Multiple sequence alignment - TraesCS7B01G239400

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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 TraesCS7B01G239400 chr7B 100.000 3901 0 0 1 3901 445424447 445420547 0.000000e+00 7204.0
1 TraesCS7B01G239400 chr7B 96.809 94 3 0 2064 2157 203138563 203138656 1.450000e-34 158.0
2 TraesCS7B01G239400 chr7B 100.000 29 0 0 2877 2905 688554301 688554329 2.000000e-03 54.7
3 TraesCS7B01G239400 chr7B 100.000 28 0 0 158 185 163743875 163743902 7.000000e-03 52.8
4 TraesCS7B01G239400 chr7D 95.618 1757 67 4 2152 3900 427630799 427629045 0.000000e+00 2809.0
5 TraesCS7B01G239400 chr7D 95.961 1114 33 4 966 2072 427631904 427630796 0.000000e+00 1797.0
6 TraesCS7B01G239400 chr7D 84.397 987 70 44 5 926 427633480 427632513 0.000000e+00 893.0
7 TraesCS7B01G239400 chr7D 90.164 122 8 3 2047 2164 616006518 616006639 5.220000e-34 156.0
8 TraesCS7B01G239400 chr7A 93.004 1601 85 9 2324 3901 505016936 505018532 0.000000e+00 2311.0
9 TraesCS7B01G239400 chr7A 89.273 1445 93 35 662 2072 505015318 505016734 0.000000e+00 1753.0
10 TraesCS7B01G239400 chr7A 86.511 556 57 8 5 555 504996809 504997351 2.590000e-166 595.0
11 TraesCS7B01G239400 chr7A 90.341 176 17 0 2152 2327 505016731 505016906 8.430000e-57 231.0
12 TraesCS7B01G239400 chr7A 98.913 92 1 0 2067 2158 20733015 20732924 8.670000e-37 165.0
13 TraesCS7B01G239400 chr2A 96.907 97 3 0 2063 2159 767024083 767023987 3.120000e-36 163.0
14 TraesCS7B01G239400 chr2A 96.907 97 3 0 2063 2159 767144139 767144235 3.120000e-36 163.0
15 TraesCS7B01G239400 chr2A 86.598 97 10 3 3648 3743 82363406 82363312 1.920000e-18 104.0
16 TraesCS7B01G239400 chr4D 96.842 95 3 0 2069 2163 10274495 10274401 4.030000e-35 159.0
17 TraesCS7B01G239400 chr4A 98.876 89 1 0 2067 2155 650851209 650851297 4.030000e-35 159.0
18 TraesCS7B01G239400 chr4A 98.876 89 1 0 2067 2155 650861412 650861500 4.030000e-35 159.0
19 TraesCS7B01G239400 chr3D 91.818 110 8 1 2047 2155 142089737 142089846 6.750000e-33 152.0
20 TraesCS7B01G239400 chr3D 85.271 129 15 1 3615 3743 33382436 33382560 3.160000e-26 130.0
21 TraesCS7B01G239400 chr3A 86.154 130 12 2 3615 3743 46168202 46168326 6.800000e-28 135.0
22 TraesCS7B01G239400 chr2B 83.846 130 15 3 3615 3743 218292338 218292462 6.850000e-23 119.0
23 TraesCS7B01G239400 chr2B 87.500 96 11 1 3648 3742 477526524 477526619 4.120000e-20 110.0
24 TraesCS7B01G239400 chr1D 86.207 87 11 1 3656 3742 27686031 27686116 4.150000e-15 93.5
25 TraesCS7B01G239400 chr1B 86.207 87 11 1 3656 3742 43324677 43324762 4.150000e-15 93.5
26 TraesCS7B01G239400 chr3B 100.000 28 0 0 158 185 103432802 103432829 7.000000e-03 52.8
27 TraesCS7B01G239400 chr1A 100.000 28 0 0 158 185 278241743 278241716 7.000000e-03 52.8


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 TraesCS7B01G239400 chr7B 445420547 445424447 3900 True 7204.000000 7204 100.000000 1 3901 1 chr7B.!!$R1 3900
1 TraesCS7B01G239400 chr7D 427629045 427633480 4435 True 1833.000000 2809 91.992000 5 3900 3 chr7D.!!$R1 3895
2 TraesCS7B01G239400 chr7A 505015318 505018532 3214 False 1431.666667 2311 90.872667 662 3901 3 chr7A.!!$F2 3239
3 TraesCS7B01G239400 chr7A 504996809 504997351 542 False 595.000000 595 86.511000 5 555 1 chr7A.!!$F1 550

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
65 66 0.317020 GACCGAATATTTGCGCAGGC 60.317 55.0 11.31 0.00 40.52 4.85 F
703 754 0.321653 GCCACCTGTTACCTCAGTGG 60.322 60.0 3.12 3.12 38.44 4.00 F
2320 3017 1.098050 GGGCACTTCACCATGATCAC 58.902 55.0 0.00 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 2164 0.459237 GCACGGTGGAGTCATCTCAG 60.459 60.0 10.60 0.00 42.05 3.35 R
2531 3260 0.889186 GCACATCACCCACGAAACCT 60.889 55.0 0.00 0.00 0.00 3.50 R
3326 4063 0.040204 AAAGAACCTCTGGGCCATGG 59.960 55.0 20.08 20.08 35.63 3.66 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
29 30 1.482593 CGCCTTTGGATGACCTAGAGT 59.517 52.381 0.00 0.00 37.04 3.24
48 49 0.611714 TTAGCCCGAAACCTCCAGAC 59.388 55.000 0.00 0.00 0.00 3.51
65 66 0.317020 GACCGAATATTTGCGCAGGC 60.317 55.000 11.31 0.00 40.52 4.85
109 110 5.208463 CTAGAACCTCTAGGCTCCATTTC 57.792 47.826 0.00 0.00 42.05 2.17
117 118 6.013379 CCTCTAGGCTCCATTTCTGTATAGA 58.987 44.000 0.00 0.00 0.00 1.98
133 134 7.411808 TCTGTATAGACCAAAAGTAGTCCTCT 58.588 38.462 0.00 0.00 33.29 3.69
165 166 9.102757 ACAAATTGTGTGTAAAAATTGCATACA 57.897 25.926 0.00 6.65 43.24 2.29
300 304 4.702131 GGCCAAAGTTGTCATCAATACTCT 59.298 41.667 0.00 0.00 35.92 3.24
385 391 5.163814 CGGAAATGAATCTCTCCACACTTTC 60.164 44.000 0.00 0.00 0.00 2.62
577 595 9.859427 AAATACTCATGTATGTCCATTTTGTTG 57.141 29.630 0.00 0.00 39.16 3.33
582 600 8.296211 TCATGTATGTCCATTTTGTTGATGAT 57.704 30.769 0.00 0.00 0.00 2.45
585 603 5.603170 ATGTCCATTTTGTTGATGATCCC 57.397 39.130 0.00 0.00 0.00 3.85
586 604 3.768757 TGTCCATTTTGTTGATGATCCCC 59.231 43.478 0.00 0.00 0.00 4.81
615 633 7.898014 TGCTACTCTCTCTGTTCCATATTAA 57.102 36.000 0.00 0.00 0.00 1.40
637 655 8.906636 TTAACTCTCGCTACTTGTACTAAATG 57.093 34.615 0.00 0.00 0.00 2.32
644 662 6.204075 GCTACTTGTACTAAATGAGCGATG 57.796 41.667 0.00 0.00 0.00 3.84
646 664 6.255887 GCTACTTGTACTAAATGAGCGATGTT 59.744 38.462 0.00 0.00 0.00 2.71
648 666 7.435068 ACTTGTACTAAATGAGCGATGTTTT 57.565 32.000 0.00 0.00 0.00 2.43
649 667 7.298122 ACTTGTACTAAATGAGCGATGTTTTG 58.702 34.615 0.00 0.00 0.00 2.44
650 668 7.172532 ACTTGTACTAAATGAGCGATGTTTTGA 59.827 33.333 0.00 0.00 0.00 2.69
651 669 7.060600 TGTACTAAATGAGCGATGTTTTGAG 57.939 36.000 0.00 0.00 0.00 3.02
652 670 6.871492 TGTACTAAATGAGCGATGTTTTGAGA 59.129 34.615 0.00 0.00 0.00 3.27
653 671 6.992063 ACTAAATGAGCGATGTTTTGAGAT 57.008 33.333 0.00 0.00 0.00 2.75
654 672 7.383102 ACTAAATGAGCGATGTTTTGAGATT 57.617 32.000 0.00 0.00 0.00 2.40
655 673 7.820648 ACTAAATGAGCGATGTTTTGAGATTT 58.179 30.769 0.00 0.00 0.00 2.17
656 674 7.965107 ACTAAATGAGCGATGTTTTGAGATTTC 59.035 33.333 0.00 0.00 0.00 2.17
657 675 4.326413 TGAGCGATGTTTTGAGATTTCG 57.674 40.909 0.00 0.00 0.00 3.46
659 677 2.177173 GCGATGTTTTGAGATTTCGCC 58.823 47.619 3.91 0.00 44.38 5.54
660 678 2.430956 CGATGTTTTGAGATTTCGCCG 58.569 47.619 0.00 0.00 0.00 6.46
700 751 2.270352 TTTGCCACCTGTTACCTCAG 57.730 50.000 0.00 0.00 35.45 3.35
703 754 0.321653 GCCACCTGTTACCTCAGTGG 60.322 60.000 3.12 3.12 38.44 4.00
779 841 3.120468 TGATTCCTCCCTCTCATCACA 57.880 47.619 0.00 0.00 0.00 3.58
780 842 3.453868 TGATTCCTCCCTCTCATCACAA 58.546 45.455 0.00 0.00 0.00 3.33
781 843 3.198635 TGATTCCTCCCTCTCATCACAAC 59.801 47.826 0.00 0.00 0.00 3.32
782 844 2.325661 TCCTCCCTCTCATCACAACA 57.674 50.000 0.00 0.00 0.00 3.33
783 845 2.837947 TCCTCCCTCTCATCACAACAT 58.162 47.619 0.00 0.00 0.00 2.71
784 846 2.768527 TCCTCCCTCTCATCACAACATC 59.231 50.000 0.00 0.00 0.00 3.06
785 847 2.502947 CCTCCCTCTCATCACAACATCA 59.497 50.000 0.00 0.00 0.00 3.07
786 848 3.136077 CCTCCCTCTCATCACAACATCAT 59.864 47.826 0.00 0.00 0.00 2.45
787 849 4.378774 CTCCCTCTCATCACAACATCATC 58.621 47.826 0.00 0.00 0.00 2.92
788 850 3.776417 TCCCTCTCATCACAACATCATCA 59.224 43.478 0.00 0.00 0.00 3.07
789 851 3.875727 CCCTCTCATCACAACATCATCAC 59.124 47.826 0.00 0.00 0.00 3.06
810 872 2.159128 CCACCACATGACACAAAGCAAA 60.159 45.455 0.00 0.00 0.00 3.68
812 874 4.261952 CCACCACATGACACAAAGCAAATA 60.262 41.667 0.00 0.00 0.00 1.40
1175 1832 3.285371 CGTAGTCGTCAAGGGGCT 58.715 61.111 0.00 0.00 0.00 5.19
1344 2015 1.671901 CCCTCCTCGTCTTCCTCTGC 61.672 65.000 0.00 0.00 0.00 4.26
1405 2076 4.911514 GAGAACCATCTCCAGAGAGTAC 57.088 50.000 3.41 0.00 45.35 2.73
1482 2164 9.290483 CTCCTTTTAAGTTTGTTTGTTCTCTTC 57.710 33.333 0.00 0.00 0.00 2.87
1510 2197 2.815211 CCACCGTGCTGATCCGTG 60.815 66.667 0.00 0.00 0.00 4.94
1536 2223 6.748333 TCCAGATTCAGATGAACAATTGTC 57.252 37.500 12.39 6.33 36.80 3.18
1537 2224 6.479006 TCCAGATTCAGATGAACAATTGTCT 58.521 36.000 12.39 1.27 36.80 3.41
1538 2225 6.373495 TCCAGATTCAGATGAACAATTGTCTG 59.627 38.462 12.39 14.28 39.47 3.51
1771 2468 5.922546 TGTATTCTTCGTCAATTTTGTCCG 58.077 37.500 0.00 0.00 0.00 4.79
1963 2660 6.384305 ACTGTCTTCTGGCTAATGGTAGTTAT 59.616 38.462 0.00 0.00 0.00 1.89
1982 2679 2.698855 TCCATGTAGCTTCTTCCTGC 57.301 50.000 0.00 0.00 0.00 4.85
2000 2697 3.632604 CCTGCTCGTCCTCTTGTATAAGA 59.367 47.826 1.67 1.67 40.53 2.10
2054 2751 1.818674 GCCGTGTCCCTCATTTCATTT 59.181 47.619 0.00 0.00 0.00 2.32
2078 2775 9.670442 TTTTAAGGTATATGATGTACTCCCTCT 57.330 33.333 0.00 0.00 0.00 3.69
2079 2776 8.651589 TTAAGGTATATGATGTACTCCCTCTG 57.348 38.462 0.00 0.00 0.00 3.35
2080 2777 6.220881 AGGTATATGATGTACTCCCTCTGT 57.779 41.667 0.00 0.00 0.00 3.41
2081 2778 7.344599 AGGTATATGATGTACTCCCTCTGTA 57.655 40.000 0.00 0.00 0.00 2.74
2082 2779 7.766628 AGGTATATGATGTACTCCCTCTGTAA 58.233 38.462 0.00 0.00 0.00 2.41
2083 2780 8.232412 AGGTATATGATGTACTCCCTCTGTAAA 58.768 37.037 0.00 0.00 0.00 2.01
2084 2781 8.305317 GGTATATGATGTACTCCCTCTGTAAAC 58.695 40.741 0.00 0.00 0.00 2.01
2085 2782 9.080097 GTATATGATGTACTCCCTCTGTAAACT 57.920 37.037 0.00 0.00 0.00 2.66
2087 2784 7.973048 ATGATGTACTCCCTCTGTAAACTAA 57.027 36.000 0.00 0.00 0.00 2.24
2088 2785 7.973048 TGATGTACTCCCTCTGTAAACTAAT 57.027 36.000 0.00 0.00 0.00 1.73
2089 2786 9.656323 ATGATGTACTCCCTCTGTAAACTAATA 57.344 33.333 0.00 0.00 0.00 0.98
2090 2787 9.656323 TGATGTACTCCCTCTGTAAACTAATAT 57.344 33.333 0.00 0.00 0.00 1.28
2096 2793 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2097 2794 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2098 2795 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2099 2796 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2100 2797 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2115 2812 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
2116 2813 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2117 2814 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
2118 2815 9.122779 AGAGCGTTTAGATCACTACTTTAGTAT 57.877 33.333 0.00 0.00 37.82 2.12
2119 2816 9.733219 GAGCGTTTAGATCACTACTTTAGTATT 57.267 33.333 0.00 0.00 37.23 1.89
2120 2817 9.733219 AGCGTTTAGATCACTACTTTAGTATTC 57.267 33.333 0.00 0.00 37.23 1.75
2121 2818 9.733219 GCGTTTAGATCACTACTTTAGTATTCT 57.267 33.333 0.00 0.00 37.23 2.40
2127 2824 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
2128 2825 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
2129 2826 9.733219 ATCACTACTTTAGTATTCTAAACGCTC 57.267 33.333 0.76 0.00 40.05 5.03
2130 2827 8.954350 TCACTACTTTAGTATTCTAAACGCTCT 58.046 33.333 0.76 0.00 40.05 4.09
2131 2828 9.570488 CACTACTTTAGTATTCTAAACGCTCTT 57.430 33.333 0.76 0.00 40.05 2.85
2145 2842 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2146 2843 9.455847 CTAAACGCTCTTATATTAGTTTACGGT 57.544 33.333 0.00 0.00 34.29 4.83
2147 2844 7.689953 AACGCTCTTATATTAGTTTACGGTG 57.310 36.000 0.00 0.00 0.00 4.94
2148 2845 6.211515 ACGCTCTTATATTAGTTTACGGTGG 58.788 40.000 0.00 0.00 0.00 4.61
2149 2846 5.632347 CGCTCTTATATTAGTTTACGGTGGG 59.368 44.000 0.00 0.00 0.00 4.61
2150 2847 6.515531 CGCTCTTATATTAGTTTACGGTGGGA 60.516 42.308 0.00 0.00 0.00 4.37
2189 2886 4.052159 ACATGATTGAGTCTTAGCCGAG 57.948 45.455 0.00 0.00 0.00 4.63
2201 2898 1.098869 TAGCCGAGTGAGCTGAGAAG 58.901 55.000 0.00 0.00 41.71 2.85
2243 2940 7.472334 AGGAGCAATTTCAAGTGTCAATATT 57.528 32.000 0.00 0.00 0.00 1.28
2320 3017 1.098050 GGGCACTTCACCATGATCAC 58.902 55.000 0.00 0.00 0.00 3.06
2354 3083 5.121380 AGACATCTGGCACCAAATATTCT 57.879 39.130 0.00 0.00 0.00 2.40
2438 3167 2.176273 GCGTGCCGATCAAGATGCT 61.176 57.895 0.00 0.00 0.00 3.79
2531 3260 3.181329 TGGAGTCATTGAGGAAGCCTTA 58.819 45.455 0.00 0.00 31.76 2.69
2551 3280 1.169661 GGTTTCGTGGGTGATGTGCA 61.170 55.000 0.00 0.00 0.00 4.57
2693 3422 6.446318 CAGTTTTGCTTTAGCCAAGAACATA 58.554 36.000 0.00 0.00 41.18 2.29
2822 3551 3.577848 CAGCAGTCCAATATAGGAGAGCT 59.422 47.826 0.00 0.00 44.94 4.09
2873 3602 6.625873 AGAAAAGACAGTAAAGGAAAGCAG 57.374 37.500 0.00 0.00 0.00 4.24
3114 3844 4.891168 GGTCCCTTTTCTTCAACTAACCAA 59.109 41.667 0.00 0.00 0.00 3.67
3220 3950 6.118170 ACATCTATTGTGATGAACTTGGAGG 58.882 40.000 10.89 0.00 44.71 4.30
3237 3967 1.494721 GAGGGGATCCACAAGCCAATA 59.505 52.381 18.46 0.00 33.97 1.90
3245 3975 1.949525 CCACAAGCCAATATTCCCTCG 59.050 52.381 0.00 0.00 0.00 4.63
3291 4028 0.745845 ATCAGGCTGGACATTGCGAC 60.746 55.000 15.73 0.00 0.00 5.19
3292 4029 1.672030 CAGGCTGGACATTGCGACA 60.672 57.895 6.61 0.00 0.00 4.35
3316 4053 1.806542 TGCTTCATTCGTTTGCCTCTC 59.193 47.619 0.00 0.00 0.00 3.20
3318 4055 1.740025 CTTCATTCGTTTGCCTCTCCC 59.260 52.381 0.00 0.00 0.00 4.30
3326 4063 0.324943 TTTGCCTCTCCCACTAGTGC 59.675 55.000 17.86 4.74 0.00 4.40
3521 4264 5.163513 CGCTTTTTCTTTGCATATGTTCCT 58.836 37.500 4.29 0.00 0.00 3.36
3529 4272 8.862325 TTCTTTGCATATGTTCCTCTTCTTTA 57.138 30.769 4.29 0.00 0.00 1.85
3581 4329 4.555262 GCTGCTTGCAATGGTTTTACTTA 58.445 39.130 0.00 0.00 42.31 2.24
3610 4358 2.128771 TGGGCCTTCTCATGTAAAGC 57.871 50.000 4.53 0.00 0.00 3.51
3642 4390 4.898320 TGCACTACAAATCTGACATCAGT 58.102 39.130 8.70 0.00 44.12 3.41
3682 4430 4.923281 GCAAATCAAACGTCTTTTATGGCT 59.077 37.500 0.00 0.00 0.00 4.75
3695 4443 6.868339 GTCTTTTATGGCTATTTGTGTTTGCT 59.132 34.615 0.00 0.00 0.00 3.91
3733 4482 1.927487 TGGCAAGCATGTCAAATCCT 58.073 45.000 0.00 0.00 38.47 3.24
3745 4494 2.413453 GTCAAATCCTGCTCAGTTCGAC 59.587 50.000 0.00 0.00 0.00 4.20
3754 4503 2.224281 TGCTCAGTTCGACTTTCCATGT 60.224 45.455 0.00 0.00 0.00 3.21
3775 4524 9.520204 CCATGTTTAAAAATATGATGTCAGACC 57.480 33.333 12.20 0.00 39.11 3.85
3776 4525 9.225201 CATGTTTAAAAATATGATGTCAGACCG 57.775 33.333 6.37 0.00 39.11 4.79
3827 4576 2.973224 CAGTGAAATCTTTGGCGAAACG 59.027 45.455 0.00 0.00 0.00 3.60
3885 4644 7.014711 TGTCTATGGTTTTGGCATCTTTGTTTA 59.985 33.333 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.102978 ATCCAAAGGCGTACAATGGC 58.897 50.000 0.00 0.00 0.00 4.40
1 2 2.097466 GTCATCCAAAGGCGTACAATGG 59.903 50.000 0.00 0.00 0.00 3.16
2 3 2.097466 GGTCATCCAAAGGCGTACAATG 59.903 50.000 0.00 0.00 0.00 2.82
3 4 2.026262 AGGTCATCCAAAGGCGTACAAT 60.026 45.455 0.00 0.00 35.89 2.71
29 30 0.611714 GTCTGGAGGTTTCGGGCTAA 59.388 55.000 0.00 0.00 0.00 3.09
48 49 1.008538 GGCCTGCGCAAATATTCGG 60.009 57.895 13.05 8.57 36.38 4.30
65 66 2.478134 GCTATCTAGAAGCGTGCAATGG 59.522 50.000 0.00 0.00 0.00 3.16
109 110 7.648039 AGAGGACTACTTTTGGTCTATACAG 57.352 40.000 0.00 0.00 33.46 2.74
117 118 5.129815 TGTTGTGTAGAGGACTACTTTTGGT 59.870 40.000 0.00 0.00 46.33 3.67
153 154 5.939296 CCAATCCAAGGTTGTATGCAATTTT 59.061 36.000 0.00 0.00 36.92 1.82
156 157 3.451902 CCCAATCCAAGGTTGTATGCAAT 59.548 43.478 0.00 0.00 36.92 3.56
165 166 3.319031 GGATCATCCCAATCCAAGGTT 57.681 47.619 0.00 0.00 42.01 3.50
196 197 5.244402 TGCATGTCTCATGAAGGTGATTTTT 59.756 36.000 12.98 0.00 0.00 1.94
197 198 4.768448 TGCATGTCTCATGAAGGTGATTTT 59.232 37.500 12.98 0.00 0.00 1.82
198 199 4.338012 TGCATGTCTCATGAAGGTGATTT 58.662 39.130 12.98 0.00 0.00 2.17
199 200 3.959293 TGCATGTCTCATGAAGGTGATT 58.041 40.909 12.98 0.00 0.00 2.57
200 201 3.639672 TGCATGTCTCATGAAGGTGAT 57.360 42.857 12.98 0.00 0.00 3.06
300 304 8.630054 TGCACTCTAAAAATTTAAAGGCTCTA 57.370 30.769 0.00 0.00 0.00 2.43
496 502 7.934120 AGCTTTATTCATGTAATCTACTCCACC 59.066 37.037 0.00 0.00 0.00 4.61
497 503 8.894768 AGCTTTATTCATGTAATCTACTCCAC 57.105 34.615 0.00 0.00 0.00 4.02
498 504 7.867909 CGAGCTTTATTCATGTAATCTACTCCA 59.132 37.037 0.00 0.00 0.00 3.86
499 505 7.148722 GCGAGCTTTATTCATGTAATCTACTCC 60.149 40.741 0.00 0.00 0.00 3.85
500 506 7.596995 AGCGAGCTTTATTCATGTAATCTACTC 59.403 37.037 0.00 0.00 0.00 2.59
557 567 7.700022 TCATCAACAAAATGGACATACATGA 57.300 32.000 0.00 0.00 0.00 3.07
558 568 7.650504 GGATCATCAACAAAATGGACATACATG 59.349 37.037 0.00 0.00 0.00 3.21
560 570 6.096705 GGGATCATCAACAAAATGGACATACA 59.903 38.462 0.00 0.00 0.00 2.29
563 573 4.406649 GGGGATCATCAACAAAATGGACAT 59.593 41.667 0.00 0.00 0.00 3.06
564 574 3.768757 GGGGATCATCAACAAAATGGACA 59.231 43.478 0.00 0.00 0.00 4.02
565 575 4.026052 AGGGGATCATCAACAAAATGGAC 58.974 43.478 0.00 0.00 0.00 4.02
577 595 4.786425 AGAGTAGCAAAAAGGGGATCATC 58.214 43.478 0.00 0.00 0.00 2.92
582 600 3.261897 CAGAGAGAGTAGCAAAAAGGGGA 59.738 47.826 0.00 0.00 0.00 4.81
585 603 4.693095 GGAACAGAGAGAGTAGCAAAAAGG 59.307 45.833 0.00 0.00 0.00 3.11
586 604 5.300752 TGGAACAGAGAGAGTAGCAAAAAG 58.699 41.667 0.00 0.00 0.00 2.27
615 633 6.678409 GCTCATTTAGTACAAGTAGCGAGAGT 60.678 42.308 0.00 0.00 0.00 3.24
644 662 2.331809 AAGCGGCGAAATCTCAAAAC 57.668 45.000 12.98 0.00 0.00 2.43
646 664 3.363341 AAAAAGCGGCGAAATCTCAAA 57.637 38.095 12.98 0.00 0.00 2.69
675 726 1.467342 GTAACAGGTGGCAAATCCGTC 59.533 52.381 0.00 0.00 37.80 4.79
700 751 4.893424 TTTACTTGTGCTTTCAGACCAC 57.107 40.909 0.00 0.00 0.00 4.16
703 754 6.237569 GCAAGTTTTTACTTGTGCTTTCAGAC 60.238 38.462 16.67 0.00 46.36 3.51
739 790 8.145767 GGAATCATTCAGGAATTATGCATTTCA 58.854 33.333 3.54 0.00 0.00 2.69
779 841 3.084039 GTCATGTGGTGGTGATGATGTT 58.916 45.455 0.00 0.00 0.00 2.71
780 842 2.040145 TGTCATGTGGTGGTGATGATGT 59.960 45.455 0.00 0.00 0.00 3.06
781 843 2.421073 GTGTCATGTGGTGGTGATGATG 59.579 50.000 0.00 0.00 0.00 3.07
782 844 2.040145 TGTGTCATGTGGTGGTGATGAT 59.960 45.455 0.00 0.00 0.00 2.45
783 845 1.419387 TGTGTCATGTGGTGGTGATGA 59.581 47.619 0.00 0.00 0.00 2.92
784 846 1.894881 TGTGTCATGTGGTGGTGATG 58.105 50.000 0.00 0.00 0.00 3.07
785 847 2.655090 TTGTGTCATGTGGTGGTGAT 57.345 45.000 0.00 0.00 0.00 3.06
786 848 2.296792 CTTTGTGTCATGTGGTGGTGA 58.703 47.619 0.00 0.00 0.00 4.02
787 849 1.269206 GCTTTGTGTCATGTGGTGGTG 60.269 52.381 0.00 0.00 0.00 4.17
788 850 1.032014 GCTTTGTGTCATGTGGTGGT 58.968 50.000 0.00 0.00 0.00 4.16
789 851 1.031235 TGCTTTGTGTCATGTGGTGG 58.969 50.000 0.00 0.00 0.00 4.61
959 1047 2.261671 GCCGTTGGCGAGAAGAGA 59.738 61.111 0.00 0.00 39.62 3.10
1284 1941 0.951040 CACGAAGGAAGTGGAGGTGC 60.951 60.000 0.00 0.00 36.06 5.01
1405 2076 5.106948 GGCATGATAACAATCCACTGTATCG 60.107 44.000 0.00 0.00 0.00 2.92
1482 2164 0.459237 GCACGGTGGAGTCATCTCAG 60.459 60.000 10.60 0.00 42.05 3.35
1510 2197 7.769220 ACAATTGTTCATCTGAATCTGGATTC 58.231 34.615 4.92 14.33 45.55 2.52
1536 2223 6.187480 CGTGCTCATAATGTAAATGACACAG 58.813 40.000 13.76 7.31 42.17 3.66
1537 2224 5.447144 GCGTGCTCATAATGTAAATGACACA 60.447 40.000 13.76 0.00 42.17 3.72
1538 2225 4.963953 GCGTGCTCATAATGTAAATGACAC 59.036 41.667 0.00 0.00 42.17 3.67
1716 2413 8.771920 TGTGATAACGAAACATAACAGAGAAT 57.228 30.769 0.00 0.00 0.00 2.40
1717 2414 8.596271 TTGTGATAACGAAACATAACAGAGAA 57.404 30.769 0.00 0.00 0.00 2.87
1771 2468 1.814394 TCTGGCACTCAAATCACATGC 59.186 47.619 0.00 0.00 35.51 4.06
1963 2660 2.169352 GAGCAGGAAGAAGCTACATGGA 59.831 50.000 0.00 0.00 42.04 3.41
2054 2751 8.232412 ACAGAGGGAGTACATCATATACCTTAA 58.768 37.037 0.00 0.00 0.00 1.85
2070 2767 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2071 2768 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2072 2769 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2073 2770 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2074 2771 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2089 2786 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2090 2787 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
2091 2788 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2092 2789 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
2093 2790 9.733219 AATACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
2094 2791 9.733219 GAATACTAAAGTAGTGATCTAAACGCT 57.267 33.333 0.00 0.00 39.81 5.07
2095 2792 9.733219 AGAATACTAAAGTAGTGATCTAAACGC 57.267 33.333 0.00 0.00 39.81 4.84
2101 2798 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
2102 2799 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
2103 2800 9.733219 GAGCGTTTAGAATACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
2104 2801 8.954350 AGAGCGTTTAGAATACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
2105 2802 9.570488 AAGAGCGTTTAGAATACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
2119 2816 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2120 2817 9.455847 ACCGTAAACTAATATAAGAGCGTTTAG 57.544 33.333 0.00 0.00 30.36 1.85
2121 2818 9.236691 CACCGTAAACTAATATAAGAGCGTTTA 57.763 33.333 0.00 0.00 0.00 2.01
2122 2819 7.223387 CCACCGTAAACTAATATAAGAGCGTTT 59.777 37.037 0.00 0.00 0.00 3.60
2123 2820 6.698766 CCACCGTAAACTAATATAAGAGCGTT 59.301 38.462 0.00 0.00 0.00 4.84
2124 2821 6.211515 CCACCGTAAACTAATATAAGAGCGT 58.788 40.000 0.00 0.00 0.00 5.07
2125 2822 5.632347 CCCACCGTAAACTAATATAAGAGCG 59.368 44.000 0.00 0.00 0.00 5.03
2126 2823 6.752168 TCCCACCGTAAACTAATATAAGAGC 58.248 40.000 0.00 0.00 0.00 4.09
2127 2824 7.949434 ACTCCCACCGTAAACTAATATAAGAG 58.051 38.462 0.00 0.00 0.00 2.85
2128 2825 7.902920 ACTCCCACCGTAAACTAATATAAGA 57.097 36.000 0.00 0.00 0.00 2.10
2129 2826 8.632679 TGTACTCCCACCGTAAACTAATATAAG 58.367 37.037 0.00 0.00 0.00 1.73
2130 2827 8.532186 TGTACTCCCACCGTAAACTAATATAA 57.468 34.615 0.00 0.00 0.00 0.98
2131 2828 8.532186 TTGTACTCCCACCGTAAACTAATATA 57.468 34.615 0.00 0.00 0.00 0.86
2132 2829 7.422465 TTGTACTCCCACCGTAAACTAATAT 57.578 36.000 0.00 0.00 0.00 1.28
2133 2830 6.849085 TTGTACTCCCACCGTAAACTAATA 57.151 37.500 0.00 0.00 0.00 0.98
2134 2831 5.743636 TTGTACTCCCACCGTAAACTAAT 57.256 39.130 0.00 0.00 0.00 1.73
2135 2832 5.743636 ATTGTACTCCCACCGTAAACTAA 57.256 39.130 0.00 0.00 0.00 2.24
2136 2833 5.743636 AATTGTACTCCCACCGTAAACTA 57.256 39.130 0.00 0.00 0.00 2.24
2137 2834 4.628963 AATTGTACTCCCACCGTAAACT 57.371 40.909 0.00 0.00 0.00 2.66
2138 2835 5.694231 AAAATTGTACTCCCACCGTAAAC 57.306 39.130 0.00 0.00 0.00 2.01
2165 2862 6.161855 TCGGCTAAGACTCAATCATGTATT 57.838 37.500 0.00 0.00 0.00 1.89
2189 2886 3.248125 GCAGCATTATCTTCTCAGCTCAC 59.752 47.826 0.00 0.00 0.00 3.51
2243 2940 6.058833 CACAGATGTAGAGAGAAGGTAGCTA 58.941 44.000 0.00 0.00 0.00 3.32
2320 3017 4.021632 TGCCAGATGTCTAGCTAGCATAAG 60.022 45.833 22.47 18.34 31.80 1.73
2438 3167 1.450134 CTGCACCCTAGCAATCGCA 60.450 57.895 0.00 0.00 45.13 5.10
2531 3260 0.889186 GCACATCACCCACGAAACCT 60.889 55.000 0.00 0.00 0.00 3.50
2693 3422 6.538263 GCTACCCATCCTCTCAAATCTTAAT 58.462 40.000 0.00 0.00 0.00 1.40
2822 3551 4.505566 CCTCCAGAAAGAGAACCATTGTCA 60.506 45.833 0.00 0.00 35.82 3.58
2873 3602 6.641474 ACCTCTAGCTAATAACACTTCCAAC 58.359 40.000 0.00 0.00 0.00 3.77
3114 3844 5.822204 TGCCCTAGTACCATACAATTGTTT 58.178 37.500 17.78 5.99 0.00 2.83
3204 3934 1.741028 TCCCCTCCAAGTTCATCACA 58.259 50.000 0.00 0.00 0.00 3.58
3220 3950 2.893489 GGAATATTGGCTTGTGGATCCC 59.107 50.000 9.90 0.85 0.00 3.85
3237 3967 1.903877 CTGGTGACTGGCGAGGGAAT 61.904 60.000 0.00 0.00 0.00 3.01
3245 3975 3.054503 CAGCTGCTGGTGACTGGC 61.055 66.667 21.71 0.00 43.76 4.85
3291 4028 3.127548 AGGCAAACGAATGAAGCATAGTG 59.872 43.478 0.00 0.00 0.00 2.74
3292 4029 3.347216 AGGCAAACGAATGAAGCATAGT 58.653 40.909 0.00 0.00 0.00 2.12
3316 4053 2.124151 GGCCATGGCACTAGTGGG 60.124 66.667 36.56 16.77 44.11 4.61
3318 4055 1.452651 CTGGGCCATGGCACTAGTG 60.453 63.158 37.64 21.29 46.30 2.74
3326 4063 0.040204 AAAGAACCTCTGGGCCATGG 59.960 55.000 20.08 20.08 35.63 3.66
3521 4264 5.067936 CCTAACTCGCATCTCCTAAAGAAGA 59.932 44.000 0.00 0.00 37.61 2.87
3529 4272 2.567615 ACAAACCTAACTCGCATCTCCT 59.432 45.455 0.00 0.00 0.00 3.69
3573 4321 3.761752 GCCCAAGCTGGTGATAAGTAAAA 59.238 43.478 0.00 0.00 35.17 1.52
3581 4329 1.000396 GAAGGCCCAAGCTGGTGAT 60.000 57.895 0.00 0.00 39.73 3.06
3610 4358 4.999950 AGATTTGTAGTGCAGTCCTTCAAG 59.000 41.667 0.00 0.00 0.00 3.02
3666 4414 6.977213 ACACAAATAGCCATAAAAGACGTTT 58.023 32.000 0.00 0.00 0.00 3.60
3682 4430 3.193267 GCCATCCTCAGCAAACACAAATA 59.807 43.478 0.00 0.00 0.00 1.40
3695 4443 3.420893 CCAACTAAACTTGCCATCCTCA 58.579 45.455 0.00 0.00 0.00 3.86
3733 4482 2.224281 ACATGGAAAGTCGAACTGAGCA 60.224 45.455 0.00 0.00 0.00 4.26
3775 4524 4.914312 TCAAACTTCGGTAATGCTAACG 57.086 40.909 0.00 0.00 39.72 3.18
3776 4525 6.837992 TGATTCAAACTTCGGTAATGCTAAC 58.162 36.000 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.