Multiple sequence alignment - TraesCS6D01G389700

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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 TraesCS6D01G389700 chr6D 100.000 3314 0 0 1 3314 465066606 465063293 0.000000e+00 6120
1 TraesCS6D01G389700 chr6D 95.850 506 19 2 2810 3314 322566631 322566127 0.000000e+00 817
2 TraesCS6D01G389700 chr6B 91.922 1993 129 16 826 2810 709559784 709561752 0.000000e+00 2760
3 TraesCS6D01G389700 chr6B 87.097 434 43 11 128 556 709558435 709558860 2.310000e-131 479
4 TraesCS6D01G389700 chr6B 86.643 277 18 6 563 826 709559450 709559720 4.180000e-74 289
5 TraesCS6D01G389700 chr6A 92.723 1168 79 3 826 1988 611706970 611705804 0.000000e+00 1681
6 TraesCS6D01G389700 chr6A 89.306 346 33 2 2469 2810 611673505 611673160 6.570000e-117 431
7 TraesCS6D01G389700 chr6A 86.321 212 12 5 626 826 611707239 611707034 7.200000e-52 215
8 TraesCS6D01G389700 chr5D 95.906 513 19 2 2803 3314 349381757 349382268 0.000000e+00 830
9 TraesCS6D01G389700 chr1D 96.252 507 15 4 2810 3314 159880835 159880331 0.000000e+00 828
10 TraesCS6D01G389700 chr1D 95.850 506 19 2 2810 3314 113816922 113817426 0.000000e+00 817
11 TraesCS6D01G389700 chr2D 96.223 503 17 2 2813 3314 2992235 2991734 0.000000e+00 822
12 TraesCS6D01G389700 chr2D 95.874 509 17 4 2808 3314 537927118 537926612 0.000000e+00 821
13 TraesCS6D01G389700 chrUn 95.850 506 19 2 2810 3314 45795751 45795247 0.000000e+00 817
14 TraesCS6D01G389700 chr4D 95.686 510 18 4 2807 3314 84171420 84170913 0.000000e+00 817
15 TraesCS6D01G389700 chr3D 95.850 506 19 2 2809 3314 394771736 394772239 0.000000e+00 817


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 TraesCS6D01G389700 chr6D 465063293 465066606 3313 True 6120 6120 100.000 1 3314 1 chr6D.!!$R2 3313
1 TraesCS6D01G389700 chr6D 322566127 322566631 504 True 817 817 95.850 2810 3314 1 chr6D.!!$R1 504
2 TraesCS6D01G389700 chr6B 709558435 709561752 3317 False 1176 2760 88.554 128 2810 3 chr6B.!!$F1 2682
3 TraesCS6D01G389700 chr6A 611705804 611707239 1435 True 948 1681 89.522 626 1988 2 chr6A.!!$R2 1362
4 TraesCS6D01G389700 chr5D 349381757 349382268 511 False 830 830 95.906 2803 3314 1 chr5D.!!$F1 511
5 TraesCS6D01G389700 chr1D 159880331 159880835 504 True 828 828 96.252 2810 3314 1 chr1D.!!$R1 504
6 TraesCS6D01G389700 chr1D 113816922 113817426 504 False 817 817 95.850 2810 3314 1 chr1D.!!$F1 504
7 TraesCS6D01G389700 chr2D 2991734 2992235 501 True 822 822 96.223 2813 3314 1 chr2D.!!$R1 501
8 TraesCS6D01G389700 chr2D 537926612 537927118 506 True 821 821 95.874 2808 3314 1 chr2D.!!$R2 506
9 TraesCS6D01G389700 chrUn 45795247 45795751 504 True 817 817 95.850 2810 3314 1 chrUn.!!$R1 504
10 TraesCS6D01G389700 chr4D 84170913 84171420 507 True 817 817 95.686 2807 3314 1 chr4D.!!$R1 507
11 TraesCS6D01G389700 chr3D 394771736 394772239 503 False 817 817 95.850 2809 3314 1 chr3D.!!$F1 505

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
841 1506 0.391661 CTTCAGCTGTATGGCACCGT 60.392 55.0 14.67 0.0 34.17 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2382 3053 0.03918 GGACCCCCAAAACGATTCCT 59.961 55.0 0.0 0.0 0.0 3.36 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
26 27 8.757789 CACGTAGTTTTAGTTAAAGTGATCACA 58.242 33.333 27.02 4.33 41.61 3.58
27 28 8.975439 ACGTAGTTTTAGTTAAAGTGATCACAG 58.025 33.333 27.02 0.00 37.78 3.66
28 29 8.975439 CGTAGTTTTAGTTAAAGTGATCACAGT 58.025 33.333 27.02 16.25 31.84 3.55
37 38 9.725019 AGTTAAAGTGATCACAGTTATTGATGA 57.275 29.630 27.02 6.78 38.53 2.92
87 88 7.872113 AGAAAATTTTAAAAATGTGGGTGCA 57.128 28.000 4.44 0.00 0.00 4.57
88 89 8.462589 AGAAAATTTTAAAAATGTGGGTGCAT 57.537 26.923 4.44 0.00 0.00 3.96
89 90 8.911965 AGAAAATTTTAAAAATGTGGGTGCATT 58.088 25.926 4.44 0.00 40.43 3.56
99 100 7.999450 AAATGTGGGTGCATTTTCAATAAAT 57.001 28.000 0.00 0.00 43.97 1.40
100 101 6.988622 ATGTGGGTGCATTTTCAATAAATG 57.011 33.333 5.99 5.99 39.84 2.32
124 125 6.856895 GCTCATAGCATTACAAAAAGGTTCT 58.143 36.000 0.00 0.00 41.89 3.01
125 126 7.315890 GCTCATAGCATTACAAAAAGGTTCTT 58.684 34.615 0.00 0.00 41.89 2.52
126 127 7.274250 GCTCATAGCATTACAAAAAGGTTCTTG 59.726 37.037 0.00 0.00 41.89 3.02
146 147 8.342634 GTTCTTGCACTTCATACACTTTTAGAA 58.657 33.333 0.00 0.00 0.00 2.10
150 151 9.515020 TTGCACTTCATACACTTTTAGAAAAAG 57.485 29.630 9.92 9.92 0.00 2.27
288 292 5.153513 CAGAATGTTCACCCATTGTTTACG 58.846 41.667 0.00 0.00 35.24 3.18
296 300 7.175119 TGTTCACCCATTGTTTACGAAATATCA 59.825 33.333 0.00 0.00 0.00 2.15
375 379 7.764695 AAACAACAGCAAATACACTAAAACC 57.235 32.000 0.00 0.00 0.00 3.27
377 381 6.868622 ACAACAGCAAATACACTAAAACCAA 58.131 32.000 0.00 0.00 0.00 3.67
378 382 6.978080 ACAACAGCAAATACACTAAAACCAAG 59.022 34.615 0.00 0.00 0.00 3.61
379 383 5.528870 ACAGCAAATACACTAAAACCAAGC 58.471 37.500 0.00 0.00 0.00 4.01
380 384 5.068460 ACAGCAAATACACTAAAACCAAGCA 59.932 36.000 0.00 0.00 0.00 3.91
381 385 5.630680 CAGCAAATACACTAAAACCAAGCAG 59.369 40.000 0.00 0.00 0.00 4.24
386 390 7.817418 AATACACTAAAACCAAGCAGAAAGA 57.183 32.000 0.00 0.00 0.00 2.52
387 391 7.817418 ATACACTAAAACCAAGCAGAAAGAA 57.183 32.000 0.00 0.00 0.00 2.52
388 392 6.524101 ACACTAAAACCAAGCAGAAAGAAA 57.476 33.333 0.00 0.00 0.00 2.52
389 393 6.930731 ACACTAAAACCAAGCAGAAAGAAAA 58.069 32.000 0.00 0.00 0.00 2.29
429 433 4.093743 ACACCAAAAAGAAAGGACAAGGT 58.906 39.130 0.00 0.00 0.00 3.50
433 437 5.105351 ACCAAAAAGAAAGGACAAGGTCTTG 60.105 40.000 8.97 8.97 45.58 3.02
497 502 7.371159 CCACATATACGAACACATACTCATCT 58.629 38.462 0.00 0.00 0.00 2.90
505 510 7.946207 ACGAACACATACTCATCTCTATGAAT 58.054 34.615 0.00 0.00 41.57 2.57
511 516 9.085250 CACATACTCATCTCTATGAATGTATGC 57.915 37.037 18.32 0.00 44.91 3.14
513 518 9.085250 CATACTCATCTCTATGAATGTATGCAC 57.915 37.037 11.58 0.00 40.56 4.57
521 526 1.086696 GAATGTATGCACGCACACCT 58.913 50.000 0.00 0.00 0.00 4.00
524 529 1.434555 TGTATGCACGCACACCTTAC 58.565 50.000 0.00 0.00 0.00 2.34
525 530 1.001520 TGTATGCACGCACACCTTACT 59.998 47.619 0.00 0.00 0.00 2.24
534 539 3.068307 ACGCACACCTTACTCCTATGATC 59.932 47.826 0.00 0.00 0.00 2.92
540 545 5.144100 CACCTTACTCCTATGATCACCTCT 58.856 45.833 0.00 0.00 0.00 3.69
543 548 5.835819 CCTTACTCCTATGATCACCTCTGAA 59.164 44.000 0.00 0.00 0.00 3.02
549 554 8.228206 ACTCCTATGATCACCTCTGAAATACTA 58.772 37.037 0.00 0.00 0.00 1.82
552 557 8.310382 CCTATGATCACCTCTGAAATACTAAGG 58.690 40.741 0.00 0.00 0.00 2.69
559 1147 6.375455 CACCTCTGAAATACTAAGGCAAACAT 59.625 38.462 0.00 0.00 0.00 2.71
560 1148 6.948309 ACCTCTGAAATACTAAGGCAAACATT 59.052 34.615 0.00 0.00 0.00 2.71
561 1149 7.094205 ACCTCTGAAATACTAAGGCAAACATTG 60.094 37.037 0.00 0.00 0.00 2.82
566 1154 7.395772 TGAAATACTAAGGCAAACATTGGATGA 59.604 33.333 0.00 0.00 0.00 2.92
571 1159 1.205417 GGCAAACATTGGATGACTGGG 59.795 52.381 0.00 0.00 0.00 4.45
637 1225 9.487790 TTTGTTCTAAAATAGCCATTCTTTTGG 57.512 29.630 0.00 0.00 39.94 3.28
653 1241 6.653526 TCTTTTGGAGAGAAATGAATGCAA 57.346 33.333 0.00 0.00 0.00 4.08
661 1249 4.093998 AGAGAAATGAATGCAAGCACGTAG 59.906 41.667 0.00 0.00 0.00 3.51
705 1301 2.398588 TGTCCTCGCCCTCTCATTTAT 58.601 47.619 0.00 0.00 0.00 1.40
755 1356 6.417191 AATACAACACTAGTAAACGGCATG 57.583 37.500 0.00 0.00 0.00 4.06
835 1500 4.744795 AAGTACTCCTTCAGCTGTATGG 57.255 45.455 14.67 13.93 0.00 2.74
838 1503 1.065854 ACTCCTTCAGCTGTATGGCAC 60.066 52.381 14.67 0.00 34.17 5.01
841 1506 0.391661 CTTCAGCTGTATGGCACCGT 60.392 55.000 14.67 0.00 34.17 4.83
867 1532 9.099454 TGTTTATTTCCACAAAAATACAACACC 57.901 29.630 0.00 0.00 33.42 4.16
884 1549 2.288666 CACCGCTAAACTGCATGGTAT 58.711 47.619 0.00 0.00 0.00 2.73
1113 1783 2.379634 CGTCTGCAACATCGGCGAA 61.380 57.895 15.93 0.00 0.00 4.70
1120 1790 1.135699 CAACATCGGCGAATGCTTGC 61.136 55.000 15.93 0.00 42.25 4.01
1221 1891 0.614134 AGAAGGGGGACTACACCGAC 60.614 60.000 0.00 0.00 41.26 4.79
1263 1933 2.936919 AATGGGCATTGCTCGATCTA 57.063 45.000 8.82 0.00 0.00 1.98
1284 1954 2.892374 TGCGATGACCTTATCACACTG 58.108 47.619 0.00 0.00 41.24 3.66
1313 1983 0.895530 GACACTGGTCGATTCCTCCA 59.104 55.000 0.00 0.00 33.68 3.86
1323 1993 3.993081 GTCGATTCCTCCATAAGAGCATG 59.007 47.826 0.00 0.00 41.74 4.06
1446 2116 0.523968 CGGGCTCAATCGTGCATTTG 60.524 55.000 0.00 0.00 33.19 2.32
1479 2149 0.393077 CTGATGTAGGGGTAAGGGCG 59.607 60.000 0.00 0.00 0.00 6.13
1587 2257 5.913137 TCGAGCAATTTTGGACCAATTAT 57.087 34.783 7.99 2.15 0.00 1.28
1673 2343 0.671781 ATCCACTCGCTCACAGTTGC 60.672 55.000 0.00 0.00 0.00 4.17
1752 2422 5.132144 GGAAACCATCTTCCCTAGTATTGGA 59.868 44.000 0.00 0.00 39.26 3.53
1782 2452 0.984995 ACCAAGGACTAACAGAGGGC 59.015 55.000 0.00 0.00 0.00 5.19
1798 2468 4.160439 CAGAGGGCGGCAGATATTATCTTA 59.840 45.833 12.47 0.00 37.58 2.10
1801 2471 4.716784 AGGGCGGCAGATATTATCTTATGA 59.283 41.667 12.47 0.00 37.58 2.15
1811 2481 9.040259 CAGATATTATCTTATGAAGTCTGGGGA 57.960 37.037 3.34 0.00 37.58 4.81
1821 2491 1.963985 AGTCTGGGGAAGATCTGCTT 58.036 50.000 0.00 0.00 37.23 3.91
1836 2506 1.007387 GCTTCTTGTGGCCAAACCG 60.007 57.895 7.24 0.00 43.94 4.44
1882 2552 4.970611 CAGTTGTTCGTAGAGTGGATATCG 59.029 45.833 0.00 0.00 38.43 2.92
1910 2580 1.433534 GTGCTTGAGCCAGTCAGTAC 58.566 55.000 0.00 0.00 41.18 2.73
1922 2592 1.153647 TCAGTACCATCGGCAAGCG 60.154 57.895 0.00 0.00 0.00 4.68
1944 2614 1.807755 GCTCTATTCGTCAGCCATGCA 60.808 52.381 0.00 0.00 0.00 3.96
1948 2618 0.813184 ATTCGTCAGCCATGCAAAGG 59.187 50.000 4.27 4.27 0.00 3.11
2017 2687 5.218139 GCATTCACTTTATAGAGCCAATGC 58.782 41.667 17.24 17.24 38.44 3.56
2059 2729 5.281727 AGCCTTCAAAAGTGACGATTTTTC 58.718 37.500 0.00 0.00 31.90 2.29
2095 2765 2.287970 CGCATCATGGTTGAATGGGATG 60.288 50.000 3.17 0.00 34.96 3.51
2106 2776 1.777272 GAATGGGATGCCCTAGAAGGT 59.223 52.381 0.00 0.00 45.70 3.50
2126 2796 1.299976 GCTTCCGTCCATTCACCCT 59.700 57.895 0.00 0.00 0.00 4.34
2136 2806 1.002134 ATTCACCCTCGCCCAAGTG 60.002 57.895 0.00 0.00 0.00 3.16
2155 2825 2.160417 GTGTTCACAGATTACTGCAGGC 59.840 50.000 19.93 4.33 46.95 4.85
2216 2886 2.774234 AGTGGGGTTACTCAGATGATGG 59.226 50.000 0.00 0.00 0.00 3.51
2262 2932 6.111382 GTCCTCTCAACTTGATGATGAATCA 58.889 40.000 0.00 0.00 43.79 2.57
2289 2959 4.286808 TCCTCTGAACTTGGTGATGAATCA 59.713 41.667 0.00 0.00 0.00 2.57
2293 2963 5.045359 TCTGAACTTGGTGATGAATCATCCT 60.045 40.000 19.38 0.00 39.87 3.24
2294 2964 5.188434 TGAACTTGGTGATGAATCATCCTC 58.812 41.667 19.38 12.47 39.87 3.71
2295 2965 4.162040 ACTTGGTGATGAATCATCCTCC 57.838 45.455 19.38 19.74 39.87 4.30
2296 2966 3.524789 ACTTGGTGATGAATCATCCTCCA 59.475 43.478 23.28 23.28 39.87 3.86
2305 2975 3.772572 TGAATCATCCTCCAACGAACCTA 59.227 43.478 0.00 0.00 0.00 3.08
2306 2976 4.224147 TGAATCATCCTCCAACGAACCTAA 59.776 41.667 0.00 0.00 0.00 2.69
2353 3023 7.016153 TGAAATCTGGATAGTTTGTAGTGGT 57.984 36.000 0.00 0.00 0.00 4.16
2379 3050 9.989869 TTAAAACAAAAATTGGAATTCCGAAAC 57.010 25.926 18.59 0.00 39.43 2.78
2382 3053 4.857509 AAAATTGGAATTCCGAAACCGA 57.142 36.364 18.59 0.00 39.43 4.69
2389 3060 3.429043 TTCCGAAACCGAGGAATCG 57.571 52.632 12.01 12.01 41.19 3.34
2398 3069 1.029947 CCGAGGAATCGTTTTGGGGG 61.030 60.000 0.00 0.00 0.00 5.40
2399 3070 0.322187 CGAGGAATCGTTTTGGGGGT 60.322 55.000 0.00 0.00 0.00 4.95
2400 3071 1.460504 GAGGAATCGTTTTGGGGGTC 58.539 55.000 0.00 0.00 0.00 4.46
2421 3092 6.014584 GGGTCCAACTAATTTTGAGTGGAAAT 60.015 38.462 8.61 0.00 30.79 2.17
2480 3151 7.351981 AGTGTTTCGGTATTTAACGGTTTTAC 58.648 34.615 0.00 0.00 0.00 2.01
2481 3152 7.011857 AGTGTTTCGGTATTTAACGGTTTTACA 59.988 33.333 0.00 0.00 0.00 2.41
2482 3153 7.802720 GTGTTTCGGTATTTAACGGTTTTACAT 59.197 33.333 0.00 0.00 0.00 2.29
2483 3154 8.348507 TGTTTCGGTATTTAACGGTTTTACATT 58.651 29.630 0.00 0.00 0.00 2.71
2484 3155 8.839914 GTTTCGGTATTTAACGGTTTTACATTC 58.160 33.333 0.00 0.00 0.00 2.67
2485 3156 7.071014 TCGGTATTTAACGGTTTTACATTCC 57.929 36.000 0.00 0.00 0.00 3.01
2487 3158 6.183360 CGGTATTTAACGGTTTTACATTCCGA 60.183 38.462 9.75 0.00 46.05 4.55
2488 3159 6.960992 GGTATTTAACGGTTTTACATTCCGAC 59.039 38.462 9.75 0.00 46.05 4.79
2489 3160 5.998454 TTTAACGGTTTTACATTCCGACA 57.002 34.783 9.75 0.00 46.05 4.35
2490 3161 6.557291 TTTAACGGTTTTACATTCCGACAT 57.443 33.333 9.75 0.00 46.05 3.06
2584 3256 2.955660 CCCAAACAAGTGCTCCTACAAA 59.044 45.455 0.00 0.00 0.00 2.83
2587 3259 4.498009 CCAAACAAGTGCTCCTACAAACAG 60.498 45.833 0.00 0.00 0.00 3.16
2600 3272 7.004555 TCCTACAAACAGTAATCATCACACT 57.995 36.000 0.00 0.00 30.92 3.55
2609 3281 5.006068 CAGTAATCATCACACTGAATCACCG 59.994 44.000 0.00 0.00 41.80 4.94
2610 3282 3.616956 ATCATCACACTGAATCACCGT 57.383 42.857 0.00 0.00 0.00 4.83
2662 3334 9.481340 GAAATATATATGCAGTGAGAGACAACA 57.519 33.333 0.00 0.00 0.00 3.33
2663 3335 9.486497 AAATATATATGCAGTGAGAGACAACAG 57.514 33.333 0.00 0.00 0.00 3.16
2664 3336 2.469274 ATGCAGTGAGAGACAACAGG 57.531 50.000 0.00 0.00 0.00 4.00
2676 3348 5.148502 AGAGACAACAGGAGGTTTAGAAGA 58.851 41.667 0.00 0.00 37.72 2.87
2693 3365 9.980780 GTTTAGAAGAATAAATCTCTTGCTGTC 57.019 33.333 0.00 0.00 37.42 3.51
2759 3431 4.963318 TTATGAGGAGGAGCTATTGGTG 57.037 45.455 0.00 0.00 0.00 4.17
2788 3460 1.663911 TAGCATGTACAACCCCAGGT 58.336 50.000 0.00 0.00 37.65 4.00
2792 3464 1.431195 ATGTACAACCCCAGGTGGCA 61.431 55.000 0.00 0.00 35.34 4.92
2799 3471 3.636231 CCCAGGTGGCAAGACGGA 61.636 66.667 0.00 0.00 0.00 4.69
2805 3477 2.031919 TGGCAAGACGGACGCATT 59.968 55.556 0.00 0.00 0.00 3.56
2831 3503 5.012975 AGGTGTTGGGGAACGTAGTAATTTA 59.987 40.000 0.00 0.00 45.00 1.40
2992 3665 1.731424 CGATCAAGTACCGAACGCACT 60.731 52.381 0.00 0.00 0.00 4.40
3111 3784 4.441495 GGTGACGATGATGATGTTCTACCA 60.441 45.833 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.757789 TGTGATCACTTTAACTAAAACTACGTG 58.242 33.333 25.55 0.00 0.00 4.49
1 2 8.876275 TGTGATCACTTTAACTAAAACTACGT 57.124 30.769 25.55 0.00 0.00 3.57
2 3 8.975439 ACTGTGATCACTTTAACTAAAACTACG 58.025 33.333 25.55 0.00 0.00 3.51
11 12 9.725019 TCATCAATAACTGTGATCACTTTAACT 57.275 29.630 25.55 11.78 33.37 2.24
61 62 9.396022 TGCACCCACATTTTTAAAATTTTCTAA 57.604 25.926 6.72 0.63 0.00 2.10
62 63 8.964476 TGCACCCACATTTTTAAAATTTTCTA 57.036 26.923 6.72 0.00 0.00 2.10
63 64 7.872113 TGCACCCACATTTTTAAAATTTTCT 57.128 28.000 6.72 0.00 0.00 2.52
64 65 9.526713 AAATGCACCCACATTTTTAAAATTTTC 57.473 25.926 6.72 0.00 45.63 2.29
76 77 7.380431 CATTTATTGAAAATGCACCCACATT 57.620 32.000 0.00 0.00 42.01 2.71
77 78 6.988622 CATTTATTGAAAATGCACCCACAT 57.011 33.333 0.00 0.00 31.82 3.21
100 101 6.856895 AGAACCTTTTTGTAATGCTATGAGC 58.143 36.000 0.00 0.00 42.82 4.26
101 102 7.274250 GCAAGAACCTTTTTGTAATGCTATGAG 59.726 37.037 0.00 0.00 0.00 2.90
102 103 7.090173 GCAAGAACCTTTTTGTAATGCTATGA 58.910 34.615 0.00 0.00 0.00 2.15
103 104 6.867816 TGCAAGAACCTTTTTGTAATGCTATG 59.132 34.615 0.00 0.00 32.74 2.23
104 105 6.868339 GTGCAAGAACCTTTTTGTAATGCTAT 59.132 34.615 0.00 0.00 32.74 2.97
105 106 6.040391 AGTGCAAGAACCTTTTTGTAATGCTA 59.960 34.615 0.00 0.00 32.74 3.49
106 107 5.049828 GTGCAAGAACCTTTTTGTAATGCT 58.950 37.500 0.00 0.00 32.74 3.79
107 108 5.049828 AGTGCAAGAACCTTTTTGTAATGC 58.950 37.500 0.00 0.00 0.00 3.56
108 109 6.756074 TGAAGTGCAAGAACCTTTTTGTAATG 59.244 34.615 0.00 0.00 0.00 1.90
109 110 6.872920 TGAAGTGCAAGAACCTTTTTGTAAT 58.127 32.000 0.00 0.00 0.00 1.89
110 111 6.274157 TGAAGTGCAAGAACCTTTTTGTAA 57.726 33.333 0.00 0.00 0.00 2.41
111 112 5.906113 TGAAGTGCAAGAACCTTTTTGTA 57.094 34.783 0.00 0.00 0.00 2.41
112 113 4.799564 TGAAGTGCAAGAACCTTTTTGT 57.200 36.364 0.00 0.00 0.00 2.83
113 114 6.198966 GTGTATGAAGTGCAAGAACCTTTTTG 59.801 38.462 0.00 0.00 0.00 2.44
114 115 6.096846 AGTGTATGAAGTGCAAGAACCTTTTT 59.903 34.615 0.00 0.00 0.00 1.94
115 116 5.594317 AGTGTATGAAGTGCAAGAACCTTTT 59.406 36.000 0.00 0.00 0.00 2.27
116 117 5.133221 AGTGTATGAAGTGCAAGAACCTTT 58.867 37.500 0.00 0.00 0.00 3.11
117 118 4.718961 AGTGTATGAAGTGCAAGAACCTT 58.281 39.130 0.00 0.00 0.00 3.50
118 119 4.357918 AGTGTATGAAGTGCAAGAACCT 57.642 40.909 0.00 0.00 0.00 3.50
119 120 5.438761 AAAGTGTATGAAGTGCAAGAACC 57.561 39.130 0.00 0.00 0.00 3.62
120 121 7.861630 TCTAAAAGTGTATGAAGTGCAAGAAC 58.138 34.615 0.00 0.00 0.00 3.01
121 122 8.445275 TTCTAAAAGTGTATGAAGTGCAAGAA 57.555 30.769 0.00 0.00 0.00 2.52
122 123 8.445275 TTTCTAAAAGTGTATGAAGTGCAAGA 57.555 30.769 0.00 0.00 0.00 3.02
123 124 9.515020 TTTTTCTAAAAGTGTATGAAGTGCAAG 57.485 29.630 0.00 0.00 0.00 4.01
124 125 9.515020 CTTTTTCTAAAAGTGTATGAAGTGCAA 57.485 29.630 0.00 0.00 0.00 4.08
125 126 8.682710 ACTTTTTCTAAAAGTGTATGAAGTGCA 58.317 29.630 14.73 0.00 38.88 4.57
258 262 7.118723 ACAATGGGTGAACATTCTGTATATGT 58.881 34.615 0.00 0.00 38.94 2.29
265 269 5.049060 TCGTAAACAATGGGTGAACATTCTG 60.049 40.000 0.00 0.00 38.94 3.02
272 276 7.689446 TGATATTTCGTAAACAATGGGTGAA 57.311 32.000 0.00 0.00 0.00 3.18
334 338 9.255304 GCTGTTGTTTTCTTACATTTCCATTTA 57.745 29.630 0.00 0.00 0.00 1.40
356 360 5.068460 TGCTTGGTTTTAGTGTATTTGCTGT 59.932 36.000 0.00 0.00 0.00 4.40
357 361 5.527951 TGCTTGGTTTTAGTGTATTTGCTG 58.472 37.500 0.00 0.00 0.00 4.41
359 363 5.768317 TCTGCTTGGTTTTAGTGTATTTGC 58.232 37.500 0.00 0.00 0.00 3.68
400 404 8.073467 TGTCCTTTCTTTTTGGTGTTCTTATT 57.927 30.769 0.00 0.00 0.00 1.40
402 406 7.363443 CCTTGTCCTTTCTTTTTGGTGTTCTTA 60.363 37.037 0.00 0.00 0.00 2.10
467 472 4.674281 TGTGTTCGTATATGTGGGCATA 57.326 40.909 0.00 0.00 41.31 3.14
468 473 3.552132 TGTGTTCGTATATGTGGGCAT 57.448 42.857 0.00 0.00 39.03 4.40
497 502 3.555547 GTGTGCGTGCATACATTCATAGA 59.444 43.478 15.58 0.00 37.86 1.98
505 510 1.001520 AGTAAGGTGTGCGTGCATACA 59.998 47.619 20.75 2.78 39.36 2.29
510 515 0.245539 TAGGAGTAAGGTGTGCGTGC 59.754 55.000 0.00 0.00 0.00 5.34
511 516 2.165641 TCATAGGAGTAAGGTGTGCGTG 59.834 50.000 0.00 0.00 0.00 5.34
513 518 3.068165 TGATCATAGGAGTAAGGTGTGCG 59.932 47.826 0.00 0.00 0.00 5.34
521 526 7.921041 ATTTCAGAGGTGATCATAGGAGTAA 57.079 36.000 0.00 0.00 30.85 2.24
524 529 7.537596 AGTATTTCAGAGGTGATCATAGGAG 57.462 40.000 0.00 0.00 30.85 3.69
525 530 9.083422 CTTAGTATTTCAGAGGTGATCATAGGA 57.917 37.037 0.00 0.00 30.85 2.94
534 539 5.705441 TGTTTGCCTTAGTATTTCAGAGGTG 59.295 40.000 0.00 0.00 0.00 4.00
540 545 7.395772 TCATCCAATGTTTGCCTTAGTATTTCA 59.604 33.333 0.00 0.00 0.00 2.69
543 548 6.891908 AGTCATCCAATGTTTGCCTTAGTATT 59.108 34.615 0.00 0.00 0.00 1.89
549 554 2.564062 CCAGTCATCCAATGTTTGCCTT 59.436 45.455 0.00 0.00 0.00 4.35
552 557 2.170166 TCCCAGTCATCCAATGTTTGC 58.830 47.619 0.00 0.00 0.00 3.68
559 1147 5.163099 CCAATAGGTATTCCCAGTCATCCAA 60.163 44.000 0.00 0.00 34.66 3.53
560 1148 4.350816 CCAATAGGTATTCCCAGTCATCCA 59.649 45.833 0.00 0.00 34.66 3.41
561 1149 4.911390 CCAATAGGTATTCCCAGTCATCC 58.089 47.826 0.00 0.00 34.66 3.51
623 1211 6.484288 TCATTTCTCTCCAAAAGAATGGCTA 58.516 36.000 0.00 0.00 40.46 3.93
624 1212 5.327732 TCATTTCTCTCCAAAAGAATGGCT 58.672 37.500 0.00 0.00 40.46 4.75
630 1218 6.653526 TTGCATTCATTTCTCTCCAAAAGA 57.346 33.333 0.00 0.00 0.00 2.52
631 1219 5.347907 GCTTGCATTCATTTCTCTCCAAAAG 59.652 40.000 0.00 0.00 0.00 2.27
636 1224 3.730061 CGTGCTTGCATTCATTTCTCTCC 60.730 47.826 0.00 0.00 0.00 3.71
637 1225 3.120060 ACGTGCTTGCATTCATTTCTCTC 60.120 43.478 0.00 0.00 0.00 3.20
653 1241 3.579709 CTTGTTCTCATGTCTACGTGCT 58.420 45.455 0.00 0.00 33.05 4.40
661 1249 3.254166 ACATTGCACCTTGTTCTCATGTC 59.746 43.478 0.00 0.00 0.00 3.06
705 1301 6.286758 TGTGGAAATAAACGTGGTACAACTA 58.713 36.000 0.00 0.00 44.16 2.24
785 1386 8.958060 AATGGAGTCGGTGGCTATATATATAT 57.042 34.615 10.10 10.10 0.00 0.86
787 1388 8.807118 CATAATGGAGTCGGTGGCTATATATAT 58.193 37.037 0.00 0.00 0.00 0.86
788 1389 8.002459 TCATAATGGAGTCGGTGGCTATATATA 58.998 37.037 0.00 0.00 0.00 0.86
826 1427 0.250727 AAACACGGTGCCATACAGCT 60.251 50.000 8.30 0.00 44.86 4.24
827 1428 1.444836 TAAACACGGTGCCATACAGC 58.555 50.000 8.30 0.00 43.56 4.40
828 1429 4.438200 GGAAATAAACACGGTGCCATACAG 60.438 45.833 8.30 0.00 0.00 2.74
835 1500 3.357166 TTGTGGAAATAAACACGGTGC 57.643 42.857 8.30 0.00 40.39 5.01
838 1503 7.932120 TGTATTTTTGTGGAAATAAACACGG 57.068 32.000 0.00 0.00 40.39 4.94
841 1506 9.099454 GGTGTTGTATTTTTGTGGAAATAAACA 57.901 29.630 0.00 0.00 34.32 2.83
867 1532 3.874543 TGGTTATACCATGCAGTTTAGCG 59.125 43.478 0.00 0.00 44.79 4.26
920 1586 5.163195 AAGGAGTACTTCACAATGGAGTTGT 60.163 40.000 3.42 0.00 40.95 3.32
948 1614 2.613977 GGCTCTTGCTTCTACTTCTGCA 60.614 50.000 0.00 0.00 39.59 4.41
1113 1783 0.311790 CGTTGTTGGACAGCAAGCAT 59.688 50.000 1.72 0.00 32.25 3.79
1120 1790 1.455786 GTCGATGTCGTTGTTGGACAG 59.544 52.381 2.04 0.00 46.55 3.51
1185 1855 1.263356 TCTCGGGGTAGTCCTTTGTG 58.737 55.000 0.00 0.00 35.33 3.33
1221 1891 3.100671 ACTAGGCTTGAAGTAGTGAGGG 58.899 50.000 2.20 0.00 0.00 4.30
1263 1933 3.461061 CAGTGTGATAAGGTCATCGCAT 58.539 45.455 2.99 0.00 44.72 4.73
1284 1954 1.429463 GACCAGTGTCGATGTTCACC 58.571 55.000 0.66 0.00 35.45 4.02
1407 2077 1.597663 GTGAACGGGTTGAGAACACAG 59.402 52.381 0.00 0.00 33.25 3.66
1446 2116 1.202580 ACATCAGGTATGCTCGCCTTC 60.203 52.381 0.00 0.00 39.39 3.46
1479 2149 2.209273 GGTTTTGTTGTCATGGCAACC 58.791 47.619 33.83 19.67 45.80 3.77
1587 2257 4.263727 ACCATGCATGTAGGTTTGTAAGGA 60.264 41.667 24.58 0.00 29.58 3.36
1673 2343 1.535462 GTTCCCCAACAACGACATCAG 59.465 52.381 0.00 0.00 32.14 2.90
1710 2380 1.827344 TCCATCGAGATTGTCAGTGCT 59.173 47.619 0.00 0.00 0.00 4.40
1713 2383 3.007940 TGGTTTCCATCGAGATTGTCAGT 59.992 43.478 0.00 0.00 0.00 3.41
1752 2422 0.179018 GTCCTTGGTGGCTTGTGTCT 60.179 55.000 0.00 0.00 35.26 3.41
1782 2452 7.490725 CCAGACTTCATAAGATAATATCTGCCG 59.509 40.741 3.20 0.00 40.13 5.69
1798 2468 2.172293 GCAGATCTTCCCCAGACTTCAT 59.828 50.000 0.00 0.00 32.83 2.57
1801 2471 1.963985 AGCAGATCTTCCCCAGACTT 58.036 50.000 0.00 0.00 32.83 3.01
1811 2481 1.074405 TGGCCACAAGAAGCAGATCTT 59.926 47.619 0.00 0.00 40.23 2.40
1821 2491 2.279935 ATAACGGTTTGGCCACAAGA 57.720 45.000 3.88 0.00 37.97 3.02
1836 2506 8.189460 ACTGGTTGATCGAGAGTAAAGTATAAC 58.811 37.037 0.00 0.00 0.00 1.89
1882 2552 1.271054 TGGCTCAAGCACCTTCTTCTC 60.271 52.381 4.13 0.00 44.36 2.87
1922 2592 1.863454 CATGGCTGACGAATAGAGCAC 59.137 52.381 0.00 0.00 34.20 4.40
1944 2614 1.375326 GTTGACGGAGAGGCCCTTT 59.625 57.895 0.00 0.00 0.00 3.11
1948 2618 4.070552 AGCGTTGACGGAGAGGCC 62.071 66.667 5.62 0.00 40.23 5.19
2017 2687 3.254892 GCTCAAAGTTCCCTCGAGTTAG 58.745 50.000 12.31 0.00 0.00 2.34
2052 2722 4.736793 CGCCTATCAGCAACATGAAAAATC 59.263 41.667 0.00 0.00 31.76 2.17
2059 2729 2.396700 TGCGCCTATCAGCAACATG 58.603 52.632 4.18 0.00 40.78 3.21
2095 2765 0.744771 CGGAAGCAACCTTCTAGGGC 60.745 60.000 3.76 0.00 45.44 5.19
2106 2776 0.608035 GGGTGAATGGACGGAAGCAA 60.608 55.000 0.00 0.00 0.00 3.91
2126 2796 0.396435 ATCTGTGAACACTTGGGCGA 59.604 50.000 6.51 0.00 0.00 5.54
2136 2806 1.740025 GGCCTGCAGTAATCTGTGAAC 59.260 52.381 13.81 0.00 43.05 3.18
2155 2825 9.745018 ATGGTATAGTTCAGAATAATGAATGGG 57.255 33.333 0.00 0.00 41.05 4.00
2192 2862 1.825474 CATCTGAGTAACCCCACTCGT 59.175 52.381 0.00 0.00 46.60 4.18
2216 2886 3.240861 CGAGTCTTCGTCGGATTCAAATC 59.759 47.826 0.00 0.00 41.84 2.17
2262 2932 2.907892 TCACCAAGTTCAGAGGAGGAT 58.092 47.619 0.00 0.00 0.00 3.24
2289 2959 2.094338 GTCGTTAGGTTCGTTGGAGGAT 60.094 50.000 0.00 0.00 0.00 3.24
2293 2963 4.582701 TTTAGTCGTTAGGTTCGTTGGA 57.417 40.909 0.00 0.00 0.00 3.53
2294 2964 5.655893 TTTTTAGTCGTTAGGTTCGTTGG 57.344 39.130 0.00 0.00 0.00 3.77
2295 2965 6.075280 CCATTTTTAGTCGTTAGGTTCGTTG 58.925 40.000 0.00 0.00 0.00 4.10
2296 2966 5.759763 ACCATTTTTAGTCGTTAGGTTCGTT 59.240 36.000 0.00 0.00 0.00 3.85
2305 2975 8.407064 TCAAACATACAACCATTTTTAGTCGTT 58.593 29.630 0.00 0.00 0.00 3.85
2306 2976 7.932335 TCAAACATACAACCATTTTTAGTCGT 58.068 30.769 0.00 0.00 0.00 4.34
2334 3004 8.212312 TGTTTTAACCACTACAAACTATCCAGA 58.788 33.333 0.00 0.00 31.59 3.86
2353 3023 9.989869 GTTTCGGAATTCCAATTTTTGTTTTAA 57.010 25.926 24.09 0.00 35.14 1.52
2365 3035 1.348366 TCCTCGGTTTCGGAATTCCAA 59.652 47.619 24.09 14.02 36.95 3.53
2366 3036 0.978151 TCCTCGGTTTCGGAATTCCA 59.022 50.000 24.09 8.75 36.95 3.53
2367 3037 2.103537 TTCCTCGGTTTCGGAATTCC 57.896 50.000 15.01 15.01 34.52 3.01
2382 3053 0.039180 GGACCCCCAAAACGATTCCT 59.961 55.000 0.00 0.00 0.00 3.36
2398 3069 9.974980 TTTATTTCCACTCAAAATTAGTTGGAC 57.025 29.630 0.00 0.00 29.60 4.02
2440 3111 8.795842 ACCGAAACACTATGGTATTATTTTGA 57.204 30.769 0.00 0.00 31.60 2.69
2449 3120 6.756074 CCGTTAAATACCGAAACACTATGGTA 59.244 38.462 0.00 0.00 40.95 3.25
2455 3126 6.375945 AAAACCGTTAAATACCGAAACACT 57.624 33.333 0.00 0.00 0.00 3.55
2462 3133 5.958949 CGGAATGTAAAACCGTTAAATACCG 59.041 40.000 0.00 0.00 41.47 4.02
2483 3154 1.278985 ACAGAGCATTTCCATGTCGGA 59.721 47.619 0.00 0.00 44.40 4.55
2484 3155 1.399440 CACAGAGCATTTCCATGTCGG 59.601 52.381 0.00 0.00 32.28 4.79
2485 3156 1.202110 GCACAGAGCATTTCCATGTCG 60.202 52.381 0.00 0.00 44.79 4.35
2486 3157 2.556534 GCACAGAGCATTTCCATGTC 57.443 50.000 0.00 0.00 44.79 3.06
2562 3234 1.771854 TGTAGGAGCACTTGTTTGGGA 59.228 47.619 0.00 0.00 0.00 4.37
2584 3256 5.877012 GGTGATTCAGTGTGATGATTACTGT 59.123 40.000 0.00 0.00 41.82 3.55
2587 3259 4.870426 ACGGTGATTCAGTGTGATGATTAC 59.130 41.667 0.00 0.00 0.00 1.89
2600 3272 2.037121 ACTCACATGTCACGGTGATTCA 59.963 45.455 14.78 8.95 42.62 2.57
2638 3310 8.093307 CCTGTTGTCTCTCACTGCATATATATT 58.907 37.037 0.00 0.00 0.00 1.28
2640 3312 6.777580 TCCTGTTGTCTCTCACTGCATATATA 59.222 38.462 0.00 0.00 0.00 0.86
2641 3313 5.600069 TCCTGTTGTCTCTCACTGCATATAT 59.400 40.000 0.00 0.00 0.00 0.86
2642 3314 4.956075 TCCTGTTGTCTCTCACTGCATATA 59.044 41.667 0.00 0.00 0.00 0.86
2643 3315 3.771479 TCCTGTTGTCTCTCACTGCATAT 59.229 43.478 0.00 0.00 0.00 1.78
2644 3316 3.165071 TCCTGTTGTCTCTCACTGCATA 58.835 45.455 0.00 0.00 0.00 3.14
2645 3317 1.973515 TCCTGTTGTCTCTCACTGCAT 59.026 47.619 0.00 0.00 0.00 3.96
2662 3334 9.898152 CAAGAGATTTATTCTTCTAAACCTCCT 57.102 33.333 0.00 0.00 33.39 3.69
2663 3335 8.616942 GCAAGAGATTTATTCTTCTAAACCTCC 58.383 37.037 0.00 0.00 33.39 4.30
2664 3336 9.389755 AGCAAGAGATTTATTCTTCTAAACCTC 57.610 33.333 0.00 0.00 33.19 3.85
2699 3371 8.721133 AACAAATAAATAGGTCTCTTTGGGTT 57.279 30.769 0.00 0.00 0.00 4.11
2700 3372 8.721133 AAACAAATAAATAGGTCTCTTTGGGT 57.279 30.769 0.00 0.00 0.00 4.51
2739 3411 2.634940 GCACCAATAGCTCCTCCTCATA 59.365 50.000 0.00 0.00 0.00 2.15
2740 3412 1.419387 GCACCAATAGCTCCTCCTCAT 59.581 52.381 0.00 0.00 0.00 2.90
2741 3413 0.833287 GCACCAATAGCTCCTCCTCA 59.167 55.000 0.00 0.00 0.00 3.86
2742 3414 0.249657 CGCACCAATAGCTCCTCCTC 60.250 60.000 0.00 0.00 0.00 3.71
2743 3415 1.826024 CGCACCAATAGCTCCTCCT 59.174 57.895 0.00 0.00 0.00 3.69
2745 3417 1.889573 GGCGCACCAATAGCTCCTC 60.890 63.158 10.83 0.00 34.14 3.71
2746 3418 2.190578 GGCGCACCAATAGCTCCT 59.809 61.111 10.83 0.00 34.14 3.69
2749 3421 1.750399 CAAGGGCGCACCAATAGCT 60.750 57.895 5.73 0.00 43.89 3.32
2759 3431 0.377203 GTACATGCTAACAAGGGCGC 59.623 55.000 0.00 0.00 0.00 6.53
2788 3460 2.031919 AATGCGTCCGTCTTGCCA 59.968 55.556 0.00 0.00 0.00 4.92
2792 3464 0.670546 CACCTCAATGCGTCCGTCTT 60.671 55.000 0.00 0.00 0.00 3.01
2799 3471 1.603455 CCCCAACACCTCAATGCGT 60.603 57.895 0.00 0.00 0.00 5.24
2805 3477 0.682852 CTACGTTCCCCAACACCTCA 59.317 55.000 0.00 0.00 32.14 3.86
2850 3523 4.564199 GCTATGCATCACCATGATCCAGTA 60.564 45.833 0.19 0.00 34.28 2.74
2853 3526 2.106857 TGCTATGCATCACCATGATCCA 59.893 45.455 0.19 0.00 34.28 3.41
2854 3527 2.786777 TGCTATGCATCACCATGATCC 58.213 47.619 0.19 0.00 34.28 3.36
2992 3665 2.343758 GCTGAACTCGGAGGTGCA 59.656 61.111 10.23 2.80 0.00 4.57


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

AutoCloner maintained by Alex Coulton.