Multiple sequence alignment - TraesCS6B01G327100

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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 TraesCS6B01G327100 chr6B 100.000 2599 0 0 1 2599 576811680 576814278 0.000000e+00 4800
1 TraesCS6B01G327100 chr6D 92.455 2094 112 18 547 2599 386161706 386163794 0.000000e+00 2950
2 TraesCS6B01G327100 chr6A 92.413 1318 55 12 547 1837 531000439 531001738 0.000000e+00 1838
3 TraesCS6B01G327100 chr6A 91.206 398 20 4 1934 2319 531001772 531002166 6.370000e-146 527
4 TraesCS6B01G327100 chr6A 90.295 237 20 3 2365 2599 531002170 531002405 9.030000e-80 307
5 TraesCS6B01G327100 chr3B 87.674 503 50 7 1 491 708392517 708392015 2.240000e-160 575
6 TraesCS6B01G327100 chr1B 87.674 503 50 10 1 491 642813116 642813618 2.240000e-160 575
7 TraesCS6B01G327100 chr1B 86.745 513 56 8 1 501 589132698 589133210 6.280000e-156 560
8 TraesCS6B01G327100 chr5B 87.879 495 51 6 1 486 596873870 596874364 8.070000e-160 573
9 TraesCS6B01G327100 chr5B 87.450 502 52 7 1 491 658466765 658467266 3.750000e-158 568
10 TraesCS6B01G327100 chr1D 86.940 513 55 10 1 501 329507061 329506549 1.350000e-157 566
11 TraesCS6B01G327100 chr7B 87.327 505 48 13 1 491 739379541 739380043 4.860000e-157 564
12 TraesCS6B01G327100 chr2D 86.576 514 56 4 1 501 304663933 304664446 2.920000e-154 555
13 TraesCS6B01G327100 chr2B 85.876 531 63 9 1 520 102127712 102128241 2.920000e-154 555


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 TraesCS6B01G327100 chr6B 576811680 576814278 2598 False 4800.000000 4800 100.000000 1 2599 1 chr6B.!!$F1 2598
1 TraesCS6B01G327100 chr6D 386161706 386163794 2088 False 2950.000000 2950 92.455000 547 2599 1 chr6D.!!$F1 2052
2 TraesCS6B01G327100 chr6A 531000439 531002405 1966 False 890.666667 1838 91.304667 547 2599 3 chr6A.!!$F1 2052
3 TraesCS6B01G327100 chr3B 708392015 708392517 502 True 575.000000 575 87.674000 1 491 1 chr3B.!!$R1 490
4 TraesCS6B01G327100 chr1B 642813116 642813618 502 False 575.000000 575 87.674000 1 491 1 chr1B.!!$F2 490
5 TraesCS6B01G327100 chr1B 589132698 589133210 512 False 560.000000 560 86.745000 1 501 1 chr1B.!!$F1 500
6 TraesCS6B01G327100 chr5B 658466765 658467266 501 False 568.000000 568 87.450000 1 491 1 chr5B.!!$F2 490
7 TraesCS6B01G327100 chr1D 329506549 329507061 512 True 566.000000 566 86.940000 1 501 1 chr1D.!!$R1 500
8 TraesCS6B01G327100 chr7B 739379541 739380043 502 False 564.000000 564 87.327000 1 491 1 chr7B.!!$F1 490
9 TraesCS6B01G327100 chr2D 304663933 304664446 513 False 555.000000 555 86.576000 1 501 1 chr2D.!!$F1 500
10 TraesCS6B01G327100 chr2B 102127712 102128241 529 False 555.000000 555 85.876000 1 520 1 chr2B.!!$F1 519

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
149 150 0.034863 AACCACGAACCCAACACACT 60.035 50.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 1879 0.030638 TTTCCGCAGCAAAGCAAGAC 59.969 50.0 0.0 0.0 0.0 3.01 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
85 86 3.339042 CCAGATCTGGCACCCCAT 58.661 61.111 28.45 0.00 44.73 4.00
125 126 2.358195 GGAGGAAACCATACCTGCCATT 60.358 50.000 0.00 0.00 38.41 3.16
143 144 2.350057 TTCATGAACCACGAACCCAA 57.650 45.000 3.38 0.00 0.00 4.12
149 150 0.034863 AACCACGAACCCAACACACT 60.035 50.000 0.00 0.00 0.00 3.55
160 161 2.561569 CCAACACACTTTCCGTCTTCT 58.438 47.619 0.00 0.00 0.00 2.85
174 175 3.739810 CCGTCTTCTAGATGTCGTCGATA 59.260 47.826 18.71 0.00 29.27 2.92
184 186 3.629438 TGTCGTCGATACAGACACAAA 57.371 42.857 0.00 0.00 39.63 2.83
285 287 1.229209 AGGTCCACCACGAGGATGT 60.229 57.895 5.68 0.00 37.52 3.06
307 309 1.743623 CGCCACCACGCCATTCTTA 60.744 57.895 0.00 0.00 0.00 2.10
316 318 3.252215 CCACGCCATTCTTACTTGAACAA 59.748 43.478 0.00 0.00 0.00 2.83
325 327 7.763985 CCATTCTTACTTGAACAAACTGGTTTT 59.236 33.333 0.00 0.00 0.00 2.43
346 348 7.720074 GGTTTTTAAATTCAACCCCAACCATAA 59.280 33.333 8.53 0.00 34.90 1.90
351 353 3.330126 TCAACCCCAACCATAAAACCA 57.670 42.857 0.00 0.00 0.00 3.67
359 361 4.285775 CCCAACCATAAAACCAATGACCTT 59.714 41.667 0.00 0.00 0.00 3.50
375 377 2.169561 GACCTTGTCAGGGAAGGATCTC 59.830 54.545 8.21 0.00 46.01 2.75
410 412 2.278857 GTCGTCATCATCGCCGCT 60.279 61.111 0.00 0.00 0.00 5.52
425 433 2.030457 CGCCGCTAAGACAATAAACAGG 59.970 50.000 0.00 0.00 0.00 4.00
538 552 3.342627 CGCCGCCACGACAAGAAA 61.343 61.111 0.00 0.00 34.06 2.52
539 553 2.887889 CGCCGCCACGACAAGAAAA 61.888 57.895 0.00 0.00 34.06 2.29
540 554 1.357334 GCCGCCACGACAAGAAAAA 59.643 52.632 0.00 0.00 0.00 1.94
541 555 0.039527 GCCGCCACGACAAGAAAAAT 60.040 50.000 0.00 0.00 0.00 1.82
542 556 1.685302 CCGCCACGACAAGAAAAATG 58.315 50.000 0.00 0.00 0.00 2.32
543 557 1.265635 CCGCCACGACAAGAAAAATGA 59.734 47.619 0.00 0.00 0.00 2.57
544 558 2.095263 CCGCCACGACAAGAAAAATGAT 60.095 45.455 0.00 0.00 0.00 2.45
545 559 3.163594 CGCCACGACAAGAAAAATGATC 58.836 45.455 0.00 0.00 0.00 2.92
645 662 0.601057 TGACCGCAGTTCGATCAGAA 59.399 50.000 0.00 0.00 35.38 3.02
719 736 1.335182 CGTACTGACTCAGCCATCGAT 59.665 52.381 5.92 0.00 34.37 3.59
751 768 0.458669 GTCGTCCGCCTAAATCTGGA 59.541 55.000 0.00 0.00 0.00 3.86
762 779 1.626356 AAATCTGGAGCGCCTGCCTA 61.626 55.000 8.34 0.00 44.31 3.93
767 784 4.840005 GAGCGCCTGCCTACACCC 62.840 72.222 2.29 0.00 44.31 4.61
790 807 1.068474 CTACAAGAACCGCTCCAACG 58.932 55.000 0.00 0.00 0.00 4.10
807 824 3.319198 GCAACCTCCTCCCCGACA 61.319 66.667 0.00 0.00 0.00 4.35
893 912 2.273588 TAAAGCCGAAATCCCCCGGG 62.274 60.000 15.80 15.80 45.42 5.73
945 967 1.705078 ATCCCCCTCCCAAATCCCC 60.705 63.158 0.00 0.00 0.00 4.81
946 968 3.438812 CCCCCTCCCAAATCCCCC 61.439 72.222 0.00 0.00 0.00 5.40
960 982 1.304464 CCCCCTCTCCCAAGCAAAC 60.304 63.158 0.00 0.00 0.00 2.93
1023 1045 2.348998 CTGGAGTGGGTGGTGCTC 59.651 66.667 0.00 0.00 0.00 4.26
1068 1090 3.125573 ATGCTGCTGCTGCTGACG 61.126 61.111 27.67 8.16 40.01 4.35
1110 1132 2.049985 CGCGGGATGATCTCCGTC 60.050 66.667 18.79 12.35 46.01 4.79
1116 1138 2.278857 ATGATCTCCGTCGTGCGC 60.279 61.111 0.00 0.00 39.71 6.09
1203 1225 3.071837 TACGAGATGCGGCCCACA 61.072 61.111 0.00 0.00 46.49 4.17
1452 1481 1.791204 GGTGTCGTTTCTTCGTCTTCC 59.209 52.381 0.00 0.00 0.00 3.46
1551 1581 2.693074 TGAGATCGTGATCCGGATTTCA 59.307 45.455 20.22 11.44 38.58 2.69
1558 1588 1.140816 GATCCGGATTTCACTAGCGC 58.859 55.000 20.22 0.00 0.00 5.92
1572 1602 3.549471 CACTAGCGCTCTGTTATCACTTG 59.451 47.826 16.34 0.00 0.00 3.16
1586 1616 1.093159 CACTTGCCTGCTTCAGATCC 58.907 55.000 0.00 0.00 32.44 3.36
1637 1667 7.562412 CGATAAAGATCATCATGAACACTGTC 58.438 38.462 0.00 0.00 31.78 3.51
1647 1677 2.665165 TGAACACTGTCCCTGCAAAAT 58.335 42.857 0.00 0.00 0.00 1.82
1648 1678 3.030291 TGAACACTGTCCCTGCAAAATT 58.970 40.909 0.00 0.00 0.00 1.82
1684 1714 6.775142 TGTGTCTCAGAACCATAAATTTGGAA 59.225 34.615 3.10 0.00 39.25 3.53
1730 1760 5.200483 TCATTAACTTGTTCCCCATGGATC 58.800 41.667 15.22 0.82 41.40 3.36
1742 1772 4.467082 TCCCCATGGATCTTTGTTGATTTG 59.533 41.667 15.22 0.00 35.03 2.32
1751 1781 7.147932 TGGATCTTTGTTGATTTGTCTTGTCAA 60.148 33.333 0.00 0.00 0.00 3.18
1795 1841 1.986882 CCCATGGGAACTGGAATAGC 58.013 55.000 28.27 0.00 35.70 2.97
1833 1879 3.659786 TGGTTGTGAAAGGTATCGAGTG 58.340 45.455 0.00 0.00 0.00 3.51
1837 1883 4.866508 TGTGAAAGGTATCGAGTGTCTT 57.133 40.909 0.00 0.00 0.00 3.01
1850 1896 1.525765 TGTCTTGCTTTGCTGCGGA 60.526 52.632 0.00 0.00 35.36 5.54
1852 1898 0.030638 GTCTTGCTTTGCTGCGGAAA 59.969 50.000 0.00 0.00 35.36 3.13
1886 1932 2.972713 GCCTTGGTGGGAGATGATAGTA 59.027 50.000 0.00 0.00 36.00 1.82
1895 1941 7.102346 GGTGGGAGATGATAGTATCAAGATTG 58.898 42.308 16.61 0.00 43.50 2.67
1896 1942 7.256475 GGTGGGAGATGATAGTATCAAGATTGT 60.256 40.741 16.61 0.00 43.50 2.71
1903 1949 8.757982 ATGATAGTATCAAGATTGTTTTGGCT 57.242 30.769 16.61 0.00 43.50 4.75
1924 1970 5.032220 GCTAATGTTTGTTATTACGGTGGC 58.968 41.667 0.00 0.00 0.00 5.01
1932 1978 4.328536 TGTTATTACGGTGGCTTGAATGT 58.671 39.130 0.00 0.00 0.00 2.71
1933 1979 4.762765 TGTTATTACGGTGGCTTGAATGTT 59.237 37.500 0.00 0.00 0.00 2.71
1934 1980 5.241949 TGTTATTACGGTGGCTTGAATGTTT 59.758 36.000 0.00 0.00 0.00 2.83
1935 1981 4.864704 ATTACGGTGGCTTGAATGTTTT 57.135 36.364 0.00 0.00 0.00 2.43
1975 2047 5.011943 TGGAAGAATGCCTGCTTTTTATTGT 59.988 36.000 0.00 0.00 31.46 2.71
1997 2069 6.341316 TGTGTGATTCTAATTCCTAGAGTGC 58.659 40.000 0.00 0.00 37.93 4.40
2006 2078 5.337578 AATTCCTAGAGTGCAAGAGACTC 57.662 43.478 0.00 0.00 40.25 3.36
2041 2114 3.390967 ACCATTTGGGAAGGGAAACAAAG 59.609 43.478 0.96 0.00 39.02 2.77
2043 2116 4.503123 CCATTTGGGAAGGGAAACAAAGAC 60.503 45.833 0.00 0.00 39.02 3.01
2069 2142 7.417570 CGAAGGTATAATACTCTGGTTCTGGTT 60.418 40.741 0.00 0.00 0.00 3.67
2128 2202 5.010820 CCTGGGTCAGCCTTTAGTATAGTAC 59.989 48.000 0.00 0.00 34.45 2.73
2137 2211 8.204836 CAGCCTTTAGTATAGTACAGGATTTGT 58.795 37.037 19.83 0.64 43.96 2.83
2139 2213 7.041984 GCCTTTAGTATAGTACAGGATTTGTGC 60.042 40.741 19.83 3.13 41.10 4.57
2160 2245 3.867493 GCTTTGCAGCTTCAGAAAACTTT 59.133 39.130 0.00 0.00 43.51 2.66
2277 2363 6.606234 TCGTTAGTTGTTGCTTGATGTTTA 57.394 33.333 0.00 0.00 0.00 2.01
2319 2405 6.849588 ATTTTTGCAACTTTCCATCTGAAC 57.150 33.333 0.00 0.00 31.05 3.18
2322 2408 4.836125 TGCAACTTTCCATCTGAACTTC 57.164 40.909 0.00 0.00 31.05 3.01
2351 2437 3.915437 AACGGCTATTGACAAGTTTGG 57.085 42.857 0.00 0.00 0.00 3.28
2359 2445 6.037610 GGCTATTGACAAGTTTGGATCAGTAG 59.962 42.308 0.00 9.03 35.57 2.57
2379 2465 6.366604 CAGTAGATGATGAATGACTGATGCTC 59.633 42.308 0.00 0.00 37.14 4.26
2411 2497 1.466167 CAACAGCAATTCTCCTGACGG 59.534 52.381 4.74 0.00 33.40 4.79
2482 2568 3.705604 CTGTCCGCTTCAAACAATTTGT 58.294 40.909 0.00 0.00 41.36 2.83
2483 2569 4.791411 GCTGTCCGCTTCAAACAATTTGTA 60.791 41.667 1.76 0.00 37.51 2.41
2491 2578 6.089249 CTTCAAACAATTTGTAGCTTCCCT 57.911 37.500 1.76 0.00 41.36 4.20
2499 2586 6.206829 ACAATTTGTAGCTTCCCTTCAAGTAC 59.793 38.462 0.00 0.00 33.25 2.73
2508 2595 5.437946 CTTCCCTTCAAGTACCTAAATCCC 58.562 45.833 0.00 0.00 0.00 3.85
2519 2606 3.081804 ACCTAAATCCCGCAGTTCAAAG 58.918 45.455 0.00 0.00 0.00 2.77
2549 2637 0.541863 CTAAATCCTGGGCCTCACGT 59.458 55.000 4.53 0.00 0.00 4.49
2567 2655 3.855379 CACGTGCATCTTTTGATCATTGG 59.145 43.478 0.82 0.00 36.97 3.16
2581 2669 5.132502 TGATCATTGGTGTGTTCTCTGTTT 58.867 37.500 0.00 0.00 0.00 2.83
2583 2671 5.499139 TCATTGGTGTGTTCTCTGTTTTC 57.501 39.130 0.00 0.00 0.00 2.29
2590 2678 5.236695 GGTGTGTTCTCTGTTTTCTAACCTC 59.763 44.000 0.00 0.00 33.15 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.147150 TGATTCGTTCAACGGCAATGA 58.853 42.857 10.69 0.00 42.81 2.57
56 57 1.137675 CAGATCTGGAGTTCGATGGCA 59.862 52.381 15.38 0.00 0.00 4.92
85 86 0.167470 CTTCGGCGTCTTAGTCGTGA 59.833 55.000 6.85 0.00 40.52 4.35
125 126 1.134068 TGTTGGGTTCGTGGTTCATGA 60.134 47.619 0.00 0.00 0.00 3.07
143 144 4.281182 ACATCTAGAAGACGGAAAGTGTGT 59.719 41.667 1.17 0.00 0.00 3.72
149 150 3.181513 CGACGACATCTAGAAGACGGAAA 60.182 47.826 20.36 0.00 0.00 3.13
160 161 4.186159 TGTGTCTGTATCGACGACATCTA 58.814 43.478 0.00 0.00 39.52 1.98
174 175 1.229428 CGGATGCAGTTTGTGTCTGT 58.771 50.000 0.00 0.00 35.60 3.41
184 186 2.685017 TCCAGGAGCGGATGCAGT 60.685 61.111 0.00 0.00 46.23 4.40
222 224 1.134818 ACGATATTTGCTCCAGCGTCA 60.135 47.619 0.00 0.00 45.83 4.35
293 295 2.812011 GTTCAAGTAAGAATGGCGTGGT 59.188 45.455 0.00 0.00 0.00 4.16
307 309 9.495572 TGAATTTAAAAACCAGTTTGTTCAAGT 57.504 25.926 0.00 0.00 32.36 3.16
316 318 6.314899 TGGGGTTGAATTTAAAAACCAGTT 57.685 33.333 17.83 0.00 44.29 3.16
325 327 7.147373 TGGTTTTATGGTTGGGGTTGAATTTAA 60.147 33.333 0.00 0.00 0.00 1.52
331 333 3.330126 TGGTTTTATGGTTGGGGTTGA 57.670 42.857 0.00 0.00 0.00 3.18
334 336 3.580895 GTCATTGGTTTTATGGTTGGGGT 59.419 43.478 0.00 0.00 0.00 4.95
346 348 2.176798 TCCCTGACAAGGTCATTGGTTT 59.823 45.455 1.83 0.00 41.94 3.27
351 353 2.348472 TCCTTCCCTGACAAGGTCATT 58.652 47.619 0.00 0.00 41.94 2.57
359 361 3.190383 TCTTGAGATCCTTCCCTGACA 57.810 47.619 0.00 0.00 0.00 3.58
375 377 5.062183 TGACGACGCTGAATAAAGATTCTTG 59.938 40.000 0.00 0.00 41.87 3.02
410 412 8.700439 AGGTTTTTAGCCTGTTTATTGTCTTA 57.300 30.769 0.00 0.00 34.56 2.10
501 515 4.821589 CCGTTCTCTGGCGGCTCC 62.822 72.222 11.43 0.00 41.53 4.70
521 535 2.381665 TTTTTCTTGTCGTGGCGGCG 62.382 55.000 0.51 0.51 32.50 6.46
522 536 0.039527 ATTTTTCTTGTCGTGGCGGC 60.040 50.000 0.00 0.00 0.00 6.53
523 537 1.265635 TCATTTTTCTTGTCGTGGCGG 59.734 47.619 0.00 0.00 0.00 6.13
524 538 2.679355 TCATTTTTCTTGTCGTGGCG 57.321 45.000 0.00 0.00 0.00 5.69
525 539 4.161333 CAGATCATTTTTCTTGTCGTGGC 58.839 43.478 0.00 0.00 0.00 5.01
526 540 4.161333 GCAGATCATTTTTCTTGTCGTGG 58.839 43.478 0.00 0.00 0.00 4.94
527 541 3.842428 CGCAGATCATTTTTCTTGTCGTG 59.158 43.478 0.00 0.00 0.00 4.35
528 542 3.745975 TCGCAGATCATTTTTCTTGTCGT 59.254 39.130 0.00 0.00 0.00 4.34
529 543 4.091945 TCTCGCAGATCATTTTTCTTGTCG 59.908 41.667 0.00 0.00 33.89 4.35
530 544 5.319931 GTCTCGCAGATCATTTTTCTTGTC 58.680 41.667 0.00 0.00 33.89 3.18
531 545 4.154918 GGTCTCGCAGATCATTTTTCTTGT 59.845 41.667 0.00 0.00 33.89 3.16
532 546 4.437930 GGGTCTCGCAGATCATTTTTCTTG 60.438 45.833 0.00 0.00 33.89 3.02
533 547 3.691609 GGGTCTCGCAGATCATTTTTCTT 59.308 43.478 0.00 0.00 33.89 2.52
534 548 3.274288 GGGTCTCGCAGATCATTTTTCT 58.726 45.455 0.00 0.00 33.89 2.52
535 549 3.009723 TGGGTCTCGCAGATCATTTTTC 58.990 45.455 0.00 0.00 33.89 2.29
536 550 3.071874 TGGGTCTCGCAGATCATTTTT 57.928 42.857 0.00 0.00 33.89 1.94
537 551 2.749621 GTTGGGTCTCGCAGATCATTTT 59.250 45.455 0.00 0.00 33.89 1.82
538 552 2.359900 GTTGGGTCTCGCAGATCATTT 58.640 47.619 0.00 0.00 33.89 2.32
539 553 1.407437 GGTTGGGTCTCGCAGATCATT 60.407 52.381 0.00 0.00 33.89 2.57
540 554 0.179000 GGTTGGGTCTCGCAGATCAT 59.821 55.000 0.00 0.00 33.89 2.45
541 555 0.904865 AGGTTGGGTCTCGCAGATCA 60.905 55.000 0.00 0.00 33.89 2.92
542 556 0.250513 AAGGTTGGGTCTCGCAGATC 59.749 55.000 0.00 0.00 33.89 2.75
543 557 1.568504 TAAGGTTGGGTCTCGCAGAT 58.431 50.000 0.00 0.00 33.89 2.90
544 558 1.001633 GTTAAGGTTGGGTCTCGCAGA 59.998 52.381 0.00 0.00 0.00 4.26
545 559 1.270625 TGTTAAGGTTGGGTCTCGCAG 60.271 52.381 0.00 0.00 0.00 5.18
579 593 3.504863 GGACGACACGAAGCAAAGTATA 58.495 45.455 0.00 0.00 0.00 1.47
698 715 0.867753 CGATGGCTGAGTCAGTACGC 60.868 60.000 21.06 7.74 33.43 4.42
740 757 1.162800 GCAGGCGCTCCAGATTTAGG 61.163 60.000 7.64 0.00 34.30 2.69
762 779 1.278127 CGGTTCTTGTAGATGGGGTGT 59.722 52.381 0.00 0.00 0.00 4.16
767 784 1.207089 TGGAGCGGTTCTTGTAGATGG 59.793 52.381 0.00 0.00 0.00 3.51
769 786 2.674177 CGTTGGAGCGGTTCTTGTAGAT 60.674 50.000 0.00 0.00 0.00 1.98
790 807 3.319198 TGTCGGGGAGGAGGTTGC 61.319 66.667 0.00 0.00 0.00 4.17
807 824 4.157120 GGGTCTATGGCGTGGCGT 62.157 66.667 0.00 0.00 0.00 5.68
945 967 0.035056 ATCGGTTTGCTTGGGAGAGG 60.035 55.000 0.00 0.00 0.00 3.69
946 968 1.065854 AGATCGGTTTGCTTGGGAGAG 60.066 52.381 0.00 0.00 0.00 3.20
1131 1153 3.813596 GGCACCACCGACATCATC 58.186 61.111 0.00 0.00 0.00 2.92
1441 1470 3.755628 CGCGGGGGAAGACGAAGA 61.756 66.667 0.00 0.00 0.00 2.87
1444 1473 1.606885 ATAAACGCGGGGGAAGACGA 61.607 55.000 12.47 0.00 0.00 4.20
1452 1481 1.093496 GGAGGAACATAAACGCGGGG 61.093 60.000 12.47 0.00 0.00 5.73
1551 1581 3.775202 CAAGTGATAACAGAGCGCTAGT 58.225 45.455 11.50 9.98 31.61 2.57
1558 1588 2.983229 AGCAGGCAAGTGATAACAGAG 58.017 47.619 0.00 0.00 0.00 3.35
1572 1602 1.377536 GAACTGGATCTGAAGCAGGC 58.622 55.000 0.00 0.00 31.51 4.85
1586 1616 8.328864 GCATAAAGACCTATTTTACTCGAACTG 58.671 37.037 0.00 0.00 0.00 3.16
1722 1752 6.276832 AGACAAATCAACAAAGATCCATGG 57.723 37.500 4.97 4.97 0.00 3.66
1730 1760 7.010738 AGCATTTGACAAGACAAATCAACAAAG 59.989 33.333 7.37 0.00 45.00 2.77
1742 1772 2.686558 TCGCAAGCATTTGACAAGAC 57.313 45.000 0.00 0.00 36.36 3.01
1751 1781 5.163513 CCTGAACTTAATTTCGCAAGCATT 58.836 37.500 1.63 0.00 37.18 3.56
1795 1841 1.206578 CAGGGCAACTAAACACGCG 59.793 57.895 3.53 3.53 0.00 6.01
1833 1879 0.030638 TTTCCGCAGCAAAGCAAGAC 59.969 50.000 0.00 0.00 0.00 3.01
1837 1883 2.727544 GGTTTCCGCAGCAAAGCA 59.272 55.556 3.21 0.00 35.50 3.91
1850 1896 0.178924 AAGGCAAGCATCTGGGGTTT 60.179 50.000 0.00 0.00 0.00 3.27
1852 1898 1.304713 CAAGGCAAGCATCTGGGGT 60.305 57.895 0.00 0.00 0.00 4.95
1886 1932 7.933033 ACAAACATTAGCCAAAACAATCTTGAT 59.067 29.630 0.00 0.00 0.00 2.57
1895 1941 7.595875 ACCGTAATAACAAACATTAGCCAAAAC 59.404 33.333 0.00 0.00 0.00 2.43
1896 1942 7.595502 CACCGTAATAACAAACATTAGCCAAAA 59.404 33.333 0.00 0.00 0.00 2.44
1903 1949 6.430308 TCAAGCCACCGTAATAACAAACATTA 59.570 34.615 0.00 0.00 0.00 1.90
1935 1981 8.623903 GCATTCTTCCATCTTGTGACATAAATA 58.376 33.333 0.00 0.00 0.00 1.40
1975 2047 6.544928 TGCACTCTAGGAATTAGAATCACA 57.455 37.500 0.00 0.00 37.93 3.58
1988 2060 2.088423 ACGAGTCTCTTGCACTCTAGG 58.912 52.381 0.00 0.00 38.55 3.02
1992 2064 5.862323 TGTAAATTACGAGTCTCTTGCACTC 59.138 40.000 0.00 0.00 37.51 3.51
1997 2069 7.310664 TGGTACTGTAAATTACGAGTCTCTTG 58.689 38.462 10.08 0.00 0.00 3.02
2006 2078 6.988622 TCCCAAATGGTACTGTAAATTACG 57.011 37.500 0.00 0.00 34.77 3.18
2041 2114 7.140048 CAGAACCAGAGTATTATACCTTCGTC 58.860 42.308 0.00 0.00 0.00 4.20
2043 2116 6.040616 ACCAGAACCAGAGTATTATACCTTCG 59.959 42.308 0.00 0.00 0.00 3.79
2128 2202 1.000506 AGCTGCAAAGCACAAATCCTG 59.999 47.619 1.02 0.00 37.25 3.86
2137 2211 2.428171 AGTTTTCTGAAGCTGCAAAGCA 59.572 40.909 1.02 0.00 37.25 3.91
2139 2213 6.364435 GGATAAAGTTTTCTGAAGCTGCAAAG 59.636 38.462 1.02 0.00 0.00 2.77
2140 2214 6.183360 TGGATAAAGTTTTCTGAAGCTGCAAA 60.183 34.615 1.02 0.00 0.00 3.68
2160 2245 6.566079 ACATGGAAGAACAGAAGATGGATA 57.434 37.500 0.00 0.00 0.00 2.59
2298 2384 5.596836 AGTTCAGATGGAAAGTTGCAAAA 57.403 34.783 0.00 0.00 37.23 2.44
2351 2437 7.063662 GCATCAGTCATTCATCATCTACTGATC 59.936 40.741 11.69 5.37 46.43 2.92
2359 2445 7.441760 ACTTAAGAGCATCAGTCATTCATCATC 59.558 37.037 10.09 0.00 37.82 2.92
2369 2455 6.545504 TGTTCAAACTTAAGAGCATCAGTC 57.454 37.500 10.09 0.00 37.82 3.51
2370 2456 6.318648 TGTTGTTCAAACTTAAGAGCATCAGT 59.681 34.615 10.09 0.00 37.82 3.41
2379 2465 7.168135 GGAGAATTGCTGTTGTTCAAACTTAAG 59.832 37.037 0.00 0.00 0.00 1.85
2411 2497 6.728200 TCACAAACACTCATTGATCAAACTC 58.272 36.000 13.09 0.00 0.00 3.01
2413 2499 9.282247 GATATCACAAACACTCATTGATCAAAC 57.718 33.333 13.09 0.00 0.00 2.93
2457 2543 6.917033 CAAATTGTTTGAAGCGGACAGCAAA 61.917 40.000 0.00 0.00 45.46 3.68
2482 2568 6.126854 GGATTTAGGTACTTGAAGGGAAGCTA 60.127 42.308 0.00 0.00 41.75 3.32
2483 2569 5.339282 GGATTTAGGTACTTGAAGGGAAGCT 60.339 44.000 0.00 0.00 41.75 3.74
2487 2573 3.453353 CGGGATTTAGGTACTTGAAGGGA 59.547 47.826 0.00 0.00 41.75 4.20
2491 2578 3.262405 ACTGCGGGATTTAGGTACTTGAA 59.738 43.478 0.00 0.00 41.75 2.69
2499 2586 3.343617 TCTTTGAACTGCGGGATTTAGG 58.656 45.455 0.00 0.00 0.00 2.69
2508 2595 1.884235 ACTTCCCTCTTTGAACTGCG 58.116 50.000 0.00 0.00 0.00 5.18
2519 2606 4.263112 GCCCAGGATTTAGATACTTCCCTC 60.263 50.000 0.00 0.00 0.00 4.30
2549 2637 4.281435 ACACACCAATGATCAAAAGATGCA 59.719 37.500 0.00 0.00 0.00 3.96
2567 2655 5.815740 TGAGGTTAGAAAACAGAGAACACAC 59.184 40.000 0.00 0.00 37.34 3.82


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

AutoCloner maintained by Alex Coulton.