATCTAGAAGTCTGACAT 59.984 40.741 10.88 0.00 0.00 3.06
4265 4372 1.510623 GCAGTGCGAATTCTGCGTG 60.511 57.895 0.00 14.46 45.42 5.34
4274 4381 1.526575 AATTCTGCGTGGTTGGCCTG 61.527 55.000 3.32 0.00 35.27 4.85
4301 4411 2.328099 CGTTCCTTCTGCAGCCACC 61.328 63.158 9.47 0.00 0.00 4.61
4336 4446 0.616371 TACAACGAGGGACATTGGGG 59.384 55.000 0.00 0.00 0.00 4.96
4363 4473 5.991861 TGCCATTTGCTTTATTGGATCATT 58.008 33.333 0.00 0.00 42.00 2.57
4498 4608 4.373116 TTCACGAGGAGGGCACGC 62.373 66.667 0.00 0.00 0.00 5.34
4517 4627 0.319813 CATGAGGCAGACACACACGA 60.320 55.000 0.00 0.00 0.00 4.35
4518 4628 0.037882 ATGAGGCAGACACACACGAG 60.038 55.000 0.00 0.00 0.00 4.18
4519 4629 1.106944 TGAGGCAGACACACACGAGA 61.107 55.000 0.00 0.00 0.00 4.04
4520 4630 0.387878 GAGGCAGACACACACGAGAG 60.388 60.000 0.00 0.00 0.00 3.20
4521 4631 2.024319 GGCAGACACACACGAGAGC 61.024 63.158 0.00 0.00 0.00 4.09
4522 4632 1.300156 GCAGACACACACGAGAGCA 60.300 57.895 0.00 0.00 0.00 4.26
4523 4633 1.552348 GCAGACACACACGAGAGCAC 61.552 60.000 0.00 0.00 0.00 4.40
4557 4668 2.646719 CATGCACGTGCTGGCTTT 59.353 55.556 37.59 14.97 42.66 3.51
4561 4672 3.594775 CACGTGCTGGCTTTGGCA 61.595 61.111 0.82 0.00 40.87 4.92
4571 4682 2.664851 CTTTGGCAGTCACCGCGA 60.665 61.111 8.23 0.00 0.00 5.87
4625 4741 0.176680 CAAGTGGTCCTGGATCCTCG 59.823 60.000 14.23 3.91 0.00 4.63
4629 4745 0.755698 TGGTCCTGGATCCTCGCTAC 60.756 60.000 14.23 4.21 0.00 3.58
4632 4748 1.109920 TCCTGGATCCTCGCTACTGC 61.110 60.000 14.23 0.00 0.00 4.40
4764 4880 2.046700 CCTTTGGAAGCGGGCGTA 60.047 61.111 0.00 0.00 0.00 4.42
4765 4881 2.106683 CCTTTGGAAGCGGGCGTAG 61.107 63.158 0.00 0.00 0.00 3.51
4766 4882 2.046700 TTTGGAAGCGGGCGTAGG 60.047 61.111 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.343069 GACAGAGGTCAGGGAAGTGT 58.657 55.000 0.00 0.00 43.73 3.55
121 122 4.814294 CGTCGGCGGAAGAAGGGG 62.814 72.222 7.21 0.00 0.00 4.79
199 200 4.767255 GCGGAGTGGTGAGGCAGG 62.767 72.222 0.00 0.00 0.00 4.85
276 284 2.614259 AGACCCGAGCATAAGATGGAT 58.386 47.619 0.00 0.00 0.00 3.41
277 285 2.088104 AGACCCGAGCATAAGATGGA 57.912 50.000 0.00 0.00 0.00 3.41
280 288 2.814919 CGAGTAGACCCGAGCATAAGAT 59.185 50.000 0.00 0.00 0.00 2.40
294 302 1.134189 TCGGATTGGAGCTCGAGTAGA 60.134 52.381 15.13 1.43 0.00 2.59
1115 1124 0.883833 CTGATGTGGTTGTTGGGAGC 59.116 55.000 0.00 0.00 0.00 4.70
1191 1201 4.571984 TGATGGATGTGTTCATCTAAAGCG 59.428 41.667 7.89 0.00 46.74 4.68
1203 1214 4.492494 TCTTATGCAGTGATGGATGTGT 57.508 40.909 0.00 0.00 0.00 3.72
1239 1250 2.203480 TGCCCTTGCAAGTGTCCC 60.203 61.111 24.35 8.55 46.66 4.46
1266 1291 8.999431 GCAGCCAGTACTAAAGCATAATTATTA 58.001 33.333 12.64 0.00 0.00 0.98
1306 1332 7.108841 AGTCAATTCAGCTCATTATGCAAAT 57.891 32.000 0.00 0.00 0.00 2.32
1390 1420 4.236935 CATGACAAGGTATGTGGTTTTGC 58.763 43.478 0.00 0.00 44.12 3.68
1391 1421 4.022068 AGCATGACAAGGTATGTGGTTTTG 60.022 41.667 0.00 0.00 44.12 2.44
1392 1422 4.151883 AGCATGACAAGGTATGTGGTTTT 58.848 39.130 0.00 0.00 44.12 2.43
1394 1424 3.439857 AGCATGACAAGGTATGTGGTT 57.560 42.857 0.00 0.00 44.12 3.67
1434 1466 7.383102 TCTATGAAAGGAATGAAAGAGCAAC 57.617 36.000 0.00 0.00 0.00 4.17
1509 1541 8.323567 CCTAACCTCAACCCTAAGTAAAATGTA 58.676 37.037 0.00 0.00 0.00 2.29
1517 1549 3.572661 TCCCTAACCTCAACCCTAAGT 57.427 47.619 0.00 0.00 0.00 2.24
1523 1555 4.008330 GCTACTTTTCCCTAACCTCAACC 58.992 47.826 0.00 0.00 0.00 3.77
1575 1612 5.009010 ACACCAAATGAGTTTGTGCTTCTAG 59.991 40.000 0.00 0.00 42.50 2.43
1659 1696 6.825610 GGAAAGAGATCCTAACTGATCACAT 58.174 40.000 0.00 0.00 42.95 3.21
1836 1875 5.726980 AATTAGCCAGAAATTCACAAGCA 57.273 34.783 0.00 0.00 0.00 3.91
1850 1889 2.785562 ACCGTGCAAGTAAATTAGCCA 58.214 42.857 0.00 0.00 0.00 4.75
1852 1891 8.953990 CATAAATAACCGTGCAAGTAAATTAGC 58.046 33.333 0.00 0.00 0.00 3.09
1867 1906 7.810766 AAACACTTTGCATCATAAATAACCG 57.189 32.000 0.00 0.00 0.00 4.44
1975 2017 0.676151 CTCCACAGCTGAAGGAAGGC 60.676 60.000 23.35 0.00 0.00 4.35
1976 2018 0.689623 ACTCCACAGCTGAAGGAAGG 59.310 55.000 23.35 16.97 0.00 3.46
1981 2023 4.940046 ACAATATTGACTCCACAGCTGAAG 59.060 41.667 23.35 16.34 0.00 3.02
2023 2065 6.835174 AGCAGAGATAAAAATCATCCTGCTA 58.165 36.000 19.10 0.00 45.22 3.49
2223 2266 2.198827 AGTTGACGCATTCCCATCAA 57.801 45.000 0.00 0.00 0.00 2.57
2276 2319 2.760092 TCATAGCTCCATTTTGGTTGGC 59.240 45.455 0.00 0.00 39.03 4.52
2308 2351 1.430632 CGATGATGGTGGTGCAAGC 59.569 57.895 0.00 0.00 0.00 4.01
2440 2483 2.309613 TGAGGTTCATTGGCATATGGC 58.690 47.619 21.76 21.76 43.74 4.40
2642 2685 3.498397 CCACCAGAGTATGTTGTTGACAC 59.502 47.826 0.00 0.00 42.04 3.67
2725 2771 1.902508 CTTGGAGTTACTGAGGCAGGA 59.097 52.381 0.00 0.00 35.51 3.86
2784 2830 2.526304 TGTCTTCCAGTGTGCAGTAC 57.474 50.000 0.00 0.00 0.00 2.73
3244 3314 4.686972 TCTGAAACTCATTAGGCAGATCG 58.313 43.478 0.00 0.00 29.90 3.69
3392 3474 2.029380 GGGGTGAAAAGTCGGGAATTTG 60.029 50.000 0.00 0.00 0.00 2.32
3393 3475 2.244695 GGGGTGAAAAGTCGGGAATTT 58.755 47.619 0.00 0.00 0.00 1.82
3394 3476 1.146152 TGGGGTGAAAAGTCGGGAATT 59.854 47.619 0.00 0.00 0.00 2.17
3395 3477 0.774908 TGGGGTGAAAAGTCGGGAAT 59.225 50.000 0.00 0.00 0.00 3.01
3396 3478 0.109723 CTGGGGTGAAAAGTCGGGAA 59.890 55.000 0.00 0.00 0.00 3.97
3400 3482 1.971695 GGGCTGGGGTGAAAAGTCG 60.972 63.158 0.00 0.00 0.00 4.18
3418 3500 9.529325 TCTGGTAAATCAAGATATAACAGAACG 57.471 33.333 0.00 0.00 0.00 3.95
3447 3529 7.228906 CAGCAGTTCATGGAGATCTAAATGATT 59.771 37.037 16.60 8.70 35.14 2.57
3474 3556 4.685169 ATTACTGAACAATTGGTCTGCG 57.315 40.909 25.26 15.60 34.54 5.18
3516 3603 6.377327 AAGACATTTGTGTTCAGGTTACAG 57.623 37.500 0.00 0.00 0.00 2.74
3521 3608 5.593909 TGATGAAAGACATTTGTGTTCAGGT 59.406 36.000 10.47 0.00 39.56 4.00
3551 3638 5.567423 GCAAATCAAAATCTGGGTGTAGCTT 60.567 40.000 0.00 0.00 0.00 3.74
3581 3668 6.064717 AGTCAATTAAGGACATCATTAGGGC 58.935 40.000 11.36 0.00 37.74 5.19
3601 3688 4.573900 GCTTTCATTCCTGAGAGAAGTCA 58.426 43.478 0.00 0.00 36.03 3.41
3602 3689 3.616379 CGCTTTCATTCCTGAGAGAAGTC 59.384 47.826 0.00 0.00 36.03 3.01
3617 3704 1.377202 GACAGATGCCCCGCTTTCA 60.377 57.895 0.00 0.00 0.00 2.69
3652 3739 2.224523 TGAAAGGATGGCAGTCTTTCGT 60.225 45.455 25.95 7.40 45.37 3.85
3677 3764 3.242867 AGAGATATTTCATCCCTCGCCA 58.757 45.455 0.00 0.00 0.00 5.69
3747 3836 3.585862 TCTGTACTCAATTTCAGCGTCC 58.414 45.455 0.00 0.00 0.00 4.79
3750 3839 3.372206 CCCTTCTGTACTCAATTTCAGCG 59.628 47.826 0.00 0.00 0.00 5.18
3816 3905 1.412343 TGCAGCTGTCTTGACAGTGTA 59.588 47.619 25.57 19.40 39.76 2.90
3867 3956 9.742144 TTTAGATCACTATACAGAGGGAGTATC 57.258 37.037 0.00 0.00 30.69 2.24
3868 3957 9.523168 GTTTAGATCACTATACAGAGGGAGTAT 57.477 37.037 0.00 0.00 30.69 2.12
3869 3958 8.500238 TGTTTAGATCACTATACAGAGGGAGTA 58.500 37.037 0.00 0.00 36.30 2.59
3870 3959 7.285858 GTGTTTAGATCACTATACAGAGGGAGT 59.714 40.741 0.00 0.00 39.71 3.85
3871 3960 7.504238 AGTGTTTAGATCACTATACAGAGGGAG 59.496 40.741 0.00 0.00 43.17 4.30
3872 3961 7.355101 AGTGTTTAGATCACTATACAGAGGGA 58.645 38.462 0.00 0.00 43.17 4.20
3873 3962 7.504238 AGAGTGTTTAGATCACTATACAGAGGG 59.496 40.741 0.00 0.00 44.68 4.30
3874 3963 8.458573 AGAGTGTTTAGATCACTATACAGAGG 57.541 38.462 0.00 0.00 44.68 3.69
3891 3980 9.379791 CCTCCGTAAAGAAATATAAGAGTGTTT 57.620 33.333 0.00 0.00 0.00 2.83
3892 3981 7.985752 CCCTCCGTAAAGAAATATAAGAGTGTT 59.014 37.037 0.00 0.00 0.00 3.32
3893 3982 7.343833 TCCCTCCGTAAAGAAATATAAGAGTGT 59.656 37.037 0.00 0.00 0.00 3.55
3894 3983 7.723324 TCCCTCCGTAAAGAAATATAAGAGTG 58.277 38.462 0.00 0.00 0.00 3.51
3895 3984 7.564292 ACTCCCTCCGTAAAGAAATATAAGAGT 59.436 37.037 0.00 0.00 0.00 3.24
3896 3985 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3897 3986 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3898 3987 8.858094 ACTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
3899 3988 8.773033 ACTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
3900 3989 8.773033 AACTACTCCCTCCGTAAAGAAATATA 57.227 34.615 0.00 0.00 0.00 0.86
3901 3990 7.201983 GGAACTACTCCCTCCGTAAAGAAATAT 60.202 40.741 0.00 0.00 38.44 1.28
3902 3991 6.097412 GGAACTACTCCCTCCGTAAAGAAATA 59.903 42.308 0.00 0.00 38.44 1.40
3903 3992 5.105023 GGAACTACTCCCTCCGTAAAGAAAT 60.105 44.000 0.00 0.00 38.44 2.17
3904 3993 4.221482 GGAACTACTCCCTCCGTAAAGAAA 59.779 45.833 0.00 0.00 38.44 2.52
3905 3994 3.766051 GGAACTACTCCCTCCGTAAAGAA 59.234 47.826 0.00 0.00 38.44 2.52
3906 3995 3.359950 GGAACTACTCCCTCCGTAAAGA 58.640 50.000 0.00 0.00 38.44 2.52
3907 3996 3.797451 GGAACTACTCCCTCCGTAAAG 57.203 52.381 0.00 0.00 38.44 1.85
3917 4006 3.913509 ACTAGGCTAAGGGAACTACTCC 58.086 50.000 0.00 0.00 42.68 3.85
3918 4007 5.047872 GCATACTAGGCTAAGGGAACTACTC 60.048 48.000 0.00 0.00 42.68 2.59
3919 4008 4.833938 GCATACTAGGCTAAGGGAACTACT 59.166 45.833 0.00 0.00 42.68 2.57
3920 4009 4.587684 TGCATACTAGGCTAAGGGAACTAC 59.412 45.833 0.00 0.00 42.68 2.73
4084 4191 7.348274 AGAGGAACATGGTGATCTTAAATAGGA 59.652 37.037 0.00 0.00 0.00 2.94
4136 4243 2.533266 CCTTTCATTTCATTGCTCCGC 58.467 47.619 0.00 0.00 0.00 5.54
4157 4264 7.532571 TCAGAATTCAAAGTAATCATGCACAG 58.467 34.615 8.44 0.00 0.00 3.66
4219 4326 2.802816 AGTCGTTGCAATGTCAGACTTC 59.197 45.455 17.94 0.00 35.70 3.01
4230 4337 0.179043 TGCCTAACCAGTCGTTGCAA 60.179 50.000 0.00 0.00 32.20 4.08
4265 4372 4.329545 TCGACAGGCAGGCCAACC 62.330 66.667 13.63 5.55 38.92 3.77
4274 4381 1.009389 CAGAAGGAACGTCGACAGGC 61.009 60.000 17.16 3.13 42.91 4.85
4277 4384 0.318699 CTGCAGAAGGAACGTCGACA 60.319 55.000 17.16 0.00 42.91 4.35
4316 4426 1.406887 CCCCAATGTCCCTCGTTGTAG 60.407 57.143 0.00 0.00 40.36 2.74
4363 4473 7.581213 ACTGGTCATTCTCAATTGTAAAACA 57.419 32.000 5.13 0.00 0.00 2.83
4498 4608 0.319813 TCGTGTGTGTCTGCCTCATG 60.320 55.000 0.00 0.00 0.00 3.07
4560 4671 2.357517 AAGGCTTCGCGGTGACTG 60.358 61.111 6.13 0.00 0.00 3.51
4561 4672 2.357517 CAAGGCTTCGCGGTGACT 60.358 61.111 6.13 3.62 0.00 3.41
4749 4865 2.046700 CCTACGCCCGCTTCCAAA 60.047 61.111 0.00 0.00 0.00 3.28
4765 4881 4.541482 TATGACGACGCCGACGCC 62.541 66.667 9.15 0.00 45.53 5.68
4766 4882 3.017314 CTATGACGACGCCGACGC 61.017 66.667 9.15 2.82 45.53 5.19
4768 4884 2.654404 GGCTATGACGACGCCGAC 60.654 66.667 0.00 0.00 39.50 4.79


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

AutoCloner maintained by Alex Coulton.