Multiple sequence alignment - TraesCS1A01G338700

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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 TraesCS1A01G338700 chr1A 100.000 2723 0 0 1 2723 528104055 528101333 0.000000e+00 4992
1 TraesCS1A01G338700 chr1D 91.500 2353 116 40 420 2722 430482731 430480413 0.000000e+00 3160
2 TraesCS1A01G338700 chr1D 86.717 399 32 9 1 398 430483252 430482874 9.010000e-115 424
3 TraesCS1A01G338700 chr1D 76.190 357 71 12 11 365 430483762 430483418 2.790000e-40 176
4 TraesCS1A01G338700 chr1B 91.809 1880 81 40 423 2278 581596878 581595048 0.000000e+00 2551
5 TraesCS1A01G338700 chr1B 89.698 398 32 5 1 398 581597680 581597292 1.460000e-137 499
6 TraesCS1A01G338700 chr1B 82.338 402 36 21 2332 2722 581594630 581594253 1.570000e-82 316
7 TraesCS1A01G338700 chr3D 76.147 763 106 53 1017 1743 378529343 378530065 5.620000e-87 331
8 TraesCS1A01G338700 chr3A 76.344 744 101 51 1017 1724 502490408 502491112 2.020000e-86 329
9 TraesCS1A01G338700 chr3B 75.393 764 119 46 1017 1743 493584578 493585309 3.410000e-79 305


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 TraesCS1A01G338700 chr1A 528101333 528104055 2722 True 4992.000000 4992 100.000000 1 2723 1 chr1A.!!$R1 2722
1 TraesCS1A01G338700 chr1D 430480413 430483762 3349 True 1253.333333 3160 84.802333 1 2722 3 chr1D.!!$R1 2721
2 TraesCS1A01G338700 chr1B 581594253 581597680 3427 True 1122.000000 2551 87.948333 1 2722 3 chr1B.!!$R1 2721
3 TraesCS1A01G338700 chr3D 378529343 378530065 722 False 331.000000 331 76.147000 1017 1743 1 chr3D.!!$F1 726
4 TraesCS1A01G338700 chr3A 502490408 502491112 704 False 329.000000 329 76.344000 1017 1724 1 chr3A.!!$F1 707
5 TraesCS1A01G338700 chr3B 493584578 493585309 731 False 305.000000 305 75.393000 1017 1743 1 chr3B.!!$F1 726

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
78 593 0.674895 CTTGGCCTTCTCCTTCACCG 60.675 60.0 3.32 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 2918 0.304705 GCACAATTAGCACCGATCCG 59.695 55.0 0.0 0.0 0.0 4.18 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
56 57 1.754803 CATAACTGCAGTCTACCCCGA 59.245 52.381 21.95 0.00 0.00 5.14
61 62 1.988406 GCAGTCTACCCCGACCCTT 60.988 63.158 0.00 0.00 34.46 3.95
78 593 0.674895 CTTGGCCTTCTCCTTCACCG 60.675 60.000 3.32 0.00 0.00 4.94
86 601 1.847328 TCTCCTTCACCGCACATCTA 58.153 50.000 0.00 0.00 0.00 1.98
109 624 2.120312 GTTTCCCCCTTTTTGGTCCAA 58.880 47.619 0.00 0.00 0.00 3.53
110 625 2.708861 GTTTCCCCCTTTTTGGTCCAAT 59.291 45.455 4.80 0.00 0.00 3.16
111 626 2.022718 TCCCCCTTTTTGGTCCAATG 57.977 50.000 4.80 0.00 0.00 2.82
112 627 1.221781 TCCCCCTTTTTGGTCCAATGT 59.778 47.619 4.80 0.00 0.00 2.71
113 628 1.623311 CCCCCTTTTTGGTCCAATGTC 59.377 52.381 4.80 0.00 0.00 3.06
114 629 1.623311 CCCCTTTTTGGTCCAATGTCC 59.377 52.381 4.80 0.00 0.00 4.02
115 630 2.324541 CCCTTTTTGGTCCAATGTCCA 58.675 47.619 4.80 0.00 0.00 4.02
116 631 2.905736 CCCTTTTTGGTCCAATGTCCAT 59.094 45.455 4.80 0.00 33.50 3.41
117 632 3.055891 CCCTTTTTGGTCCAATGTCCATC 60.056 47.826 4.80 0.00 33.50 3.51
118 633 3.834231 CCTTTTTGGTCCAATGTCCATCT 59.166 43.478 4.80 0.00 33.50 2.90
119 634 4.322198 CCTTTTTGGTCCAATGTCCATCTG 60.322 45.833 4.80 0.00 33.50 2.90
120 635 3.805066 TTTGGTCCAATGTCCATCTGA 57.195 42.857 4.80 0.00 33.50 3.27
121 636 4.320546 TTTGGTCCAATGTCCATCTGAT 57.679 40.909 4.80 0.00 33.50 2.90
173 688 2.125512 CCGCCTTCTCCTTCACCG 60.126 66.667 0.00 0.00 0.00 4.94
179 694 2.788191 CTTCTCCTTCACCGCGCCTT 62.788 60.000 0.00 0.00 0.00 4.35
191 706 2.548295 GCGCCTTTGACGTTTCCCA 61.548 57.895 0.00 0.00 0.00 4.37
259 775 2.646175 CCTCGACCTCCGCCTTCAA 61.646 63.158 0.00 0.00 38.37 2.69
267 783 2.203280 CCGCCTTCAACACACCCA 60.203 61.111 0.00 0.00 0.00 4.51
369 885 0.721718 CTCGCACGTTTTCCCTGATC 59.278 55.000 0.00 0.00 0.00 2.92
395 911 7.613022 CCAGCCAATATGATAACTTGACCATAT 59.387 37.037 0.00 0.00 34.68 1.78
475 1381 7.685155 GCCAGATATAATTTTGCAGGTTCACAT 60.685 37.037 0.00 0.00 0.00 3.21
489 1395 6.258507 GCAGGTTCACATTGATTTGAAAAGTT 59.741 34.615 0.00 0.00 33.58 2.66
496 1402 7.804600 TCACATTGATTTGAAAAGTTGAGATCG 59.195 33.333 0.00 0.00 0.00 3.69
515 1421 2.832129 TCGAAGTGCAGTCCTATCCTTT 59.168 45.455 0.00 0.00 0.00 3.11
516 1422 3.260884 TCGAAGTGCAGTCCTATCCTTTT 59.739 43.478 0.00 0.00 0.00 2.27
520 1426 4.833390 AGTGCAGTCCTATCCTTTTACAC 58.167 43.478 0.00 0.00 0.00 2.90
560 1466 6.611613 TCTTTACATCTCTCACAACTCCAT 57.388 37.500 0.00 0.00 0.00 3.41
660 1566 8.014263 TCACCTCTTATGGTAGGTATATTTCCA 58.986 37.037 0.00 0.00 44.43 3.53
710 1617 4.022068 AGCACAACAATACCATGACAAAGG 60.022 41.667 0.00 0.00 0.00 3.11
711 1618 4.808558 CACAACAATACCATGACAAAGGG 58.191 43.478 0.00 0.00 0.00 3.95
791 1702 2.857748 CTGAAAACCGGCAAGAAAACAC 59.142 45.455 0.00 0.00 0.00 3.32
862 1775 2.171870 ACCTCACGGTCAAAGGAAGAAA 59.828 45.455 7.53 0.00 40.27 2.52
865 1778 4.278419 CCTCACGGTCAAAGGAAGAAAAAT 59.722 41.667 0.00 0.00 31.44 1.82
866 1779 5.472137 CCTCACGGTCAAAGGAAGAAAAATA 59.528 40.000 0.00 0.00 31.44 1.40
867 1780 6.016610 CCTCACGGTCAAAGGAAGAAAAATAA 60.017 38.462 0.00 0.00 31.44 1.40
930 1843 2.439880 CCTTCTTATTCCCACTCCCTCC 59.560 54.545 0.00 0.00 0.00 4.30
950 1865 4.410400 CGTCCCTGAACCCAGCCC 62.410 72.222 0.00 0.00 39.07 5.19
984 1899 0.683973 CTTCTCCATCCATCCCCGAG 59.316 60.000 0.00 0.00 0.00 4.63
1620 2598 1.597461 CTTCTTCCTCCACCCGTCC 59.403 63.158 0.00 0.00 0.00 4.79
1623 2601 3.925914 CTTCCTCCACCCGTCCCCT 62.926 68.421 0.00 0.00 0.00 4.79
1732 2720 4.838486 CGGAGTGAGCGAGCCGAC 62.838 72.222 0.00 0.00 46.29 4.79
1733 2721 3.444805 GGAGTGAGCGAGCCGACT 61.445 66.667 0.00 0.00 0.00 4.18
1735 2723 2.360600 AGTGAGCGAGCCGACTCT 60.361 61.111 0.00 6.10 41.09 3.24
1760 2748 2.397252 GCGTAGAGCGTACGACGT 59.603 61.111 21.65 5.52 44.73 4.34
1761 2749 1.631072 GCGTAGAGCGTACGACGTA 59.369 57.895 21.65 2.97 44.73 3.57
1762 2750 0.649065 GCGTAGAGCGTACGACGTAC 60.649 60.000 24.85 24.85 44.73 3.67
1811 2799 2.407428 TAGCTCGTCCTCGGTGCTG 61.407 63.158 14.65 0.00 42.77 4.41
1812 2800 4.803426 GCTCGTCCTCGGTGCTGG 62.803 72.222 0.00 0.00 37.69 4.85
1813 2801 3.374402 CTCGTCCTCGGTGCTGGT 61.374 66.667 0.00 0.00 37.69 4.00
1837 2825 5.086058 AGTATGTTGTAATTTTTGCTCGCG 58.914 37.500 0.00 0.00 0.00 5.87
1839 2827 3.696898 TGTTGTAATTTTTGCTCGCGTT 58.303 36.364 5.77 0.00 0.00 4.84
1921 2918 2.093235 CCTCCTCTGTTCTTGGTGGATC 60.093 54.545 0.00 0.00 36.83 3.36
1922 2919 1.550524 TCCTCTGTTCTTGGTGGATCG 59.449 52.381 0.00 0.00 0.00 3.69
1923 2920 1.406069 CCTCTGTTCTTGGTGGATCGG 60.406 57.143 0.00 0.00 0.00 4.18
1924 2921 1.550524 CTCTGTTCTTGGTGGATCGGA 59.449 52.381 0.00 0.00 0.00 4.55
1925 2922 2.169352 CTCTGTTCTTGGTGGATCGGAT 59.831 50.000 0.00 0.00 0.00 4.18
1955 2952 7.065803 TGCTAATTGTGCCTAATTTACTCTCAC 59.934 37.037 1.29 0.00 32.79 3.51
2009 3006 9.256477 GTTAATTTCCGGAAAATATTTCCCATC 57.744 33.333 32.03 10.05 36.54 3.51
2089 3100 4.028852 CTACCAAAGCTTAATTTCCGCC 57.971 45.455 0.00 0.00 0.00 6.13
2105 3116 1.217882 CGCCAAGATACGAACCATCC 58.782 55.000 0.00 0.00 0.00 3.51
2113 3124 3.383825 AGATACGAACCATCCACTGTACC 59.616 47.826 0.00 0.00 0.00 3.34
2119 3130 4.331717 CGAACCATCCACTGTACCAATAAC 59.668 45.833 0.00 0.00 0.00 1.89
2154 3165 6.949352 TCAGAATTCTTCCCAAATCTATGC 57.051 37.500 4.86 0.00 0.00 3.14
2214 3226 2.679349 GCCAGAATTCTCCTCAGTGTCC 60.679 54.545 4.57 0.00 0.00 4.02
2215 3227 2.093235 CCAGAATTCTCCTCAGTGTCCC 60.093 54.545 4.57 0.00 0.00 4.46
2217 3229 4.026744 CAGAATTCTCCTCAGTGTCCCTA 58.973 47.826 4.57 0.00 0.00 3.53
2229 3241 5.762279 TCAGTGTCCCTAATTAAATTCCCC 58.238 41.667 0.00 0.00 0.00 4.81
2252 3264 2.794820 AAGGCCGCAAGAGTCAGAGC 62.795 60.000 0.00 0.00 43.02 4.09
2341 3717 2.558359 TCAGAGAGATTGCAGTGTCGAA 59.442 45.455 0.54 0.00 0.00 3.71
2342 3718 2.922387 CAGAGAGATTGCAGTGTCGAAG 59.078 50.000 0.54 0.00 0.00 3.79
2346 3722 2.413453 GAGATTGCAGTGTCGAAGGAAC 59.587 50.000 0.00 0.00 0.00 3.62
2351 3728 1.261619 GCAGTGTCGAAGGAACAACAG 59.738 52.381 0.00 0.00 0.00 3.16
2353 3730 2.540101 CAGTGTCGAAGGAACAACAGAC 59.460 50.000 0.00 0.00 0.00 3.51
2388 3765 0.317160 TCACATCGAGCCGTGACTTT 59.683 50.000 10.17 0.00 37.23 2.66
2392 3769 2.230508 ACATCGAGCCGTGACTTTTAGA 59.769 45.455 0.00 0.00 0.00 2.10
2428 3805 9.822185 ATTGCAACTTTGAATTTCTCTTTTACT 57.178 25.926 0.00 0.00 0.00 2.24
2430 3807 9.730420 TGCAACTTTGAATTTCTCTTTTACTAC 57.270 29.630 0.00 0.00 0.00 2.73
2448 3825 8.856153 TTTACTACATTTATGTGCCTTGAAGA 57.144 30.769 5.64 0.00 41.89 2.87
2453 3830 6.006449 ACATTTATGTGCCTTGAAGAGTTCT 58.994 36.000 0.00 0.00 40.03 3.01
2454 3831 5.947228 TTTATGTGCCTTGAAGAGTTCTG 57.053 39.130 0.00 0.00 0.00 3.02
2459 3836 2.368548 TGCCTTGAAGAGTTCTGTGCTA 59.631 45.455 0.00 0.00 0.00 3.49
2460 3837 2.999355 GCCTTGAAGAGTTCTGTGCTAG 59.001 50.000 0.00 0.00 0.00 3.42
2471 3848 4.109050 GTTCTGTGCTAGTGCTAGTGATC 58.891 47.826 7.90 0.00 40.48 2.92
2472 3849 3.625853 TCTGTGCTAGTGCTAGTGATCT 58.374 45.455 7.90 0.00 40.48 2.75
2473 3850 3.379688 TCTGTGCTAGTGCTAGTGATCTG 59.620 47.826 7.90 2.29 40.48 2.90
2474 3851 2.428530 TGTGCTAGTGCTAGTGATCTGG 59.571 50.000 7.90 0.00 40.48 3.86
2483 3860 0.390492 TAGTGATCTGGCTGGCATCG 59.610 55.000 3.74 0.00 0.00 3.84
2501 3878 1.002502 GGGTTCGGGTCAAAGGAGG 60.003 63.158 0.00 0.00 0.00 4.30
2513 3890 0.179067 AAAGGAGGCGTCGTTGTCAA 60.179 50.000 14.39 0.00 31.13 3.18
2531 3908 3.267860 GCATCCAGCCGAGAAGCG 61.268 66.667 0.00 0.00 38.01 4.68
2547 3924 3.068881 CGGCACAAGGAAGGAGGA 58.931 61.111 0.00 0.00 0.00 3.71
2548 3925 1.078848 CGGCACAAGGAAGGAGGAG 60.079 63.158 0.00 0.00 0.00 3.69
2551 3935 1.528129 GCACAAGGAAGGAGGAGTTG 58.472 55.000 0.00 0.00 0.00 3.16
2569 3953 1.668151 GGACTGTCCAGTTGACCGC 60.668 63.158 21.70 0.00 43.78 5.68
2570 3954 1.668151 GACTGTCCAGTTGACCGCC 60.668 63.158 0.79 0.00 43.78 6.13
2694 4085 2.562912 CTTGGTGGTGCGTGCATC 59.437 61.111 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.175471 TGCAGTTATGATCAAGTTGTCAGAT 58.825 36.000 0.00 0.00 0.00 2.90
27 28 6.036517 GGTAGACTGCAGTTATGATCAAGTTG 59.963 42.308 22.65 0.00 0.00 3.16
56 57 0.772124 TGAAGGAGAAGGCCAAGGGT 60.772 55.000 5.01 0.00 0.00 4.34
61 62 3.068881 CGGTGAAGGAGAAGGCCA 58.931 61.111 5.01 0.00 0.00 5.36
86 601 2.394632 GACCAAAAAGGGGGAAACACT 58.605 47.619 0.00 0.00 43.89 3.55
97 612 4.523943 TCAGATGGACATTGGACCAAAAAG 59.476 41.667 11.82 7.05 42.05 2.27
109 624 6.065976 TGGTGAAGTTAATCAGATGGACAT 57.934 37.500 0.00 0.00 0.00 3.06
110 625 5.497464 TGGTGAAGTTAATCAGATGGACA 57.503 39.130 0.00 0.00 0.00 4.02
111 626 6.115446 TCATGGTGAAGTTAATCAGATGGAC 58.885 40.000 0.00 0.00 0.00 4.02
112 627 6.312141 TCATGGTGAAGTTAATCAGATGGA 57.688 37.500 0.00 0.00 0.00 3.41
113 628 7.423199 CAATCATGGTGAAGTTAATCAGATGG 58.577 38.462 0.00 0.00 0.00 3.51
114 629 6.916387 GCAATCATGGTGAAGTTAATCAGATG 59.084 38.462 0.00 0.00 0.00 2.90
115 630 6.604396 TGCAATCATGGTGAAGTTAATCAGAT 59.396 34.615 0.00 0.00 0.00 2.90
116 631 5.945191 TGCAATCATGGTGAAGTTAATCAGA 59.055 36.000 0.00 0.00 0.00 3.27
117 632 6.198650 TGCAATCATGGTGAAGTTAATCAG 57.801 37.500 0.00 0.00 0.00 2.90
118 633 6.587206 TTGCAATCATGGTGAAGTTAATCA 57.413 33.333 0.00 0.00 0.00 2.57
119 634 7.486647 AGATTGCAATCATGGTGAAGTTAATC 58.513 34.615 34.59 9.10 37.89 1.75
120 635 7.414222 AGATTGCAATCATGGTGAAGTTAAT 57.586 32.000 34.59 11.41 37.89 1.40
121 636 6.839124 AGATTGCAATCATGGTGAAGTTAA 57.161 33.333 34.59 0.00 37.89 2.01
173 688 1.862602 ATGGGAAACGTCAAAGGCGC 61.863 55.000 0.00 0.00 0.00 6.53
206 721 8.627403 AGGTTGCAGTTATGATCAATTTATCAG 58.373 33.333 8.23 0.00 39.18 2.90
259 775 3.228188 ACAGAAACATCATGGGTGTGT 57.772 42.857 5.59 0.73 0.00 3.72
353 869 0.804989 CTGGATCAGGGAAAACGTGC 59.195 55.000 0.00 0.00 35.01 5.34
361 877 2.705148 TCATATTGGCTGGATCAGGGA 58.295 47.619 0.00 0.00 31.21 4.20
369 885 5.132502 TGGTCAAGTTATCATATTGGCTGG 58.867 41.667 0.00 0.00 0.00 4.85
408 924 0.175989 TTTTTGGGAAACGTGTGGCC 59.824 50.000 0.00 0.00 0.00 5.36
409 925 3.742983 TTTTTGGGAAACGTGTGGC 57.257 47.368 0.00 0.00 0.00 5.01
442 1348 5.300034 TGCAAAATTATATCTGGCCTCTGTG 59.700 40.000 3.32 0.00 0.00 3.66
444 1350 5.048224 CCTGCAAAATTATATCTGGCCTCTG 60.048 44.000 3.32 0.00 0.00 3.35
445 1351 5.075493 CCTGCAAAATTATATCTGGCCTCT 58.925 41.667 3.32 0.00 0.00 3.69
475 1381 7.857389 CACTTCGATCTCAACTTTTCAAATCAA 59.143 33.333 0.00 0.00 0.00 2.57
489 1395 1.550327 AGGACTGCACTTCGATCTCA 58.450 50.000 0.00 0.00 0.00 3.27
496 1402 5.351740 GTGTAAAAGGATAGGACTGCACTTC 59.648 44.000 0.00 0.00 0.00 3.01
539 1445 6.611613 AGATGGAGTTGTGAGAGATGTAAA 57.388 37.500 0.00 0.00 0.00 2.01
555 1461 7.910999 AGAGTACTCTGGTACCATAAGATGGAG 60.911 44.444 24.62 21.40 46.81 3.86
560 1466 9.537852 TTTTTAGAGTACTCTGGTACCATAAGA 57.462 33.333 31.47 14.67 46.81 2.10
591 1497 2.860735 GCTACGCTCGACATTTGAATCT 59.139 45.455 0.00 0.00 0.00 2.40
603 1509 0.315625 TACGATTGACGCTACGCTCG 60.316 55.000 0.00 0.00 46.94 5.03
619 1525 4.810790 AGAGGTGAAATTGTGAGAGTACG 58.189 43.478 0.00 0.00 0.00 3.67
624 1530 6.126863 ACCATAAGAGGTGAAATTGTGAGA 57.873 37.500 0.00 0.00 41.30 3.27
682 1589 3.255395 TCATGGTATTGTTGTGCTTGTGG 59.745 43.478 0.00 0.00 0.00 4.17
721 1632 8.722480 AAAAAGTCTTTTCATTTTCTTGGGAG 57.278 30.769 10.95 0.00 28.09 4.30
747 1658 7.777910 TCAGTTCACCAATTCTCTTTTTCCTAA 59.222 33.333 0.00 0.00 0.00 2.69
748 1659 7.287061 TCAGTTCACCAATTCTCTTTTTCCTA 58.713 34.615 0.00 0.00 0.00 2.94
749 1660 6.129179 TCAGTTCACCAATTCTCTTTTTCCT 58.871 36.000 0.00 0.00 0.00 3.36
750 1661 6.391227 TCAGTTCACCAATTCTCTTTTTCC 57.609 37.500 0.00 0.00 0.00 3.13
751 1662 8.595533 GTTTTCAGTTCACCAATTCTCTTTTTC 58.404 33.333 0.00 0.00 0.00 2.29
752 1663 7.549134 GGTTTTCAGTTCACCAATTCTCTTTTT 59.451 33.333 0.00 0.00 0.00 1.94
867 1780 9.787532 GTTGTGATGCATGTAGTGTTATTTATT 57.212 29.630 2.46 0.00 0.00 1.40
881 1794 1.012086 CGAGGGAGTTGTGATGCATG 58.988 55.000 2.46 0.00 0.00 4.06
930 1843 4.760047 CTGGGTTCAGGGACGGCG 62.760 72.222 4.80 4.80 37.36 6.46
984 1899 2.035632 TCCATTGTTGGTTGGTTGGTC 58.964 47.619 0.00 0.00 44.06 4.02
1732 2720 2.895865 TCTACGCGGCGGAGAGAG 60.896 66.667 31.95 16.77 42.31 3.20
1762 2750 0.308684 TCAGTAATAGTACGCCGCCG 59.691 55.000 0.00 0.00 41.14 6.46
1763 2751 2.497107 TTCAGTAATAGTACGCCGCC 57.503 50.000 0.00 0.00 35.20 6.13
1811 2799 6.468000 GCGAGCAAAAATTACAACATACTACC 59.532 38.462 0.00 0.00 0.00 3.18
1812 2800 6.192137 CGCGAGCAAAAATTACAACATACTAC 59.808 38.462 0.00 0.00 0.00 2.73
1813 2801 6.128499 ACGCGAGCAAAAATTACAACATACTA 60.128 34.615 15.93 0.00 0.00 1.82
1904 2896 1.550524 TCCGATCCACCAAGAACAGAG 59.449 52.381 0.00 0.00 0.00 3.35
1921 2918 0.304705 GCACAATTAGCACCGATCCG 59.695 55.000 0.00 0.00 0.00 4.18
1922 2919 0.663153 GGCACAATTAGCACCGATCC 59.337 55.000 4.67 0.00 0.00 3.36
1923 2920 1.668419 AGGCACAATTAGCACCGATC 58.332 50.000 4.67 0.00 0.00 3.69
1924 2921 3.275617 TTAGGCACAATTAGCACCGAT 57.724 42.857 4.67 0.00 0.00 4.18
1925 2922 2.772077 TTAGGCACAATTAGCACCGA 57.228 45.000 4.67 0.00 0.00 4.69
1955 2952 6.480524 TGATGAAACGGAGACAGTTAATTG 57.519 37.500 0.00 0.00 0.00 2.32
1966 2963 4.944962 TTAACTGCATGATGAAACGGAG 57.055 40.909 0.00 0.00 0.00 4.63
2009 3006 4.643784 CCATGAATGAGAGGAAAGAAAGGG 59.356 45.833 0.00 0.00 0.00 3.95
2089 3100 3.861840 ACAGTGGATGGTTCGTATCTTG 58.138 45.455 0.00 0.00 0.00 3.02
2105 3116 2.809119 TGCAACCGTTATTGGTACAGTG 59.191 45.455 0.00 0.00 42.89 3.66
2113 3124 3.119884 TCTGAATGCTGCAACCGTTATTG 60.120 43.478 6.36 0.00 0.00 1.90
2119 3130 2.163010 AGAATTCTGAATGCTGCAACCG 59.837 45.455 10.13 0.88 0.00 4.44
2214 3226 4.037565 GCCTTGTCGGGGAATTTAATTAGG 59.962 45.833 0.00 0.00 0.00 2.69
2215 3227 4.037565 GGCCTTGTCGGGGAATTTAATTAG 59.962 45.833 0.00 0.00 0.00 1.73
2217 3229 2.764010 GGCCTTGTCGGGGAATTTAATT 59.236 45.455 0.00 0.00 0.00 1.40
2229 3241 2.357517 ACTCTTGCGGCCTTGTCG 60.358 61.111 0.00 0.00 0.00 4.35
2252 3264 5.525012 TGATTCTACGCCATTGAAGAAGATG 59.475 40.000 0.00 0.00 31.90 2.90
2287 3299 2.285368 TACAGGGGAGGGGCACTG 60.285 66.667 0.00 0.00 37.01 3.66
2288 3300 2.285442 GTACAGGGGAGGGGCACT 60.285 66.667 0.00 0.00 0.00 4.40
2289 3301 1.923909 AAGTACAGGGGAGGGGCAC 60.924 63.158 0.00 0.00 0.00 5.01
2290 3302 1.923395 CAAGTACAGGGGAGGGGCA 60.923 63.158 0.00 0.00 0.00 5.36
2291 3303 1.498176 AACAAGTACAGGGGAGGGGC 61.498 60.000 0.00 0.00 0.00 5.80
2294 3306 1.279271 CAGGAACAAGTACAGGGGAGG 59.721 57.143 0.00 0.00 0.00 4.30
2295 3307 1.978580 ACAGGAACAAGTACAGGGGAG 59.021 52.381 0.00 0.00 0.00 4.30
2296 3308 2.112279 ACAGGAACAAGTACAGGGGA 57.888 50.000 0.00 0.00 0.00 4.81
2341 3717 1.940613 GCTTGTTCGTCTGTTGTTCCT 59.059 47.619 0.00 0.00 0.00 3.36
2342 3718 1.002792 GGCTTGTTCGTCTGTTGTTCC 60.003 52.381 0.00 0.00 0.00 3.62
2346 3722 2.307363 ACGGCTTGTTCGTCTGTTG 58.693 52.632 0.00 0.00 35.87 3.33
2353 3730 0.163788 GTGACATGACGGCTTGTTCG 59.836 55.000 11.59 0.00 33.10 3.95
2388 3765 9.210329 TCAAAGTTGCAATAATTCTACGTCTAA 57.790 29.630 0.59 0.00 0.00 2.10
2392 3769 9.691362 AAATTCAAAGTTGCAATAATTCTACGT 57.309 25.926 0.59 0.00 0.00 3.57
2419 3796 8.946085 TCAAGGCACATAAATGTAGTAAAAGAG 58.054 33.333 0.00 0.00 39.39 2.85
2428 3805 7.119699 CAGAACTCTTCAAGGCACATAAATGTA 59.880 37.037 0.00 0.00 39.39 2.29
2429 3806 6.006449 AGAACTCTTCAAGGCACATAAATGT 58.994 36.000 0.00 0.00 42.84 2.71
2430 3807 6.072286 ACAGAACTCTTCAAGGCACATAAATG 60.072 38.462 0.00 0.00 0.00 2.32
2448 3825 3.157881 TCACTAGCACTAGCACAGAACT 58.842 45.455 4.58 0.00 45.49 3.01
2453 3830 2.428530 CCAGATCACTAGCACTAGCACA 59.571 50.000 4.58 0.00 45.49 4.57
2454 3831 2.801342 GCCAGATCACTAGCACTAGCAC 60.801 54.545 4.58 0.00 45.49 4.40
2459 3836 0.829333 CCAGCCAGATCACTAGCACT 59.171 55.000 0.00 0.00 33.44 4.40
2460 3837 0.813210 GCCAGCCAGATCACTAGCAC 60.813 60.000 0.00 0.00 33.44 4.40
2471 3848 2.825836 GAACCCGATGCCAGCCAG 60.826 66.667 0.00 0.00 0.00 4.85
2472 3849 4.776322 CGAACCCGATGCCAGCCA 62.776 66.667 0.00 0.00 38.22 4.75
2483 3860 1.002502 CCTCCTTTGACCCGAACCC 60.003 63.158 0.00 0.00 0.00 4.11
2501 3878 1.132640 GGATGCTTGACAACGACGC 59.867 57.895 0.00 0.00 0.00 5.19
2513 3890 2.188994 GCTTCTCGGCTGGATGCT 59.811 61.111 11.95 0.00 42.39 3.79
2524 3901 1.301677 CCTTCCTTGTGCCGCTTCTC 61.302 60.000 0.00 0.00 0.00 2.87
2525 3902 1.302832 CCTTCCTTGTGCCGCTTCT 60.303 57.895 0.00 0.00 0.00 2.85
2526 3903 1.301677 CTCCTTCCTTGTGCCGCTTC 61.302 60.000 0.00 0.00 0.00 3.86
2527 3904 1.302832 CTCCTTCCTTGTGCCGCTT 60.303 57.895 0.00 0.00 0.00 4.68
2531 3908 0.402121 AACTCCTCCTTCCTTGTGCC 59.598 55.000 0.00 0.00 0.00 5.01
2623 4009 2.045708 TGCACCGATGATGGGTTGC 61.046 57.895 11.81 11.81 34.97 4.17
2670 4061 3.305516 GCACCACCAAGGCCAAGG 61.306 66.667 5.01 9.04 43.14 3.61
2679 4070 2.977456 GTGATGCACGCACCACCA 60.977 61.111 5.11 0.00 34.47 4.17
2694 4085 1.470979 GCCCATACGTACTGACCTGTG 60.471 57.143 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.