Multiple sequence alignment - TraesCS7D01G257000

Loading Multiple Alignment...

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 TraesCS7D01G257000 chr7D 100.000 3937 0 0 1 3937 232410502 232406566 0 7271
1 TraesCS7D01G257000 chr7B 87.912 4004 296 99 4 3927 203030796 203026901 0 4540
2 TraesCS7D01G257000 chr7A 90.212 1982 117 31 2 1939 244606058 244604110 0 2514
3 TraesCS7D01G257000 chr7A 90.661 1724 73 34 1990 3681 244604100 244602433 0 2211


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 TraesCS7D01G257000 chr7D 232406566 232410502 3936 True 7271.0 7271 100.0000 1 3937 1 chr7D.!!$R1 3936
1 TraesCS7D01G257000 chr7B 203026901 203030796 3895 True 4540.0 4540 87.9120 4 3927 1 chr7B.!!$R1 3923
2 TraesCS7D01G257000 chr7A 244602433 244606058 3625 True 2362.5 2514 90.4365 2 3681 2 chr7A.!!$R1 3679

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
729 747 0.033109 CCTCCTCCCCATCCCAAAAC 60.033 60.0 0.0 0.0 0.00 2.43 F
2116 2200 0.387367 ACTACGTGCAGTCGCTTCAG 60.387 55.0 0.0 0.0 39.64 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 2405 0.250901 GTGATGAACAGCAGGGGTGT 60.251 55.0 0.0 0.0 46.58 4.16 R
3586 3746 0.040067 CGGCACTCAGTTTTTGGAGC 60.040 55.0 0.0 0.0 34.48 4.70 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
17 18 3.320359 CGCCTCCAGGTACCCAAT 58.680 61.111 8.74 0.00 37.57 3.16
20 21 1.227383 CCTCCAGGTACCCAATGCC 59.773 63.158 8.74 0.00 0.00 4.40
26 27 2.516225 GTACCCAATGCCGCTCCC 60.516 66.667 0.00 0.00 0.00 4.30
48 49 2.364579 TCCTACCAATCGGGCGGT 60.365 61.111 0.00 0.00 42.05 5.68
76 77 1.071471 ACCAAGGGAACACGAGCAG 59.929 57.895 0.00 0.00 0.00 4.24
102 103 2.425773 GCAGCGAGCAACAACACG 60.426 61.111 0.00 0.00 44.79 4.49
114 115 4.015406 AACACGATGAGGCGGGCA 62.015 61.111 3.78 0.00 38.49 5.36
116 117 2.514592 CACGATGAGGCGGGCAAT 60.515 61.111 3.78 0.00 35.12 3.56
129 130 1.024271 GGGCAATGTGCGATATGTGT 58.976 50.000 0.00 0.00 46.21 3.72
216 217 3.120477 CGAAGGCGCATAACAACTGTTTA 60.120 43.478 10.83 0.00 39.31 2.01
227 228 9.337091 GCATAACAACTGTTTAACGAAATGTAT 57.663 29.630 0.00 0.00 39.31 2.29
239 241 6.751514 AACGAAATGTATGAGGCAAATGTA 57.248 33.333 0.00 0.00 0.00 2.29
257 259 7.377662 GCAAATGTAAGTTTTAGTGCGTTAAGT 59.622 33.333 0.00 0.00 0.00 2.24
268 270 7.832503 TTAGTGCGTTAAGTTTTAGGGTATC 57.167 36.000 0.00 0.00 0.00 2.24
366 368 0.398318 GATGAGACCAGCCATACCCC 59.602 60.000 0.00 0.00 0.00 4.95
368 370 3.462199 GAGACCAGCCATACCCCGC 62.462 68.421 0.00 0.00 0.00 6.13
379 381 5.010617 CAGCCATACCCCGCTTTAATTTTAT 59.989 40.000 0.00 0.00 31.40 1.40
457 463 3.244422 TGGCACTGGTAGTTCCTTGTAAG 60.244 47.826 0.00 0.00 32.48 2.34
473 479 5.120830 CCTTGTAAGTTACTCTGCATCACAC 59.879 44.000 14.00 0.00 0.00 3.82
550 558 6.980397 GCGAAAATCCATGTGAAAAATCCTAT 59.020 34.615 0.00 0.00 0.00 2.57
551 559 7.043192 GCGAAAATCCATGTGAAAAATCCTATG 60.043 37.037 0.00 0.00 0.00 2.23
553 561 7.427989 AAATCCATGTGAAAAATCCTATGCT 57.572 32.000 0.00 0.00 0.00 3.79
565 573 4.569023 TATGCTGAGCCGCGGTCG 62.569 66.667 28.70 17.85 32.15 4.79
602 610 3.432588 CTCCGTCGACCGAGCACT 61.433 66.667 18.68 0.00 39.56 4.40
643 657 2.492088 GCCAACCAGGAACAGAATTACC 59.508 50.000 0.00 0.00 41.22 2.85
729 747 0.033109 CCTCCTCCCCATCCCAAAAC 60.033 60.000 0.00 0.00 0.00 2.43
825 843 2.124151 CCCAATTGCCCCTCCTCG 60.124 66.667 0.00 0.00 0.00 4.63
929 953 1.142748 CTCCGGCTGCTCTCGATTT 59.857 57.895 0.00 0.00 0.00 2.17
931 955 2.176273 CCGGCTGCTCTCGATTTGG 61.176 63.158 0.00 0.00 0.00 3.28
984 1019 2.747686 GGTTCTTGGACGGCTCCA 59.252 61.111 0.00 2.10 45.68 3.86
1042 1077 0.526954 CGGTAGCGGCGACTACATTT 60.527 55.000 28.91 4.51 43.61 2.32
1438 1491 3.853330 CGCCATTGACGCTGACCG 61.853 66.667 0.00 0.00 44.21 4.79
1486 1539 1.985116 GTCGGGGAGCAGAAGGAGT 60.985 63.158 0.00 0.00 0.00 3.85
1701 1754 2.662596 CTGGCAGAGCGGGTACAA 59.337 61.111 9.42 0.00 0.00 2.41
1736 1797 3.702792 TGCTGCTTCTCCTTCTAGTAGT 58.297 45.455 0.00 0.00 0.00 2.73
1816 1877 3.269381 AGGTGAGAAGAGAGAGGATCAGT 59.731 47.826 0.00 0.00 37.82 3.41
1866 1927 3.517296 TCCAGGATGCAACAAGGTAAA 57.483 42.857 0.00 0.00 31.97 2.01
1869 1930 5.575157 TCCAGGATGCAACAAGGTAAATAA 58.425 37.500 0.00 0.00 31.97 1.40
1871 1932 6.667414 TCCAGGATGCAACAAGGTAAATAATT 59.333 34.615 0.00 0.00 31.97 1.40
1872 1933 7.180051 TCCAGGATGCAACAAGGTAAATAATTT 59.820 33.333 0.00 0.00 31.97 1.82
1873 1934 7.278424 CCAGGATGCAACAAGGTAAATAATTTG 59.722 37.037 0.00 0.00 31.97 2.32
1875 1936 8.034804 AGGATGCAACAAGGTAAATAATTTGTC 58.965 33.333 0.00 0.00 32.97 3.18
1900 1981 9.647797 TCATTTCATTCAAAATGAGAAATCAGG 57.352 29.630 7.72 0.00 45.85 3.86
1939 2023 8.198778 AGCACATGATAATTTTGATGCACATTA 58.801 29.630 0.00 0.00 34.27 1.90
2023 2107 6.646267 AGACAGTCTTTGTGTACAAGGTTAA 58.354 36.000 0.00 0.00 41.05 2.01
2028 2112 7.643764 CAGTCTTTGTGTACAAGGTTAACAATG 59.356 37.037 8.10 8.03 37.15 2.82
2116 2200 0.387367 ACTACGTGCAGTCGCTTCAG 60.387 55.000 0.00 0.00 39.64 3.02
2147 2231 1.295423 GTAAGAAGAGCGTGGGCCA 59.705 57.895 0.00 0.00 41.24 5.36
2172 2256 2.260844 AACCATCCGATGCCATGTAG 57.739 50.000 2.53 0.00 0.00 2.74
2174 2258 2.325484 ACCATCCGATGCCATGTAGTA 58.675 47.619 2.53 0.00 0.00 1.82
2176 2260 2.562738 CCATCCGATGCCATGTAGTAGA 59.437 50.000 2.53 0.00 0.00 2.59
2177 2261 3.367806 CCATCCGATGCCATGTAGTAGAG 60.368 52.174 2.53 0.00 0.00 2.43
2178 2262 2.945456 TCCGATGCCATGTAGTAGAGT 58.055 47.619 0.00 0.00 0.00 3.24
2179 2263 2.623416 TCCGATGCCATGTAGTAGAGTG 59.377 50.000 0.00 0.00 0.00 3.51
2181 2265 2.362397 CGATGCCATGTAGTAGAGTGGT 59.638 50.000 0.00 0.00 34.23 4.16
2182 2266 3.568430 CGATGCCATGTAGTAGAGTGGTA 59.432 47.826 0.00 0.00 34.23 3.25
2183 2267 4.037565 CGATGCCATGTAGTAGAGTGGTAA 59.962 45.833 0.00 0.00 34.23 2.85
2184 2268 4.730949 TGCCATGTAGTAGAGTGGTAAC 57.269 45.455 0.00 0.00 34.23 2.50
2186 2270 3.129988 GCCATGTAGTAGAGTGGTAACGT 59.870 47.826 0.00 0.00 42.51 3.99
2187 2271 4.669318 CCATGTAGTAGAGTGGTAACGTG 58.331 47.826 0.00 0.00 42.51 4.49
2188 2272 3.837213 TGTAGTAGAGTGGTAACGTGC 57.163 47.619 0.00 0.00 42.51 5.34
2190 2274 1.624336 AGTAGAGTGGTAACGTGCCA 58.376 50.000 7.90 7.90 42.51 4.92
2201 2285 3.181510 GGTAACGTGCCACTGAATGAATC 60.182 47.826 4.72 0.00 0.00 2.52
2232 2316 2.037772 TCCTCCTCTGTTTCTGTTGCTC 59.962 50.000 0.00 0.00 0.00 4.26
2316 2400 1.215014 TGCACAAAGACGTGAGCTCG 61.215 55.000 9.64 0.45 39.34 5.03
2321 2405 1.858458 CAAAGACGTGAGCTCGAAACA 59.142 47.619 9.64 0.00 34.70 2.83
2340 2424 0.250901 ACACCCCTGCTGTTCATCAC 60.251 55.000 0.00 0.00 0.00 3.06
2342 2426 1.379044 CCCCTGCTGTTCATCACCC 60.379 63.158 0.00 0.00 0.00 4.61
2343 2427 1.687612 CCCTGCTGTTCATCACCCT 59.312 57.895 0.00 0.00 0.00 4.34
2364 2448 4.799473 CGCGCCGTAACGAGTCGA 62.799 66.667 21.50 0.00 34.06 4.20
2366 2450 1.010797 GCGCCGTAACGAGTCGATA 60.011 57.895 21.50 9.30 34.06 2.92
2500 2584 1.065410 TTCCAGTCCTTCCTGCCCAA 61.065 55.000 0.00 0.00 0.00 4.12
2549 2633 2.289532 GCTGGACCTGGCTCTGTCT 61.290 63.158 0.00 0.00 0.00 3.41
2564 2651 4.680237 TCTCAGGCCACCAACGCG 62.680 66.667 5.01 3.53 0.00 6.01
2643 2730 6.183360 GGTGATAACTCTTGCCTTCAGAATTC 60.183 42.308 0.00 0.00 0.00 2.17
2689 2777 7.928167 TGACGTAGAATCGTTAGAGACCTTATA 59.072 37.037 0.00 0.00 44.21 0.98
2690 2778 8.668510 ACGTAGAATCGTTAGAGACCTTATAA 57.331 34.615 0.00 0.00 41.37 0.98
2691 2779 9.282569 ACGTAGAATCGTTAGAGACCTTATAAT 57.717 33.333 0.00 0.00 41.37 1.28
2796 2892 0.620700 AGAGCCAGGATAACGGGGTT 60.621 55.000 0.00 0.00 45.34 4.11
2799 2895 0.750546 GCCAGGATAACGGGGTTTCC 60.751 60.000 0.00 0.00 34.66 3.13
2838 2934 4.478699 GTTAGTTAAAAGCCCGCGATTTT 58.521 39.130 8.23 14.18 33.42 1.82
2888 2984 1.544246 TGACATCGTCACTGAACGGAT 59.456 47.619 7.31 0.00 42.80 4.18
2915 3022 1.922369 AGGTGATCTGCAGGCAGGT 60.922 57.895 20.19 14.33 43.75 4.00
3075 3199 7.008941 TGTAATTAGGCTCTACTACTAAGGGG 58.991 42.308 0.00 0.00 31.02 4.79
3299 3452 8.519526 AGTTTTAATATCTGTGGCGATGAAAAA 58.480 29.630 0.00 0.00 0.00 1.94
3314 3467 4.620589 TGAAAAACCCCGTCAGTATACA 57.379 40.909 5.50 0.00 0.00 2.29
3514 3669 1.820481 CCGTCTCGTCTCCTCTCCC 60.820 68.421 0.00 0.00 0.00 4.30
3546 3706 2.168621 CTGCGTCGCGTGTTCTTG 59.831 61.111 13.38 0.00 0.00 3.02
3578 3738 2.590007 CGCTCAGCCCTGCCATAC 60.590 66.667 0.00 0.00 0.00 2.39
3579 3739 2.914289 GCTCAGCCCTGCCATACT 59.086 61.111 0.00 0.00 0.00 2.12
3580 3740 1.225704 GCTCAGCCCTGCCATACTT 59.774 57.895 0.00 0.00 0.00 2.24
3581 3741 0.469917 GCTCAGCCCTGCCATACTTA 59.530 55.000 0.00 0.00 0.00 2.24
3582 3742 1.811941 GCTCAGCCCTGCCATACTTAC 60.812 57.143 0.00 0.00 0.00 2.34
3584 3744 0.179018 CAGCCCTGCCATACTTACCC 60.179 60.000 0.00 0.00 0.00 3.69
3585 3745 0.623324 AGCCCTGCCATACTTACCCA 60.623 55.000 0.00 0.00 0.00 4.51
3586 3746 0.179018 GCCCTGCCATACTTACCCAG 60.179 60.000 0.00 0.00 0.00 4.45
3587 3747 0.179018 CCCTGCCATACTTACCCAGC 60.179 60.000 0.00 0.00 0.00 4.85
3588 3748 0.839946 CCTGCCATACTTACCCAGCT 59.160 55.000 0.00 0.00 0.00 4.24
3589 3749 1.202698 CCTGCCATACTTACCCAGCTC 60.203 57.143 0.00 0.00 0.00 4.09
3591 3751 0.837272 GCCATACTTACCCAGCTCCA 59.163 55.000 0.00 0.00 0.00 3.86
3593 3753 2.356741 GCCATACTTACCCAGCTCCAAA 60.357 50.000 0.00 0.00 0.00 3.28
3594 3754 3.876156 GCCATACTTACCCAGCTCCAAAA 60.876 47.826 0.00 0.00 0.00 2.44
3595 3755 4.340617 CCATACTTACCCAGCTCCAAAAA 58.659 43.478 0.00 0.00 0.00 1.94
3596 3756 4.157840 CCATACTTACCCAGCTCCAAAAAC 59.842 45.833 0.00 0.00 0.00 2.43
3597 3757 3.595190 ACTTACCCAGCTCCAAAAACT 57.405 42.857 0.00 0.00 0.00 2.66
3601 3768 1.215423 ACCCAGCTCCAAAAACTGAGT 59.785 47.619 0.00 0.00 33.10 3.41
3605 3772 0.040067 GCTCCAAAAACTGAGTGCCG 60.040 55.000 0.00 0.00 0.00 5.69
3611 3778 1.507141 AAAACTGAGTGCCGGCTTCG 61.507 55.000 29.70 20.63 0.00 3.79
3639 3806 5.163602 CGTGCCTAGTTTCTTCAGAGATACT 60.164 44.000 5.19 5.19 43.63 2.12
3640 3807 6.038382 CGTGCCTAGTTTCTTCAGAGATACTA 59.962 42.308 6.58 6.58 40.82 1.82
3693 3861 2.002018 TTTCACAAGGGCGGGAAGGT 62.002 55.000 0.00 0.00 0.00 3.50
3694 3862 2.672996 CACAAGGGCGGGAAGGTG 60.673 66.667 0.00 0.00 0.00 4.00
3695 3863 4.660938 ACAAGGGCGGGAAGGTGC 62.661 66.667 0.00 0.00 0.00 5.01
3701 3869 2.908015 GCGGGAAGGTGCCATCTA 59.092 61.111 0.00 0.00 0.00 1.98
3702 3870 1.523938 GCGGGAAGGTGCCATCTAC 60.524 63.158 0.00 0.00 0.00 2.59
3703 3871 1.972660 GCGGGAAGGTGCCATCTACT 61.973 60.000 0.00 0.00 0.00 2.57
3704 3872 0.179073 CGGGAAGGTGCCATCTACTG 60.179 60.000 0.00 0.00 0.00 2.74
3708 3876 2.766828 GGAAGGTGCCATCTACTGTACT 59.233 50.000 0.00 0.00 0.00 2.73
3709 3877 3.958798 GGAAGGTGCCATCTACTGTACTA 59.041 47.826 0.00 0.00 0.00 1.82
3711 3879 5.340439 AAGGTGCCATCTACTGTACTAAC 57.660 43.478 0.00 0.00 0.00 2.34
3712 3880 3.705072 AGGTGCCATCTACTGTACTAACC 59.295 47.826 0.00 0.00 0.00 2.85
3713 3881 3.449737 GGTGCCATCTACTGTACTAACCA 59.550 47.826 0.00 0.00 0.00 3.67
3714 3882 4.081309 GGTGCCATCTACTGTACTAACCAA 60.081 45.833 0.00 0.00 0.00 3.67
3715 3883 4.868734 GTGCCATCTACTGTACTAACCAAC 59.131 45.833 0.00 0.00 0.00 3.77
3716 3884 4.110482 GCCATCTACTGTACTAACCAACG 58.890 47.826 0.00 0.00 0.00 4.10
3717 3885 4.142315 GCCATCTACTGTACTAACCAACGA 60.142 45.833 0.00 0.00 0.00 3.85
3718 3886 5.579718 CCATCTACTGTACTAACCAACGAG 58.420 45.833 0.00 0.00 0.00 4.18
3723 3891 2.987149 CTGTACTAACCAACGAGCTGTG 59.013 50.000 0.00 0.00 0.00 3.66
3727 3895 0.105964 TAACCAACGAGCTGTGCACT 59.894 50.000 19.41 0.00 0.00 4.40
3733 3901 2.807045 GAGCTGTGCACTCCGTCG 60.807 66.667 19.41 0.79 0.00 5.12
3802 3970 0.453282 CAGGCTGTTGCGACGAAATG 60.453 55.000 6.28 0.00 40.82 2.32
3866 4034 1.202940 ACAGCAAAAGGGAGGAAGGAC 60.203 52.381 0.00 0.00 0.00 3.85
3892 4060 1.962306 GCCCGTCGCTTTACACCAA 60.962 57.895 0.00 0.00 0.00 3.67
3895 4063 1.489824 CGTCGCTTTACACCAACCG 59.510 57.895 0.00 0.00 0.00 4.44
3901 4069 2.702261 GCTTTACACCAACCGGATACA 58.298 47.619 9.46 0.00 35.59 2.29
3915 4083 4.467082 ACCGGATACAACCAACTGTATACA 59.533 41.667 9.46 5.25 41.48 2.29
3922 4090 4.984161 ACAACCAACTGTATACACACGTAC 59.016 41.667 0.08 0.00 0.00 3.67
3927 4095 4.600012 ACTGTATACACACGTACGTACC 57.400 45.455 22.34 4.57 0.00 3.34
3928 4096 4.000325 ACTGTATACACACGTACGTACCA 59.000 43.478 22.34 7.10 0.00 3.25
3929 4097 4.142902 ACTGTATACACACGTACGTACCAC 60.143 45.833 22.34 13.03 0.00 4.16
3930 4098 2.919666 ATACACACGTACGTACCACC 57.080 50.000 22.34 0.00 0.00 4.61
3931 4099 1.598882 TACACACGTACGTACCACCA 58.401 50.000 22.34 1.50 0.00 4.17
3932 4100 0.030638 ACACACGTACGTACCACCAC 59.969 55.000 22.34 0.00 0.00 4.16
3933 4101 0.664166 CACACGTACGTACCACCACC 60.664 60.000 22.34 0.00 0.00 4.61
3934 4102 1.442520 CACGTACGTACCACCACCG 60.443 63.158 22.34 8.88 0.00 4.94
3935 4103 2.179018 CGTACGTACCACCACCGG 59.821 66.667 19.67 0.00 0.00 5.28
3936 4104 2.573340 GTACGTACCACCACCGGG 59.427 66.667 15.00 0.00 41.29 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.496336 GAGCTGGGGAGCGGCATT 62.496 66.667 1.45 0.00 40.27 3.56
20 21 3.541713 GGTAGGAGCTGGGGAGCG 61.542 72.222 0.00 0.00 40.27 5.03
26 27 1.447643 CCCGATTGGTAGGAGCTGG 59.552 63.158 0.00 0.00 0.00 4.85
34 35 2.184836 CGAACCGCCCGATTGGTA 59.815 61.111 0.00 0.00 37.54 3.25
48 49 1.401318 TTCCCTTGGTGGACGTCGAA 61.401 55.000 9.92 1.79 38.35 3.71
90 91 0.166814 GCCTCATCGTGTTGTTGCTC 59.833 55.000 0.00 0.00 0.00 4.26
102 103 3.113745 CACATTGCCCGCCTCATC 58.886 61.111 0.00 0.00 0.00 2.92
114 115 2.944349 TGCATCACACATATCGCACATT 59.056 40.909 0.00 0.00 0.00 2.71
116 117 2.021355 TGCATCACACATATCGCACA 57.979 45.000 0.00 0.00 0.00 4.57
216 217 5.643379 ACATTTGCCTCATACATTTCGTT 57.357 34.783 0.00 0.00 0.00 3.85
227 228 5.561919 CGCACTAAAACTTACATTTGCCTCA 60.562 40.000 0.00 0.00 0.00 3.86
228 229 4.851558 CGCACTAAAACTTACATTTGCCTC 59.148 41.667 0.00 0.00 0.00 4.70
229 230 4.277423 ACGCACTAAAACTTACATTTGCCT 59.723 37.500 0.00 0.00 0.00 4.75
230 231 4.542735 ACGCACTAAAACTTACATTTGCC 58.457 39.130 0.00 0.00 0.00 4.52
239 241 7.067372 ACCCTAAAACTTAACGCACTAAAACTT 59.933 33.333 0.00 0.00 0.00 2.66
247 249 4.033243 CCGATACCCTAAAACTTAACGCAC 59.967 45.833 0.00 0.00 0.00 5.34
257 259 7.678837 TGTCTTTTCTAACCGATACCCTAAAA 58.321 34.615 0.00 0.00 0.00 1.52
314 316 7.783042 AGAGAAGTATAAACTGCCGAGTATTT 58.217 34.615 0.00 0.00 35.62 1.40
366 368 8.757164 AGGGTCAGAAAAATAAAATTAAAGCG 57.243 30.769 0.00 0.00 0.00 4.68
419 422 8.916628 ACCAGTGCCAAATATTAAATTTTGTT 57.083 26.923 0.00 0.00 32.23 2.83
457 463 1.649171 CGTCGTGTGATGCAGAGTAAC 59.351 52.381 0.00 0.00 0.00 2.50
473 479 2.372040 TTTGGTGTCCACTCCCGTCG 62.372 60.000 0.00 0.00 30.78 5.12
489 495 6.418141 GGAAACACGTGGAATTTCAAATTTG 58.582 36.000 23.46 12.15 34.63 2.32
643 657 2.888534 CCGTAATGACCGGTGGCG 60.889 66.667 14.63 8.88 40.59 5.69
729 747 4.440112 GGCTTTAATGGAATCCTGTTTCGG 60.440 45.833 0.00 0.00 0.00 4.30
825 843 1.347378 GAGGAGGAGGAATGGATGCTC 59.653 57.143 0.00 0.00 45.19 4.26
929 953 2.023223 GTCGTTCCTTTACGCGCCA 61.023 57.895 5.73 0.00 41.16 5.69
931 955 2.389143 CGTCGTTCCTTTACGCGC 59.611 61.111 5.73 0.00 41.16 6.86
1026 1061 0.818938 TGGAAATGTAGTCGCCGCTA 59.181 50.000 0.00 0.00 0.00 4.26
1042 1077 2.363018 CGAGGTGAGGAGGCTGGA 60.363 66.667 0.00 0.00 0.00 3.86
1438 1491 0.725784 CAACACAATTGACGCGGCTC 60.726 55.000 15.80 0.43 0.00 4.70
1486 1539 4.373116 GCACCTCTTGCCGTCCGA 62.373 66.667 0.00 0.00 46.63 4.55
1701 1754 3.510531 AGCAGCATGATCATTCAGGAT 57.489 42.857 5.16 0.00 39.69 3.24
1736 1797 3.003897 GGACAAACCGAAGCAACAACATA 59.996 43.478 0.00 0.00 0.00 2.29
1816 1877 3.273434 CTGGAGAAATTTCATCCGCTGA 58.727 45.455 19.99 7.36 35.78 4.26
1872 1933 9.984190 TGATTTCTCATTTTGAATGAAATGACA 57.016 25.926 8.50 3.73 45.90 3.58
1875 1936 9.647797 TCCTGATTTCTCATTTTGAATGAAATG 57.352 29.630 8.56 4.42 44.51 2.32
1910 1994 7.063662 TGTGCATCAAAATTATCATGTGCTTTC 59.936 33.333 0.00 0.00 32.87 2.62
1911 1995 6.874664 TGTGCATCAAAATTATCATGTGCTTT 59.125 30.769 0.00 0.00 32.87 3.51
1989 2073 9.601217 GTACACAAAGACTGTCTTCCATTATAT 57.399 33.333 22.24 2.60 35.27 0.86
1990 2074 8.590204 TGTACACAAAGACTGTCTTCCATTATA 58.410 33.333 22.24 8.74 35.27 0.98
1991 2075 7.450074 TGTACACAAAGACTGTCTTCCATTAT 58.550 34.615 22.24 4.04 35.27 1.28
1992 2076 6.822442 TGTACACAAAGACTGTCTTCCATTA 58.178 36.000 22.24 9.85 35.27 1.90
1993 2077 5.680619 TGTACACAAAGACTGTCTTCCATT 58.319 37.500 22.24 10.72 35.27 3.16
2023 2107 6.096564 ACACAAAATTTGGCCAATTTCATTGT 59.903 30.769 24.39 24.39 43.20 2.71
2028 2112 5.065731 TCACACACAAAATTTGGCCAATTTC 59.934 36.000 21.26 0.00 43.20 2.17
2116 2200 0.389426 TTCTTACCTCGACTTGCCGC 60.389 55.000 0.00 0.00 0.00 6.53
2147 2231 0.749454 GGCATCGGATGGTTTCAGCT 60.749 55.000 18.96 0.00 0.00 4.24
2178 2262 1.070914 TCATTCAGTGGCACGTTACCA 59.929 47.619 12.71 2.88 33.84 3.25
2179 2263 1.803334 TCATTCAGTGGCACGTTACC 58.197 50.000 12.71 0.00 0.00 2.85
2181 2265 3.006940 GGATTCATTCAGTGGCACGTTA 58.993 45.455 12.71 1.33 0.00 3.18
2182 2266 1.812571 GGATTCATTCAGTGGCACGTT 59.187 47.619 12.71 0.00 0.00 3.99
2183 2267 1.003580 AGGATTCATTCAGTGGCACGT 59.996 47.619 12.71 0.00 0.00 4.49
2184 2268 1.399440 CAGGATTCATTCAGTGGCACG 59.601 52.381 12.71 7.55 0.00 5.34
2186 2270 3.054213 TGATCAGGATTCATTCAGTGGCA 60.054 43.478 0.00 0.00 0.00 4.92
2187 2271 3.548770 TGATCAGGATTCATTCAGTGGC 58.451 45.455 0.00 0.00 0.00 5.01
2188 2272 5.191426 AGTTGATCAGGATTCATTCAGTGG 58.809 41.667 0.00 0.00 0.00 4.00
2190 2274 5.191323 AGGAGTTGATCAGGATTCATTCAGT 59.809 40.000 0.00 0.00 0.00 3.41
2192 2276 5.397221 GGAGGAGTTGATCAGGATTCATTCA 60.397 44.000 0.00 0.00 0.00 2.57
2193 2277 5.062528 GGAGGAGTTGATCAGGATTCATTC 58.937 45.833 0.00 0.00 0.00 2.67
2194 2278 4.725810 AGGAGGAGTTGATCAGGATTCATT 59.274 41.667 0.00 0.00 0.00 2.57
2195 2279 4.305524 AGGAGGAGTTGATCAGGATTCAT 58.694 43.478 0.00 0.00 0.00 2.57
2201 2285 2.465813 ACAGAGGAGGAGTTGATCAGG 58.534 52.381 0.00 0.00 0.00 3.86
2232 2316 1.558756 AGCTTCATGGAGAGGAACTGG 59.441 52.381 4.75 0.00 41.55 4.00
2316 2400 0.668535 GAACAGCAGGGGTGTGTTTC 59.331 55.000 1.45 0.00 43.73 2.78
2321 2405 0.250901 GTGATGAACAGCAGGGGTGT 60.251 55.000 0.00 0.00 46.58 4.16
2340 2424 2.960129 GTTACGGCGCGATGAGGG 60.960 66.667 12.10 0.00 0.00 4.30
2342 2426 2.277692 TCGTTACGGCGCGATGAG 60.278 61.111 12.10 0.00 31.76 2.90
2343 2427 2.277692 CTCGTTACGGCGCGATGA 60.278 61.111 12.10 5.79 36.50 2.92
2364 2448 5.713861 ACGGACAAGGTGAGTAAGTAACTAT 59.286 40.000 0.00 0.00 39.07 2.12
2366 2450 3.893813 ACGGACAAGGTGAGTAAGTAACT 59.106 43.478 0.00 0.00 42.80 2.24
2500 2584 1.298993 CACTGGCTCTCCATGCTGT 59.701 57.895 0.00 0.00 42.51 4.40
2624 2711 3.077359 CGGAATTCTGAAGGCAAGAGTT 58.923 45.455 8.73 0.00 0.00 3.01
2626 2713 2.417933 CACGGAATTCTGAAGGCAAGAG 59.582 50.000 21.21 0.00 0.00 2.85
2643 2730 4.054455 CGACGCGAACAACCACGG 62.054 66.667 15.93 0.00 0.00 4.94
2689 2777 4.154195 GCACAACGAAACTGTATCAGGATT 59.846 41.667 0.00 0.00 35.51 3.01
2690 2778 3.684788 GCACAACGAAACTGTATCAGGAT 59.315 43.478 0.00 0.00 35.51 3.24
2691 2779 3.064207 GCACAACGAAACTGTATCAGGA 58.936 45.455 0.00 0.00 35.51 3.86
2915 3022 5.431765 GGCTAGAACTCCATTTTCATCTGA 58.568 41.667 0.00 0.00 0.00 3.27
2965 3072 5.562506 TTCTTCCTATGTACAGACTGTCG 57.437 43.478 12.39 0.34 0.00 4.35
2969 3076 7.962995 TCTTGATTCTTCCTATGTACAGACT 57.037 36.000 0.33 0.00 0.00 3.24
3075 3199 5.554636 CAGAATATGACACAAGAAACTCGC 58.445 41.667 0.00 0.00 0.00 5.03
3182 3316 4.202121 ACACACACTGTAACTGATCGTTCT 60.202 41.667 6.27 0.00 37.05 3.01
3299 3452 4.141779 GGAAATTCTGTATACTGACGGGGT 60.142 45.833 11.60 0.00 0.00 4.95
3314 3467 4.582973 AGCTAAGCTCCAAGGAAATTCT 57.417 40.909 0.00 0.00 30.62 2.40
3343 3497 0.309612 CGCAACAAACGGCTTAAGGT 59.690 50.000 4.29 0.00 0.00 3.50
3514 3669 2.584418 CAGCGTGAGATCCAGCGG 60.584 66.667 0.00 0.00 34.34 5.52
3566 3726 0.623324 TGGGTAAGTATGGCAGGGCT 60.623 55.000 0.00 0.00 0.00 5.19
3567 3727 0.179018 CTGGGTAAGTATGGCAGGGC 60.179 60.000 0.00 0.00 0.00 5.19
3569 3729 0.839946 AGCTGGGTAAGTATGGCAGG 59.160 55.000 0.00 0.00 0.00 4.85
3570 3730 1.202698 GGAGCTGGGTAAGTATGGCAG 60.203 57.143 0.00 0.00 0.00 4.85
3571 3731 0.837272 GGAGCTGGGTAAGTATGGCA 59.163 55.000 0.00 0.00 0.00 4.92
3572 3732 0.837272 TGGAGCTGGGTAAGTATGGC 59.163 55.000 0.00 0.00 0.00 4.40
3574 3734 5.010282 AGTTTTTGGAGCTGGGTAAGTATG 58.990 41.667 0.00 0.00 0.00 2.39
3575 3735 5.010282 CAGTTTTTGGAGCTGGGTAAGTAT 58.990 41.667 0.00 0.00 0.00 2.12
3578 3738 3.486383 TCAGTTTTTGGAGCTGGGTAAG 58.514 45.455 0.00 0.00 0.00 2.34
3579 3739 3.117663 ACTCAGTTTTTGGAGCTGGGTAA 60.118 43.478 0.00 0.00 41.61 2.85
3580 3740 2.441750 ACTCAGTTTTTGGAGCTGGGTA 59.558 45.455 0.00 0.00 41.61 3.69
3581 3741 1.215423 ACTCAGTTTTTGGAGCTGGGT 59.785 47.619 0.00 0.00 38.94 4.51
3582 3742 1.610522 CACTCAGTTTTTGGAGCTGGG 59.389 52.381 0.00 0.00 36.82 4.45
3584 3744 1.000938 GGCACTCAGTTTTTGGAGCTG 60.001 52.381 0.00 0.00 34.48 4.24
3585 3745 1.322442 GGCACTCAGTTTTTGGAGCT 58.678 50.000 0.00 0.00 34.48 4.09
3586 3746 0.040067 CGGCACTCAGTTTTTGGAGC 60.040 55.000 0.00 0.00 34.48 4.70
3587 3747 0.593128 CCGGCACTCAGTTTTTGGAG 59.407 55.000 0.00 0.00 37.18 3.86
3588 3748 1.452145 GCCGGCACTCAGTTTTTGGA 61.452 55.000 24.80 0.00 0.00 3.53
3589 3749 1.007387 GCCGGCACTCAGTTTTTGG 60.007 57.895 24.80 0.00 0.00 3.28
3591 3751 0.668535 GAAGCCGGCACTCAGTTTTT 59.331 50.000 31.54 10.77 0.00 1.94
3593 3753 1.961277 CGAAGCCGGCACTCAGTTT 60.961 57.895 31.54 12.51 0.00 2.66
3594 3754 2.357517 CGAAGCCGGCACTCAGTT 60.358 61.111 31.54 13.38 0.00 3.16
3639 3806 2.989909 TGCAGCTACGGTAGTACAGTA 58.010 47.619 16.05 11.98 0.00 2.74
3640 3807 1.830279 TGCAGCTACGGTAGTACAGT 58.170 50.000 16.05 10.94 0.00 3.55
3693 3861 4.381185 CGTTGGTTAGTACAGTAGATGGCA 60.381 45.833 0.00 0.00 0.00 4.92
3694 3862 4.110482 CGTTGGTTAGTACAGTAGATGGC 58.890 47.826 0.00 0.00 0.00 4.40
3695 3863 5.571784 TCGTTGGTTAGTACAGTAGATGG 57.428 43.478 0.00 0.00 0.00 3.51
3697 3865 4.948621 AGCTCGTTGGTTAGTACAGTAGAT 59.051 41.667 0.00 0.00 0.00 1.98
3698 3866 4.155462 CAGCTCGTTGGTTAGTACAGTAGA 59.845 45.833 0.00 0.00 0.00 2.59
3699 3867 4.082895 ACAGCTCGTTGGTTAGTACAGTAG 60.083 45.833 0.00 0.00 0.00 2.57
3700 3868 3.822735 ACAGCTCGTTGGTTAGTACAGTA 59.177 43.478 0.00 0.00 0.00 2.74
3701 3869 2.626743 ACAGCTCGTTGGTTAGTACAGT 59.373 45.455 0.00 0.00 0.00 3.55
3702 3870 2.987149 CACAGCTCGTTGGTTAGTACAG 59.013 50.000 0.00 0.00 0.00 2.74
3703 3871 2.864882 GCACAGCTCGTTGGTTAGTACA 60.865 50.000 0.00 0.00 0.00 2.90
3704 3872 1.725164 GCACAGCTCGTTGGTTAGTAC 59.275 52.381 0.00 0.00 0.00 2.73
3708 3876 0.105964 AGTGCACAGCTCGTTGGTTA 59.894 50.000 21.04 0.00 0.00 2.85
3709 3877 1.153168 AGTGCACAGCTCGTTGGTT 60.153 52.632 21.04 0.00 0.00 3.67
3711 3879 2.320587 GGAGTGCACAGCTCGTTGG 61.321 63.158 21.04 0.00 34.00 3.77
3712 3880 2.661566 CGGAGTGCACAGCTCGTTG 61.662 63.158 21.04 0.00 34.00 4.10
3713 3881 2.356313 CGGAGTGCACAGCTCGTT 60.356 61.111 21.04 0.00 34.00 3.85
3714 3882 3.606662 ACGGAGTGCACAGCTCGT 61.607 61.111 21.04 18.41 42.51 4.18
3757 3925 2.742116 TACATTCTCCGGGCTGGGC 61.742 63.158 13.58 0.00 38.76 5.36
3758 3926 1.146263 GTACATTCTCCGGGCTGGG 59.854 63.158 13.58 3.32 38.76 4.45
3759 3927 1.227263 CGTACATTCTCCGGGCTGG 60.227 63.158 5.83 5.83 40.09 4.85
3760 3928 1.883084 GCGTACATTCTCCGGGCTG 60.883 63.158 0.00 0.00 0.00 4.85
3761 3929 2.499685 GCGTACATTCTCCGGGCT 59.500 61.111 0.00 0.00 0.00 5.19
3792 3960 3.181377 TCATTTTGTTTGCATTTCGTCGC 59.819 39.130 0.00 0.00 0.00 5.19
3802 3970 3.679502 GGTGGTGCTATCATTTTGTTTGC 59.320 43.478 0.00 0.00 0.00 3.68
3835 4003 0.394938 TTTTGCTGTCAGTCCGGCTA 59.605 50.000 0.00 0.00 0.00 3.93
3840 4008 1.528129 CTCCCTTTTGCTGTCAGTCC 58.472 55.000 0.93 0.00 0.00 3.85
3892 4060 4.467082 TGTATACAGTTGGTTGTATCCGGT 59.533 41.667 0.08 0.00 41.92 5.28
3895 4063 5.290158 CGTGTGTATACAGTTGGTTGTATCC 59.710 44.000 5.62 0.00 41.92 2.59
3901 4069 4.229096 CGTACGTGTGTATACAGTTGGTT 58.771 43.478 5.62 0.00 37.52 3.67
3915 4083 1.659794 GGTGGTGGTACGTACGTGT 59.340 57.895 30.25 7.45 0.00 4.49


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

AutoCloner maintained by Alex Coulton.