Multiple sequence alignment - TraesCS5A01G308600

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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 TraesCS5A01G308600 chr5A 100.000 3236 0 0 1 3236 521024014 521020779 0.000000e+00 5976
1 TraesCS5A01G308600 chr5B 87.945 1966 160 31 1 1915 491585435 491583496 0.000000e+00 2246
2 TraesCS5A01G308600 chr5B 88.974 780 37 12 1806 2538 491583496 491582719 0.000000e+00 918
3 TraesCS5A01G308600 chr5B 87.904 711 54 12 2535 3236 491582639 491581952 0.000000e+00 808
4 TraesCS5A01G308600 chr5D 87.146 1906 132 37 1 1846 409940911 409939059 0.000000e+00 2058
5 TraesCS5A01G308600 chr5D 80.412 1067 113 35 2078 3072 409938711 409937669 0.000000e+00 725
6 TraesCS5A01G308600 chr2A 90.270 185 14 2 1156 1337 739439862 739439679 4.170000e-59 239


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 TraesCS5A01G308600 chr5A 521020779 521024014 3235 True 5976.0 5976 100.000000 1 3236 1 chr5A.!!$R1 3235
1 TraesCS5A01G308600 chr5B 491581952 491585435 3483 True 1324.0 2246 88.274333 1 3236 3 chr5B.!!$R1 3235
2 TraesCS5A01G308600 chr5D 409937669 409940911 3242 True 1391.5 2058 83.779000 1 3072 2 chr5D.!!$R1 3071

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
343 350 0.603065 GGGGTTTGGTCTTGTCATGC 59.397 55.000 0.0 0.0 0.0 4.06 F
380 387 1.134037 ACAAGTGTAGACCCCGCAAAA 60.134 47.619 0.0 0.0 0.0 2.44 F
1601 1654 0.168128 ATTCGCCGCAAACTAAGCAC 59.832 50.000 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1635 0.168128 GTGCTTAGTTTGCGGCGAAT 59.832 50.000 12.98 0.0 0.00 3.34 R
1825 1998 0.178953 AGCAAAGGGGATGCAACTGT 60.179 50.000 0.00 0.0 46.22 3.55 R
2899 3387 1.069978 GCTAGATGCTTGACCTCTCCC 59.930 57.143 0.00 0.0 38.95 4.30 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
123 124 6.362551 CACGGTATCACGGAGTAATATCTTTG 59.637 42.308 0.00 0.00 41.61 2.77
186 187 6.640518 TCAGACGAAGCACTTCCTAAATATT 58.359 36.000 4.86 0.00 36.27 1.28
187 188 7.778083 TCAGACGAAGCACTTCCTAAATATTA 58.222 34.615 4.86 0.00 36.27 0.98
188 189 7.921214 TCAGACGAAGCACTTCCTAAATATTAG 59.079 37.037 4.86 0.00 36.27 1.73
190 191 8.258708 AGACGAAGCACTTCCTAAATATTAGTT 58.741 33.333 4.86 0.00 36.27 2.24
191 192 8.788325 ACGAAGCACTTCCTAAATATTAGTTT 57.212 30.769 4.86 0.00 36.27 2.66
192 193 9.880157 ACGAAGCACTTCCTAAATATTAGTTTA 57.120 29.630 4.86 0.00 36.27 2.01
230 235 2.163613 ACACTGCAATCACAGCATCATG 59.836 45.455 0.00 0.00 41.82 3.07
242 247 5.997129 TCACAGCATCATGACTTGTTTTCTA 59.003 36.000 0.00 0.00 0.00 2.10
244 249 6.745907 CACAGCATCATGACTTGTTTTCTATG 59.254 38.462 0.00 0.00 0.00 2.23
312 319 2.408050 CTCTGTGTGTAGGTTGTGCTC 58.592 52.381 0.00 0.00 0.00 4.26
343 350 0.603065 GGGGTTTGGTCTTGTCATGC 59.397 55.000 0.00 0.00 0.00 4.06
370 377 4.879545 GGTCCAAGAAAACACAAGTGTAGA 59.120 41.667 6.24 0.00 44.13 2.59
372 379 4.879545 TCCAAGAAAACACAAGTGTAGACC 59.120 41.667 6.24 0.00 44.13 3.85
380 387 1.134037 ACAAGTGTAGACCCCGCAAAA 60.134 47.619 0.00 0.00 0.00 2.44
471 489 2.076863 CCTTGGTGGAAAGATGACGAC 58.923 52.381 0.00 0.00 38.35 4.34
485 503 1.472878 TGACGACTGCAGACCATAGAC 59.527 52.381 23.35 2.64 0.00 2.59
511 531 1.589716 GGTGCCATGCCAAGTGAGAC 61.590 60.000 0.00 0.00 0.00 3.36
572 592 5.060427 TCTTTTCCTTTGATCCTTGGTGA 57.940 39.130 0.00 0.00 0.00 4.02
659 682 7.487829 CAGAAGATAGAAAGAGAGAAGAAACCG 59.512 40.741 0.00 0.00 0.00 4.44
741 765 2.526304 TAATATCCACTCGTGCTGCC 57.474 50.000 0.00 0.00 0.00 4.85
764 788 6.591448 GCCTATGCAGCTGTTTTTATTTTCTT 59.409 34.615 16.64 0.00 37.47 2.52
765 789 7.759433 GCCTATGCAGCTGTTTTTATTTTCTTA 59.241 33.333 16.64 0.00 37.47 2.10
766 790 9.807649 CCTATGCAGCTGTTTTTATTTTCTTAT 57.192 29.630 16.64 0.00 0.00 1.73
807 831 8.548877 ACTTGGATGATGATGATGATGATGATA 58.451 33.333 0.00 0.00 0.00 2.15
808 832 8.964476 TTGGATGATGATGATGATGATGATAG 57.036 34.615 0.00 0.00 0.00 2.08
837 864 4.870426 TCGGAGTACATCTCATTTTGCTTC 59.130 41.667 0.00 0.00 44.40 3.86
919 951 3.058914 ACACGTACGGTTACAGTACAGTC 60.059 47.826 21.06 0.03 43.24 3.51
920 952 2.157668 ACGTACGGTTACAGTACAGTCG 59.842 50.000 21.06 12.33 43.24 4.18
1337 1379 1.885049 TCTCTGAGGAGGGGAATTGG 58.115 55.000 4.59 0.00 39.86 3.16
1373 1415 4.101448 ATGGCGCTGGTCTGGGAC 62.101 66.667 7.64 0.00 0.00 4.46
1438 1480 2.092323 GGGGATGGTAAGTGCAAACTC 58.908 52.381 0.00 0.00 0.00 3.01
1439 1481 2.092323 GGGATGGTAAGTGCAAACTCC 58.908 52.381 0.00 0.00 0.00 3.85
1440 1482 1.737793 GGATGGTAAGTGCAAACTCCG 59.262 52.381 0.00 0.00 0.00 4.63
1441 1483 2.614481 GGATGGTAAGTGCAAACTCCGA 60.614 50.000 0.00 0.00 0.00 4.55
1442 1484 2.851263 TGGTAAGTGCAAACTCCGAT 57.149 45.000 0.00 0.00 0.00 4.18
1444 1486 3.857052 TGGTAAGTGCAAACTCCGATAG 58.143 45.455 0.00 0.00 0.00 2.08
1448 1490 4.744795 AAGTGCAAACTCCGATAGAGAT 57.255 40.909 0.00 0.00 46.50 2.75
1450 1492 6.412362 AAGTGCAAACTCCGATAGAGATAT 57.588 37.500 0.00 0.00 46.50 1.63
1453 1495 6.926272 AGTGCAAACTCCGATAGAGATATTTC 59.074 38.462 0.00 0.00 46.50 2.17
1458 1500 6.582677 ACTCCGATAGAGATATTTCTGGTG 57.417 41.667 6.03 3.10 46.50 4.17
1469 1511 7.071698 AGAGATATTTCTGGTGAAGAAGCCATA 59.928 37.037 0.00 0.00 45.64 2.74
1478 1520 4.578105 GGTGAAGAAGCCATATTCTGAAGG 59.422 45.833 0.00 0.00 39.47 3.46
1480 1522 5.882557 GTGAAGAAGCCATATTCTGAAGGAA 59.117 40.000 0.00 0.00 39.47 3.36
1485 1527 5.526506 AGCCATATTCTGAAGGAATTTGC 57.473 39.130 0.00 0.00 41.42 3.68
1488 1530 5.287226 CCATATTCTGAAGGAATTTGCTGC 58.713 41.667 0.00 0.00 41.42 5.25
1496 1538 5.129634 TGAAGGAATTTGCTGCGGATAATA 58.870 37.500 0.00 0.00 0.00 0.98
1498 1540 5.886960 AGGAATTTGCTGCGGATAATATC 57.113 39.130 0.00 0.00 0.00 1.63
1499 1541 4.702131 AGGAATTTGCTGCGGATAATATCC 59.298 41.667 9.23 9.23 46.22 2.59
1520 1572 6.065976 TCCCTATCTGAATGTGTGAAATGT 57.934 37.500 0.00 0.00 0.00 2.71
1527 1579 5.067544 TCTGAATGTGTGAAATGTTGCAAGA 59.932 36.000 0.00 0.00 0.00 3.02
1528 1580 5.845103 TGAATGTGTGAAATGTTGCAAGAT 58.155 33.333 2.67 2.67 0.00 2.40
1550 1602 3.843893 TGCTTGCTATTAGGATGCTGA 57.156 42.857 19.14 0.00 37.55 4.26
1551 1603 3.470709 TGCTTGCTATTAGGATGCTGAC 58.529 45.455 19.14 0.00 37.55 3.51
1556 1608 5.557576 TGCTATTAGGATGCTGACAGATT 57.442 39.130 6.65 0.00 0.00 2.40
1557 1609 5.303165 TGCTATTAGGATGCTGACAGATTG 58.697 41.667 6.65 0.00 0.00 2.67
1569 1622 2.948979 TGACAGATTGTTGGTTCGCTTT 59.051 40.909 0.00 0.00 0.00 3.51
1572 1625 4.134563 ACAGATTGTTGGTTCGCTTTACT 58.865 39.130 0.00 0.00 0.00 2.24
1582 1635 5.412640 TGGTTCGCTTTACTCGATGATTTA 58.587 37.500 0.00 0.00 35.75 1.40
1590 1643 1.792949 ACTCGATGATTTATTCGCCGC 59.207 47.619 0.00 0.00 0.00 6.53
1601 1654 0.168128 ATTCGCCGCAAACTAAGCAC 59.832 50.000 0.00 0.00 0.00 4.40
1605 1658 1.072666 GCCGCAAACTAAGCACATGC 61.073 55.000 0.00 0.00 42.49 4.06
1617 1670 1.955762 GCACATGCGTTTCTTCAGAC 58.044 50.000 0.00 0.00 0.00 3.51
1633 1686 4.553330 TCAGACACCCTCCTTATTGAAC 57.447 45.455 0.00 0.00 0.00 3.18
1634 1687 3.263425 TCAGACACCCTCCTTATTGAACC 59.737 47.826 0.00 0.00 0.00 3.62
1639 1692 1.006832 CCTCCTTATTGAACCGTGCG 58.993 55.000 0.00 0.00 0.00 5.34
1641 1694 1.393539 CTCCTTATTGAACCGTGCGTG 59.606 52.381 0.00 0.00 0.00 5.34
1642 1695 1.153353 CCTTATTGAACCGTGCGTGT 58.847 50.000 0.00 0.00 0.00 4.49
1643 1696 1.533731 CCTTATTGAACCGTGCGTGTT 59.466 47.619 0.00 0.00 0.00 3.32
1644 1697 2.570169 CTTATTGAACCGTGCGTGTTG 58.430 47.619 3.89 0.00 0.00 3.33
1645 1698 1.867166 TATTGAACCGTGCGTGTTGA 58.133 45.000 3.89 0.00 0.00 3.18
1646 1699 0.586319 ATTGAACCGTGCGTGTTGAG 59.414 50.000 3.89 0.00 0.00 3.02
1647 1700 0.741574 TTGAACCGTGCGTGTTGAGT 60.742 50.000 3.89 0.00 0.00 3.41
1652 1712 2.331451 GTGCGTGTTGAGTTGGCC 59.669 61.111 0.00 0.00 0.00 5.36
1698 1761 3.696281 TGACAGTTCATGTGCTTGTTG 57.304 42.857 0.00 0.00 44.17 3.33
1736 1799 3.485463 TCTGCCCAATAATAGGTTCCG 57.515 47.619 0.00 0.00 0.00 4.30
1803 1866 4.638421 ACAATTCAGAGTCTCTCGAGGTAG 59.362 45.833 13.56 3.43 35.36 3.18
1804 1867 2.992124 TCAGAGTCTCTCGAGGTAGG 57.008 55.000 13.56 1.10 35.36 3.18
1816 1989 7.231115 GTCTCTCGAGGTAGGATATTTAACCTT 59.769 40.741 13.56 0.00 42.40 3.50
1817 1990 7.447853 TCTCTCGAGGTAGGATATTTAACCTTC 59.552 40.741 13.56 0.00 42.40 3.46
1820 1993 7.064866 TCGAGGTAGGATATTTAACCTTCAGA 58.935 38.462 0.00 4.31 42.40 3.27
1823 1996 8.024145 AGGTAGGATATTTAACCTTCAGACAG 57.976 38.462 0.00 0.00 39.32 3.51
1825 1998 8.483758 GGTAGGATATTTAACCTTCAGACAGAA 58.516 37.037 0.00 0.00 37.68 3.02
1854 2027 1.106285 CCCCTTTGCTGATTGCTACC 58.894 55.000 0.00 0.00 43.37 3.18
1888 2061 5.254115 TGATAGTATCATCTACCTGTCCCG 58.746 45.833 8.84 0.00 33.59 5.14
1890 2063 4.180377 AGTATCATCTACCTGTCCCGAA 57.820 45.455 0.00 0.00 0.00 4.30
1938 2130 4.289672 ACTGTCACCCTGAATATTTCCACT 59.710 41.667 0.00 0.00 0.00 4.00
1988 2314 2.205074 CGGGCTAGACATTGCTAACTG 58.795 52.381 0.00 0.00 0.00 3.16
2018 2344 6.485984 CAGCAGCTATATCCTGAATTCTTTGT 59.514 38.462 7.05 0.00 32.03 2.83
2105 2431 7.488322 TCCTTTTCCTTAGTTGTGATGTTTTG 58.512 34.615 0.00 0.00 0.00 2.44
2151 2477 1.565156 CGCTTCAAGGTGCGCTTACA 61.565 55.000 9.73 0.00 45.50 2.41
2181 2507 5.007626 CGGTAACATAACAATGTGCATAGCT 59.992 40.000 0.00 0.00 34.56 3.32
2222 2548 3.219281 GGTCCCAAGAAAGCACTAACAA 58.781 45.455 0.00 0.00 0.00 2.83
2595 3059 5.009510 CCTCGTCTGATACTGATCACTGAAT 59.990 44.000 0.00 0.00 37.15 2.57
2596 3060 5.825507 TCGTCTGATACTGATCACTGAATG 58.174 41.667 0.00 0.00 37.15 2.67
2597 3061 5.358160 TCGTCTGATACTGATCACTGAATGT 59.642 40.000 0.00 0.00 37.15 2.71
2598 3062 6.038985 CGTCTGATACTGATCACTGAATGTT 58.961 40.000 0.00 0.00 37.15 2.71
2599 3063 7.067008 TCGTCTGATACTGATCACTGAATGTTA 59.933 37.037 0.00 0.00 37.15 2.41
2600 3064 7.378194 CGTCTGATACTGATCACTGAATGTTAG 59.622 40.741 0.00 0.00 37.15 2.34
2601 3065 8.194104 GTCTGATACTGATCACTGAATGTTAGT 58.806 37.037 0.00 0.00 37.15 2.24
2602 3066 9.408648 TCTGATACTGATCACTGAATGTTAGTA 57.591 33.333 0.00 0.00 37.15 1.82
2603 3067 9.457110 CTGATACTGATCACTGAATGTTAGTAC 57.543 37.037 0.00 0.00 37.15 2.73
2604 3068 8.414003 TGATACTGATCACTGAATGTTAGTACC 58.586 37.037 0.00 0.00 37.15 3.34
2605 3069 6.859112 ACTGATCACTGAATGTTAGTACCT 57.141 37.500 0.00 0.00 0.00 3.08
2632 3096 6.403866 TCACATTCACCTTTGCATACTTTT 57.596 33.333 0.00 0.00 0.00 2.27
2637 3101 5.811399 TCACCTTTGCATACTTTTATCCG 57.189 39.130 0.00 0.00 0.00 4.18
2643 3107 6.866248 CCTTTGCATACTTTTATCCGTTGTTT 59.134 34.615 0.00 0.00 0.00 2.83
2680 3145 3.070748 TCGATGTGAAATTCCTGCGAAA 58.929 40.909 0.00 0.00 0.00 3.46
2690 3155 0.179032 TCCTGCGAAACAAAGAGGCA 60.179 50.000 0.00 0.00 0.00 4.75
2892 3380 3.414700 GTCGCTGGTGCCTTGTCG 61.415 66.667 0.00 0.00 35.36 4.35
2894 3382 3.414700 CGCTGGTGCCTTGTCGAC 61.415 66.667 9.11 9.11 35.36 4.20
2935 3423 3.889815 TCTAGCATGGGAATGAAACCTG 58.110 45.455 0.00 0.00 0.00 4.00
3096 3584 0.665835 CAGCAAACCTTACGTGCCAA 59.334 50.000 0.00 0.00 39.13 4.52
3111 3599 3.005367 CGTGCCAATAAAACTGGGAAACT 59.995 43.478 0.00 0.00 35.88 2.66
3112 3600 4.216687 CGTGCCAATAAAACTGGGAAACTA 59.783 41.667 0.00 0.00 35.88 2.24
3113 3601 5.466819 GTGCCAATAAAACTGGGAAACTAC 58.533 41.667 0.00 0.00 35.88 2.73
3115 3603 5.242838 TGCCAATAAAACTGGGAAACTACAG 59.757 40.000 0.00 0.00 40.48 2.74
3116 3604 5.709966 CCAATAAAACTGGGAAACTACAGC 58.290 41.667 0.00 0.00 38.25 4.40
3117 3605 5.242838 CCAATAAAACTGGGAAACTACAGCA 59.757 40.000 0.00 0.00 38.25 4.41
3118 3606 5.959618 ATAAAACTGGGAAACTACAGCAC 57.040 39.130 0.00 0.00 38.25 4.40
3119 3607 3.290948 AAACTGGGAAACTACAGCACA 57.709 42.857 0.00 0.00 38.25 4.57
3120 3608 3.508845 AACTGGGAAACTACAGCACAT 57.491 42.857 0.00 0.00 38.25 3.21
3121 3609 4.634012 AACTGGGAAACTACAGCACATA 57.366 40.909 0.00 0.00 38.25 2.29
3123 3611 5.179452 ACTGGGAAACTACAGCACATAAT 57.821 39.130 0.00 0.00 38.25 1.28
3124 3612 6.308015 ACTGGGAAACTACAGCACATAATA 57.692 37.500 0.00 0.00 38.25 0.98
3126 3614 7.172342 ACTGGGAAACTACAGCACATAATAAA 58.828 34.615 0.00 0.00 38.25 1.40
3127 3615 7.120726 ACTGGGAAACTACAGCACATAATAAAC 59.879 37.037 0.00 0.00 38.25 2.01
3128 3616 7.172342 TGGGAAACTACAGCACATAATAAACT 58.828 34.615 0.00 0.00 0.00 2.66
3129 3617 8.322828 TGGGAAACTACAGCACATAATAAACTA 58.677 33.333 0.00 0.00 0.00 2.24
3130 3618 9.338622 GGGAAACTACAGCACATAATAAACTAT 57.661 33.333 0.00 0.00 0.00 2.12
3155 3643 2.288666 ACAGAACTTCTTGCGCTTCAA 58.711 42.857 9.73 0.00 0.00 2.69
3166 3654 2.288666 TGCGCTTCAAAACTCAGAACT 58.711 42.857 9.73 0.00 0.00 3.01
3174 3662 5.248870 TCAAAACTCAGAACTTTTCAGCC 57.751 39.130 0.00 0.00 0.00 4.85
3182 3670 2.872858 AGAACTTTTCAGCCTCGTTGTC 59.127 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.483491 GCCATAGCTGCTCTTTAGATGC 59.517 50.000 4.91 0.00 35.50 3.91
187 188 9.381038 AGTGTCCATCATATATGGTACTAAACT 57.619 33.333 12.78 2.79 40.06 2.66
188 189 9.424319 CAGTGTCCATCATATATGGTACTAAAC 57.576 37.037 12.78 0.64 40.06 2.01
190 191 7.234577 TGCAGTGTCCATCATATATGGTACTAA 59.765 37.037 12.78 0.00 40.06 2.24
191 192 6.723977 TGCAGTGTCCATCATATATGGTACTA 59.276 38.462 12.78 0.00 40.06 1.82
192 193 5.543790 TGCAGTGTCCATCATATATGGTACT 59.456 40.000 12.78 3.31 40.06 2.73
211 216 2.422479 GTCATGATGCTGTGATTGCAGT 59.578 45.455 0.00 0.00 44.04 4.40
230 235 7.301054 CAACAGATGGTCATAGAAAACAAGTC 58.699 38.462 0.00 0.00 0.00 3.01
242 247 4.720127 TGCGCAACAGATGGTCAT 57.280 50.000 8.16 0.00 0.00 3.06
343 350 5.299279 ACACTTGTGTTTTCTTGGACCATAG 59.701 40.000 0.00 0.00 0.00 2.23
370 377 2.520741 CCAGTGGTTTTGCGGGGT 60.521 61.111 0.00 0.00 0.00 4.95
372 379 3.989787 GCCCAGTGGTTTTGCGGG 61.990 66.667 8.74 0.00 40.11 6.13
380 387 2.496679 AGTATATCCAGCCCAGTGGT 57.503 50.000 8.74 0.00 38.88 4.16
423 441 2.302260 TGTTCTTGGCGATTTGGTCAA 58.698 42.857 0.00 0.00 0.00 3.18
471 489 1.227380 GGCCGTCTATGGTCTGCAG 60.227 63.158 7.63 7.63 0.00 4.41
499 517 1.451504 CCTGGTGTCTCACTTGGCA 59.548 57.895 0.06 0.00 34.40 4.92
500 518 1.302832 CCCTGGTGTCTCACTTGGC 60.303 63.158 0.00 0.00 34.40 4.52
501 519 0.035458 GACCCTGGTGTCTCACTTGG 59.965 60.000 0.00 3.19 34.40 3.61
502 520 0.758734 TGACCCTGGTGTCTCACTTG 59.241 55.000 13.91 0.00 36.21 3.16
503 521 0.759346 GTGACCCTGGTGTCTCACTT 59.241 55.000 13.91 0.00 36.21 3.16
511 531 2.030562 GTCACGGTGACCCTGGTG 59.969 66.667 26.86 0.00 41.37 4.17
572 592 7.936847 TCCTACAATGTTACACAGACATCTTTT 59.063 33.333 0.00 0.00 36.76 2.27
590 612 7.964293 AGAGGTTATCCCTATGAATCCTACAAT 59.036 37.037 0.00 0.00 46.51 2.71
593 615 6.381707 GGAGAGGTTATCCCTATGAATCCTAC 59.618 46.154 0.00 0.00 46.51 3.18
659 682 2.627945 TGATAAATCCACCAGCACGTC 58.372 47.619 0.00 0.00 0.00 4.34
690 713 4.851558 GTCACAAGAAATGCAAACGGATAC 59.148 41.667 0.00 0.00 0.00 2.24
764 788 7.335673 TCATCCAAGTTTGCAACTCGATTAATA 59.664 33.333 0.00 0.00 41.91 0.98
765 789 5.957842 TCCAAGTTTGCAACTCGATTAAT 57.042 34.783 0.00 0.00 41.91 1.40
766 790 5.471797 TCATCCAAGTTTGCAACTCGATTAA 59.528 36.000 0.00 0.00 41.91 1.40
807 831 2.294074 GAGATGTACTCCGAGACTGCT 58.706 52.381 1.33 0.00 39.53 4.24
808 832 2.017782 TGAGATGTACTCCGAGACTGC 58.982 52.381 1.33 0.00 44.34 4.40
837 864 8.250332 TGGTTAATAATTTTCAAGCTGCCTTAG 58.750 33.333 0.00 0.00 0.00 2.18
900 932 2.762472 CGACTGTACTGTAACCGTACG 58.238 52.381 8.69 8.69 39.98 3.67
919 951 1.448540 GGACCCATCAGTCAGTGCG 60.449 63.158 0.00 0.00 38.59 5.34
920 952 0.392193 CTGGACCCATCAGTCAGTGC 60.392 60.000 0.00 0.00 38.59 4.40
933 965 2.841442 AGCTTCTGTACAACTGGACC 57.159 50.000 0.00 0.00 0.00 4.46
1274 1309 5.755861 AGAAATAGTTCGGAGCTTCAATAGC 59.244 40.000 0.00 0.00 43.47 2.97
1279 1314 3.055819 AGCAGAAATAGTTCGGAGCTTCA 60.056 43.478 7.25 0.00 37.72 3.02
1337 1379 3.050275 GCCGTCACCCTGCAAGTC 61.050 66.667 0.00 0.00 0.00 3.01
1392 1434 2.440599 GCCCTTCCAGCCCTTCAA 59.559 61.111 0.00 0.00 0.00 2.69
1438 1480 7.220741 TCTTCACCAGAAATATCTCTATCGG 57.779 40.000 0.00 0.00 32.03 4.18
1439 1481 7.328249 GCTTCTTCACCAGAAATATCTCTATCG 59.672 40.741 0.00 0.00 41.25 2.92
1440 1482 7.602265 GGCTTCTTCACCAGAAATATCTCTATC 59.398 40.741 0.00 0.00 41.25 2.08
1441 1483 7.071698 TGGCTTCTTCACCAGAAATATCTCTAT 59.928 37.037 0.00 0.00 41.25 1.98
1442 1484 6.384015 TGGCTTCTTCACCAGAAATATCTCTA 59.616 38.462 0.00 0.00 41.25 2.43
1444 1486 5.431765 TGGCTTCTTCACCAGAAATATCTC 58.568 41.667 0.00 0.00 41.25 2.75
1446 1488 7.992754 ATATGGCTTCTTCACCAGAAATATC 57.007 36.000 0.00 0.00 41.25 1.63
1448 1490 7.500227 CAGAATATGGCTTCTTCACCAGAAATA 59.500 37.037 2.20 0.00 41.25 1.40
1450 1492 5.649395 CAGAATATGGCTTCTTCACCAGAAA 59.351 40.000 2.20 0.00 41.25 2.52
1453 1495 4.774124 TCAGAATATGGCTTCTTCACCAG 58.226 43.478 2.20 0.00 39.88 4.00
1458 1500 7.579761 AATTCCTTCAGAATATGGCTTCTTC 57.420 36.000 0.00 0.00 44.75 2.87
1496 1538 6.666678 ACATTTCACACATTCAGATAGGGAT 58.333 36.000 0.00 0.00 0.00 3.85
1498 1540 6.558009 CAACATTTCACACATTCAGATAGGG 58.442 40.000 0.00 0.00 0.00 3.53
1499 1541 6.032094 GCAACATTTCACACATTCAGATAGG 58.968 40.000 0.00 0.00 0.00 2.57
1500 1542 6.614160 TGCAACATTTCACACATTCAGATAG 58.386 36.000 0.00 0.00 0.00 2.08
1507 1549 6.950545 CAAATCTTGCAACATTTCACACATT 58.049 32.000 9.43 0.00 0.00 2.71
1527 1579 5.009410 GTCAGCATCCTAATAGCAAGCAAAT 59.991 40.000 0.00 0.00 0.00 2.32
1528 1580 4.336433 GTCAGCATCCTAATAGCAAGCAAA 59.664 41.667 0.00 0.00 0.00 3.68
1533 1585 5.557576 ATCTGTCAGCATCCTAATAGCAA 57.442 39.130 0.00 0.00 0.00 3.91
1536 1588 6.204301 CCAACAATCTGTCAGCATCCTAATAG 59.796 42.308 0.00 0.00 0.00 1.73
1537 1589 6.057533 CCAACAATCTGTCAGCATCCTAATA 58.942 40.000 0.00 0.00 0.00 0.98
1546 1598 1.400242 GCGAACCAACAATCTGTCAGC 60.400 52.381 0.00 0.00 0.00 4.26
1550 1602 4.134563 AGTAAAGCGAACCAACAATCTGT 58.865 39.130 0.00 0.00 0.00 3.41
1551 1603 4.666655 CGAGTAAAGCGAACCAACAATCTG 60.667 45.833 0.00 0.00 0.00 2.90
1556 1608 2.512485 TCGAGTAAAGCGAACCAACA 57.488 45.000 0.00 0.00 34.45 3.33
1557 1609 2.991190 TCATCGAGTAAAGCGAACCAAC 59.009 45.455 0.00 0.00 41.52 3.77
1569 1622 2.984471 GCGGCGAATAAATCATCGAGTA 59.016 45.455 12.98 0.00 41.43 2.59
1572 1625 1.859383 TGCGGCGAATAAATCATCGA 58.141 45.000 12.98 0.00 41.43 3.59
1582 1635 0.168128 GTGCTTAGTTTGCGGCGAAT 59.832 50.000 12.98 0.00 0.00 3.34
1590 1643 3.888934 AGAAACGCATGTGCTTAGTTTG 58.111 40.909 6.08 0.00 39.32 2.93
1601 1654 1.197721 GGGTGTCTGAAGAAACGCATG 59.802 52.381 11.69 0.00 42.70 4.06
1605 1658 1.344763 AGGAGGGTGTCTGAAGAAACG 59.655 52.381 0.00 0.00 33.06 3.60
1616 1669 1.982958 ACGGTTCAATAAGGAGGGTGT 59.017 47.619 0.00 0.00 0.00 4.16
1617 1670 2.356135 CACGGTTCAATAAGGAGGGTG 58.644 52.381 0.00 0.00 0.00 4.61
1633 1686 2.631428 CCAACTCAACACGCACGG 59.369 61.111 0.00 0.00 0.00 4.94
1634 1687 2.052237 GCCAACTCAACACGCACG 60.052 61.111 0.00 0.00 0.00 5.34
1639 1692 0.388659 TGCAATGGCCAACTCAACAC 59.611 50.000 10.96 0.00 40.13 3.32
1641 1694 1.069049 ACTTGCAATGGCCAACTCAAC 59.931 47.619 10.96 0.00 40.13 3.18
1642 1695 1.412079 ACTTGCAATGGCCAACTCAA 58.588 45.000 10.96 12.89 40.13 3.02
1643 1696 2.161855 CTACTTGCAATGGCCAACTCA 58.838 47.619 10.96 4.57 40.13 3.41
1644 1697 1.135286 GCTACTTGCAATGGCCAACTC 60.135 52.381 10.96 1.38 42.31 3.01
1645 1698 0.890683 GCTACTTGCAATGGCCAACT 59.109 50.000 10.96 0.00 42.31 3.16
1646 1699 3.423848 GCTACTTGCAATGGCCAAC 57.576 52.632 10.96 2.55 42.31 3.77
1674 1734 3.501062 ACAAGCACATGAACTGTCATCAG 59.499 43.478 0.00 0.00 42.88 2.90
1698 1761 3.916776 GCAGAAATGCAAGCTTGTTAGTC 59.083 43.478 26.55 18.17 34.41 2.59
1708 1771 5.069516 ACCTATTATTGGGCAGAAATGCAAG 59.930 40.000 2.29 0.00 36.33 4.01
1736 1799 4.577246 ATCGCTCCGCCGAGAAGC 62.577 66.667 6.23 0.00 40.97 3.86
1766 1829 6.150140 ACTCTGAATTGTAGAAGAAATGCCAC 59.850 38.462 0.00 0.00 0.00 5.01
1803 1866 7.824779 ACTGTTCTGTCTGAAGGTTAAATATCC 59.175 37.037 0.00 0.00 35.01 2.59
1804 1867 8.779354 ACTGTTCTGTCTGAAGGTTAAATATC 57.221 34.615 0.00 0.00 35.01 1.63
1816 1989 2.550855 GGGATGCAACTGTTCTGTCTGA 60.551 50.000 0.00 0.00 0.00 3.27
1817 1990 1.808945 GGGATGCAACTGTTCTGTCTG 59.191 52.381 0.00 0.00 0.00 3.51
1820 1993 0.773644 AGGGGATGCAACTGTTCTGT 59.226 50.000 0.00 0.00 0.00 3.41
1823 1996 1.337167 GCAAAGGGGATGCAACTGTTC 60.337 52.381 0.00 0.00 43.29 3.18
1825 1998 0.178953 AGCAAAGGGGATGCAACTGT 60.179 50.000 0.00 0.00 46.22 3.55
1854 2027 9.619316 GTAGATGATACTATCAAGCAACTAGTG 57.381 37.037 0.00 0.00 43.50 2.74
1888 2061 4.574599 AGTGAAGACAGCCACAAAATTC 57.425 40.909 0.00 0.00 35.84 2.17
1890 2063 3.701040 ACAAGTGAAGACAGCCACAAAAT 59.299 39.130 0.00 0.00 35.84 1.82
1954 2161 5.537295 TGTCTAGCCCGCTAATTATCAAGTA 59.463 40.000 0.00 0.00 0.00 2.24
2018 2344 5.067674 ACTCATTCAGCAAAACTAACAAGCA 59.932 36.000 0.00 0.00 0.00 3.91
2063 2389 6.352137 GGAAAAGGAACATGGGCAGAATAATT 60.352 38.462 0.00 0.00 0.00 1.40
2105 2431 2.028385 AGTACCTGTGGAATTCGGACAC 60.028 50.000 4.34 5.45 35.75 3.67
2145 2471 5.808540 TGTTATGTTACCGATCACTGTAAGC 59.191 40.000 0.00 0.00 37.60 3.09
2148 2474 7.276878 CACATTGTTATGTTACCGATCACTGTA 59.723 37.037 0.00 0.00 42.29 2.74
2151 2477 5.064707 GCACATTGTTATGTTACCGATCACT 59.935 40.000 0.00 0.00 42.29 3.41
2222 2548 3.857157 ACACAGGTTATGGACTGTTGT 57.143 42.857 0.00 0.00 45.03 3.32
2351 2704 3.092301 TCTCGAATCAGGTGTGACAGAT 58.908 45.455 0.00 0.00 34.75 2.90
2548 2998 4.413969 CACGCTTGCATGTCATTCAAATA 58.586 39.130 0.00 0.00 0.00 1.40
2573 3023 5.358160 ACATTCAGTGATCAGTATCAGACGA 59.642 40.000 1.86 0.00 42.80 4.20
2574 3024 5.586339 ACATTCAGTGATCAGTATCAGACG 58.414 41.667 1.86 0.00 42.80 4.18
2595 3059 6.013725 AGGTGAATGTGAATCAGGTACTAACA 60.014 38.462 0.00 0.00 36.02 2.41
2596 3060 6.407202 AGGTGAATGTGAATCAGGTACTAAC 58.593 40.000 0.00 0.00 36.02 2.34
2597 3061 6.620877 AGGTGAATGTGAATCAGGTACTAA 57.379 37.500 0.00 0.00 36.02 2.24
2598 3062 6.620877 AAGGTGAATGTGAATCAGGTACTA 57.379 37.500 0.00 0.00 36.02 1.82
2599 3063 5.505181 AAGGTGAATGTGAATCAGGTACT 57.495 39.130 0.00 0.00 43.88 2.73
2600 3064 5.619981 GCAAAGGTGAATGTGAATCAGGTAC 60.620 44.000 0.00 0.00 0.00 3.34
2601 3065 4.458989 GCAAAGGTGAATGTGAATCAGGTA 59.541 41.667 0.00 0.00 0.00 3.08
2602 3066 3.256631 GCAAAGGTGAATGTGAATCAGGT 59.743 43.478 0.00 0.00 0.00 4.00
2603 3067 3.256383 TGCAAAGGTGAATGTGAATCAGG 59.744 43.478 0.00 0.00 0.00 3.86
2604 3068 4.508461 TGCAAAGGTGAATGTGAATCAG 57.492 40.909 0.00 0.00 0.00 2.90
2605 3069 5.711506 AGTATGCAAAGGTGAATGTGAATCA 59.288 36.000 0.00 0.00 0.00 2.57
2632 3096 6.140786 CGATTCGATCTCTAAACAACGGATA 58.859 40.000 0.00 0.00 0.00 2.59
2680 3145 1.678101 GTGCTTCAAGTGCCTCTTTGT 59.322 47.619 0.00 0.00 33.63 2.83
2690 3155 2.162681 GTAGGGCAATGTGCTTCAAGT 58.837 47.619 0.00 0.00 44.28 3.16
2720 3185 2.143419 ATGAGGGAGGGCATCGTCC 61.143 63.158 0.00 0.00 44.78 4.79
2763 3228 7.891498 AAGTACCAGGAAGTGTTTATTTTGT 57.109 32.000 0.00 0.00 0.00 2.83
2767 3232 6.370453 ACCAAAGTACCAGGAAGTGTTTATT 58.630 36.000 0.00 0.00 0.00 1.40
2875 3363 3.414700 CGACAAGGCACCAGCGAC 61.415 66.667 0.00 0.00 43.41 5.19
2894 3382 4.148825 CTTGACCTCTCCCCGCCG 62.149 72.222 0.00 0.00 0.00 6.46
2899 3387 1.069978 GCTAGATGCTTGACCTCTCCC 59.930 57.143 0.00 0.00 38.95 4.30
2902 3390 2.104451 CCATGCTAGATGCTTGACCTCT 59.896 50.000 0.00 0.00 46.07 3.69
2922 3410 1.273327 CCAAGTGCAGGTTTCATTCCC 59.727 52.381 0.00 0.00 0.00 3.97
2935 3423 3.357079 CTGCGTCCACCCAAGTGC 61.357 66.667 0.00 0.00 43.09 4.40
2994 3482 4.100084 CCACCCTCCGATGCTGCA 62.100 66.667 4.13 4.13 0.00 4.41
3096 3584 5.381757 TGTGCTGTAGTTTCCCAGTTTTAT 58.618 37.500 0.00 0.00 0.00 1.40
3123 3611 9.872757 CGCAAGAAGTTCTGTTTTTATAGTTTA 57.127 29.630 6.06 0.00 43.02 2.01
3124 3612 7.378728 GCGCAAGAAGTTCTGTTTTTATAGTTT 59.621 33.333 6.06 0.00 43.02 2.66
3126 3614 6.204882 AGCGCAAGAAGTTCTGTTTTTATAGT 59.795 34.615 11.47 0.00 43.02 2.12
3127 3615 6.603095 AGCGCAAGAAGTTCTGTTTTTATAG 58.397 36.000 11.47 0.00 43.02 1.31
3128 3616 6.554334 AGCGCAAGAAGTTCTGTTTTTATA 57.446 33.333 11.47 0.00 43.02 0.98
3129 3617 5.438761 AGCGCAAGAAGTTCTGTTTTTAT 57.561 34.783 11.47 0.00 43.02 1.40
3130 3618 4.893424 AGCGCAAGAAGTTCTGTTTTTA 57.107 36.364 11.47 0.00 43.02 1.52
3131 3619 3.782889 AGCGCAAGAAGTTCTGTTTTT 57.217 38.095 11.47 0.00 43.02 1.94
3132 3620 3.128589 TGAAGCGCAAGAAGTTCTGTTTT 59.871 39.130 11.47 0.00 43.02 2.43
3133 3621 2.682856 TGAAGCGCAAGAAGTTCTGTTT 59.317 40.909 11.47 0.00 43.02 2.83
3134 3622 2.288666 TGAAGCGCAAGAAGTTCTGTT 58.711 42.857 11.47 0.00 43.02 3.16
3135 3623 1.953559 TGAAGCGCAAGAAGTTCTGT 58.046 45.000 11.47 0.00 43.02 3.41
3136 3624 3.338818 TTTGAAGCGCAAGAAGTTCTG 57.661 42.857 11.47 2.23 37.87 3.02
3137 3625 3.378427 AGTTTTGAAGCGCAAGAAGTTCT 59.622 39.130 11.47 0.00 37.87 3.01
3146 3634 2.288666 AGTTCTGAGTTTTGAAGCGCA 58.711 42.857 11.47 0.00 0.00 6.09
3155 3643 3.561725 CGAGGCTGAAAAGTTCTGAGTTT 59.438 43.478 0.00 0.00 0.00 2.66
3166 3654 3.671262 TCGACAACGAGGCTGAAAA 57.329 47.368 0.00 0.00 43.81 2.29
3185 3673 3.277715 AGAAGATAAGGAAGCAGCAAGC 58.722 45.455 0.00 0.00 46.19 4.01
3191 3679 9.574516 AAAAAGTAAAGAGAAGATAAGGAAGCA 57.425 29.630 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.