Multiple sequence alignment - TraesCS3A01G106600

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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 TraesCS3A01G106600 chr3A 100.000 3545 0 0 1 3545 70847476 70851020 0.000000e+00 6547.0
1 TraesCS3A01G106600 chr3B 91.390 2834 141 32 163 2940 99499923 99502709 0.000000e+00 3786.0
2 TraesCS3A01G106600 chr3B 87.342 237 19 7 3313 3539 99503080 99503315 9.760000e-66 261.0
3 TraesCS3A01G106600 chr3B 94.611 167 8 1 1 167 99499637 99499802 1.260000e-64 257.0
4 TraesCS3A01G106600 chr3D 93.155 2469 99 33 346 2785 61802094 61804521 0.000000e+00 3559.0
5 TraesCS3A01G106600 chr3D 87.030 771 67 19 2779 3539 61804609 61805356 0.000000e+00 839.0
6 TraesCS3A01G106600 chr3D 90.449 356 22 5 1 347 61801580 61801932 3.220000e-125 459.0
7 TraesCS3A01G106600 chr4D 71.309 833 181 42 1655 2455 34089867 34090673 1.020000e-35 161.0
8 TraesCS3A01G106600 chr4A 70.923 791 172 42 1697 2455 568193751 568194515 2.220000e-27 134.0
9 TraesCS3A01G106600 chr4A 100.000 28 0 0 249 276 155317715 155317688 6.000000e-03 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 TraesCS3A01G106600 chr3A 70847476 70851020 3544 False 6547.000000 6547 100.000000 1 3545 1 chr3A.!!$F1 3544
1 TraesCS3A01G106600 chr3B 99499637 99503315 3678 False 1434.666667 3786 91.114333 1 3539 3 chr3B.!!$F1 3538
2 TraesCS3A01G106600 chr3D 61801580 61805356 3776 False 1619.000000 3559 90.211333 1 3539 3 chr3D.!!$F1 3538

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
351 649 0.320374 ACCTGCACGCTGCTAGTTTA 59.680 50.0 10.54 0.0 45.31 2.01 F
1449 1796 0.031515 TGGAGAAGATAAGGGGCGGA 60.032 55.0 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 1799 0.250770 GGTCAGGGTCAAACCTCACC 60.251 60.0 0.0 0.0 39.34 4.02 R
3371 3876 0.179034 GTGCCATGACTGAGATCCCC 60.179 60.0 0.0 0.0 0.00 4.81 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
100 109 8.861033 TCGCGTATAGTATGTCTTACATTTTT 57.139 30.769 5.77 0.00 39.88 1.94
181 315 6.532657 GCCAACGTACTATGTTACACTTACAT 59.467 38.462 0.00 0.00 39.44 2.29
209 343 5.627499 TGTCTAACAAATGGTGCAATCTC 57.373 39.130 0.00 0.00 0.00 2.75
225 359 4.141846 GCAATCTCCATGTCTTCTACTCCA 60.142 45.833 0.00 0.00 0.00 3.86
228 362 4.871822 TCTCCATGTCTTCTACTCCATCA 58.128 43.478 0.00 0.00 0.00 3.07
238 373 7.955750 TGTCTTCTACTCCATCATCCCATAATA 59.044 37.037 0.00 0.00 0.00 0.98
329 464 5.394553 CCTCAAGCACAAAAGAGAAAAAGGT 60.395 40.000 0.00 0.00 0.00 3.50
351 649 0.320374 ACCTGCACGCTGCTAGTTTA 59.680 50.000 10.54 0.00 45.31 2.01
368 666 9.944376 TGCTAGTTTATAACAGAAGACTGAATT 57.056 29.630 0.00 0.00 46.03 2.17
394 692 7.966812 TGAAGGCAGAGAAATATTAGCTATCA 58.033 34.615 0.00 0.00 0.00 2.15
421 719 9.912634 TTGTTAAATCTTTCCTTGCTTATCTTG 57.087 29.630 0.00 0.00 0.00 3.02
426 724 5.376625 TCTTTCCTTGCTTATCTTGTGTGT 58.623 37.500 0.00 0.00 0.00 3.72
428 726 5.689383 TTCCTTGCTTATCTTGTGTGTTC 57.311 39.130 0.00 0.00 0.00 3.18
434 732 9.113838 CCTTGCTTATCTTGTGTGTTCTATAAT 57.886 33.333 0.00 0.00 0.00 1.28
442 740 8.362464 TCTTGTGTGTTCTATAATGGTACTCT 57.638 34.615 0.00 0.00 0.00 3.24
476 774 9.643693 CTTTGTGCTAAATCAAGGTCAATTAAT 57.356 29.630 0.00 0.00 0.00 1.40
496 794 4.314440 GTCCGGTCACTGCCAGCA 62.314 66.667 0.00 0.00 0.00 4.41
513 811 4.057428 AGCGTGTCCGGAGCTGTC 62.057 66.667 15.34 0.00 40.07 3.51
542 840 1.056660 CCATGGGCGTATAGGGACTT 58.943 55.000 2.85 0.00 41.75 3.01
593 892 7.885922 TGCTCTAACCATTGGTAAAATCTTACA 59.114 33.333 9.20 0.00 39.43 2.41
596 895 9.967451 TCTAACCATTGGTAAAATCTTACATCA 57.033 29.630 9.20 0.00 39.43 3.07
600 899 8.686334 ACCATTGGTAAAATCTTACATCATGTC 58.314 33.333 6.54 0.00 39.43 3.06
605 904 8.544622 TGGTAAAATCTTACATCATGTCAGGTA 58.455 33.333 0.00 0.00 39.43 3.08
623 922 8.890472 TGTCAGGTAATAGGAATATTAGCCATT 58.110 33.333 11.57 0.00 39.77 3.16
784 1109 1.339929 GGGCAACTTTGACAACCGAAT 59.660 47.619 0.00 0.00 38.18 3.34
842 1189 5.905331 TGCCTATATATATCCCCAAGACCAG 59.095 44.000 0.00 0.00 0.00 4.00
866 1213 1.195115 GATCACCACACCCAGCTCTA 58.805 55.000 0.00 0.00 0.00 2.43
869 1216 1.158705 ACCACACCCAGCTCTACCT 59.841 57.895 0.00 0.00 0.00 3.08
898 1245 3.365666 CGCATTCACATTCTTGAGCTGTT 60.366 43.478 0.00 0.00 0.00 3.16
900 1247 4.082895 GCATTCACATTCTTGAGCTGTTCT 60.083 41.667 0.00 0.00 0.00 3.01
932 1279 3.073874 GCCATTGCATTGCGTTGCG 62.074 57.895 3.84 0.66 45.77 4.85
946 1293 0.944386 GTTGCGAGCTTTCAACCTCA 59.056 50.000 16.59 0.00 37.26 3.86
958 1305 2.851195 TCAACCTCAAAAGAGTCCTGC 58.149 47.619 0.00 0.00 0.00 4.85
1092 1439 3.072468 TACTTCGCCGGGTGGAGG 61.072 66.667 19.80 8.98 37.49 4.30
1449 1796 0.031515 TGGAGAAGATAAGGGGCGGA 60.032 55.000 0.00 0.00 0.00 5.54
1452 1799 2.485657 GGAGAAGATAAGGGGCGGAAAG 60.486 54.545 0.00 0.00 0.00 2.62
1485 1832 3.188786 GACCGCATCGTGCTCACC 61.189 66.667 8.07 0.00 42.25 4.02
1563 1910 2.028190 CTGCTCATCCCTACGCCG 59.972 66.667 0.00 0.00 0.00 6.46
1585 1932 0.325602 CTACCCGGGGTAAGCAACAA 59.674 55.000 27.92 4.13 37.76 2.83
1586 1933 0.325602 TACCCGGGGTAAGCAACAAG 59.674 55.000 27.92 0.00 34.97 3.16
1653 2004 4.246206 CTGACATGCATGGCGCCG 62.246 66.667 29.41 15.73 39.17 6.46
1926 2277 1.738908 GACGAGATATACTCCGGCTCC 59.261 57.143 0.00 0.00 42.18 4.70
2019 2370 0.389817 TGCACATCGTGTACAGCCTC 60.390 55.000 0.00 0.00 35.75 4.70
2372 2723 2.821366 GTGGGACCTGATGCTGCG 60.821 66.667 0.00 0.00 0.00 5.18
2550 2901 2.810400 GCAGGAACAGCACTAGACCAAA 60.810 50.000 0.00 0.00 41.82 3.28
2633 2986 7.795482 CAAATCCATTGCCATTGTAATCAAT 57.205 32.000 0.00 0.00 37.19 2.57
2634 2987 8.215926 CAAATCCATTGCCATTGTAATCAATT 57.784 30.769 0.00 0.00 35.85 2.32
2832 3280 3.791320 TGTCCTCACTCAACCTCCTAAT 58.209 45.455 0.00 0.00 0.00 1.73
2839 3287 6.372937 CCTCACTCAACCTCCTAATCTTTTTC 59.627 42.308 0.00 0.00 0.00 2.29
2860 3308 8.690203 TTTTCTATCCACTCTGATTTGTTTCA 57.310 30.769 0.00 0.00 0.00 2.69
2876 3324 9.590088 GATTTGTTTCAAAAATCAGCAAATCTC 57.410 29.630 15.51 0.00 43.11 2.75
2920 3423 4.400529 AACGAGTGATGCCATACATACA 57.599 40.909 0.00 0.00 39.84 2.29
2945 3448 4.088056 TCCTTTGTCCGATTTTGGTACA 57.912 40.909 0.00 0.00 0.00 2.90
2970 3474 1.254975 ACCGATCACACCGTCCATGA 61.255 55.000 0.00 0.00 0.00 3.07
2980 3484 2.355756 CACCGTCCATGAATAGGCAAAG 59.644 50.000 0.00 0.00 0.00 2.77
3008 3512 3.324556 CCCCAACCATTTGATTGACTGTT 59.675 43.478 0.00 0.00 34.24 3.16
3024 3528 6.862711 TGACTGTTGTATAGAGATCGTAGG 57.137 41.667 0.00 0.00 0.00 3.18
3026 3530 7.225011 TGACTGTTGTATAGAGATCGTAGGAT 58.775 38.462 0.00 0.00 34.96 3.24
3027 3531 8.373220 TGACTGTTGTATAGAGATCGTAGGATA 58.627 37.037 0.00 0.00 31.51 2.59
3029 3533 9.570468 ACTGTTGTATAGAGATCGTAGGATAAA 57.430 33.333 0.00 0.00 31.51 1.40
3064 3568 6.679327 GGAGTAGTTGCCGAAAAGAAATAT 57.321 37.500 0.00 0.00 0.00 1.28
3065 3569 6.487103 GGAGTAGTTGCCGAAAAGAAATATG 58.513 40.000 0.00 0.00 0.00 1.78
3066 3570 6.315393 GGAGTAGTTGCCGAAAAGAAATATGA 59.685 38.462 0.00 0.00 0.00 2.15
3067 3571 7.148306 GGAGTAGTTGCCGAAAAGAAATATGAA 60.148 37.037 0.00 0.00 0.00 2.57
3199 3704 7.310423 GGGGTTTTGCTATTTATCAAGAAACCT 60.310 37.037 12.64 0.00 35.23 3.50
3256 3761 8.857098 CAAATCATTGGATCCAAACATCTAGAT 58.143 33.333 30.28 19.21 39.55 1.98
3265 3770 4.081142 TCCAAACATCTAGATCCTCGCAAA 60.081 41.667 1.03 0.00 0.00 3.68
3277 3782 7.121974 AGATCCTCGCAAATATAAAATCACG 57.878 36.000 0.00 0.00 0.00 4.35
3298 3803 4.677832 ACGACAAATGTTTTATCAAACGGC 59.322 37.500 0.00 0.00 44.76 5.68
3300 3805 5.174035 CGACAAATGTTTTATCAAACGGCAA 59.826 36.000 0.00 0.00 44.76 4.52
3301 3806 6.128956 CGACAAATGTTTTATCAAACGGCAAT 60.129 34.615 0.00 0.00 44.76 3.56
3302 3807 7.116061 ACAAATGTTTTATCAAACGGCAATC 57.884 32.000 0.00 0.00 44.76 2.67
3303 3808 6.128956 ACAAATGTTTTATCAAACGGCAATCG 60.129 34.615 0.00 0.00 44.76 3.34
3304 3809 4.750952 TGTTTTATCAAACGGCAATCGA 57.249 36.364 0.00 0.00 44.76 3.59
3305 3810 5.303747 TGTTTTATCAAACGGCAATCGAT 57.696 34.783 0.00 0.00 44.76 3.59
3306 3811 5.092105 TGTTTTATCAAACGGCAATCGATG 58.908 37.500 0.00 0.00 44.76 3.84
3307 3812 4.955925 TTTATCAAACGGCAATCGATGT 57.044 36.364 0.00 0.00 42.43 3.06
3308 3813 2.830772 ATCAAACGGCAATCGATGTG 57.169 45.000 0.00 0.79 42.43 3.21
3309 3814 0.801872 TCAAACGGCAATCGATGTGG 59.198 50.000 0.00 0.00 42.43 4.17
3310 3815 0.801872 CAAACGGCAATCGATGTGGA 59.198 50.000 0.00 0.00 42.43 4.02
3311 3816 1.401552 CAAACGGCAATCGATGTGGAT 59.598 47.619 0.00 0.00 42.43 3.41
3320 3825 5.602458 CAATCGATGTGGATTGTGGATAG 57.398 43.478 0.00 0.00 45.19 2.08
3328 3833 6.126863 TGTGGATTGTGGATAGAGAAAACT 57.873 37.500 0.00 0.00 0.00 2.66
3355 3860 6.132791 TCTAAGTTGACTCGGCTATAGTTG 57.867 41.667 0.84 0.00 0.00 3.16
3371 3876 6.150140 GCTATAGTTGCTCCCTATCAAAATGG 59.850 42.308 0.84 0.00 0.00 3.16
3372 3877 3.635591 AGTTGCTCCCTATCAAAATGGG 58.364 45.455 0.00 0.00 42.20 4.00
3381 3886 4.660168 CCTATCAAAATGGGGGATCTCAG 58.340 47.826 0.00 0.00 30.00 3.35
3390 3904 0.179034 GGGGATCTCAGTCATGGCAC 60.179 60.000 0.00 0.00 0.00 5.01
3397 3918 1.136891 CTCAGTCATGGCACCGATGTA 59.863 52.381 0.00 0.00 0.00 2.29
3426 3947 8.970691 ATCAAAACAATGTTAACACTAGCATC 57.029 30.769 11.22 0.00 29.48 3.91
3432 3953 5.818136 ATGTTAACACTAGCATCGCAAAT 57.182 34.783 11.22 0.00 0.00 2.32
3450 3971 4.840239 GCAAATGAAACAAAAATGCTACGC 59.160 37.500 0.00 0.00 0.00 4.42
3491 4012 1.564348 GCAGATTTCCTCCTACCCCAA 59.436 52.381 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.519455 GAGGTTGGAGCCGACATCG 60.519 63.158 9.05 0.00 32.55 3.84
69 78 9.454435 TGTAAGACATACTATACGCGATACGGC 62.454 44.444 15.93 0.00 39.80 5.68
75 84 8.748582 CAAAAATGTAAGACATACTATACGCGA 58.251 33.333 15.93 0.00 37.97 5.87
181 315 7.987750 TTGCACCATTTGTTAGACATACTAA 57.012 32.000 0.00 0.00 38.56 2.24
200 334 4.764172 AGTAGAAGACATGGAGATTGCAC 58.236 43.478 0.00 0.00 0.00 4.57
209 343 4.262808 GGGATGATGGAGTAGAAGACATGG 60.263 50.000 0.00 0.00 0.00 3.66
276 411 7.117397 ACATGAGTGGTAGCTAGTACTCTTTA 58.883 38.462 25.80 14.20 40.07 1.85
351 649 6.716628 TGCCTTCAAATTCAGTCTTCTGTTAT 59.283 34.615 0.00 0.00 41.91 1.89
368 666 8.432013 TGATAGCTAATATTTCTCTGCCTTCAA 58.568 33.333 0.00 0.00 0.00 2.69
403 701 5.376625 ACACACAAGATAAGCAAGGAAAGA 58.623 37.500 0.00 0.00 0.00 2.52
412 710 8.438676 ACCATTATAGAACACACAAGATAAGC 57.561 34.615 0.00 0.00 0.00 3.09
434 732 7.241042 AGCACAAAGTTAATAGAGAGTACCA 57.759 36.000 0.00 0.00 0.00 3.25
442 740 9.515226 ACCTTGATTTAGCACAAAGTTAATAGA 57.485 29.630 0.00 0.00 0.00 1.98
476 774 1.897423 CTGGCAGTGACCGGACATA 59.103 57.895 9.46 0.00 38.48 2.29
496 794 4.057428 GACAGCTCCGGACACGCT 62.057 66.667 10.73 10.73 39.22 5.07
505 803 3.628280 GACACGTCCGGACAGCTCC 62.628 68.421 32.80 14.27 0.00 4.70
506 804 2.126424 GACACGTCCGGACAGCTC 60.126 66.667 32.80 18.97 0.00 4.09
507 805 3.681835 GGACACGTCCGGACAGCT 61.682 66.667 32.80 14.63 40.36 4.24
516 814 0.386476 TATACGCCCATGGACACGTC 59.614 55.000 24.42 3.20 39.78 4.34
517 815 0.387929 CTATACGCCCATGGACACGT 59.612 55.000 24.23 24.23 42.22 4.49
518 816 0.319555 CCTATACGCCCATGGACACG 60.320 60.000 15.22 16.31 0.00 4.49
519 817 0.034896 CCCTATACGCCCATGGACAC 59.965 60.000 15.22 0.78 0.00 3.67
520 818 0.105401 TCCCTATACGCCCATGGACA 60.105 55.000 15.22 0.00 0.00 4.02
555 853 5.172687 TGGTTAGAGCATGTTCAACCATA 57.827 39.130 26.88 15.25 42.73 2.74
563 862 6.909550 TTTTACCAATGGTTAGAGCATGTT 57.090 33.333 11.41 0.00 36.31 2.71
596 895 8.449423 TGGCTAATATTCCTATTACCTGACAT 57.551 34.615 0.00 0.00 30.43 3.06
715 1039 4.996793 AGCCCCAAAATTTTAAAATGGCT 58.003 34.783 25.17 25.17 37.73 4.75
728 1052 1.754226 GTTGTCACAAGAGCCCCAAAA 59.246 47.619 0.00 0.00 0.00 2.44
817 1164 6.276248 TGGTCTTGGGGATATATATAGGCAA 58.724 40.000 0.00 0.00 0.00 4.52
830 1177 2.788230 ATCCTGGCTGGTCTTGGGGA 62.788 60.000 10.44 0.00 37.07 4.81
842 1189 2.044946 GGGTGTGGTGATCCTGGC 60.045 66.667 0.00 0.00 34.23 4.85
922 1269 0.310543 TTGAAAGCTCGCAACGCAAT 59.689 45.000 0.00 0.00 0.00 3.56
927 1274 3.755697 GAGGTTGAAAGCTCGCAAC 57.244 52.632 18.35 18.35 42.77 4.17
946 1293 2.165998 GCAATGGAGCAGGACTCTTTT 58.834 47.619 0.00 0.00 45.48 2.27
958 1305 2.189594 TGGAGTGACAAGCAATGGAG 57.810 50.000 0.00 0.00 0.00 3.86
1092 1439 4.185059 GGGTCGTCGTCGTAGGCC 62.185 72.222 0.00 0.00 38.33 5.19
1341 1688 3.688673 AGACAAGCAAGATAAAGCAGAGC 59.311 43.478 0.00 0.00 0.00 4.09
1449 1796 1.850345 TCAGGGTCAAACCTCACCTTT 59.150 47.619 0.00 0.00 39.34 3.11
1452 1799 0.250770 GGTCAGGGTCAAACCTCACC 60.251 60.000 0.00 0.00 39.34 4.02
1551 1898 0.595095 GGTAGTACGGCGTAGGGATG 59.405 60.000 21.64 0.00 0.00 3.51
1563 1910 1.134699 GTTGCTTACCCCGGGTAGTAC 60.135 57.143 21.85 10.34 39.52 2.73
1585 1932 0.825010 CTTGCTCTGGTTGGTTGGCT 60.825 55.000 0.00 0.00 0.00 4.75
1586 1933 1.662044 CTTGCTCTGGTTGGTTGGC 59.338 57.895 0.00 0.00 0.00 4.52
1653 2004 0.321653 AGTCCCGATCAAACCTGCAC 60.322 55.000 0.00 0.00 0.00 4.57
1728 2079 2.432628 GCGACCGTGACCTGGAAG 60.433 66.667 0.00 0.00 0.00 3.46
2019 2370 2.612115 AGCCCCAGGTCCTTGGAG 60.612 66.667 10.73 2.25 40.87 3.86
2175 2526 0.902984 TGGTGCGGATGTACTCCTGT 60.903 55.000 8.96 0.00 42.47 4.00
2350 2701 2.124983 CATCAGGTCCCACAGCCG 60.125 66.667 0.00 0.00 0.00 5.52
2372 2723 0.723981 GATGTTGAGCTTCACCTCGC 59.276 55.000 0.00 0.00 34.56 5.03
2532 2883 3.944087 AGATTTGGTCTAGTGCTGTTCC 58.056 45.455 0.00 0.00 34.69 3.62
2627 2980 5.579511 CGGTTACGTACTTCCTCAATTGATT 59.420 40.000 8.96 0.00 34.81 2.57
2628 2981 5.105635 TCGGTTACGTACTTCCTCAATTGAT 60.106 40.000 8.96 0.00 41.85 2.57
2629 2982 4.218200 TCGGTTACGTACTTCCTCAATTGA 59.782 41.667 8.12 8.12 41.85 2.57
2630 2983 4.487948 TCGGTTACGTACTTCCTCAATTG 58.512 43.478 0.00 0.00 41.85 2.32
2631 2984 4.789012 TCGGTTACGTACTTCCTCAATT 57.211 40.909 0.00 0.00 41.85 2.32
2632 2985 4.202090 GGATCGGTTACGTACTTCCTCAAT 60.202 45.833 0.00 0.00 41.85 2.57
2633 2986 3.129287 GGATCGGTTACGTACTTCCTCAA 59.871 47.826 0.00 0.00 41.85 3.02
2634 2987 2.684881 GGATCGGTTACGTACTTCCTCA 59.315 50.000 0.00 0.00 41.85 3.86
2740 3093 7.596494 TGCAAAGAAGACTTATTCCAAGAATG 58.404 34.615 0.00 0.00 35.05 2.67
2809 3257 2.408565 AGGAGGTTGAGTGAGGACAAA 58.591 47.619 0.00 0.00 0.00 2.83
2812 3260 4.027437 AGATTAGGAGGTTGAGTGAGGAC 58.973 47.826 0.00 0.00 0.00 3.85
2832 3280 8.924511 AACAAATCAGAGTGGATAGAAAAAGA 57.075 30.769 0.00 0.00 0.00 2.52
2839 3287 9.918630 ATTTTTGAAACAAATCAGAGTGGATAG 57.081 29.630 0.00 0.00 0.00 2.08
2860 3308 9.774413 AAGAAATGAAGAGATTTGCTGATTTTT 57.226 25.926 0.00 0.00 0.00 1.94
2897 3345 4.808895 TGTATGTATGGCATCACTCGTTTC 59.191 41.667 1.65 0.00 38.94 2.78
2898 3346 4.765273 TGTATGTATGGCATCACTCGTTT 58.235 39.130 1.65 0.00 38.94 3.60
2900 3348 4.119862 GTTGTATGTATGGCATCACTCGT 58.880 43.478 1.65 0.00 38.94 4.18
2901 3349 4.119136 TGTTGTATGTATGGCATCACTCG 58.881 43.478 1.65 0.00 38.94 4.18
2920 3423 3.895041 ACCAAAATCGGACAAAGGATGTT 59.105 39.130 0.00 0.00 44.12 2.71
2945 3448 0.971386 ACGGTGTGATCGGTAGGTTT 59.029 50.000 0.00 0.00 0.00 3.27
2980 3484 1.004679 CAAATGGTTGGGGCTGCAC 60.005 57.895 0.50 0.00 0.00 4.57
3026 3530 7.333423 GGCAACTACTCCGCATATGATATTTTA 59.667 37.037 6.97 0.00 0.00 1.52
3027 3531 6.149474 GGCAACTACTCCGCATATGATATTTT 59.851 38.462 6.97 0.00 0.00 1.82
3029 3533 5.178797 GGCAACTACTCCGCATATGATATT 58.821 41.667 6.97 0.00 0.00 1.28
3032 3536 2.610479 CGGCAACTACTCCGCATATGAT 60.610 50.000 6.97 0.00 39.14 2.45
3038 3542 0.249953 TTTTCGGCAACTACTCCGCA 60.250 50.000 0.00 0.00 44.91 5.69
3039 3543 0.442699 CTTTTCGGCAACTACTCCGC 59.557 55.000 0.00 0.00 44.91 5.54
3040 3544 2.074547 TCTTTTCGGCAACTACTCCG 57.925 50.000 0.00 0.00 46.52 4.63
3083 3587 6.212388 TGGGGTGCATTATTGTAATTTTGTCT 59.788 34.615 0.00 0.00 0.00 3.41
3091 3595 5.247110 ACAACATTGGGGTGCATTATTGTAA 59.753 36.000 0.00 0.00 0.00 2.41
3098 3602 0.602562 CGACAACATTGGGGTGCATT 59.397 50.000 0.00 0.00 0.00 3.56
3148 3653 7.491372 CCATTTTGGTGAGATCAAAAGATGATG 59.509 37.037 0.00 2.14 44.12 3.07
3149 3654 7.364408 CCCATTTTGGTGAGATCAAAAGATGAT 60.364 37.037 0.00 0.00 44.12 2.45
3216 3721 8.774890 TCCAATGATTTGTTACCATTGATTTG 57.225 30.769 13.83 0.73 45.91 2.32
3224 3729 6.268617 TGTTTGGATCCAATGATTTGTTACCA 59.731 34.615 27.53 5.29 35.70 3.25
3256 3761 5.813157 TGTCGTGATTTTATATTTGCGAGGA 59.187 36.000 0.00 0.00 0.00 3.71
3259 3764 7.965655 ACATTTGTCGTGATTTTATATTTGCGA 59.034 29.630 0.00 0.00 0.00 5.10
3277 3782 6.517914 TTGCCGTTTGATAAAACATTTGTC 57.482 33.333 6.49 0.00 33.08 3.18
3300 3805 4.835056 TCTCTATCCACAATCCACATCGAT 59.165 41.667 0.00 0.00 0.00 3.59
3301 3806 4.215109 TCTCTATCCACAATCCACATCGA 58.785 43.478 0.00 0.00 0.00 3.59
3302 3807 4.590850 TCTCTATCCACAATCCACATCG 57.409 45.455 0.00 0.00 0.00 3.84
3303 3808 6.825721 AGTTTTCTCTATCCACAATCCACATC 59.174 38.462 0.00 0.00 0.00 3.06
3304 3809 6.725364 AGTTTTCTCTATCCACAATCCACAT 58.275 36.000 0.00 0.00 0.00 3.21
3305 3810 6.126863 AGTTTTCTCTATCCACAATCCACA 57.873 37.500 0.00 0.00 0.00 4.17
3306 3811 8.738645 AATAGTTTTCTCTATCCACAATCCAC 57.261 34.615 0.00 0.00 31.24 4.02
3307 3812 9.396022 GAAATAGTTTTCTCTATCCACAATCCA 57.604 33.333 0.00 0.00 38.56 3.41
3308 3813 9.620259 AGAAATAGTTTTCTCTATCCACAATCC 57.380 33.333 0.00 0.00 46.88 3.01
3320 3825 8.648968 CCGAGTCAACTTAGAAATAGTTTTCTC 58.351 37.037 4.36 0.00 46.88 2.87
3328 3833 8.461249 ACTATAGCCGAGTCAACTTAGAAATA 57.539 34.615 0.00 0.00 0.00 1.40
3355 3860 1.499007 TCCCCCATTTTGATAGGGAGC 59.501 52.381 0.00 0.00 45.80 4.70
3371 3876 0.179034 GTGCCATGACTGAGATCCCC 60.179 60.000 0.00 0.00 0.00 4.81
3372 3877 0.179034 GGTGCCATGACTGAGATCCC 60.179 60.000 0.00 0.00 0.00 3.85
3381 3886 2.309528 TTCTACATCGGTGCCATGAC 57.690 50.000 0.00 0.00 0.00 3.06
3390 3904 9.619316 TTAACATTGTTTTGATTTCTACATCGG 57.381 29.630 7.45 0.00 0.00 4.18
3397 3918 9.463443 GCTAGTGTTAACATTGTTTTGATTTCT 57.537 29.630 12.26 1.90 0.00 2.52
3426 3947 5.065661 CGTAGCATTTTTGTTTCATTTGCG 58.934 37.500 0.00 0.00 33.99 4.85
3450 3971 2.273557 CGGTAAGTTGGGTTCCGTATG 58.726 52.381 0.00 0.00 36.99 2.39
3452 3973 0.607620 CCGGTAAGTTGGGTTCCGTA 59.392 55.000 0.00 0.00 39.62 4.02
3459 3980 1.743394 GAAATCTGCCGGTAAGTTGGG 59.257 52.381 1.90 0.00 0.00 4.12
3506 4028 6.410540 TGAATGTTTTTGGGGTAAATATGCC 58.589 36.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.