Multiple sequence alignment - TraesCS1B01G031600

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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 TraesCS1B01G031600 chr1B 100.000 4770 0 0 1 4770 15452124 15447355 0.000000e+00 8809.0
1 TraesCS1B01G031600 chr1B 84.314 306 42 6 241 541 15451624 15451320 1.300000e-75 294.0
2 TraesCS1B01G031600 chr1B 84.314 306 42 6 501 805 15451884 15451584 1.300000e-75 294.0
3 TraesCS1B01G031600 chr1B 94.828 58 2 1 425 481 15451663 15451606 6.580000e-14 89.8
4 TraesCS1B01G031600 chr1B 94.828 58 2 1 462 519 15451700 15451644 6.580000e-14 89.8
5 TraesCS1B01G031600 chr1D 94.816 3742 164 20 729 4455 10436150 10432424 0.000000e+00 5808.0
6 TraesCS1B01G031600 chr1D 88.948 751 46 24 19 743 10436839 10436100 0.000000e+00 893.0
7 TraesCS1B01G031600 chr1D 90.123 324 20 5 4455 4770 10432389 10432070 1.240000e-110 411.0
8 TraesCS1B01G031600 chr1D 89.571 326 22 4 4455 4768 10406113 10405788 2.070000e-108 403.0
9 TraesCS1B01G031600 chr1D 84.395 314 34 9 501 805 10436618 10436311 1.300000e-75 294.0
10 TraesCS1B01G031600 chr1D 82.101 257 29 13 241 481 10436351 10436096 2.250000e-48 204.0
11 TraesCS1B01G031600 chr1D 96.552 58 0 2 425 481 10436389 10436333 1.410000e-15 95.3
12 TraesCS1B01G031600 chr1D 94.828 58 0 2 462 519 10436424 10436370 2.360000e-13 87.9
13 TraesCS1B01G031600 chr1A 93.708 2956 143 28 1524 4455 12159686 12156750 0.000000e+00 4388.0
14 TraesCS1B01G031600 chr1A 93.359 783 49 1 743 1525 12160589 12159810 0.000000e+00 1155.0
15 TraesCS1B01G031600 chr1A 88.331 617 47 17 85 686 12161192 12160586 0.000000e+00 717.0
16 TraesCS1B01G031600 chr1A 89.815 324 18 6 4455 4770 12156158 12155842 7.440000e-108 401.0
17 TraesCS1B01G031600 chr1A 83.828 303 40 7 507 805 12161038 12160741 3.640000e-71 279.0
18 TraesCS1B01G031600 chr1A 91.379 58 4 1 462 519 12160856 12160800 1.420000e-10 78.7
19 TraesCS1B01G031600 chr7B 91.372 1553 123 9 1850 3396 553107499 553109046 0.000000e+00 2115.0
20 TraesCS1B01G031600 chr7B 86.882 587 40 17 1850 2429 438373281 438372725 1.460000e-174 623.0


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 TraesCS1B01G031600 chr1B 15447355 15452124 4769 True 1915.320000 8809 91.656800 1 4770 5 chr1B.!!$R1 4769
1 TraesCS1B01G031600 chr1D 10432070 10436839 4769 True 1113.314286 5808 90.251857 19 4770 7 chr1D.!!$R2 4751
2 TraesCS1B01G031600 chr1A 12155842 12161192 5350 True 1169.783333 4388 90.070000 85 4770 6 chr1A.!!$R1 4685
3 TraesCS1B01G031600 chr7B 553107499 553109046 1547 False 2115.000000 2115 91.372000 1850 3396 1 chr7B.!!$F1 1546
4 TraesCS1B01G031600 chr7B 438372725 438373281 556 True 623.000000 623 86.882000 1850 2429 1 chr7B.!!$R1 579

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
990 1020 0.331278 CCCCTGTGGTTGCATTCCTA 59.669 55.0 9.35 0.00 0.0 2.94 F
1035 1065 0.530650 CTGTCAGTCGCAGGTGTGTT 60.531 55.0 0.00 0.00 0.0 3.32 F
2843 3006 1.772819 ATATCTCCCAGCCCGGCTTG 61.773 60.0 9.99 6.32 36.4 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2843 3006 0.906282 TTAGTCCCCGGTCAGGTTCC 60.906 60.000 0.0 0.0 38.74 3.62 R
2855 3018 2.633488 GTCATCTGCCAAGTTAGTCCC 58.367 52.381 0.0 0.0 0.00 4.46 R
4268 4447 0.734889 GTTTGCGATGGAGATGGTGG 59.265 55.000 0.0 0.0 0.00 4.61 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
58 59 4.084485 GGACTTTCAACGCTCAAGTCTTAC 60.084 45.833 13.80 0.00 44.00 2.34
82 83 0.389817 TCAGCTGATTTGGTCGGTCG 60.390 55.000 13.74 0.00 35.53 4.79
103 104 3.430790 CGGTCAGCAGGAGTAATCAATCA 60.431 47.826 0.00 0.00 0.00 2.57
104 105 4.517285 GGTCAGCAGGAGTAATCAATCAA 58.483 43.478 0.00 0.00 0.00 2.57
105 106 5.128919 GGTCAGCAGGAGTAATCAATCAAT 58.871 41.667 0.00 0.00 0.00 2.57
106 107 5.238214 GGTCAGCAGGAGTAATCAATCAATC 59.762 44.000 0.00 0.00 0.00 2.67
107 108 5.238214 GTCAGCAGGAGTAATCAATCAATCC 59.762 44.000 0.00 0.00 0.00 3.01
108 109 4.518211 CAGCAGGAGTAATCAATCAATCCC 59.482 45.833 0.00 0.00 0.00 3.85
109 110 3.499918 GCAGGAGTAATCAATCAATCCCG 59.500 47.826 0.00 0.00 0.00 5.14
148 149 1.797635 GTCTCTCAAGTTGACTGCAGC 59.202 52.381 15.27 7.45 0.00 5.25
191 192 1.726791 ACTCGTTGTGATGTTCGATGC 59.273 47.619 0.00 0.00 0.00 3.91
192 193 1.061131 CTCGTTGTGATGTTCGATGCC 59.939 52.381 0.00 0.00 0.00 4.40
230 235 1.005630 AGGCTGTCAGCGTCTTGTC 60.006 57.895 18.44 2.93 43.62 3.18
239 244 1.299926 GCGTCTTGTCGGTCACTGT 60.300 57.895 0.00 0.00 0.00 3.55
256 261 2.884639 ACTGTAATGTGTTCTGGTTGGC 59.115 45.455 0.00 0.00 0.00 4.52
257 262 2.884012 CTGTAATGTGTTCTGGTTGGCA 59.116 45.455 0.00 0.00 0.00 4.92
271 276 5.357878 TCTGGTTGGCAATTAGTTCATCATC 59.642 40.000 1.92 0.00 0.00 2.92
288 298 2.625314 TCATCCATAAGTCAGAGAGGCG 59.375 50.000 0.00 0.00 0.00 5.52
296 306 0.390472 GTCAGAGAGGCGGGTTTCTG 60.390 60.000 0.00 0.00 38.67 3.02
299 309 1.065854 CAGAGAGGCGGGTTTCTGAAT 60.066 52.381 0.00 0.00 39.46 2.57
304 314 3.009143 AGAGGCGGGTTTCTGAATTTAGT 59.991 43.478 0.00 0.00 0.00 2.24
320 330 9.143631 CTGAATTTAGTTCCAGGCAAAATTTAG 57.856 33.333 0.00 0.00 35.91 1.85
321 331 8.093927 TGAATTTAGTTCCAGGCAAAATTTAGG 58.906 33.333 0.00 0.00 35.91 2.69
383 400 2.353269 TCGTGTTGTTCGATGCTTTTGT 59.647 40.909 0.00 0.00 32.30 2.83
533 551 3.490800 TGGTCATTTGTTCATCATGCG 57.509 42.857 0.00 0.00 0.00 4.73
562 580 3.137360 AGAGAGGCAGGTTTCTCAACTTT 59.863 43.478 3.88 0.00 41.78 2.66
596 615 7.115236 GGCAAAAATTTAAACTACCACTTACCG 59.885 37.037 0.00 0.00 0.00 4.02
597 616 7.648908 GCAAAAATTTAAACTACCACTTACCGT 59.351 33.333 0.00 0.00 0.00 4.83
599 618 9.734620 AAAAATTTAAACTACCACTTACCGTTC 57.265 29.630 0.00 0.00 0.00 3.95
606 625 1.615392 ACCACTTACCGTTCGTTAGCT 59.385 47.619 0.00 0.00 0.00 3.32
618 637 2.809446 TCGTTAGCTGTCCATTCATCG 58.191 47.619 0.00 0.00 0.00 3.84
625 645 2.033407 GCTGTCCATTCATCGTGAATCG 60.033 50.000 9.38 5.14 43.03 3.34
629 649 3.370978 GTCCATTCATCGTGAATCGTTGT 59.629 43.478 9.38 0.00 43.03 3.32
630 650 3.370672 TCCATTCATCGTGAATCGTTGTG 59.629 43.478 9.38 1.89 43.03 3.33
640 660 5.234543 TCGTGAATCGTTGTGTTGTTTGATA 59.765 36.000 0.00 0.00 40.80 2.15
642 662 6.195868 GTGAATCGTTGTGTTGTTTGATACA 58.804 36.000 0.00 0.00 34.12 2.29
651 671 7.106439 TGTGTTGTTTGATACATTTGAGGTT 57.894 32.000 0.00 0.00 36.44 3.50
652 672 6.977502 TGTGTTGTTTGATACATTTGAGGTTG 59.022 34.615 0.00 0.00 36.44 3.77
653 673 7.148000 TGTGTTGTTTGATACATTTGAGGTTGA 60.148 33.333 0.00 0.00 36.44 3.18
660 690 9.829507 TTTGATACATTTGAGGTTGAACAATTT 57.170 25.926 0.00 0.00 0.00 1.82
681 711 4.200838 TCAAACTGTCAGTGTCTTGTGA 57.799 40.909 6.18 1.55 0.00 3.58
689 719 6.101650 TGTCAGTGTCTTGTGAGTCATTAT 57.898 37.500 0.00 0.00 0.00 1.28
690 720 7.039714 ACTGTCAGTGTCTTGTGAGTCATTATA 60.040 37.037 4.21 0.00 0.00 0.98
691 721 7.666623 TGTCAGTGTCTTGTGAGTCATTATAA 58.333 34.615 0.00 0.00 0.00 0.98
692 722 8.314021 TGTCAGTGTCTTGTGAGTCATTATAAT 58.686 33.333 0.00 0.00 0.00 1.28
693 723 9.803315 GTCAGTGTCTTGTGAGTCATTATAATA 57.197 33.333 0.00 0.00 0.00 0.98
713 743 6.808008 AATATGTTCTGGTTGTCAGTCTTG 57.192 37.500 0.00 0.00 43.76 3.02
714 744 3.904800 TGTTCTGGTTGTCAGTCTTGA 57.095 42.857 0.00 0.00 43.76 3.02
715 745 4.214986 TGTTCTGGTTGTCAGTCTTGAA 57.785 40.909 0.00 0.00 43.76 2.69
716 746 4.584874 TGTTCTGGTTGTCAGTCTTGAAA 58.415 39.130 0.00 0.00 43.76 2.69
717 747 5.007034 TGTTCTGGTTGTCAGTCTTGAAAA 58.993 37.500 0.00 0.00 43.76 2.29
718 748 5.475220 TGTTCTGGTTGTCAGTCTTGAAAAA 59.525 36.000 0.00 0.00 43.76 1.94
745 775 8.458843 AGGAAAAATAATATGTTCTGGTTGTCG 58.541 33.333 0.00 0.00 0.00 4.35
786 816 9.874205 AAATAATATGTTCTGGTTGGTCATTTG 57.126 29.630 0.00 0.00 0.00 2.32
800 830 4.038883 TGGTCATTTGTTCATCATGCACAA 59.961 37.500 0.00 0.00 32.02 3.33
835 865 5.466728 TCTGCAATGTCACTTTCTTGTACTC 59.533 40.000 0.00 0.00 0.00 2.59
838 868 5.239525 GCAATGTCACTTTCTTGTACTCCTT 59.760 40.000 0.00 0.00 0.00 3.36
841 871 3.498777 GTCACTTTCTTGTACTCCTTGGC 59.501 47.826 0.00 0.00 0.00 4.52
938 968 2.181975 TCAGCATGATCTCTGTGGACA 58.818 47.619 0.00 0.00 42.56 4.02
948 978 3.435275 TCTCTGTGGACAATGAGTAGCT 58.565 45.455 0.00 0.00 0.00 3.32
988 1018 1.984026 CCCCCTGTGGTTGCATTCC 60.984 63.158 0.00 0.00 0.00 3.01
990 1020 0.331278 CCCCTGTGGTTGCATTCCTA 59.669 55.000 9.35 0.00 0.00 2.94
1009 1039 3.997021 CCTATACTGGATCATGGCGAAAC 59.003 47.826 0.00 0.00 0.00 2.78
1012 1042 0.933097 CTGGATCATGGCGAAACTCG 59.067 55.000 0.00 0.00 43.89 4.18
1035 1065 0.530650 CTGTCAGTCGCAGGTGTGTT 60.531 55.000 0.00 0.00 0.00 3.32
1055 1085 5.464389 GTGTTCCTTTTTCACGCTCTACTTA 59.536 40.000 0.00 0.00 0.00 2.24
1069 1099 5.692204 CGCTCTACTTATGATTCGAATTGGT 59.308 40.000 12.81 9.27 0.00 3.67
1075 1105 7.915293 ACTTATGATTCGAATTGGTTGTACA 57.085 32.000 12.81 3.24 0.00 2.90
1083 1113 2.194201 ATTGGTTGTACACTTCCCCG 57.806 50.000 0.00 0.00 0.00 5.73
1110 1140 7.205297 CAGTTAATATTTCCCCATTTGCTCTG 58.795 38.462 0.00 0.00 0.00 3.35
1291 1321 8.226819 TCAGTGTAATAACCACATTGTTTTGA 57.773 30.769 0.00 0.00 35.70 2.69
1424 1454 2.760092 GCTTAACCATGCCTGGAATTCA 59.240 45.455 15.66 0.00 46.37 2.57
1568 1723 5.189342 TGATATGGTGTCCATTTGGCAAAAT 59.811 36.000 17.70 5.79 42.23 1.82
1579 1734 5.065474 CCATTTGGCAAAATATTCTGCTTGG 59.935 40.000 17.70 11.65 38.65 3.61
1589 1744 7.440523 AAATATTCTGCTTGGATAATCGGTC 57.559 36.000 0.00 0.00 0.00 4.79
1590 1745 2.910688 TCTGCTTGGATAATCGGTCC 57.089 50.000 0.00 0.00 36.26 4.46
1609 1764 5.642063 CGGTCCGCATAGATTAACCATTTAT 59.358 40.000 0.00 0.00 0.00 1.40
1634 1789 7.997773 ATTGATTACATCCATTCCTGATCAG 57.002 36.000 16.24 16.24 0.00 2.90
1665 1820 9.360093 CACCTCTACTAGATTTTGTTCACTAAG 57.640 37.037 0.00 0.00 0.00 2.18
1893 2049 8.624701 ACATTTTGAGAAATATCTTGCATTCG 57.375 30.769 0.00 0.00 35.54 3.34
1905 2061 9.764363 AATATCTTGCATTCGTATCTCTTTGTA 57.236 29.630 0.00 0.00 0.00 2.41
2031 2187 2.093500 TGGGTCTTCATGTTCATCTCCG 60.093 50.000 0.00 0.00 0.00 4.63
2038 2194 6.147164 GTCTTCATGTTCATCTCCGTTGTTAA 59.853 38.462 0.00 0.00 0.00 2.01
2132 2290 6.150140 CAGAAGTCCTAAATTCTGTTCCCTTG 59.850 42.308 7.29 0.00 44.75 3.61
2536 2698 3.159984 GCGCTACTGTGCTGTCAC 58.840 61.111 0.00 0.00 45.43 3.67
2570 2732 9.918630 CTGTTCCTCTGATTGTAATTTGAAATT 57.081 29.630 8.35 8.35 0.00 1.82
2606 2768 3.259064 GCTTCTTTATGCACGTACCTCA 58.741 45.455 0.00 0.00 0.00 3.86
2746 2908 7.442364 CACTCTTCAGTTCTCCAGACAATTTTA 59.558 37.037 0.00 0.00 0.00 1.52
2754 2916 8.954350 AGTTCTCCAGACAATTTTATCTTGATG 58.046 33.333 0.00 0.00 0.00 3.07
2776 2938 7.601508 TGATGTGAGAACTGACATATGCATATC 59.398 37.037 16.46 8.22 32.85 1.63
2816 2979 9.797556 AGGTACATCAAACTTGTTAAGAAAAAC 57.202 29.630 0.00 0.00 0.00 2.43
2843 3006 1.772819 ATATCTCCCAGCCCGGCTTG 61.773 60.000 9.99 6.32 36.40 4.01
2855 3018 2.359975 GGCTTGGAACCTGACCGG 60.360 66.667 0.00 0.00 39.35 5.28
2967 3130 9.683069 GAAACATATTTCTTTGTTCTGATGTGT 57.317 29.630 0.00 0.00 41.01 3.72
3053 3216 1.271543 CCTCATCTTCCACCTTGTGCA 60.272 52.381 0.00 0.00 31.34 4.57
3097 3260 3.443099 TGCTGAGTTCTATCCACATCG 57.557 47.619 0.00 0.00 0.00 3.84
3098 3261 2.131183 GCTGAGTTCTATCCACATCGC 58.869 52.381 0.00 0.00 0.00 4.58
3109 3272 7.142306 TCTATCCACATCGCTACTATTACAC 57.858 40.000 0.00 0.00 0.00 2.90
3110 3273 4.219143 TCCACATCGCTACTATTACACG 57.781 45.455 0.00 0.00 0.00 4.49
3217 3381 4.113815 TCAAGGGAGGCATGGCGG 62.114 66.667 14.30 1.04 0.00 6.13
3333 3497 3.426695 CCTGAACGCAGAATGATTTGGTC 60.427 47.826 0.00 0.00 45.17 4.02
3369 3533 0.693049 ACTTCGCCCTCAGGAAATGT 59.307 50.000 0.00 0.00 33.47 2.71
3429 3597 4.941325 ATTTCAGCAGCAGCATATATCG 57.059 40.909 3.17 0.00 45.49 2.92
3453 3621 2.293399 ACTGAATTGTTTTGGTCCTCGC 59.707 45.455 0.00 0.00 0.00 5.03
3454 3622 1.611491 TGAATTGTTTTGGTCCTCGCC 59.389 47.619 0.00 0.00 0.00 5.54
3455 3623 1.886542 GAATTGTTTTGGTCCTCGCCT 59.113 47.619 0.00 0.00 0.00 5.52
3456 3624 1.534729 ATTGTTTTGGTCCTCGCCTC 58.465 50.000 0.00 0.00 0.00 4.70
3574 3743 5.118664 CAGATATTTTGCGTATCAGGTACCG 59.881 44.000 6.18 1.56 32.26 4.02
3575 3744 1.361793 TTTTGCGTATCAGGTACCGC 58.638 50.000 6.18 5.59 35.13 5.68
3581 3750 0.599558 GTATCAGGTACCGCGGCATA 59.400 55.000 28.58 8.52 0.00 3.14
3607 3779 3.758023 CCAACCTGCTGATTTGTATGTGA 59.242 43.478 0.00 0.00 0.00 3.58
3613 3785 7.056006 ACCTGCTGATTTGTATGTGATGAATA 58.944 34.615 0.00 0.00 0.00 1.75
3696 3868 0.257039 GAGTGGGGCATGTTCCAGAT 59.743 55.000 9.00 2.62 33.13 2.90
3701 3873 0.548031 GGGCATGTTCCAGATGAGGA 59.452 55.000 0.00 0.00 35.41 3.71
3818 3990 3.056536 CCTCGTCTCCATGTTTTCTCTCA 60.057 47.826 0.00 0.00 0.00 3.27
3868 4040 4.075682 TCTACTCGGATGATGGAGATGAC 58.924 47.826 0.00 0.00 34.40 3.06
3922 4097 8.924303 TGTATAGGTTTTAGATGCATGTAGAGT 58.076 33.333 2.46 0.00 0.00 3.24
3961 4137 3.829886 ATCAACCAACATTACAGTGCG 57.170 42.857 0.00 0.00 0.00 5.34
3962 4138 1.265635 TCAACCAACATTACAGTGCGC 59.734 47.619 0.00 0.00 0.00 6.09
4063 4239 7.984422 TTTCAGATTGTACCTGCATATATGG 57.016 36.000 14.51 0.52 0.00 2.74
4112 4291 3.188048 GCATGATAGTAATGAGCACCAGC 59.812 47.826 0.00 0.00 42.56 4.85
4254 4433 1.303888 CACCATTGCCAGGCAGTCT 60.304 57.895 15.50 0.34 40.61 3.24
4268 4447 2.583593 GTCTGGCGGCGATGAGTC 60.584 66.667 12.98 0.00 0.00 3.36
4332 4511 0.614979 CTTCCTGGTCTCCTTCCGGA 60.615 60.000 0.00 0.00 37.82 5.14
4455 5198 1.311059 GGGGCCCAATGGATGAAGT 59.689 57.895 26.86 0.00 0.00 3.01
4456 5199 0.555769 GGGGCCCAATGGATGAAGTA 59.444 55.000 26.86 0.00 0.00 2.24
4458 5201 1.322442 GGCCCAATGGATGAAGTAGC 58.678 55.000 0.00 0.00 0.00 3.58
4507 5293 1.067985 TGGTGCAAGTTTGTGTGTGTG 60.068 47.619 0.00 0.00 0.00 3.82
4549 5335 8.706492 CAGTATGTGTGATTGCCATTATTTTT 57.294 30.769 0.00 0.00 0.00 1.94
4682 5468 1.839994 TCCTGAGCTGAAATGGGGTAG 59.160 52.381 0.00 0.00 0.00 3.18
4688 5474 3.421844 AGCTGAAATGGGGTAGTTTCAC 58.578 45.455 0.00 0.00 38.88 3.18
4704 5490 9.865321 GGTAGTTTCACATATGTAGAACACTTA 57.135 33.333 24.14 12.61 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.309656 GCTTACGGGGAACTATATAAACTACAT 58.690 37.037 0.00 0.00 0.00 2.29
3 4 7.287466 TGCTTACGGGGAACTATATAAACTACA 59.713 37.037 0.00 0.00 0.00 2.74
4 5 7.661040 TGCTTACGGGGAACTATATAAACTAC 58.339 38.462 0.00 0.00 0.00 2.73
5 6 7.838079 TGCTTACGGGGAACTATATAAACTA 57.162 36.000 0.00 0.00 0.00 2.24
6 7 6.736110 TGCTTACGGGGAACTATATAAACT 57.264 37.500 0.00 0.00 0.00 2.66
7 8 8.309656 AGTATGCTTACGGGGAACTATATAAAC 58.690 37.037 4.27 0.00 33.32 2.01
8 9 8.426569 AGTATGCTTACGGGGAACTATATAAA 57.573 34.615 4.27 0.00 33.32 1.40
9 10 8.308931 CAAGTATGCTTACGGGGAACTATATAA 58.691 37.037 0.00 0.00 32.87 0.98
10 11 7.093640 CCAAGTATGCTTACGGGGAACTATATA 60.094 40.741 13.86 0.00 32.87 0.86
11 12 6.295688 CCAAGTATGCTTACGGGGAACTATAT 60.296 42.308 13.86 0.00 32.87 0.86
12 13 5.011329 CCAAGTATGCTTACGGGGAACTATA 59.989 44.000 13.86 0.00 32.87 1.31
13 14 4.202326 CCAAGTATGCTTACGGGGAACTAT 60.202 45.833 13.86 0.00 32.87 2.12
14 15 3.133362 CCAAGTATGCTTACGGGGAACTA 59.867 47.826 13.86 0.00 32.87 2.24
15 16 2.093128 CCAAGTATGCTTACGGGGAACT 60.093 50.000 13.86 0.00 32.87 3.01
16 17 2.093341 TCCAAGTATGCTTACGGGGAAC 60.093 50.000 17.29 0.00 34.52 3.62
17 18 2.093341 GTCCAAGTATGCTTACGGGGAA 60.093 50.000 19.69 8.05 37.25 3.97
58 59 3.941483 ACCGACCAAATCAGCTGATTAAG 59.059 43.478 35.78 30.18 43.41 1.85
82 83 4.142609 TGATTGATTACTCCTGCTGACC 57.857 45.455 0.00 0.00 0.00 4.02
103 104 3.477530 GCTCTAATTAAGCACCGGGATT 58.522 45.455 6.32 2.08 39.61 3.01
104 105 2.224548 GGCTCTAATTAAGCACCGGGAT 60.225 50.000 6.32 0.00 41.66 3.85
105 106 1.140252 GGCTCTAATTAAGCACCGGGA 59.860 52.381 6.32 0.00 41.66 5.14
106 107 1.134220 TGGCTCTAATTAAGCACCGGG 60.134 52.381 6.32 0.00 41.66 5.73
107 108 2.213499 CTGGCTCTAATTAAGCACCGG 58.787 52.381 0.00 0.00 41.66 5.28
108 109 2.213499 CCTGGCTCTAATTAAGCACCG 58.787 52.381 16.35 7.77 41.66 4.94
109 110 3.118223 AGACCTGGCTCTAATTAAGCACC 60.118 47.826 16.35 4.90 41.66 5.01
174 175 1.061131 GAGGCATCGAACATCACAACG 59.939 52.381 0.00 0.00 0.00 4.10
191 192 2.886523 TGCAATTGTTCAACCTCAGAGG 59.113 45.455 15.72 15.72 42.49 3.69
192 193 3.057736 CCTGCAATTGTTCAACCTCAGAG 60.058 47.826 7.40 0.00 0.00 3.35
230 235 2.736721 CCAGAACACATTACAGTGACCG 59.263 50.000 0.00 0.00 42.05 4.79
239 244 5.772672 ACTAATTGCCAACCAGAACACATTA 59.227 36.000 0.00 0.00 0.00 1.90
256 261 9.551734 TCTGACTTATGGATGATGAACTAATTG 57.448 33.333 0.00 0.00 0.00 2.32
257 262 9.775854 CTCTGACTTATGGATGATGAACTAATT 57.224 33.333 0.00 0.00 0.00 1.40
271 276 0.390860 CCCGCCTCTCTGACTTATGG 59.609 60.000 0.00 0.00 0.00 2.74
288 298 4.082190 GCCTGGAACTAAATTCAGAAACCC 60.082 45.833 0.00 0.00 39.30 4.11
296 306 7.064609 GCCTAAATTTTGCCTGGAACTAAATTC 59.935 37.037 0.00 0.00 33.40 2.17
299 309 5.542251 AGCCTAAATTTTGCCTGGAACTAAA 59.458 36.000 0.00 0.00 0.00 1.85
304 314 4.672899 AGTAGCCTAAATTTTGCCTGGAA 58.327 39.130 0.00 0.00 0.00 3.53
320 330 5.045668 GGCTAATAAGTCGTAGAGTAGCC 57.954 47.826 4.11 4.11 46.53 3.93
321 331 4.761227 AGGGCTAATAAGTCGTAGAGTAGC 59.239 45.833 0.00 0.00 40.67 3.58
373 390 5.989551 AATTGTTCAACCACAAAAGCATC 57.010 34.783 0.00 0.00 40.07 3.91
401 418 2.046892 CCCCCAAGACGCTGACAG 60.047 66.667 0.00 0.00 0.00 3.51
493 511 6.208599 TGACCAACCAGAACATATTCTTTTCC 59.791 38.462 0.00 0.00 42.91 3.13
533 551 3.259625 AGAAACCTGCCTCTCTGACTTAC 59.740 47.826 0.00 0.00 0.00 2.34
562 580 5.852827 AGTTTAAATTTTTGCCTGCAGCTA 58.147 33.333 8.66 0.00 44.23 3.32
596 615 3.000322 CGATGAATGGACAGCTAACGAAC 60.000 47.826 0.00 0.00 0.00 3.95
597 616 3.186909 CGATGAATGGACAGCTAACGAA 58.813 45.455 0.00 0.00 0.00 3.85
599 618 2.282555 CACGATGAATGGACAGCTAACG 59.717 50.000 0.00 0.00 0.00 3.18
606 625 3.245518 ACGATTCACGATGAATGGACA 57.754 42.857 20.65 0.00 46.20 4.02
618 637 6.195868 TGTATCAAACAACACAACGATTCAC 58.804 36.000 0.00 0.00 34.29 3.18
623 643 6.786207 TCAAATGTATCAAACAACACAACGA 58.214 32.000 0.00 0.00 42.70 3.85
625 645 6.978080 ACCTCAAATGTATCAAACAACACAAC 59.022 34.615 0.00 0.00 42.70 3.32
629 649 7.340122 TCAACCTCAAATGTATCAAACAACA 57.660 32.000 0.00 0.00 42.70 3.33
630 650 7.704472 TGTTCAACCTCAAATGTATCAAACAAC 59.296 33.333 0.00 0.00 42.70 3.32
651 671 6.150976 AGACACTGACAGTTTGAAATTGTTCA 59.849 34.615 5.04 6.54 42.12 3.18
652 672 6.555315 AGACACTGACAGTTTGAAATTGTTC 58.445 36.000 5.04 1.51 0.00 3.18
653 673 6.515272 AGACACTGACAGTTTGAAATTGTT 57.485 33.333 5.04 0.00 0.00 2.83
660 690 4.183865 CTCACAAGACACTGACAGTTTGA 58.816 43.478 20.27 9.71 0.00 2.69
689 719 7.676004 TCAAGACTGACAACCAGAACATATTA 58.324 34.615 0.00 0.00 45.78 0.98
690 720 6.533730 TCAAGACTGACAACCAGAACATATT 58.466 36.000 0.00 0.00 45.78 1.28
691 721 6.114187 TCAAGACTGACAACCAGAACATAT 57.886 37.500 0.00 0.00 45.78 1.78
692 722 5.545063 TCAAGACTGACAACCAGAACATA 57.455 39.130 0.00 0.00 45.78 2.29
693 723 4.422073 TCAAGACTGACAACCAGAACAT 57.578 40.909 0.00 0.00 45.78 2.71
694 724 3.904800 TCAAGACTGACAACCAGAACA 57.095 42.857 0.00 0.00 45.78 3.18
695 725 5.560966 TTTTCAAGACTGACAACCAGAAC 57.439 39.130 0.00 0.00 45.78 3.01
719 749 8.458843 CGACAACCAGAACATATTATTTTTCCT 58.541 33.333 0.00 0.00 0.00 3.36
720 750 8.455682 TCGACAACCAGAACATATTATTTTTCC 58.544 33.333 0.00 0.00 0.00 3.13
723 753 9.396022 AGATCGACAACCAGAACATATTATTTT 57.604 29.630 0.00 0.00 0.00 1.82
724 754 8.964476 AGATCGACAACCAGAACATATTATTT 57.036 30.769 0.00 0.00 0.00 1.40
725 755 8.830580 CAAGATCGACAACCAGAACATATTATT 58.169 33.333 0.00 0.00 0.00 1.40
726 756 8.204160 TCAAGATCGACAACCAGAACATATTAT 58.796 33.333 0.00 0.00 0.00 1.28
727 757 7.552459 TCAAGATCGACAACCAGAACATATTA 58.448 34.615 0.00 0.00 0.00 0.98
785 815 3.366577 GCATGACTTGTGCATGATGAACA 60.367 43.478 1.12 1.12 44.49 3.18
786 816 3.176708 GCATGACTTGTGCATGATGAAC 58.823 45.455 7.68 0.00 44.49 3.18
812 842 5.334414 GGAGTACAAGAAAGTGACATTGCAG 60.334 44.000 0.00 0.00 0.00 4.41
826 856 1.544691 GAGACGCCAAGGAGTACAAGA 59.455 52.381 0.00 0.00 0.00 3.02
841 871 0.742281 CAAGCCCATGGTGAGAGACG 60.742 60.000 11.73 0.00 0.00 4.18
907 937 0.745486 TCATGCTGATGGAGTTGCGG 60.745 55.000 0.00 0.00 0.00 5.69
938 968 1.407258 GAGCGAGGACAGCTACTCATT 59.593 52.381 11.38 0.96 46.13 2.57
948 978 2.049156 CACTTGCGAGCGAGGACA 60.049 61.111 15.92 0.00 0.00 4.02
984 1014 4.096681 TCGCCATGATCCAGTATAGGAAT 58.903 43.478 0.00 0.00 41.92 3.01
988 1018 4.887748 AGTTTCGCCATGATCCAGTATAG 58.112 43.478 0.00 0.00 0.00 1.31
990 1020 3.733337 GAGTTTCGCCATGATCCAGTAT 58.267 45.455 0.00 0.00 0.00 2.12
1009 1039 3.177920 GCGACTGACAGCTGCGAG 61.178 66.667 15.27 12.36 0.00 5.03
1012 1042 3.117171 CCTGCGACTGACAGCTGC 61.117 66.667 15.27 7.45 33.65 5.25
1035 1065 6.032956 TCATAAGTAGAGCGTGAAAAAGGA 57.967 37.500 0.00 0.00 0.00 3.36
1055 1085 6.128007 GGAAGTGTACAACCAATTCGAATCAT 60.128 38.462 11.83 0.00 39.61 2.45
1069 1099 1.373435 CTGCCGGGGAAGTGTACAA 59.627 57.895 2.18 0.00 0.00 2.41
1075 1105 3.945640 AATATTAACTGCCGGGGAAGT 57.054 42.857 2.18 0.00 35.00 3.01
1083 1113 5.056480 GCAAATGGGGAAATATTAACTGCC 58.944 41.667 0.00 0.00 0.00 4.85
1291 1321 8.883731 CAAATAAGTTACTCTGTTCCGATGAAT 58.116 33.333 0.00 0.00 31.98 2.57
1424 1454 3.181440 TGTTCTCCCTTGCATTTCTGACT 60.181 43.478 0.00 0.00 0.00 3.41
1568 1723 4.560716 CGGACCGATTATCCAAGCAGAATA 60.561 45.833 8.64 0.00 35.83 1.75
1579 1734 5.519206 GGTTAATCTATGCGGACCGATTATC 59.481 44.000 20.50 10.71 30.91 1.75
1634 1789 7.656137 TGAACAAAATCTAGTAGAGGTGAACAC 59.344 37.037 5.98 0.00 0.00 3.32
1757 1912 1.078918 CCTGCGCAGATGGAAGTCA 60.079 57.895 38.06 0.00 0.00 3.41
1872 2028 9.330063 AGATACGAATGCAAGATATTTCTCAAA 57.670 29.630 0.00 0.00 0.00 2.69
2009 2165 3.539604 GGAGATGAACATGAAGACCCAG 58.460 50.000 0.00 0.00 0.00 4.45
2013 2169 3.997021 ACAACGGAGATGAACATGAAGAC 59.003 43.478 0.00 0.00 33.32 3.01
2126 2284 1.823169 GCACCAGACGGTACAAGGGA 61.823 60.000 0.00 0.00 46.94 4.20
2132 2290 0.949105 CACCAAGCACCAGACGGTAC 60.949 60.000 0.00 0.00 46.94 3.34
2397 2559 4.900635 AGCGAAATTGTCAGAAAACTGT 57.099 36.364 0.00 0.00 0.00 3.55
2534 2696 2.281070 AGGAACAGCCAGCACGTG 60.281 61.111 12.28 12.28 40.02 4.49
2536 2698 2.031516 CAGAGGAACAGCCAGCACG 61.032 63.158 0.00 0.00 40.02 5.34
2570 2732 8.818057 GCATAAAGAAGCGTTAGAAGAAGATTA 58.182 33.333 0.00 0.00 0.00 1.75
2746 2908 6.482641 GCATATGTCAGTTCTCACATCAAGAT 59.517 38.462 4.29 0.00 34.92 2.40
2754 2916 5.347093 CCGATATGCATATGTCAGTTCTCAC 59.653 44.000 23.76 4.01 0.00 3.51
2776 2938 3.322211 TGTACCTGTAATCCAACACCG 57.678 47.619 0.00 0.00 0.00 4.94
2843 3006 0.906282 TTAGTCCCCGGTCAGGTTCC 60.906 60.000 0.00 0.00 38.74 3.62
2855 3018 2.633488 GTCATCTGCCAAGTTAGTCCC 58.367 52.381 0.00 0.00 0.00 4.46
2966 3129 4.976116 CACAAGTTGCCAGCTTAAGTTAAC 59.024 41.667 1.81 0.00 0.00 2.01
2967 3130 4.642885 ACACAAGTTGCCAGCTTAAGTTAA 59.357 37.500 1.81 0.00 0.00 2.01
3053 3216 5.730296 AGAGGATAATAAGCACATACGCT 57.270 39.130 0.00 0.00 46.67 5.07
3097 3260 7.172875 TCAGTTAGATCTCCGTGTAATAGTAGC 59.827 40.741 0.00 0.00 0.00 3.58
3098 3261 8.497554 GTCAGTTAGATCTCCGTGTAATAGTAG 58.502 40.741 0.00 0.00 0.00 2.57
3109 3272 0.930742 GCGCGTCAGTTAGATCTCCG 60.931 60.000 8.43 0.00 0.00 4.63
3110 3273 0.595310 GGCGCGTCAGTTAGATCTCC 60.595 60.000 5.47 0.00 0.00 3.71
3217 3381 5.065914 ACCTGAATCATATGCCATACACAC 58.934 41.667 0.00 0.00 0.00 3.82
3220 3384 5.072193 ACTGACCTGAATCATATGCCATACA 59.928 40.000 0.00 0.00 0.00 2.29
3400 3568 2.353406 GCTGCTGCTGAAATTCCACAAT 60.353 45.455 10.92 0.00 36.03 2.71
3402 3570 0.599558 GCTGCTGCTGAAATTCCACA 59.400 50.000 10.92 0.00 36.03 4.17
3406 3574 5.106791 ACGATATATGCTGCTGCTGAAATTC 60.107 40.000 17.00 6.13 40.48 2.17
3412 3580 4.091075 CAGTAACGATATATGCTGCTGCTG 59.909 45.833 17.00 0.77 40.48 4.41
3413 3581 4.021981 TCAGTAACGATATATGCTGCTGCT 60.022 41.667 17.00 5.09 40.48 4.24
3414 3582 4.237724 TCAGTAACGATATATGCTGCTGC 58.762 43.478 8.89 8.89 40.20 5.25
3429 3597 5.449304 CGAGGACCAAAACAATTCAGTAAC 58.551 41.667 0.00 0.00 0.00 2.50
3453 3621 1.451567 CATGAGCAGGCTGTGGAGG 60.452 63.158 17.16 0.00 0.00 4.30
3454 3622 0.462225 CTCATGAGCAGGCTGTGGAG 60.462 60.000 17.16 11.57 0.00 3.86
3455 3623 0.906282 TCTCATGAGCAGGCTGTGGA 60.906 55.000 18.36 6.02 0.00 4.02
3456 3624 0.035725 TTCTCATGAGCAGGCTGTGG 60.036 55.000 18.36 1.73 0.00 4.17
3556 3725 1.361793 GCGGTACCTGATACGCAAAA 58.638 50.000 10.90 0.00 35.05 2.44
3559 3728 2.410060 CGCGGTACCTGATACGCA 59.590 61.111 10.90 0.00 34.79 5.24
3581 3750 0.971386 CAAATCAGCAGGTTGGCCTT 59.029 50.000 3.32 0.00 44.18 4.35
3589 3759 5.823209 TTCATCACATACAAATCAGCAGG 57.177 39.130 0.00 0.00 0.00 4.85
3607 3779 2.005370 CCTTGCCCTGCCATATTCAT 57.995 50.000 0.00 0.00 0.00 2.57
3818 3990 1.340405 GGGCTTGTCATGTCATCCACT 60.340 52.381 11.64 0.00 0.00 4.00
3868 4040 1.247261 CGTCGTCGTCATCGTCATCG 61.247 60.000 0.00 0.00 38.33 3.84
3922 4097 8.049721 TGGTTGATACATAACACCATCATGTAA 58.950 33.333 0.00 0.00 38.33 2.41
4041 4217 6.686484 ACCATATATGCAGGTACAATCTGA 57.314 37.500 7.24 0.00 34.36 3.27
4070 4249 6.539826 TCATGCAATCTGGTTCAGTAGTATTG 59.460 38.462 0.00 0.00 32.61 1.90
4112 4291 1.406069 GGATGCACCACCACAGACTAG 60.406 57.143 0.00 0.00 38.79 2.57
4115 4294 1.675641 GGGATGCACCACCACAGAC 60.676 63.158 7.49 0.00 41.20 3.51
4118 4297 2.858476 AGGGGATGCACCACCACA 60.858 61.111 0.00 0.00 44.65 4.17
4120 4299 2.424842 GAACAGGGGATGCACCACCA 62.425 60.000 0.00 0.00 44.65 4.17
4254 4433 4.451150 GTGGACTCATCGCCGCCA 62.451 66.667 0.00 0.00 0.00 5.69
4268 4447 0.734889 GTTTGCGATGGAGATGGTGG 59.265 55.000 0.00 0.00 0.00 4.61
4332 4511 2.800881 TATCGATGCACGCAATCTCT 57.199 45.000 8.54 0.00 42.26 3.10
4439 5182 1.133668 AGCTACTTCATCCATTGGGCC 60.134 52.381 2.09 0.00 0.00 5.80
4441 5184 3.474600 CTCAGCTACTTCATCCATTGGG 58.525 50.000 2.09 0.00 0.00 4.12
4444 5187 3.806380 CAGCTCAGCTACTTCATCCATT 58.194 45.455 0.00 0.00 36.40 3.16
4446 5189 1.134580 GCAGCTCAGCTACTTCATCCA 60.135 52.381 0.00 0.00 36.40 3.41
4447 5190 1.134580 TGCAGCTCAGCTACTTCATCC 60.135 52.381 0.00 0.00 36.40 3.51
4455 5198 4.291047 GCAGTTGCAGCTCAGCTA 57.709 55.556 0.00 0.00 36.40 3.32
4507 5293 6.757010 CACATACTGTGTTAATACCTGTCCTC 59.243 42.308 0.00 0.00 43.08 3.71
4615 5401 3.493129 GCGAAAAGGACCAAAATCCAAAC 59.507 43.478 0.00 0.00 41.73 2.93
4654 5440 4.404715 CCATTTCAGCTCAGGATCCAATTT 59.595 41.667 15.82 0.00 0.00 1.82
4655 5441 3.958798 CCATTTCAGCTCAGGATCCAATT 59.041 43.478 15.82 0.00 0.00 2.32
4656 5442 3.563223 CCATTTCAGCTCAGGATCCAAT 58.437 45.455 15.82 0.00 0.00 3.16
4657 5443 2.357465 CCCATTTCAGCTCAGGATCCAA 60.357 50.000 15.82 0.00 0.00 3.53
4663 5449 1.561542 ACTACCCCATTTCAGCTCAGG 59.438 52.381 0.00 0.00 0.00 3.86
4664 5450 3.356529 AACTACCCCATTTCAGCTCAG 57.643 47.619 0.00 0.00 0.00 3.35
4737 5523 3.004315 ACGAACATTTCCATGTGTGAACC 59.996 43.478 0.00 0.00 43.34 3.62


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

AutoCloner maintained by Alex Coulton.