Multiple sequence alignment - TraesCS5D01G309000

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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 TraesCS5D01G309000 chr5D 100.000 4819 0 0 1 4819 406330399 406335217 0.000000e+00 8900.0
1 TraesCS5D01G309000 chr5A 94.751 4420 161 33 13 4409 511902750 511907121 0.000000e+00 6811.0
2 TraesCS5D01G309000 chr5A 93.519 216 11 3 4447 4662 511914150 511914362 7.780000e-83 318.0
3 TraesCS5D01G309000 chr5A 91.549 142 4 3 4670 4804 511914419 511914559 6.370000e-44 189.0
4 TraesCS5D01G309000 chr5A 100.000 32 0 0 4788 4819 511914569 511914600 5.210000e-05 60.2
5 TraesCS5D01G309000 chr5B 93.394 3860 141 42 772 4582 487220241 487224035 0.000000e+00 5611.0
6 TraesCS5D01G309000 chr5B 93.046 719 29 8 1 708 487219517 487220225 0.000000e+00 1031.0
7 TraesCS5D01G309000 chr5B 89.773 176 4 7 4656 4819 487224130 487224303 3.780000e-51 213.0
8 TraesCS5D01G309000 chr1A 90.821 207 19 0 3360 3566 566111186 566111392 1.320000e-70 278.0
9 TraesCS5D01G309000 chr1B 90.338 207 20 0 3360 3566 655849215 655849421 6.150000e-69 272.0
10 TraesCS5D01G309000 chr1D 89.855 207 21 0 3360 3566 471841334 471841540 2.860000e-67 267.0


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 TraesCS5D01G309000 chr5D 406330399 406335217 4818 False 8900 8900 100.000 1 4819 1 chr5D.!!$F1 4818
1 TraesCS5D01G309000 chr5A 511902750 511907121 4371 False 6811 6811 94.751 13 4409 1 chr5A.!!$F1 4396
2 TraesCS5D01G309000 chr5B 487219517 487224303 4786 False 2285 5611 92.071 1 4819 3 chr5B.!!$F1 4818

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
374 386 1.065782 CGGGAGTGAGACAGAGAGAGA 60.066 57.143 0.00 0.00 0.00 3.10 F
765 779 1.084370 CCGGCTTCGTCAGTCAATCC 61.084 60.000 0.00 0.00 0.00 3.01 F
1166 1189 1.110442 ATCGCCTCTGACTGGAAGAG 58.890 55.000 2.78 2.78 40.79 2.85 F
1726 1755 2.698855 ATGTTTGCTGACGGATAGCT 57.301 45.000 8.83 0.00 41.66 3.32 F
2061 2092 6.034577 GGAAAGTTGCAGTTTTGTTTAGTCAC 59.965 38.462 2.66 0.00 0.00 3.67 F
3440 3476 3.495331 GAGATGGCTGAGATAGTCCTGA 58.505 50.000 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2092 2.113860 TTTCCTTCCTTCCATCTGCG 57.886 50.000 0.00 0.00 0.00 5.18 R
2513 2544 6.091441 GCAACCAACACATTAAGAAAAACACA 59.909 34.615 0.00 0.00 0.00 3.72 R
3023 3056 5.068855 TGGTTCTCAAATTGCAATTCTGTCA 59.931 36.000 24.28 13.27 0.00 3.58 R
3440 3476 0.034616 AGCTGCTTGTTCTCGAAGCT 59.965 50.000 7.50 3.08 45.14 3.74 R
3502 3538 1.570813 TGAGCGTGTTGTCAGAGTTG 58.429 50.000 0.00 0.00 0.00 3.16 R
4606 4695 0.178932 TCCACAGGCTCTGGTACTGT 60.179 55.000 8.75 0.00 45.62 3.55 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
22 27 2.115348 TAGCCTAAAAGCGACGATCG 57.885 50.000 14.88 14.88 43.89 3.69
35 40 2.543031 CGACGATCGGATCCAGCTAAAA 60.543 50.000 20.98 0.00 36.00 1.52
100 112 3.282271 CTCGTCAGCCTGAGCAGA 58.718 61.111 0.00 0.00 43.56 4.26
103 115 2.813042 GTCAGCCTGAGCAGACGC 60.813 66.667 0.00 0.00 44.29 5.19
104 116 3.305516 TCAGCCTGAGCAGACGCA 61.306 61.111 0.00 0.00 43.56 5.24
360 372 3.637273 GGGTTGACCTGCGGGAGT 61.637 66.667 21.41 0.00 35.85 3.85
374 386 1.065782 CGGGAGTGAGACAGAGAGAGA 60.066 57.143 0.00 0.00 0.00 3.10
462 476 1.673337 GGCATGCTGCTGTGAGTGA 60.673 57.895 18.92 0.00 44.28 3.41
470 484 1.296715 GCTGTGAGTGACGGGGAAT 59.703 57.895 0.00 0.00 0.00 3.01
593 607 5.105513 TGTTTTGTCCCTTCTTGGAAGAAAC 60.106 40.000 8.64 10.24 43.84 2.78
606 620 3.127895 TGGAAGAAACGAAACCACACAAG 59.872 43.478 0.00 0.00 0.00 3.16
731 745 3.285484 AGTGATGGATGCTCATTTGACC 58.715 45.455 0.00 0.00 0.00 4.02
762 776 2.035237 AACCCGGCTTCGTCAGTCAA 62.035 55.000 0.00 0.00 0.00 3.18
765 779 1.084370 CCGGCTTCGTCAGTCAATCC 61.084 60.000 0.00 0.00 0.00 3.01
793 807 1.369091 GCTAATGTGGCCGGTCAGTG 61.369 60.000 10.28 0.00 0.00 3.66
797 811 2.048127 GTGGCCGGTCAGTGTCTC 60.048 66.667 10.28 0.00 0.00 3.36
832 846 6.240894 TGATTGAATAGACATGATTAGGCCC 58.759 40.000 0.00 0.00 0.00 5.80
884 900 3.614588 GTGTTGAAACAAGTTCTACGCC 58.385 45.455 0.00 0.00 42.83 5.68
888 904 5.235616 TGTTGAAACAAGTTCTACGCCTTAG 59.764 40.000 0.00 0.00 42.73 2.18
889 905 4.952460 TGAAACAAGTTCTACGCCTTAGT 58.048 39.130 0.00 0.00 37.13 2.24
890 906 5.362263 TGAAACAAGTTCTACGCCTTAGTT 58.638 37.500 0.00 0.00 37.13 2.24
893 909 4.304939 ACAAGTTCTACGCCTTAGTTGTC 58.695 43.478 0.00 0.00 0.00 3.18
894 910 4.038883 ACAAGTTCTACGCCTTAGTTGTCT 59.961 41.667 0.00 0.00 0.00 3.41
895 911 5.242393 ACAAGTTCTACGCCTTAGTTGTCTA 59.758 40.000 0.00 0.00 0.00 2.59
900 917 6.069684 TCTACGCCTTAGTTGTCTATAAGC 57.930 41.667 0.00 0.00 0.00 3.09
901 918 5.826737 TCTACGCCTTAGTTGTCTATAAGCT 59.173 40.000 0.00 0.00 0.00 3.74
904 921 4.441634 CGCCTTAGTTGTCTATAAGCTGGT 60.442 45.833 0.00 0.00 0.00 4.00
912 929 3.756434 TGTCTATAAGCTGGTTGTTTGGC 59.244 43.478 1.72 0.00 0.00 4.52
1047 1070 1.604915 GGACTTGGAGAAGGAGCCC 59.395 63.158 0.00 0.00 32.95 5.19
1086 1109 1.663074 GCGGATCTCGATCACTGGC 60.663 63.158 8.97 3.33 42.43 4.85
1166 1189 1.110442 ATCGCCTCTGACTGGAAGAG 58.890 55.000 2.78 2.78 40.79 2.85
1350 1373 7.065683 GTCATCATGTACAACAACACCATGATA 59.934 37.037 11.74 1.53 46.23 2.15
1433 1456 6.999272 CAGTACTAGCTTCTATGGACCTCTTA 59.001 42.308 0.00 0.00 0.00 2.10
1480 1509 6.978674 AGATGCTAACTGCTATTGTAGGTA 57.021 37.500 0.00 0.00 43.37 3.08
1726 1755 2.698855 ATGTTTGCTGACGGATAGCT 57.301 45.000 8.83 0.00 41.66 3.32
1860 1889 7.951347 ATCTTTGAAGACCATCTTATTTGCT 57.049 32.000 0.00 0.00 36.73 3.91
1938 1967 8.741603 AATACGTAATGGTTTGGTAAGCTTAT 57.258 30.769 9.88 0.00 32.98 1.73
1959 1990 7.218963 GCTTATAAGCGATGAAAAAGAAACTGG 59.781 37.037 21.10 0.00 42.88 4.00
2036 2067 9.009327 CAACTACAATAATTTTGACCTAATGCG 57.991 33.333 7.18 0.00 0.00 4.73
2061 2092 6.034577 GGAAAGTTGCAGTTTTGTTTAGTCAC 59.965 38.462 2.66 0.00 0.00 3.67
2109 2140 7.945033 ATTACAACAGCAAAACAATAACCTG 57.055 32.000 0.00 0.00 0.00 4.00
2535 2566 8.908903 TCTATGTGTTTTTCTTAATGTGTTGGT 58.091 29.630 0.00 0.00 0.00 3.67
2536 2567 9.528018 CTATGTGTTTTTCTTAATGTGTTGGTT 57.472 29.630 0.00 0.00 0.00 3.67
2537 2568 7.588143 TGTGTTTTTCTTAATGTGTTGGTTG 57.412 32.000 0.00 0.00 0.00 3.77
2538 2569 6.091441 TGTGTTTTTCTTAATGTGTTGGTTGC 59.909 34.615 0.00 0.00 0.00 4.17
2539 2570 6.312672 GTGTTTTTCTTAATGTGTTGGTTGCT 59.687 34.615 0.00 0.00 0.00 3.91
2540 2571 6.876257 TGTTTTTCTTAATGTGTTGGTTGCTT 59.124 30.769 0.00 0.00 0.00 3.91
2541 2572 7.064016 TGTTTTTCTTAATGTGTTGGTTGCTTC 59.936 33.333 0.00 0.00 0.00 3.86
3023 3056 8.812513 TTCATATGAGATGTTGATTTCCAGTT 57.187 30.769 5.39 0.00 0.00 3.16
3440 3476 3.495331 GAGATGGCTGAGATAGTCCTGA 58.505 50.000 0.00 0.00 0.00 3.86
3588 3624 5.215845 ACCCTCCCAAAATTTTCAGAAGAA 58.784 37.500 0.00 0.00 0.00 2.52
3634 3670 6.041296 ACACATATACAGATGCTCATCAGTCA 59.959 38.462 10.51 2.73 38.32 3.41
3794 3830 2.759795 GTCCAGCTTGGCTCCCTT 59.240 61.111 0.00 0.00 36.40 3.95
3962 4000 1.615392 GCTTGGTGCAAGAGGATGTTT 59.385 47.619 0.00 0.00 43.42 2.83
4085 4124 8.150296 CCATTGTTTTGGACCTTCTTTTAGAAT 58.850 33.333 0.00 0.00 39.25 2.40
4220 4260 2.428890 CCTCTCTAGACATGGCGTTTCT 59.571 50.000 0.00 0.46 0.00 2.52
4222 4262 3.849911 TCTCTAGACATGGCGTTTCTTG 58.150 45.455 0.00 0.00 0.00 3.02
4267 4307 3.497879 CCCAAATCGAACGGGCTC 58.502 61.111 4.40 0.00 31.89 4.70
4284 4324 3.602483 GGCTCACCGTCTTTATTTGGTA 58.398 45.455 0.00 0.00 32.29 3.25
4291 4331 3.302870 CCGTCTTTATTTGGTATTCGGCG 60.303 47.826 0.00 0.00 0.00 6.46
4296 4336 1.842052 ATTTGGTATTCGGCGGGTTT 58.158 45.000 7.21 0.00 0.00 3.27
4510 4599 7.429051 GTGAAAAACCATTAAAAAGCAGCAAAG 59.571 33.333 0.00 0.00 0.00 2.77
4518 4607 1.230324 AAAGCAGCAAAGACTCGGAC 58.770 50.000 0.00 0.00 0.00 4.79
4540 4629 6.226988 ACAATTCCATGAAAAATCGCAAAC 57.773 33.333 0.00 0.00 0.00 2.93
4550 4639 6.418956 TGAAAAATCGCAAACGCTATATCTC 58.581 36.000 0.00 0.00 39.84 2.75
4554 4643 1.497991 GCAAACGCTATATCTCGCCA 58.502 50.000 0.00 0.00 0.00 5.69
4585 4674 2.124736 GCCCGTGCTTGCCTCATA 60.125 61.111 0.00 0.00 33.53 2.15
4586 4675 2.182842 GCCCGTGCTTGCCTCATAG 61.183 63.158 0.00 0.00 33.53 2.23
4587 4676 2.182842 CCCGTGCTTGCCTCATAGC 61.183 63.158 0.00 0.00 37.89 2.97
4588 4677 2.528743 CCGTGCTTGCCTCATAGCG 61.529 63.158 0.00 0.00 40.26 4.26
4589 4678 2.711924 GTGCTTGCCTCATAGCGC 59.288 61.111 0.00 0.00 40.26 5.92
4590 4679 2.514592 TGCTTGCCTCATAGCGCC 60.515 61.111 2.29 0.00 40.26 6.53
4591 4680 3.282920 GCTTGCCTCATAGCGCCC 61.283 66.667 2.29 0.00 34.65 6.13
4592 4681 2.507944 CTTGCCTCATAGCGCCCT 59.492 61.111 2.29 0.00 34.65 5.19
4593 4682 1.890979 CTTGCCTCATAGCGCCCTG 60.891 63.158 2.29 1.21 34.65 4.45
4594 4683 2.315781 CTTGCCTCATAGCGCCCTGA 62.316 60.000 2.29 6.55 34.65 3.86
4595 4684 1.699054 TTGCCTCATAGCGCCCTGAT 61.699 55.000 2.29 0.00 34.65 2.90
4596 4685 1.670406 GCCTCATAGCGCCCTGATG 60.670 63.158 2.29 5.74 0.00 3.07
4597 4686 1.670406 CCTCATAGCGCCCTGATGC 60.670 63.158 2.29 0.00 0.00 3.91
4619 4708 3.068881 TGGCACAGTACCAGAGCC 58.931 61.111 14.70 14.70 42.19 4.70
4644 4733 4.459337 GTGGAAAGAGAGGGTTGGTATTTG 59.541 45.833 0.00 0.00 0.00 2.32
4649 4738 6.650427 AAGAGAGGGTTGGTATTTGTTTTC 57.350 37.500 0.00 0.00 0.00 2.29
4650 4739 4.760204 AGAGAGGGTTGGTATTTGTTTTCG 59.240 41.667 0.00 0.00 0.00 3.46
4657 4746 6.271566 GGTTGGTATTTGTTTTCGTGGTTTA 58.728 36.000 0.00 0.00 0.00 2.01
4663 4810 8.533965 GGTATTTGTTTTCGTGGTTTAGTTTTC 58.466 33.333 0.00 0.00 0.00 2.29
4668 4815 6.913673 TGTTTTCGTGGTTTAGTTTTCTATGC 59.086 34.615 0.00 0.00 31.96 3.14
4675 4822 7.356962 CGTGGTTTAGTTTTCTATGCGTTTTTC 60.357 37.037 0.00 0.00 31.96 2.29
4714 4864 9.631452 CTATTTTCCTTCTTTTTCATTGTCTCC 57.369 33.333 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.360551 CTGGATCCGATCGTCGCTT 59.639 57.895 15.09 0.00 38.82 4.68
22 27 1.101635 GCCGGGTTTTAGCTGGATCC 61.102 60.000 4.20 4.20 44.77 3.36
96 108 0.108424 AAGAGATGAGGTGCGTCTGC 60.108 55.000 0.00 0.00 42.88 4.26
97 109 2.376808 AAAGAGATGAGGTGCGTCTG 57.623 50.000 0.00 0.00 42.88 3.51
98 110 2.354203 GGAAAAGAGATGAGGTGCGTCT 60.354 50.000 0.00 0.00 45.48 4.18
99 111 2.003301 GGAAAAGAGATGAGGTGCGTC 58.997 52.381 0.00 0.00 0.00 5.19
100 112 1.625818 AGGAAAAGAGATGAGGTGCGT 59.374 47.619 0.00 0.00 0.00 5.24
101 113 2.275318 GAGGAAAAGAGATGAGGTGCG 58.725 52.381 0.00 0.00 0.00 5.34
102 114 2.637947 GGAGGAAAAGAGATGAGGTGC 58.362 52.381 0.00 0.00 0.00 5.01
103 115 2.092699 GGGGAGGAAAAGAGATGAGGTG 60.093 54.545 0.00 0.00 0.00 4.00
104 116 2.200955 GGGGAGGAAAAGAGATGAGGT 58.799 52.381 0.00 0.00 0.00 3.85
221 233 2.048127 GTCGCAGGACCAGTGGAC 60.048 66.667 18.40 10.15 37.19 4.02
360 372 5.163468 GCCATAATTGTCTCTCTCTGTCTCA 60.163 44.000 0.00 0.00 0.00 3.27
462 476 4.619227 CGCGCCCATATTCCCCGT 62.619 66.667 0.00 0.00 0.00 5.28
593 607 0.179029 AGACCCCTTGTGTGGTTTCG 60.179 55.000 0.00 0.00 34.20 3.46
606 620 4.448210 TGACGAAAGCAATAATAGACCCC 58.552 43.478 0.00 0.00 0.00 4.95
680 694 2.903855 CACAGGATGGCGGATGGC 60.904 66.667 0.00 0.00 43.62 4.40
731 745 1.134098 AGCCGGGTTCAATCATACCAG 60.134 52.381 0.00 0.00 36.10 4.00
762 776 3.009723 CCACATTAGCAAACGTGAGGAT 58.990 45.455 0.00 0.00 0.00 3.24
765 779 1.135689 GGCCACATTAGCAAACGTGAG 60.136 52.381 0.00 0.00 0.00 3.51
884 900 7.907214 AACAACCAGCTTATAGACAACTAAG 57.093 36.000 0.00 0.00 32.04 2.18
888 904 5.699839 CCAAACAACCAGCTTATAGACAAC 58.300 41.667 0.00 0.00 0.00 3.32
889 905 4.217550 GCCAAACAACCAGCTTATAGACAA 59.782 41.667 0.00 0.00 0.00 3.18
890 906 3.756434 GCCAAACAACCAGCTTATAGACA 59.244 43.478 0.00 0.00 0.00 3.41
893 909 4.989279 ATGCCAAACAACCAGCTTATAG 57.011 40.909 0.00 0.00 0.00 1.31
894 910 6.184068 TCTTATGCCAAACAACCAGCTTATA 58.816 36.000 0.00 0.00 0.00 0.98
895 911 5.016173 TCTTATGCCAAACAACCAGCTTAT 58.984 37.500 0.00 0.00 0.00 1.73
900 917 4.789012 ACATCTTATGCCAAACAACCAG 57.211 40.909 0.00 0.00 0.00 4.00
901 918 6.849085 ATAACATCTTATGCCAAACAACCA 57.151 33.333 0.00 0.00 0.00 3.67
904 921 8.986847 CAAACAATAACATCTTATGCCAAACAA 58.013 29.630 0.00 0.00 0.00 2.83
912 929 8.394877 TCTTACGGCAAACAATAACATCTTATG 58.605 33.333 0.00 0.00 0.00 1.90
1047 1070 1.137872 AGCTTCTCGAATGGCCAGTAG 59.862 52.381 13.05 9.79 0.00 2.57
1086 1109 1.819632 GGCTATGAACCCACCAGCG 60.820 63.158 0.00 0.00 35.59 5.18
1166 1189 2.076863 CCTCTTCCATGTGTTCGTTCC 58.923 52.381 0.00 0.00 0.00 3.62
1491 1520 4.163458 ACAGACAGACCTAAACCTTTGTCA 59.837 41.667 5.38 0.00 37.87 3.58
1578 1607 8.520119 AGCCCCCTTTATTATATAAGAAGTGA 57.480 34.615 15.07 0.00 0.00 3.41
1753 1782 6.983890 ACCTTGCAAAAAGTACACCAATAAAG 59.016 34.615 0.00 0.00 0.00 1.85
1856 1885 3.196901 TGCGAGATAAAAGGTAGGAGCAA 59.803 43.478 0.00 0.00 0.00 3.91
1860 1889 7.732025 TGAATATTGCGAGATAAAAGGTAGGA 58.268 34.615 0.00 0.00 0.00 2.94
1938 1967 5.048991 GGACCAGTTTCTTTTTCATCGCTTA 60.049 40.000 0.00 0.00 0.00 3.09
1947 1976 6.764379 TGTTTTCAAGGACCAGTTTCTTTTT 58.236 32.000 0.00 0.00 0.00 1.94
1952 1981 5.660460 ACAATGTTTTCAAGGACCAGTTTC 58.340 37.500 0.00 0.00 0.00 2.78
1959 1990 2.882137 TCGGGACAATGTTTTCAAGGAC 59.118 45.455 0.00 0.00 0.00 3.85
2036 2067 6.034577 GTGACTAAACAAAACTGCAACTTTCC 59.965 38.462 0.00 0.00 0.00 3.13
2061 2092 2.113860 TTTCCTTCCTTCCATCTGCG 57.886 50.000 0.00 0.00 0.00 5.18
2131 2162 8.037166 GCAGGAAGGAAATTGAAGTTCAATAAT 58.963 33.333 27.15 19.97 45.57 1.28
2513 2544 6.091441 GCAACCAACACATTAAGAAAAACACA 59.909 34.615 0.00 0.00 0.00 3.72
2793 2826 7.287005 AGACATACCAGTACCGAATTTGATAGA 59.713 37.037 0.00 0.00 0.00 1.98
2803 2836 6.594788 AAAAAGTAGACATACCAGTACCGA 57.405 37.500 0.00 0.00 31.78 4.69
2850 2883 9.471084 TCATGCAAAATCTATTTCATGCTAATG 57.529 29.630 11.40 8.65 35.57 1.90
2911 2944 6.094464 CAGTCCATTAATTGTCATCTCAGCAA 59.906 38.462 0.00 0.00 0.00 3.91
3023 3056 5.068855 TGGTTCTCAAATTGCAATTCTGTCA 59.931 36.000 24.28 13.27 0.00 3.58
3241 3277 5.520649 GGTAGGATGAGAACGAAGATTCAAC 59.479 44.000 0.00 0.00 0.00 3.18
3440 3476 0.034616 AGCTGCTTGTTCTCGAAGCT 59.965 50.000 7.50 3.08 45.14 3.74
3502 3538 1.570813 TGAGCGTGTTGTCAGAGTTG 58.429 50.000 0.00 0.00 0.00 3.16
3588 3624 6.150976 TGTGTGACTGAACAGAACAAAAAGAT 59.849 34.615 8.87 0.00 33.11 2.40
3634 3670 5.482878 AGGCAGAATTTGGATTCAGTTTGAT 59.517 36.000 2.41 0.00 43.35 2.57
4052 4091 2.161609 GGTCCAAAACAATGGCTCGTAG 59.838 50.000 0.00 0.00 40.46 3.51
4117 4156 9.698309 TCTTCCTCTGCTAGAAATATATTTTCG 57.302 33.333 11.92 5.35 33.86 3.46
4130 4169 9.748708 GAGCAAATATATATCTTCCTCTGCTAG 57.251 37.037 7.40 0.00 36.60 3.42
4220 4260 9.261180 CTATTCTATGCCTCGAGAAATTAACAA 57.739 33.333 15.71 0.00 35.40 2.83
4222 4262 9.646427 ATCTATTCTATGCCTCGAGAAATTAAC 57.354 33.333 15.71 0.00 35.40 2.01
4267 4307 4.495184 GCCGAATACCAAATAAAGACGGTG 60.495 45.833 0.00 0.00 39.95 4.94
4284 4324 0.879090 GAACAAGAAACCCGCCGAAT 59.121 50.000 0.00 0.00 0.00 3.34
4291 4331 7.097192 ACAAAGAAAAAGAGAACAAGAAACCC 58.903 34.615 0.00 0.00 0.00 4.11
4296 4336 9.626045 GAAGAAACAAAGAAAAAGAGAACAAGA 57.374 29.630 0.00 0.00 0.00 3.02
4362 4402 6.348621 ACTGTGAACATGTTTCAAAAATGC 57.651 33.333 13.36 0.00 0.00 3.56
4379 4419 5.897050 AGCCACGAATTTTAAAAACTGTGA 58.103 33.333 21.59 0.00 0.00 3.58
4457 4546 9.161629 CGGCTTTTTCAGGGAAATAATTTAATT 57.838 29.630 0.00 0.00 31.34 1.40
4458 4547 7.768582 CCGGCTTTTTCAGGGAAATAATTTAAT 59.231 33.333 0.00 0.00 31.34 1.40
4459 4548 7.100409 CCGGCTTTTTCAGGGAAATAATTTAA 58.900 34.615 0.00 0.00 31.34 1.52
4460 4549 6.211785 ACCGGCTTTTTCAGGGAAATAATTTA 59.788 34.615 0.00 0.00 31.34 1.40
4461 4550 5.012664 ACCGGCTTTTTCAGGGAAATAATTT 59.987 36.000 0.00 0.00 31.34 1.82
4462 4551 4.530553 ACCGGCTTTTTCAGGGAAATAATT 59.469 37.500 0.00 0.00 31.34 1.40
4503 4592 2.160417 GGAATTGTCCGAGTCTTTGCTG 59.840 50.000 0.00 0.00 33.05 4.41
4518 4607 5.307368 CGTTTGCGATTTTTCATGGAATTG 58.693 37.500 0.00 0.00 41.33 2.32
4540 4629 3.317150 TCACAATTGGCGAGATATAGCG 58.683 45.455 10.83 0.00 0.00 4.26
4550 4639 3.609175 CGGGCTATATTTCACAATTGGCG 60.609 47.826 10.83 0.27 0.00 5.69
4554 4643 4.568152 GCACGGGCTATATTTCACAATT 57.432 40.909 0.00 0.00 36.96 2.32
4589 4678 4.478371 TGCCAGCTCGCATCAGGG 62.478 66.667 0.32 0.00 32.62 4.45
4590 4679 3.200593 GTGCCAGCTCGCATCAGG 61.201 66.667 9.85 0.00 41.70 3.86
4591 4680 2.435410 TGTGCCAGCTCGCATCAG 60.435 61.111 9.85 0.00 41.70 2.90
4592 4681 1.887344 TACTGTGCCAGCTCGCATCA 61.887 55.000 9.85 8.66 41.70 3.07
4593 4682 1.153568 TACTGTGCCAGCTCGCATC 60.154 57.895 9.85 4.18 41.70 3.91
4594 4683 1.448540 GTACTGTGCCAGCTCGCAT 60.449 57.895 9.85 0.00 41.70 4.73
4595 4684 2.048222 GTACTGTGCCAGCTCGCA 60.048 61.111 0.32 0.32 34.37 5.10
4596 4685 2.815647 GGTACTGTGCCAGCTCGC 60.816 66.667 10.24 0.00 34.37 5.03
4597 4686 1.446792 CTGGTACTGTGCCAGCTCG 60.447 63.158 27.93 9.42 45.72 5.03
4598 4687 4.606071 CTGGTACTGTGCCAGCTC 57.394 61.111 27.93 0.00 45.72 4.09
4604 4693 1.674057 ACAGGCTCTGGTACTGTGC 59.326 57.895 7.06 0.00 43.29 4.57
4606 4695 0.178932 TCCACAGGCTCTGGTACTGT 60.179 55.000 8.75 0.00 45.62 3.55
4607 4696 0.976641 TTCCACAGGCTCTGGTACTG 59.023 55.000 8.75 0.00 35.51 2.74
4608 4697 1.625818 CTTTCCACAGGCTCTGGTACT 59.374 52.381 8.75 0.00 35.51 2.73
4609 4698 1.623811 TCTTTCCACAGGCTCTGGTAC 59.376 52.381 8.75 0.00 35.51 3.34
4610 4699 1.902508 CTCTTTCCACAGGCTCTGGTA 59.097 52.381 8.75 0.00 35.51 3.25
4611 4700 0.689623 CTCTTTCCACAGGCTCTGGT 59.310 55.000 8.75 0.00 35.51 4.00
4612 4701 0.979665 TCTCTTTCCACAGGCTCTGG 59.020 55.000 1.83 1.83 35.51 3.86
4613 4702 1.066286 CCTCTCTTTCCACAGGCTCTG 60.066 57.143 1.16 1.16 37.52 3.35
4614 4703 1.274712 CCTCTCTTTCCACAGGCTCT 58.725 55.000 0.00 0.00 0.00 4.09
4615 4704 0.251634 CCCTCTCTTTCCACAGGCTC 59.748 60.000 0.00 0.00 0.00 4.70
4616 4705 0.474660 ACCCTCTCTTTCCACAGGCT 60.475 55.000 0.00 0.00 0.00 4.58
4617 4706 0.402121 AACCCTCTCTTTCCACAGGC 59.598 55.000 0.00 0.00 0.00 4.85
4618 4707 1.271597 CCAACCCTCTCTTTCCACAGG 60.272 57.143 0.00 0.00 0.00 4.00
4619 4708 1.421646 ACCAACCCTCTCTTTCCACAG 59.578 52.381 0.00 0.00 0.00 3.66
4644 4733 6.085849 CGCATAGAAAACTAAACCACGAAAAC 59.914 38.462 0.00 0.00 0.00 2.43
4649 4738 4.657075 ACGCATAGAAAACTAAACCACG 57.343 40.909 0.00 0.00 0.00 4.94
4650 4739 7.096353 GGAAAAACGCATAGAAAACTAAACCAC 60.096 37.037 0.00 0.00 0.00 4.16
4657 4746 7.039313 AGAAAGGAAAAACGCATAGAAAACT 57.961 32.000 0.00 0.00 0.00 2.66
4663 4810 9.626045 AGATAAAAAGAAAGGAAAAACGCATAG 57.374 29.630 0.00 0.00 0.00 2.23
4771 4930 8.433421 TTCATATTTTCCTAAGACCGAATCAC 57.567 34.615 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.