Multiple sequence alignment - TraesCS1D01G255600

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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 TraesCS1D01G255600 chr1D 100.000 3668 0 0 1 3668 348050835 348054502 0.000000e+00 6774
1 TraesCS1D01G255600 chr1B 93.951 2397 91 28 488 2875 469968909 469971260 0.000000e+00 3574
2 TraesCS1D01G255600 chr1B 92.468 624 38 2 2969 3584 595587857 595587235 0.000000e+00 883
3 TraesCS1D01G255600 chr1B 97.674 86 1 1 398 482 469968713 469968798 2.950000e-31 147
4 TraesCS1D01G255600 chr1B 94.118 85 5 0 3584 3668 469971398 469971482 2.970000e-26 130
5 TraesCS1D01G255600 chr1A 93.822 2347 94 16 627 2951 448913358 448915675 0.000000e+00 3483
6 TraesCS1D01G255600 chr1A 84.381 493 38 19 2 485 448912462 448912924 7.230000e-122 448
7 TraesCS1D01G255600 chr1A 97.674 43 1 0 3584 3626 448915682 448915724 1.410000e-09 75
8 TraesCS1D01G255600 chr3B 87.447 1896 218 12 778 2664 672101476 672099592 0.000000e+00 2165
9 TraesCS1D01G255600 chr3B 93.248 622 33 2 2968 3581 141630157 141629537 0.000000e+00 907
10 TraesCS1D01G255600 chr3B 92.777 623 36 2 2967 3581 817224526 817225147 0.000000e+00 893
11 TraesCS1D01G255600 chr3B 92.516 628 37 3 2969 3587 257776089 257775463 0.000000e+00 891
12 TraesCS1D01G255600 chr3A 87.302 1898 219 13 778 2664 646850528 646848642 0.000000e+00 2150
13 TraesCS1D01G255600 chr3D 87.151 1899 220 16 778 2664 509250478 509248592 0.000000e+00 2134
14 TraesCS1D01G255600 chr6A 94.194 620 26 5 2970 3581 443413185 443412568 0.000000e+00 937
15 TraesCS1D01G255600 chr2B 93.559 621 31 2 2969 3581 756568427 756569046 0.000000e+00 917
16 TraesCS1D01G255600 chr5B 93.506 616 36 3 2970 3582 707481563 707480949 0.000000e+00 913
17 TraesCS1D01G255600 chr7B 93.226 620 33 2 2970 3581 439694545 439695163 0.000000e+00 904
18 TraesCS1D01G255600 chr7A 94.930 572 28 1 2987 3558 735136944 735136374 0.000000e+00 894


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 TraesCS1D01G255600 chr1D 348050835 348054502 3667 False 6774.000000 6774 100.000000 1 3668 1 chr1D.!!$F1 3667
1 TraesCS1D01G255600 chr1B 469968713 469971482 2769 False 1283.666667 3574 95.247667 398 3668 3 chr1B.!!$F1 3270
2 TraesCS1D01G255600 chr1B 595587235 595587857 622 True 883.000000 883 92.468000 2969 3584 1 chr1B.!!$R1 615
3 TraesCS1D01G255600 chr1A 448912462 448915724 3262 False 1335.333333 3483 91.959000 2 3626 3 chr1A.!!$F1 3624
4 TraesCS1D01G255600 chr3B 672099592 672101476 1884 True 2165.000000 2165 87.447000 778 2664 1 chr3B.!!$R3 1886
5 TraesCS1D01G255600 chr3B 141629537 141630157 620 True 907.000000 907 93.248000 2968 3581 1 chr3B.!!$R1 613
6 TraesCS1D01G255600 chr3B 817224526 817225147 621 False 893.000000 893 92.777000 2967 3581 1 chr3B.!!$F1 614
7 TraesCS1D01G255600 chr3B 257775463 257776089 626 True 891.000000 891 92.516000 2969 3587 1 chr3B.!!$R2 618
8 TraesCS1D01G255600 chr3A 646848642 646850528 1886 True 2150.000000 2150 87.302000 778 2664 1 chr3A.!!$R1 1886
9 TraesCS1D01G255600 chr3D 509248592 509250478 1886 True 2134.000000 2134 87.151000 778 2664 1 chr3D.!!$R1 1886
10 TraesCS1D01G255600 chr6A 443412568 443413185 617 True 937.000000 937 94.194000 2970 3581 1 chr6A.!!$R1 611
11 TraesCS1D01G255600 chr2B 756568427 756569046 619 False 917.000000 917 93.559000 2969 3581 1 chr2B.!!$F1 612
12 TraesCS1D01G255600 chr5B 707480949 707481563 614 True 913.000000 913 93.506000 2970 3582 1 chr5B.!!$R1 612
13 TraesCS1D01G255600 chr7B 439694545 439695163 618 False 904.000000 904 93.226000 2970 3581 1 chr7B.!!$F1 611
14 TraesCS1D01G255600 chr7A 735136374 735136944 570 True 894.000000 894 94.930000 2987 3558 1 chr7A.!!$R1 571

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
571 703 0.249120 CATCCAGTCCAGCAACCGTA 59.751 55.0 0.0 0.0 0.00 4.02 F
1021 1366 1.087501 GGAATCAACAGCGGAAGGTC 58.912 55.0 0.0 0.0 41.81 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 2283 0.392193 GTGCCACTCCACCATCAGAG 60.392 60.0 0.00 0.0 36.16 3.35 R
2951 3364 0.249120 CCCATCGGCCGCATCTTATA 59.751 55.0 23.51 0.0 0.00 0.98 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
55 56 4.785453 CTGGAAGCCACCGCCTCC 62.785 72.222 0.00 0.00 44.77 4.30
102 103 2.662866 TGTCCCTCAAGTATAGACGGG 58.337 52.381 0.00 0.00 0.00 5.28
107 108 1.111116 TCAAGTATAGACGGGGCCGG 61.111 60.000 9.88 9.88 44.69 6.13
132 133 2.103941 CTGGATCCAAGGTAAGGAGAGC 59.896 54.545 17.00 0.00 38.83 4.09
134 135 1.069358 GATCCAAGGTAAGGAGAGCGG 59.931 57.143 0.00 0.00 38.83 5.52
144 145 1.428869 AGGAGAGCGGGCATCTTATT 58.571 50.000 0.00 0.00 0.00 1.40
147 148 2.224402 GGAGAGCGGGCATCTTATTTCT 60.224 50.000 0.00 0.00 0.00 2.52
149 150 1.876156 GAGCGGGCATCTTATTTCTGG 59.124 52.381 0.00 0.00 0.00 3.86
176 177 4.636206 GGTTCGTCTGCAAATCCTTCTTAT 59.364 41.667 0.00 0.00 0.00 1.73
188 195 8.724229 GCAAATCCTTCTTATTGCTTTTCAAAT 58.276 29.630 2.33 0.00 43.58 2.32
193 200 9.480053 TCCTTCTTATTGCTTTTCAAATCAAAG 57.520 29.630 0.00 0.00 38.34 2.77
214 221 9.703892 TCAAAGGAATGTGTATAAATTTGGTTG 57.296 29.630 0.00 0.00 0.00 3.77
215 222 9.487790 CAAAGGAATGTGTATAAATTTGGTTGT 57.512 29.630 0.00 0.00 0.00 3.32
216 223 9.705290 AAAGGAATGTGTATAAATTTGGTTGTC 57.295 29.630 0.00 0.00 0.00 3.18
217 224 7.836842 AGGAATGTGTATAAATTTGGTTGTCC 58.163 34.615 0.00 0.00 0.00 4.02
218 225 7.039270 GGAATGTGTATAAATTTGGTTGTCCC 58.961 38.462 0.00 0.00 0.00 4.46
219 226 5.630661 TGTGTATAAATTTGGTTGTCCCG 57.369 39.130 0.00 0.00 35.15 5.14
220 227 5.071370 TGTGTATAAATTTGGTTGTCCCGT 58.929 37.500 0.00 0.00 35.15 5.28
221 228 5.048643 TGTGTATAAATTTGGTTGTCCCGTG 60.049 40.000 0.00 0.00 35.15 4.94
222 229 5.048573 GTGTATAAATTTGGTTGTCCCGTGT 60.049 40.000 0.00 0.00 35.15 4.49
223 230 6.149142 GTGTATAAATTTGGTTGTCCCGTGTA 59.851 38.462 0.00 0.00 35.15 2.90
224 231 6.885376 TGTATAAATTTGGTTGTCCCGTGTAT 59.115 34.615 0.00 0.00 35.15 2.29
225 232 6.844097 ATAAATTTGGTTGTCCCGTGTATT 57.156 33.333 0.00 0.00 35.15 1.89
226 233 5.538849 AAATTTGGTTGTCCCGTGTATTT 57.461 34.783 0.00 0.00 35.15 1.40
227 234 5.538849 AATTTGGTTGTCCCGTGTATTTT 57.461 34.783 0.00 0.00 35.15 1.82
228 235 5.538849 ATTTGGTTGTCCCGTGTATTTTT 57.461 34.783 0.00 0.00 35.15 1.94
263 270 1.860641 TGTTTCTATCTCCCCGCTGA 58.139 50.000 0.00 0.00 0.00 4.26
277 289 3.443045 CTGACACGGGCATTGGGC 61.443 66.667 0.00 0.00 43.74 5.36
300 312 3.429543 GGTAACGTTTATGTGCTGAACGA 59.570 43.478 5.91 0.00 46.49 3.85
301 313 3.788434 AACGTTTATGTGCTGAACGAG 57.212 42.857 13.81 0.00 46.49 4.18
302 314 2.750948 ACGTTTATGTGCTGAACGAGT 58.249 42.857 13.81 0.00 46.49 4.18
303 315 3.128349 ACGTTTATGTGCTGAACGAGTT 58.872 40.909 13.81 0.00 46.49 3.01
304 316 4.300803 ACGTTTATGTGCTGAACGAGTTA 58.699 39.130 13.81 0.00 46.49 2.24
305 317 4.149396 ACGTTTATGTGCTGAACGAGTTAC 59.851 41.667 13.81 0.00 46.49 2.50
306 318 4.384846 CGTTTATGTGCTGAACGAGTTACT 59.615 41.667 2.02 0.00 46.49 2.24
307 319 5.107607 CGTTTATGTGCTGAACGAGTTACTT 60.108 40.000 2.02 0.00 46.49 2.24
308 320 6.088483 CGTTTATGTGCTGAACGAGTTACTTA 59.912 38.462 2.02 0.00 46.49 2.24
318 330 8.870879 GCTGAACGAGTTACTTATATTTCAACT 58.129 33.333 0.00 0.00 32.33 3.16
345 357 2.089980 TGTCTGGAGTAGTTAGACGCC 58.910 52.381 9.85 0.00 42.80 5.68
356 368 1.916000 GTTAGACGCCGTGTATGTGTC 59.084 52.381 0.00 0.00 42.21 3.67
367 379 3.994392 CGTGTATGTGTCTGGCTTAGTTT 59.006 43.478 0.00 0.00 0.00 2.66
368 380 4.091509 CGTGTATGTGTCTGGCTTAGTTTC 59.908 45.833 0.00 0.00 0.00 2.78
369 381 4.091509 GTGTATGTGTCTGGCTTAGTTTCG 59.908 45.833 0.00 0.00 0.00 3.46
370 382 2.902705 TGTGTCTGGCTTAGTTTCGT 57.097 45.000 0.00 0.00 0.00 3.85
371 383 2.750948 TGTGTCTGGCTTAGTTTCGTC 58.249 47.619 0.00 0.00 0.00 4.20
373 385 3.181469 TGTGTCTGGCTTAGTTTCGTCTT 60.181 43.478 0.00 0.00 0.00 3.01
374 386 3.429207 GTGTCTGGCTTAGTTTCGTCTTC 59.571 47.826 0.00 0.00 0.00 2.87
375 387 3.069016 TGTCTGGCTTAGTTTCGTCTTCA 59.931 43.478 0.00 0.00 0.00 3.02
376 388 4.246458 GTCTGGCTTAGTTTCGTCTTCAT 58.754 43.478 0.00 0.00 0.00 2.57
471 485 4.393062 ACTGGCACTCTTAAATCACAATCG 59.607 41.667 0.00 0.00 0.00 3.34
542 674 2.376808 CAGTAGGACTGCTGGTTCTG 57.623 55.000 9.24 0.00 39.62 3.02
552 684 1.275291 TGCTGGTTCTGTACTAGTGCC 59.725 52.381 5.39 0.00 37.64 5.01
561 693 2.101582 CTGTACTAGTGCCATCCAGTCC 59.898 54.545 5.39 0.00 0.00 3.85
566 698 1.303561 GTGCCATCCAGTCCAGCAA 60.304 57.895 0.00 0.00 34.79 3.91
567 699 1.303561 TGCCATCCAGTCCAGCAAC 60.304 57.895 0.00 0.00 0.00 4.17
568 700 2.048603 GCCATCCAGTCCAGCAACC 61.049 63.158 0.00 0.00 0.00 3.77
569 701 1.746615 CCATCCAGTCCAGCAACCG 60.747 63.158 0.00 0.00 0.00 4.44
570 702 1.003355 CATCCAGTCCAGCAACCGT 60.003 57.895 0.00 0.00 0.00 4.83
571 703 0.249120 CATCCAGTCCAGCAACCGTA 59.751 55.000 0.00 0.00 0.00 4.02
586 718 4.094294 GCAACCGTAGACAATGATAGCAAA 59.906 41.667 0.00 0.00 0.00 3.68
602 734 4.985044 AGCAAACGTAGTAACATCACAC 57.015 40.909 0.00 0.00 45.00 3.82
628 940 3.717400 TTATTCTCGTGCTAGGCTGAG 57.283 47.619 0.00 0.00 34.71 3.35
679 991 5.061721 ACCATTGGTTTCCTCTGTAAACT 57.938 39.130 1.37 0.00 37.09 2.66
708 1020 6.409185 CAGTTTGAGCAAAATACGAATCGATC 59.591 38.462 10.55 0.00 31.33 3.69
745 1080 5.844301 CGTTTTCTTGAATGAAAATGGGG 57.156 39.130 11.77 0.00 44.42 4.96
749 1084 1.907936 CTTGAATGAAAATGGGGGCCA 59.092 47.619 4.39 0.00 38.19 5.36
751 1086 1.838715 TGAATGAAAATGGGGGCCATG 59.161 47.619 4.39 0.00 44.40 3.66
752 1087 1.839354 GAATGAAAATGGGGGCCATGT 59.161 47.619 4.39 0.00 44.40 3.21
753 1088 1.205966 ATGAAAATGGGGGCCATGTG 58.794 50.000 4.39 0.00 44.40 3.21
754 1089 1.221566 GAAAATGGGGGCCATGTGC 59.778 57.895 4.39 0.00 44.40 4.57
950 1295 2.281539 TGGGATCATGCTAATGCCTG 57.718 50.000 5.25 0.00 35.76 4.85
1019 1364 1.402968 CATGGAATCAACAGCGGAAGG 59.597 52.381 0.00 0.00 0.00 3.46
1021 1366 1.087501 GGAATCAACAGCGGAAGGTC 58.912 55.000 0.00 0.00 41.81 3.85
1206 1551 1.370900 GGTGTGCTTTGCTTCTGCG 60.371 57.895 0.00 0.00 43.34 5.18
1323 1671 2.359975 GGCCCAAGGACAACCGAG 60.360 66.667 0.00 0.00 41.83 4.63
1324 1672 2.359975 GCCCAAGGACAACCGAGG 60.360 66.667 0.00 0.00 41.83 4.63
1325 1673 2.890766 GCCCAAGGACAACCGAGGA 61.891 63.158 0.00 0.00 41.83 3.71
1696 2044 2.427506 CTTTAGGTGAGAAGGGTGTGC 58.572 52.381 0.00 0.00 0.00 4.57
1749 2097 3.243907 GCGACCTGGAAGAGCTATATGTT 60.244 47.826 0.00 0.00 34.07 2.71
1769 2117 5.852827 TGTTATGAACGATGGCATATCAGA 58.147 37.500 0.00 0.11 0.00 3.27
1935 2283 1.300233 CTCCGCGACAAGGATAGGC 60.300 63.158 8.23 0.00 37.13 3.93
2190 2538 7.243604 TGAAATGGCAGGAAATGAAATAACT 57.756 32.000 0.00 0.00 0.00 2.24
2283 2631 3.715315 AGAATGAGCTGAAGGATGATGGA 59.285 43.478 0.00 0.00 0.00 3.41
2316 2664 2.165998 GCAAAATCTCTGCAGGAAGGT 58.834 47.619 15.13 0.00 39.69 3.50
2446 2794 7.121020 TGAACATCAATTCGAATTTCATCTCCA 59.879 33.333 20.56 10.57 0.00 3.86
2449 2797 6.816134 TCAATTCGAATTTCATCTCCAACA 57.184 33.333 20.56 0.00 0.00 3.33
2559 2907 1.144936 CCCTGAAGATGGCGAGGAC 59.855 63.158 0.00 0.00 0.00 3.85
2577 2925 1.157276 CGAGGAGGATGGGGAGGAT 59.843 63.158 0.00 0.00 0.00 3.24
2579 2927 1.463018 AGGAGGATGGGGAGGATGC 60.463 63.158 0.00 0.00 0.00 3.91
2644 2995 4.774503 GCTCGAAGCTGCAGGGCT 62.775 66.667 17.12 5.02 45.30 5.19
2732 3088 3.181520 CCGGTTAGCTTCTGAAATGTTCG 60.182 47.826 0.00 0.00 0.00 3.95
2770 3127 6.566197 ATTTTCACATGAAGAGAACTCACC 57.434 37.500 0.00 0.00 35.21 4.02
2840 3197 4.802563 GCGGTTTATCTGTACTTCTGTACC 59.197 45.833 0.00 0.00 46.19 3.34
2922 3335 1.202533 ACCTACACTATGCCGTGATGC 60.203 52.381 5.09 0.00 38.27 3.91
2947 3360 3.766644 CGCAGGATCCATGAGTTGA 57.233 52.632 15.82 0.00 0.00 3.18
2948 3361 1.293924 CGCAGGATCCATGAGTTGAC 58.706 55.000 15.82 0.00 0.00 3.18
2949 3362 1.134580 CGCAGGATCCATGAGTTGACT 60.135 52.381 15.82 0.00 0.00 3.41
2950 3363 2.101415 CGCAGGATCCATGAGTTGACTA 59.899 50.000 15.82 0.00 0.00 2.59
2951 3364 3.244009 CGCAGGATCCATGAGTTGACTAT 60.244 47.826 15.82 0.00 0.00 2.12
2952 3365 4.021981 CGCAGGATCCATGAGTTGACTATA 60.022 45.833 15.82 0.00 0.00 1.31
2953 3366 5.337089 CGCAGGATCCATGAGTTGACTATAT 60.337 44.000 15.82 0.00 0.00 0.86
2954 3367 6.127619 CGCAGGATCCATGAGTTGACTATATA 60.128 42.308 15.82 0.00 0.00 0.86
2955 3368 7.577616 CGCAGGATCCATGAGTTGACTATATAA 60.578 40.741 15.82 0.00 0.00 0.98
2957 3370 9.029368 CAGGATCCATGAGTTGACTATATAAGA 57.971 37.037 15.82 0.00 0.00 2.10
2958 3371 9.781425 AGGATCCATGAGTTGACTATATAAGAT 57.219 33.333 15.82 0.00 0.00 2.40
2959 3372 9.814899 GGATCCATGAGTTGACTATATAAGATG 57.185 37.037 6.95 0.00 0.00 2.90
2961 3374 7.315890 TCCATGAGTTGACTATATAAGATGCG 58.684 38.462 0.00 0.00 0.00 4.73
2962 3375 6.533012 CCATGAGTTGACTATATAAGATGCGG 59.467 42.308 0.00 0.00 0.00 5.69
2963 3376 5.470368 TGAGTTGACTATATAAGATGCGGC 58.530 41.667 0.00 0.00 0.00 6.53
2964 3377 4.822026 AGTTGACTATATAAGATGCGGCC 58.178 43.478 0.00 0.00 0.00 6.13
2965 3378 3.503827 TGACTATATAAGATGCGGCCG 57.496 47.619 24.05 24.05 0.00 6.13
3116 3529 1.437986 CCGAGGTAGCTAGCGCTTT 59.562 57.895 18.68 4.38 46.47 3.51
3118 3531 1.066605 CCGAGGTAGCTAGCGCTTTTA 59.933 52.381 18.68 2.80 46.47 1.52
3169 3582 4.498345 GCGTTTTGGACCATGTAAGAAACA 60.498 41.667 14.51 0.00 43.86 2.83
3254 3667 6.245408 TGGTTACCGAGTAGTTTCTTACCTA 58.755 40.000 0.00 0.00 0.00 3.08
3469 3882 2.569059 AGCTACCTCGACGTTGCTATA 58.431 47.619 18.36 0.00 41.94 1.31
3509 3922 5.100259 CGAGCTATGACGTTTCTAAAAGGA 58.900 41.667 0.00 0.00 0.00 3.36
3511 3924 6.074782 CGAGCTATGACGTTTCTAAAAGGATC 60.075 42.308 0.00 0.00 0.00 3.36
3584 4005 0.818040 AATAGTGATTTCGGCCCGGC 60.818 55.000 1.90 0.00 0.00 6.13
3585 4006 2.676163 ATAGTGATTTCGGCCCGGCC 62.676 60.000 19.64 19.64 46.75 6.13
3637 4058 1.136363 CGTGTGCGTGTGGTTTCTATG 60.136 52.381 0.00 0.00 0.00 2.23
3648 4069 7.426410 CGTGTGGTTTCTATGTATCTACAGAT 58.574 38.462 0.00 0.00 39.92 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 2.662866 CCCGTCTATACTTGAGGGACA 58.337 52.381 0.00 0.00 40.69 4.02
107 108 1.473434 CCTTACCTTGGATCCAGACGC 60.473 57.143 15.53 0.00 0.00 5.19
132 133 2.348411 ACCCAGAAATAAGATGCCCG 57.652 50.000 0.00 0.00 0.00 6.13
134 135 3.365472 ACCAACCCAGAAATAAGATGCC 58.635 45.455 0.00 0.00 0.00 4.40
144 145 0.534203 GCAGACGAACCAACCCAGAA 60.534 55.000 0.00 0.00 0.00 3.02
147 148 0.394488 TTTGCAGACGAACCAACCCA 60.394 50.000 0.00 0.00 0.00 4.51
149 150 1.068541 GGATTTGCAGACGAACCAACC 60.069 52.381 0.00 0.00 0.00 3.77
176 177 6.822676 ACACATTCCTTTGATTTGAAAAGCAA 59.177 30.769 2.50 2.50 41.91 3.91
188 195 9.703892 CAACCAAATTTATACACATTCCTTTGA 57.296 29.630 0.00 0.00 0.00 2.69
193 200 7.039270 GGGACAACCAAATTTATACACATTCC 58.961 38.462 0.00 0.00 39.85 3.01
277 289 3.719763 CGTTCAGCACATAAACGTTACCG 60.720 47.826 0.00 0.00 40.51 4.02
292 304 8.870879 AGTTGAAATATAAGTAACTCGTTCAGC 58.129 33.333 0.00 0.00 0.00 4.26
328 340 1.093159 ACGGCGTCTAACTACTCCAG 58.907 55.000 6.77 0.00 0.00 3.86
345 357 3.232213 ACTAAGCCAGACACATACACG 57.768 47.619 0.00 0.00 0.00 4.49
356 368 5.613358 AAATGAAGACGAAACTAAGCCAG 57.387 39.130 0.00 0.00 0.00 4.85
381 393 5.630121 TCCAATCTTACTTGAGCAGGAAAA 58.370 37.500 0.00 0.00 0.00 2.29
385 397 4.478206 TCTCCAATCTTACTTGAGCAGG 57.522 45.455 0.00 0.00 0.00 4.85
386 398 4.272991 GCATCTCCAATCTTACTTGAGCAG 59.727 45.833 0.00 0.00 0.00 4.24
393 405 2.688446 TCGTCGCATCTCCAATCTTACT 59.312 45.455 0.00 0.00 0.00 2.24
485 505 8.609478 TTTCAAAACACGATAACTTCAACTTC 57.391 30.769 0.00 0.00 0.00 3.01
486 506 7.220108 GCTTTCAAAACACGATAACTTCAACTT 59.780 33.333 0.00 0.00 0.00 2.66
488 508 6.470877 TGCTTTCAAAACACGATAACTTCAAC 59.529 34.615 0.00 0.00 0.00 3.18
489 509 6.556212 TGCTTTCAAAACACGATAACTTCAA 58.444 32.000 0.00 0.00 0.00 2.69
490 510 6.125327 TGCTTTCAAAACACGATAACTTCA 57.875 33.333 0.00 0.00 0.00 3.02
491 511 7.623268 ATTGCTTTCAAAACACGATAACTTC 57.377 32.000 0.00 0.00 35.56 3.01
492 512 9.341899 GATATTGCTTTCAAAACACGATAACTT 57.658 29.630 0.00 0.00 35.56 2.66
493 513 8.730680 AGATATTGCTTTCAAAACACGATAACT 58.269 29.630 0.00 0.00 35.56 2.24
525 655 2.826725 AGTACAGAACCAGCAGTCCTAC 59.173 50.000 0.00 0.00 0.00 3.18
542 674 2.101582 CTGGACTGGATGGCACTAGTAC 59.898 54.545 0.00 8.25 33.66 2.73
552 684 0.249120 TACGGTTGCTGGACTGGATG 59.751 55.000 0.00 0.00 0.00 3.51
561 693 3.246226 GCTATCATTGTCTACGGTTGCTG 59.754 47.826 0.00 0.00 0.00 4.41
566 698 3.863424 CGTTTGCTATCATTGTCTACGGT 59.137 43.478 0.00 0.00 0.00 4.83
567 699 3.863424 ACGTTTGCTATCATTGTCTACGG 59.137 43.478 0.00 0.00 0.00 4.02
568 700 5.742453 ACTACGTTTGCTATCATTGTCTACG 59.258 40.000 0.00 0.00 0.00 3.51
569 701 8.529911 GTTACTACGTTTGCTATCATTGTCTAC 58.470 37.037 0.00 0.00 0.00 2.59
570 702 8.245491 TGTTACTACGTTTGCTATCATTGTCTA 58.755 33.333 0.00 0.00 0.00 2.59
571 703 7.094631 TGTTACTACGTTTGCTATCATTGTCT 58.905 34.615 0.00 0.00 0.00 3.41
602 734 6.646653 TCAGCCTAGCACGAGAATAAATAATG 59.353 38.462 0.00 0.00 0.00 1.90
615 747 2.105930 GGAGCTCAGCCTAGCACG 59.894 66.667 17.19 0.00 45.30 5.34
628 940 7.553881 TTAGCAATTACAGAATAACAGGAGC 57.446 36.000 0.00 0.00 0.00 4.70
660 972 5.070685 GGTCAGTTTACAGAGGAAACCAAT 58.929 41.667 1.40 0.00 37.48 3.16
679 991 4.130857 TCGTATTTTGCTCAAACTGGTCA 58.869 39.130 0.00 0.00 0.00 4.02
708 1020 4.981794 AGAAAACGGAGAACAACAACTTG 58.018 39.130 0.00 0.00 0.00 3.16
749 1084 4.985538 TCTTCTTCTTAAAGTGGGCACAT 58.014 39.130 0.00 0.00 33.95 3.21
750 1085 4.431416 TCTTCTTCTTAAAGTGGGCACA 57.569 40.909 0.00 0.00 33.95 4.57
751 1086 5.767816 TTTCTTCTTCTTAAAGTGGGCAC 57.232 39.130 0.00 0.00 33.95 5.01
752 1087 6.783708 TTTTTCTTCTTCTTAAAGTGGGCA 57.216 33.333 0.00 0.00 33.95 5.36
753 1088 7.433680 TCATTTTTCTTCTTCTTAAAGTGGGC 58.566 34.615 0.00 0.00 33.95 5.36
754 1089 9.415544 CATCATTTTTCTTCTTCTTAAAGTGGG 57.584 33.333 0.00 0.00 33.95 4.61
755 1090 9.971922 ACATCATTTTTCTTCTTCTTAAAGTGG 57.028 29.630 0.00 0.00 33.95 4.00
1019 1364 0.744771 GAATGTTCGGGGCTGGAGAC 60.745 60.000 0.00 0.00 0.00 3.36
1021 1366 0.462759 GAGAATGTTCGGGGCTGGAG 60.463 60.000 0.00 0.00 0.00 3.86
1206 1551 3.277715 CTCCTTCTTGAAATGCTCCTCC 58.722 50.000 0.00 0.00 0.00 4.30
1323 1671 0.954452 CAACAGGTGCTTCTGGTTCC 59.046 55.000 10.66 0.00 38.98 3.62
1324 1672 1.680338 ACAACAGGTGCTTCTGGTTC 58.320 50.000 10.66 0.00 38.98 3.62
1325 1673 1.750778 CAACAACAGGTGCTTCTGGTT 59.249 47.619 10.66 4.53 38.98 3.67
1696 2044 0.740164 AGCAGCTCTGTGAATGCTCG 60.740 55.000 0.00 0.00 45.57 5.03
1749 2097 4.772100 TCCTCTGATATGCCATCGTTCATA 59.228 41.667 0.00 0.00 0.00 2.15
1935 2283 0.392193 GTGCCACTCCACCATCAGAG 60.392 60.000 0.00 0.00 36.16 3.35
2283 2631 2.816087 AGATTTTGCGATTGTCACTGCT 59.184 40.909 0.00 0.00 0.00 4.24
2316 2664 1.330655 GCTCCTTCAGATCCGGGTGA 61.331 60.000 0.00 0.00 0.00 4.02
2391 2739 2.143876 AACCTGGCTTGTTTGTGACT 57.856 45.000 0.00 0.00 0.00 3.41
2395 2743 1.134175 CACGAAACCTGGCTTGTTTGT 59.866 47.619 9.17 5.97 36.13 2.83
2446 2794 1.064825 ACCTCATCGACCCCTTTGTT 58.935 50.000 0.00 0.00 0.00 2.83
2449 2797 1.279271 CTTCACCTCATCGACCCCTTT 59.721 52.381 0.00 0.00 0.00 3.11
2559 2907 1.157276 ATCCTCCCCATCCTCCTCG 59.843 63.158 0.00 0.00 0.00 4.63
2577 2925 1.667154 CCTTCTCCTCGTCATCGGCA 61.667 60.000 0.00 0.00 37.69 5.69
2579 2927 0.382515 GTCCTTCTCCTCGTCATCGG 59.617 60.000 0.00 0.00 37.69 4.18
2644 2995 0.491823 TCCTCCTCCTCCACCTTCAA 59.508 55.000 0.00 0.00 0.00 2.69
2770 3127 2.794350 GGTTCAAAACAATTGAGCCACG 59.206 45.455 13.59 0.00 45.47 4.94
2881 3239 3.904800 TCCCAAAATATCTCAGCGACA 57.095 42.857 0.00 0.00 0.00 4.35
2882 3240 3.312697 GGTTCCCAAAATATCTCAGCGAC 59.687 47.826 0.00 0.00 0.00 5.19
2931 3344 9.029368 TCTTATATAGTCAACTCATGGATCCTG 57.971 37.037 14.23 8.97 0.00 3.86
2932 3345 9.781425 ATCTTATATAGTCAACTCATGGATCCT 57.219 33.333 14.23 0.00 0.00 3.24
2942 3355 4.618460 CGGCCGCATCTTATATAGTCAACT 60.618 45.833 14.67 0.00 0.00 3.16
2944 3357 3.508402 TCGGCCGCATCTTATATAGTCAA 59.492 43.478 23.51 0.00 0.00 3.18
2946 3359 3.777465 TCGGCCGCATCTTATATAGTC 57.223 47.619 23.51 0.00 0.00 2.59
2947 3360 3.181475 CCATCGGCCGCATCTTATATAGT 60.181 47.826 23.51 0.00 0.00 2.12
2948 3361 3.384668 CCATCGGCCGCATCTTATATAG 58.615 50.000 23.51 0.00 0.00 1.31
2949 3362 2.102420 CCCATCGGCCGCATCTTATATA 59.898 50.000 23.51 0.00 0.00 0.86
2950 3363 1.134401 CCCATCGGCCGCATCTTATAT 60.134 52.381 23.51 2.39 0.00 0.86
2951 3364 0.249120 CCCATCGGCCGCATCTTATA 59.751 55.000 23.51 0.00 0.00 0.98
2952 3365 1.003355 CCCATCGGCCGCATCTTAT 60.003 57.895 23.51 4.20 0.00 1.73
2953 3366 2.425592 CCCATCGGCCGCATCTTA 59.574 61.111 23.51 1.11 0.00 2.10
2963 3376 4.342092 AGAATAATGAAAAAGGCCCATCGG 59.658 41.667 0.00 0.00 0.00 4.18
2964 3377 5.067674 TCAGAATAATGAAAAAGGCCCATCG 59.932 40.000 0.00 0.00 0.00 3.84
2965 3378 6.276091 GTCAGAATAATGAAAAAGGCCCATC 58.724 40.000 0.00 0.00 0.00 3.51
3076 3489 1.885887 GTTGCTATGTTGGGCAGAACA 59.114 47.619 4.07 4.07 40.08 3.18
3077 3490 1.135689 CGTTGCTATGTTGGGCAGAAC 60.136 52.381 0.00 0.00 39.68 3.01
3116 3529 3.139850 TCGGCGTTTCTTTGTTGGATAA 58.860 40.909 6.85 0.00 0.00 1.75
3118 3531 1.535462 CTCGGCGTTTCTTTGTTGGAT 59.465 47.619 6.85 0.00 0.00 3.41
3169 3582 1.302993 AAACGCCAACGCCTATGGT 60.303 52.632 0.00 0.00 45.53 3.55
3254 3667 0.391263 CGGCCTTCTTAGAAACGCCT 60.391 55.000 22.38 0.00 34.14 5.52
3459 3872 3.275617 TTCTGCCCAATATAGCAACGT 57.724 42.857 0.00 0.00 38.82 3.99
3488 3901 6.879400 AGATCCTTTTAGAAACGTCATAGCT 58.121 36.000 0.00 0.00 0.00 3.32
3511 3924 9.447040 TCGACATAAAAGTATTTCACGATCTAG 57.553 33.333 0.00 0.00 37.28 2.43
3543 3956 1.902508 TGACCCAACTTTGCCACAAAA 59.097 42.857 0.00 0.00 0.00 2.44
3550 3963 5.195001 TCACTATTTTGACCCAACTTTGC 57.805 39.130 0.00 0.00 0.00 3.68
3585 4006 3.190849 CTGCCACTGCCGACATCG 61.191 66.667 0.00 0.00 36.33 3.84
3586 4007 2.265739 TCTGCCACTGCCGACATC 59.734 61.111 0.00 0.00 36.33 3.06


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

AutoCloner maintained by Alex Coulton.