Multiple sequence alignment - TraesCS3B01G288900

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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 TraesCS3B01G288900 chr3B 100.000 7686 0 0 1 7686 463250377 463258062 0.000000e+00 14194.0
1 TraesCS3B01G288900 chr3B 95.927 7169 148 29 5 7080 455682737 455675620 0.000000e+00 11489.0
2 TraesCS3B01G288900 chr3B 95.327 535 24 1 7152 7686 686997345 686997878 0.000000e+00 848.0
3 TraesCS3B01G288900 chr3B 89.333 75 7 1 7082 7155 523626418 523626344 8.210000e-15 93.5
4 TraesCS3B01G288900 chr3A 94.117 5575 208 35 1482 6987 473718314 473712791 0.000000e+00 8368.0
5 TraesCS3B01G288900 chr3A 92.144 611 19 8 803 1409 473719303 473718718 0.000000e+00 835.0
6 TraesCS3B01G288900 chr3A 86.308 650 53 19 5 642 473721649 473721024 0.000000e+00 675.0
7 TraesCS3B01G288900 chr3A 86.047 129 9 3 666 787 473719481 473719355 6.260000e-26 130.0
8 TraesCS3B01G288900 chr3D 96.170 4883 133 12 1716 6562 355168394 355163530 0.000000e+00 7932.0
9 TraesCS3B01G288900 chr3D 86.989 1468 69 49 163 1567 355169802 355168394 0.000000e+00 1541.0
10 TraesCS3B01G288900 chr3D 87.965 565 31 14 6540 7080 355163514 355162963 3.910000e-177 632.0
11 TraesCS3B01G288900 chr3D 89.610 77 8 0 25 101 355169877 355169801 1.770000e-16 99.0
12 TraesCS3B01G288900 chr3D 100.000 28 0 0 7083 7110 55674845 55674872 1.400000e-02 52.8
13 TraesCS3B01G288900 chr2B 96.140 544 15 5 7147 7686 255312625 255313166 0.000000e+00 883.0
14 TraesCS3B01G288900 chr2B 95.404 544 19 5 7147 7686 247406790 247406249 0.000000e+00 861.0
15 TraesCS3B01G288900 chr4B 95.888 535 18 3 7156 7686 531000626 531001160 0.000000e+00 863.0
16 TraesCS3B01G288900 chr7B 95.018 542 23 4 7147 7686 267506587 267507126 0.000000e+00 848.0
17 TraesCS3B01G288900 chr6D 92.944 496 25 4 7200 7686 462305349 462304855 0.000000e+00 713.0
18 TraesCS3B01G288900 chr6D 92.415 501 29 3 7194 7686 466394025 466394524 0.000000e+00 706.0
19 TraesCS3B01G288900 chr6D 89.011 91 8 2 7148 7237 174146694 174146605 2.270000e-20 111.0
20 TraesCS3B01G288900 chr7D 89.362 94 9 1 7149 7241 53403193 53403100 4.870000e-22 117.0
21 TraesCS3B01G288900 chr1B 89.362 94 9 1 7149 7241 246755140 246755233 4.870000e-22 117.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G288900 chr3B 463250377 463258062 7685 False 14194 14194 100.0000 1 7686 1 chr3B.!!$F1 7685
1 TraesCS3B01G288900 chr3B 455675620 455682737 7117 True 11489 11489 95.9270 5 7080 1 chr3B.!!$R1 7075
2 TraesCS3B01G288900 chr3B 686997345 686997878 533 False 848 848 95.3270 7152 7686 1 chr3B.!!$F2 534
3 TraesCS3B01G288900 chr3A 473712791 473721649 8858 True 2502 8368 89.6540 5 6987 4 chr3A.!!$R1 6982
4 TraesCS3B01G288900 chr3D 355162963 355169877 6914 True 2551 7932 90.1835 25 7080 4 chr3D.!!$R1 7055
5 TraesCS3B01G288900 chr2B 255312625 255313166 541 False 883 883 96.1400 7147 7686 1 chr2B.!!$F1 539
6 TraesCS3B01G288900 chr2B 247406249 247406790 541 True 861 861 95.4040 7147 7686 1 chr2B.!!$R1 539
7 TraesCS3B01G288900 chr4B 531000626 531001160 534 False 863 863 95.8880 7156 7686 1 chr4B.!!$F1 530
8 TraesCS3B01G288900 chr7B 267506587 267507126 539 False 848 848 95.0180 7147 7686 1 chr7B.!!$F1 539

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
738 2299 0.255890 ATGGTAAATCGCCAGGTGCT 59.744 50.000 0.00 0.0 39.65 4.40 F
2509 4480 0.751277 TGAACACCCCTGTGCAAGTG 60.751 55.000 0.00 0.0 46.86 3.16 F
3358 5345 0.250124 CCTGACAGTGGCGTAAACCA 60.250 55.000 0.93 0.0 37.38 3.67 F
4161 6148 3.841255 CCTAGGGAAAGGAAGTCTTCAGT 59.159 47.826 14.49 0.0 39.15 3.41 F
4757 6747 4.464008 CAAGGATATAGGAAGCAGGCAAA 58.536 43.478 0.00 0.0 0.00 3.68 F
6350 8373 1.798813 CTCCAGAAAACGAGGGAAACG 59.201 52.381 0.00 0.0 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2511 4482 0.179215 GCTCACGCTTACACACATGC 60.179 55.000 0.00 0.0 0.00 4.06 R
3694 5681 0.749649 CGCTAGAAGCAGATGACCCT 59.250 55.000 0.00 0.0 42.58 4.34 R
4341 6328 2.795329 CTTGTTGCTTCCTGGGTGTAT 58.205 47.619 0.00 0.0 0.00 2.29 R
6104 8127 1.435408 GCTCGGCCATCTCTCTTTGC 61.435 60.000 2.24 0.0 0.00 3.68 R
6403 8426 0.534203 GAAGCTTGGGGTGAACGTGA 60.534 55.000 2.10 0.0 0.00 4.35 R
7152 9241 1.660242 ACCATACCCGTACCCACTTT 58.340 50.000 0.00 0.0 0.00 2.66 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
21 22 3.209429 GCGAATGCGTGATGACAAG 57.791 52.632 0.00 0.00 40.36 3.16
27 28 2.317609 GCGTGATGACAAGGCGTGT 61.318 57.895 5.57 5.57 45.74 4.49
33 34 4.021650 GACAAGGCGTGTCGAACA 57.978 55.556 17.40 0.00 46.99 3.18
80 82 1.266718 CTCAACATTGTGAACCGGGTG 59.733 52.381 6.32 0.00 0.00 4.61
107 109 7.013274 GGAAATATGACATTTGCAAGGCTAGTA 59.987 37.037 0.00 0.00 31.05 1.82
113 115 5.009631 ACATTTGCAAGGCTAGTATGTGAA 58.990 37.500 9.30 0.00 0.00 3.18
144 163 1.087501 GTTTGTTCCGAGAGATGGGC 58.912 55.000 0.00 0.00 0.00 5.36
145 164 0.690192 TTTGTTCCGAGAGATGGGCA 59.310 50.000 0.00 0.00 0.00 5.36
161 180 4.620589 TGGGCATTTTGATTGACAATGT 57.379 36.364 5.14 0.00 38.36 2.71
189 208 1.064654 GAATGTCGCAAAGCCATCTCC 59.935 52.381 0.00 0.00 0.00 3.71
191 210 1.078143 GTCGCAAAGCCATCTCCCT 60.078 57.895 0.00 0.00 0.00 4.20
193 212 1.377725 CGCAAAGCCATCTCCCTGT 60.378 57.895 0.00 0.00 0.00 4.00
229 248 8.050930 TGTTACTCCCTCCATTCTAAAATAACC 58.949 37.037 0.00 0.00 0.00 2.85
408 439 7.611213 ATTTGACGTAGAATAAACCCAGAAG 57.389 36.000 0.00 0.00 0.00 2.85
515 546 6.179756 TCAGTAAATTTATGGCTCTCTGCAA 58.820 36.000 0.31 0.00 45.15 4.08
516 547 6.830324 TCAGTAAATTTATGGCTCTCTGCAAT 59.170 34.615 0.31 0.00 45.15 3.56
517 548 7.012704 TCAGTAAATTTATGGCTCTCTGCAATC 59.987 37.037 0.31 0.00 45.15 2.67
518 549 7.013083 CAGTAAATTTATGGCTCTCTGCAATCT 59.987 37.037 0.31 0.00 45.15 2.40
519 550 5.769484 AATTTATGGCTCTCTGCAATCTG 57.231 39.130 0.00 0.00 45.15 2.90
520 551 2.251409 TATGGCTCTCTGCAATCTGC 57.749 50.000 0.00 0.00 45.15 4.26
566 598 5.155905 AGAGGGTAGTCTCTTCCAAAAAGA 58.844 41.667 0.00 0.00 40.93 2.52
738 2299 0.255890 ATGGTAAATCGCCAGGTGCT 59.744 50.000 0.00 0.00 39.65 4.40
1032 2639 8.466798 GGAGAGGAAGCATCTTCTATAATACTC 58.533 40.741 3.33 0.00 41.66 2.59
1559 3505 1.134401 ACGGAGTACTCGATTACGGGA 60.134 52.381 16.56 0.00 40.69 5.14
1643 3590 5.183713 GCATAGAAATAATATGGCCACTGCA 59.816 40.000 8.16 0.00 40.13 4.41
2033 3993 8.853077 TGTCTTTATCTGATGTCTGAAATTGT 57.147 30.769 0.00 0.00 0.00 2.71
2081 4041 6.588204 ACACACAGTTTATAGTTTGAGGACA 58.412 36.000 0.00 0.00 0.00 4.02
2089 4049 9.003658 AGTTTATAGTTTGAGGACAATCACTTG 57.996 33.333 0.00 0.00 35.85 3.16
2090 4050 5.886960 ATAGTTTGAGGACAATCACTTGC 57.113 39.130 0.00 0.00 35.69 4.01
2104 4064 4.524316 TCACTTGCATCTCATTTTTGGG 57.476 40.909 0.00 0.00 0.00 4.12
2509 4480 0.751277 TGAACACCCCTGTGCAAGTG 60.751 55.000 0.00 0.00 46.86 3.16
2510 4481 0.751643 GAACACCCCTGTGCAAGTGT 60.752 55.000 0.00 0.00 46.86 3.55
2511 4482 1.037030 AACACCCCTGTGCAAGTGTG 61.037 55.000 8.05 9.73 46.86 3.82
2595 4582 0.754957 CACCAACCCAACAAGAGGCA 60.755 55.000 0.00 0.00 0.00 4.75
2766 4753 2.360165 GGTGCAGCCAATCTGGATAAAG 59.640 50.000 4.03 0.00 45.05 1.85
2809 4796 3.804786 TCATTGCAAGCCCATATGTTG 57.195 42.857 4.94 1.22 0.00 3.33
2877 4864 8.659491 TCGAAATATTGACAATCTGTTTCTCAG 58.341 33.333 20.02 11.81 44.85 3.35
3005 4992 1.065551 GACTTGTGCGCTTTTCTGGTT 59.934 47.619 9.73 0.00 0.00 3.67
3123 5110 4.639310 CCTATTTTCTGCTGTGCTCTCATT 59.361 41.667 0.00 0.00 0.00 2.57
3358 5345 0.250124 CCTGACAGTGGCGTAAACCA 60.250 55.000 0.93 0.00 37.38 3.67
3603 5590 7.556275 GGATGGTAAATTGACAGACCTGAATTA 59.444 37.037 3.76 0.00 32.87 1.40
4078 6065 7.116805 CACTTTTGAATGCTTTGGTATTCTTCC 59.883 37.037 7.93 0.00 42.41 3.46
4161 6148 3.841255 CCTAGGGAAAGGAAGTCTTCAGT 59.159 47.826 14.49 0.00 39.15 3.41
4341 6328 9.176460 TGAATCAACTGCTTATATGAATGACAA 57.824 29.630 0.00 0.00 0.00 3.18
4757 6747 4.464008 CAAGGATATAGGAAGCAGGCAAA 58.536 43.478 0.00 0.00 0.00 3.68
5065 7055 6.351327 ACTCTCTTTTCAAGAACAGAAACG 57.649 37.500 0.94 0.00 37.02 3.60
5106 7099 6.072199 AGGAGCAAACAAAGAGGATATTCT 57.928 37.500 0.00 0.00 0.00 2.40
5174 7167 4.659111 TCTGACGAGGAAACAAGTACAA 57.341 40.909 0.00 0.00 0.00 2.41
5255 7248 9.354673 TGTTCAATAAGAATTCTGGAAAGTCTT 57.645 29.630 9.17 13.39 38.76 3.01
5639 7641 6.358974 ACAAAATTTCTGGGGATAACTTGG 57.641 37.500 0.00 0.00 0.00 3.61
5941 7943 6.071896 CCAAGACTTCTGTTAGGGAAAATTCC 60.072 42.308 3.49 3.49 46.82 3.01
6104 8127 2.822399 GGGAGGTAGCACCCGATG 59.178 66.667 11.87 0.00 39.75 3.84
6267 8290 1.800286 GCAATCTTCGCCAAATCCTGC 60.800 52.381 0.00 0.00 0.00 4.85
6350 8373 1.798813 CTCCAGAAAACGAGGGAAACG 59.201 52.381 0.00 0.00 0.00 3.60
6385 8408 2.028930 AGAGACCCTGAAAGTAAGCACG 60.029 50.000 0.00 0.00 0.00 5.34
6403 8426 2.433446 CCAACAGCTGGTCCTGCT 59.567 61.111 19.93 17.06 40.78 4.24
6487 8510 0.246635 CCAATCGCCGGTAGGGATAG 59.753 60.000 1.90 0.00 46.80 2.08
6709 8770 3.935818 TGTACAGAACTTGGGGTTTCA 57.064 42.857 0.00 0.00 38.41 2.69
6728 8792 8.888716 GGGTTTCATTCAAATTTGTTTGTACTT 58.111 29.630 17.47 0.00 33.82 2.24
6855 8925 6.764085 TCTTCAATTACTTCGGACAAACTTCA 59.236 34.615 0.00 0.00 0.00 3.02
6871 8941 3.074412 ACTTCAGAATTGCTACCCGTTG 58.926 45.455 0.00 0.00 0.00 4.10
6895 8965 0.238289 CGCGTGAAGATTTGCTTGGT 59.762 50.000 0.00 0.00 36.83 3.67
6963 9052 1.470051 GGTTACCGGGCATGTTCATT 58.530 50.000 6.32 0.00 0.00 2.57
7048 9137 8.297470 ACAATGTCTTAATTTGTAGCATGGAT 57.703 30.769 0.00 0.00 32.09 3.41
7080 9169 5.123186 TGTTTACAATACAAGAGGCAATCCG 59.877 40.000 0.00 0.00 37.47 4.18
7081 9170 3.627395 ACAATACAAGAGGCAATCCGA 57.373 42.857 0.00 0.00 37.47 4.55
7082 9171 3.535561 ACAATACAAGAGGCAATCCGAG 58.464 45.455 0.00 0.00 37.47 4.63
7083 9172 2.874701 CAATACAAGAGGCAATCCGAGG 59.125 50.000 0.00 0.00 37.47 4.63
7084 9173 0.830648 TACAAGAGGCAATCCGAGGG 59.169 55.000 0.00 0.00 37.47 4.30
7085 9174 0.909610 ACAAGAGGCAATCCGAGGGA 60.910 55.000 0.00 0.00 37.47 4.20
7086 9175 0.471617 CAAGAGGCAATCCGAGGGAT 59.528 55.000 0.00 0.00 45.46 3.85
7087 9176 0.471617 AAGAGGCAATCCGAGGGATG 59.528 55.000 0.00 0.00 42.27 3.51
7088 9177 1.072159 GAGGCAATCCGAGGGATGG 59.928 63.158 0.00 0.00 42.27 3.51
7091 9180 4.984194 CAATCCGAGGGATGGCAA 57.016 55.556 0.00 0.00 42.27 4.52
7092 9181 3.426903 CAATCCGAGGGATGGCAAT 57.573 52.632 0.00 0.00 42.27 3.56
7093 9182 0.956633 CAATCCGAGGGATGGCAATG 59.043 55.000 0.00 0.00 42.27 2.82
7094 9183 0.178981 AATCCGAGGGATGGCAATGG 60.179 55.000 0.00 0.00 42.27 3.16
7095 9184 1.061905 ATCCGAGGGATGGCAATGGA 61.062 55.000 0.00 0.00 41.43 3.41
7096 9185 1.061905 TCCGAGGGATGGCAATGGAT 61.062 55.000 0.00 0.00 0.00 3.41
7097 9186 0.692476 CCGAGGGATGGCAATGGATA 59.308 55.000 0.00 0.00 0.00 2.59
7098 9187 1.611673 CCGAGGGATGGCAATGGATAC 60.612 57.143 0.00 0.00 0.00 2.24
7099 9188 1.611673 CGAGGGATGGCAATGGATACC 60.612 57.143 0.00 0.00 0.00 2.73
7100 9189 1.707427 GAGGGATGGCAATGGATACCT 59.293 52.381 0.00 0.00 0.00 3.08
7101 9190 2.912956 GAGGGATGGCAATGGATACCTA 59.087 50.000 0.00 0.00 0.00 3.08
7102 9191 3.525199 GAGGGATGGCAATGGATACCTAT 59.475 47.826 0.00 0.00 0.00 2.57
7103 9192 3.925370 AGGGATGGCAATGGATACCTATT 59.075 43.478 0.00 0.00 0.00 1.73
7104 9193 5.108026 AGGGATGGCAATGGATACCTATTA 58.892 41.667 0.00 0.00 0.00 0.98
7105 9194 5.044846 AGGGATGGCAATGGATACCTATTAC 60.045 44.000 0.00 0.00 0.00 1.89
7106 9195 5.193679 GGATGGCAATGGATACCTATTACC 58.806 45.833 0.00 0.00 0.00 2.85
7107 9196 4.650972 TGGCAATGGATACCTATTACCC 57.349 45.455 0.00 0.00 0.00 3.69
7108 9197 3.984090 TGGCAATGGATACCTATTACCCA 59.016 43.478 0.00 0.00 0.00 4.51
7109 9198 4.202524 TGGCAATGGATACCTATTACCCAC 60.203 45.833 0.00 0.00 0.00 4.61
7110 9199 4.000988 GCAATGGATACCTATTACCCACG 58.999 47.826 0.00 0.00 0.00 4.94
7111 9200 4.504340 GCAATGGATACCTATTACCCACGT 60.504 45.833 0.00 0.00 0.00 4.49
7112 9201 5.279607 GCAATGGATACCTATTACCCACGTA 60.280 44.000 0.00 0.00 0.00 3.57
7113 9202 5.990120 ATGGATACCTATTACCCACGTAC 57.010 43.478 0.00 0.00 0.00 3.67
7114 9203 4.151883 TGGATACCTATTACCCACGTACC 58.848 47.826 0.00 0.00 0.00 3.34
7115 9204 3.511540 GGATACCTATTACCCACGTACCC 59.488 52.174 0.00 0.00 0.00 3.69
7116 9205 1.402787 ACCTATTACCCACGTACCCG 58.597 55.000 0.00 0.00 40.83 5.28
7117 9206 0.675633 CCTATTACCCACGTACCCGG 59.324 60.000 0.00 0.00 38.78 5.73
7118 9207 0.032540 CTATTACCCACGTACCCGGC 59.967 60.000 0.00 0.00 38.78 6.13
7119 9208 1.733402 TATTACCCACGTACCCGGCG 61.733 60.000 0.00 0.00 38.78 6.46
7150 9239 4.771338 CCTATTAGGGTAAGGGTATGGGT 58.229 47.826 1.37 0.00 0.00 4.51
7151 9240 5.167921 CCTATTAGGGTAAGGGTATGGGTT 58.832 45.833 1.37 0.00 0.00 4.11
7152 9241 6.333479 CCTATTAGGGTAAGGGTATGGGTTA 58.667 44.000 1.37 0.00 0.00 2.85
7153 9242 6.793988 CCTATTAGGGTAAGGGTATGGGTTAA 59.206 42.308 1.37 0.00 0.00 2.01
7203 9292 2.635915 CCATACCCGTGTACCCATGTAT 59.364 50.000 0.00 0.00 0.00 2.29
7404 9497 5.107607 CGTTGTCTCAACAAGCGTAATAACT 60.108 40.000 12.08 0.00 45.78 2.24
7432 9525 6.978338 TGTCCAGAATCTTATACGTGATACC 58.022 40.000 0.00 0.00 0.00 2.73
7434 9527 7.085116 GTCCAGAATCTTATACGTGATACCTG 58.915 42.308 0.00 4.01 0.00 4.00
7522 9615 1.543802 AGCCGATCGATCTCATCTTCC 59.456 52.381 22.43 2.86 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.296145 GTCATCACGCATTCGCACG 60.296 57.895 0.00 0.00 39.84 5.34
2 3 0.443478 CTTGTCATCACGCATTCGCA 59.557 50.000 0.00 0.00 39.84 5.10
10 11 3.951332 ACACGCCTTGTCATCACG 58.049 55.556 0.00 0.00 29.79 4.35
21 22 0.865769 AGACAAATGTTCGACACGCC 59.134 50.000 0.00 0.00 0.00 5.68
27 28 3.057596 GCCCATTCAAGACAAATGTTCGA 60.058 43.478 0.00 0.00 33.22 3.71
32 33 5.294356 CCATATGCCCATTCAAGACAAATG 58.706 41.667 0.00 0.00 34.55 2.32
33 34 4.202284 GCCATATGCCCATTCAAGACAAAT 60.202 41.667 0.00 0.00 0.00 2.32
80 82 4.122046 GCCTTGCAAATGTCATATTTCCC 58.878 43.478 0.00 0.00 0.00 3.97
107 109 4.840115 ACAAACCATCAATTCCCTTCACAT 59.160 37.500 0.00 0.00 0.00 3.21
113 115 2.825532 CGGAACAAACCATCAATTCCCT 59.174 45.455 0.00 0.00 36.29 4.20
161 180 3.623060 GGCTTTGCGACATTCATCTTCTA 59.377 43.478 0.00 0.00 0.00 2.10
189 208 4.941873 GGGAGTAACATAAAAGGACACAGG 59.058 45.833 0.00 0.00 0.00 4.00
191 210 5.280317 GGAGGGAGTAACATAAAAGGACACA 60.280 44.000 0.00 0.00 0.00 3.72
193 212 4.847512 TGGAGGGAGTAACATAAAAGGACA 59.152 41.667 0.00 0.00 0.00 4.02
225 244 9.158233 CTTGTGATAAACCTAGAATTTCGGTTA 57.842 33.333 8.55 0.00 39.97 2.85
229 248 8.251750 TGACTTGTGATAAACCTAGAATTTCG 57.748 34.615 0.00 0.00 0.00 3.46
248 267 6.804534 TCAAACGTAAGCAAATTTGACTTG 57.195 33.333 25.23 17.16 45.62 3.16
257 276 3.942748 AGAGTTGGTCAAACGTAAGCAAA 59.057 39.130 10.49 0.00 44.04 3.68
408 439 8.674607 ACTACCTCCATTTCGAAATAATTGAAC 58.325 33.333 22.33 0.00 0.00 3.18
444 475 1.131126 GTCAAGCACATCAACATCGGG 59.869 52.381 0.00 0.00 0.00 5.14
445 476 1.131126 GGTCAAGCACATCAACATCGG 59.869 52.381 0.00 0.00 0.00 4.18
515 546 3.600187 TGCACATTGGGATGCAGAT 57.400 47.368 0.00 0.00 46.63 2.90
519 550 0.454600 CAGTCTGCACATTGGGATGC 59.545 55.000 0.00 0.00 42.40 3.91
520 551 1.100510 CCAGTCTGCACATTGGGATG 58.899 55.000 0.00 0.00 39.25 3.51
521 552 3.583054 CCAGTCTGCACATTGGGAT 57.417 52.632 0.00 0.00 0.00 3.85
574 608 7.586349 TGAATAGATTATTCCTGAAAAGGGCT 58.414 34.615 6.41 0.00 43.00 5.19
738 2299 1.416401 GCGGGGATCTTAGGATGACAA 59.584 52.381 0.00 0.00 31.46 3.18
1032 2639 1.452108 CGGGGCTGCTTTAGAAGGG 60.452 63.158 0.00 0.00 0.00 3.95
1300 2915 0.725686 CAATCTTGCTGAGACGCCAG 59.274 55.000 0.00 0.00 37.17 4.85
1559 3505 7.229581 AGAAACGTCTAGAGTGGACTTTATT 57.770 36.000 0.00 0.00 29.93 1.40
1643 3590 4.969484 AGACCAATCACCTAAACGAAACT 58.031 39.130 0.00 0.00 0.00 2.66
1705 3652 5.882557 AGATAGATCAACACAATGGACCAAC 59.117 40.000 0.00 0.00 0.00 3.77
2033 3993 9.725019 TGTCTGCTTCTCTTAATGATAAGAAAA 57.275 29.630 0.54 0.00 45.20 2.29
2081 4041 5.484715 CCCAAAAATGAGATGCAAGTGATT 58.515 37.500 0.00 0.00 0.00 2.57
2089 4049 5.052481 GGAAATAGCCCAAAAATGAGATGC 58.948 41.667 0.00 0.00 0.00 3.91
2090 4050 5.163519 ACGGAAATAGCCCAAAAATGAGATG 60.164 40.000 0.00 0.00 0.00 2.90
2104 4064 5.211174 ACCCTATCAACTACGGAAATAGC 57.789 43.478 0.00 0.00 0.00 2.97
2509 4480 0.865111 TCACGCTTACACACATGCAC 59.135 50.000 0.00 0.00 0.00 4.57
2510 4481 1.147473 CTCACGCTTACACACATGCA 58.853 50.000 0.00 0.00 0.00 3.96
2511 4482 0.179215 GCTCACGCTTACACACATGC 60.179 55.000 0.00 0.00 0.00 4.06
2512 4483 1.136252 GTGCTCACGCTTACACACATG 60.136 52.381 0.00 0.00 36.97 3.21
2513 4484 1.148310 GTGCTCACGCTTACACACAT 58.852 50.000 0.00 0.00 36.97 3.21
2514 4485 0.878523 GGTGCTCACGCTTACACACA 60.879 55.000 0.00 0.00 36.97 3.72
2515 4486 0.878523 TGGTGCTCACGCTTACACAC 60.879 55.000 0.00 0.00 36.97 3.82
2516 4487 0.599991 CTGGTGCTCACGCTTACACA 60.600 55.000 0.00 0.00 36.97 3.72
2595 4582 1.261480 AGTCATGGTCAGCGAGAACT 58.739 50.000 0.00 0.00 34.06 3.01
2766 4753 5.444663 AAAAAGAAAGGAGCATGTCACTC 57.555 39.130 0.00 0.00 0.00 3.51
2809 4796 9.220767 AGTACCTTCTGAACTGAATAACAATTC 57.779 33.333 0.00 0.00 35.62 2.17
3123 5110 4.102996 TCAGGGCAGAAATAGATATGTGCA 59.897 41.667 0.00 0.00 32.42 4.57
3694 5681 0.749649 CGCTAGAAGCAGATGACCCT 59.250 55.000 0.00 0.00 42.58 4.34
4059 6046 7.631717 AAGTAGGAAGAATACCAAAGCATTC 57.368 36.000 0.00 0.00 0.00 2.67
4341 6328 2.795329 CTTGTTGCTTCCTGGGTGTAT 58.205 47.619 0.00 0.00 0.00 2.29
4757 6747 4.382901 CCTGCTCTCTTGATCAAAGCTAGT 60.383 45.833 24.05 0.00 35.69 2.57
5065 7055 4.155644 GCTCCTAAATCATAAGATGGCTGC 59.844 45.833 0.00 0.00 33.90 5.25
5106 7099 2.972713 GGTGGGCTAGTATCATTCAGGA 59.027 50.000 0.00 0.00 0.00 3.86
5122 7115 4.641989 CCATCTGAATCAAAAGTAGGTGGG 59.358 45.833 0.00 0.00 36.28 4.61
5174 7167 5.387113 TGGGTCCTTAAGATATGCATGTT 57.613 39.130 10.16 2.72 0.00 2.71
5255 7248 9.465199 TTCATGATCTTCAATAACATCAGGAAA 57.535 29.630 0.00 0.00 40.94 3.13
5639 7641 4.391140 CTTCTAAGGACTGTTTTCGCAC 57.609 45.455 0.00 0.00 0.00 5.34
5941 7943 1.457346 GCACCCCACTCTCTTGAATG 58.543 55.000 0.00 0.00 0.00 2.67
6104 8127 1.435408 GCTCGGCCATCTCTCTTTGC 61.435 60.000 2.24 0.00 0.00 3.68
6267 8290 3.864686 CGGGAGGTTCAATGCGCG 61.865 66.667 0.00 0.00 0.00 6.86
6403 8426 0.534203 GAAGCTTGGGGTGAACGTGA 60.534 55.000 2.10 0.00 0.00 4.35
6478 8501 7.555554 ACCGTATACATGTATGTCTATCCCTAC 59.444 40.741 25.48 11.99 41.97 3.18
6487 8510 7.997107 TTCTCAAACCGTATACATGTATGTC 57.003 36.000 25.48 17.21 41.97 3.06
6728 8792 3.555795 GGTCTGAGCTTGAGTCACAATGA 60.556 47.826 0.00 0.00 37.88 2.57
6855 8925 1.339727 GGGTCAACGGGTAGCAATTCT 60.340 52.381 0.00 0.00 0.00 2.40
6871 8941 1.794222 CAAATCTTCACGCGGGGTC 59.206 57.895 9.32 0.00 0.00 4.46
6895 8965 5.872617 GTGACATGCAATTGTACCACTACTA 59.127 40.000 7.40 0.00 0.00 1.82
7080 9169 1.707427 AGGTATCCATTGCCATCCCTC 59.293 52.381 0.00 0.00 0.00 4.30
7081 9170 1.838611 AGGTATCCATTGCCATCCCT 58.161 50.000 0.00 0.00 0.00 4.20
7082 9171 4.322057 AATAGGTATCCATTGCCATCCC 57.678 45.455 0.00 0.00 0.00 3.85
7083 9172 5.193679 GGTAATAGGTATCCATTGCCATCC 58.806 45.833 0.00 0.00 37.01 3.51
7084 9173 5.193679 GGGTAATAGGTATCCATTGCCATC 58.806 45.833 3.89 0.00 38.31 3.51
7085 9174 4.605813 TGGGTAATAGGTATCCATTGCCAT 59.394 41.667 3.89 0.00 38.13 4.40
7086 9175 3.984090 TGGGTAATAGGTATCCATTGCCA 59.016 43.478 3.89 0.00 38.13 4.92
7087 9176 4.332828 GTGGGTAATAGGTATCCATTGCC 58.667 47.826 0.00 0.00 45.13 4.52
7088 9177 4.000988 CGTGGGTAATAGGTATCCATTGC 58.999 47.826 0.00 0.00 45.13 3.56
7089 9178 5.223449 ACGTGGGTAATAGGTATCCATTG 57.777 43.478 0.00 0.00 45.13 2.82
7090 9179 5.246883 GGTACGTGGGTAATAGGTATCCATT 59.753 44.000 0.00 0.00 45.13 3.16
7091 9180 4.774200 GGTACGTGGGTAATAGGTATCCAT 59.226 45.833 0.00 0.00 45.13 3.41
7092 9181 4.151883 GGTACGTGGGTAATAGGTATCCA 58.848 47.826 0.00 0.00 41.01 3.41
7093 9182 3.511540 GGGTACGTGGGTAATAGGTATCC 59.488 52.174 0.00 0.00 33.92 2.59
7094 9183 3.191371 CGGGTACGTGGGTAATAGGTATC 59.809 52.174 0.00 0.00 34.81 2.24
7095 9184 3.157087 CGGGTACGTGGGTAATAGGTAT 58.843 50.000 0.00 0.00 34.81 2.73
7096 9185 2.582052 CGGGTACGTGGGTAATAGGTA 58.418 52.381 0.00 0.00 34.81 3.08
7097 9186 1.402787 CGGGTACGTGGGTAATAGGT 58.597 55.000 0.00 0.00 34.81 3.08
7098 9187 0.675633 CCGGGTACGTGGGTAATAGG 59.324 60.000 0.00 0.00 38.78 2.57
7099 9188 0.032540 GCCGGGTACGTGGGTAATAG 59.967 60.000 2.18 0.00 38.78 1.73
7100 9189 1.733402 CGCCGGGTACGTGGGTAATA 61.733 60.000 2.18 0.00 38.78 0.98
7101 9190 2.902584 GCCGGGTACGTGGGTAAT 59.097 61.111 2.18 0.00 38.78 1.89
7102 9191 3.757828 CGCCGGGTACGTGGGTAA 61.758 66.667 2.18 0.00 38.78 2.85
7128 9217 4.771338 ACCCATACCCTTACCCTAATAGG 58.229 47.826 0.00 0.00 34.30 2.57
7129 9218 7.876978 TTAACCCATACCCTTACCCTAATAG 57.123 40.000 0.00 0.00 0.00 1.73
7130 9219 7.856121 ACTTTAACCCATACCCTTACCCTAATA 59.144 37.037 0.00 0.00 0.00 0.98
7131 9220 6.684243 ACTTTAACCCATACCCTTACCCTAAT 59.316 38.462 0.00 0.00 0.00 1.73
7132 9221 6.037949 ACTTTAACCCATACCCTTACCCTAA 58.962 40.000 0.00 0.00 0.00 2.69
7133 9222 5.429435 CACTTTAACCCATACCCTTACCCTA 59.571 44.000 0.00 0.00 0.00 3.53
7134 9223 4.228895 CACTTTAACCCATACCCTTACCCT 59.771 45.833 0.00 0.00 0.00 4.34
7135 9224 4.529897 CACTTTAACCCATACCCTTACCC 58.470 47.826 0.00 0.00 0.00 3.69
7136 9225 4.529897 CCACTTTAACCCATACCCTTACC 58.470 47.826 0.00 0.00 0.00 2.85
7137 9226 4.018141 ACCCACTTTAACCCATACCCTTAC 60.018 45.833 0.00 0.00 0.00 2.34
7138 9227 4.185518 ACCCACTTTAACCCATACCCTTA 58.814 43.478 0.00 0.00 0.00 2.69
7139 9228 2.998186 ACCCACTTTAACCCATACCCTT 59.002 45.455 0.00 0.00 0.00 3.95
7140 9229 2.651190 ACCCACTTTAACCCATACCCT 58.349 47.619 0.00 0.00 0.00 4.34
7141 9230 3.682436 CGTACCCACTTTAACCCATACCC 60.682 52.174 0.00 0.00 0.00 3.69
7142 9231 3.534554 CGTACCCACTTTAACCCATACC 58.465 50.000 0.00 0.00 0.00 2.73
7143 9232 3.534554 CCGTACCCACTTTAACCCATAC 58.465 50.000 0.00 0.00 0.00 2.39
7144 9233 2.504996 CCCGTACCCACTTTAACCCATA 59.495 50.000 0.00 0.00 0.00 2.74
7145 9234 1.282738 CCCGTACCCACTTTAACCCAT 59.717 52.381 0.00 0.00 0.00 4.00
7146 9235 0.691904 CCCGTACCCACTTTAACCCA 59.308 55.000 0.00 0.00 0.00 4.51
7147 9236 0.692476 ACCCGTACCCACTTTAACCC 59.308 55.000 0.00 0.00 0.00 4.11
7148 9237 3.534554 CATACCCGTACCCACTTTAACC 58.465 50.000 0.00 0.00 0.00 2.85
7149 9238 3.055167 ACCATACCCGTACCCACTTTAAC 60.055 47.826 0.00 0.00 0.00 2.01
7150 9239 3.180507 ACCATACCCGTACCCACTTTAA 58.819 45.455 0.00 0.00 0.00 1.52
7151 9240 2.831565 ACCATACCCGTACCCACTTTA 58.168 47.619 0.00 0.00 0.00 1.85
7152 9241 1.660242 ACCATACCCGTACCCACTTT 58.340 50.000 0.00 0.00 0.00 2.66
7153 9242 1.660242 AACCATACCCGTACCCACTT 58.340 50.000 0.00 0.00 0.00 3.16
7203 9292 7.182817 AGCCTATTTGTAGATTATATGCGGA 57.817 36.000 0.00 0.00 0.00 5.54
7275 9368 6.327386 AGCATGATTAGGTCTTTTTAGGGA 57.673 37.500 0.00 0.00 0.00 4.20
7404 9497 6.693466 TCACGTATAAGATTCTGGACAAACA 58.307 36.000 0.00 0.00 0.00 2.83
7432 9525 7.221645 CACGCAGATATAGCCATATAAAGACAG 59.778 40.741 0.00 0.00 0.00 3.51
7434 9527 7.258441 TCACGCAGATATAGCCATATAAAGAC 58.742 38.462 0.00 0.00 0.00 3.01
7661 9754 4.684623 CCAATCCATGGTCCCCAC 57.315 61.111 12.58 0.00 44.85 4.61


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

AutoCloner maintained by Alex Coulton.