Multiple sequence alignment - TraesCS1A01G064700

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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 TraesCS1A01G064700 chr1A 100.000 2933 0 0 1 2933 46440846 46443778 0.000000e+00 5417.0
1 TraesCS1A01G064700 chr1A 86.025 322 44 1 711 1032 46854991 46854671 7.780000e-91 344.0
2 TraesCS1A01G064700 chr1A 97.727 44 1 0 2890 2933 337427165 337427208 3.130000e-10 76.8
3 TraesCS1A01G064700 chr1B 94.374 1422 73 4 532 1953 66943664 66942250 0.000000e+00 2176.0
4 TraesCS1A01G064700 chr1B 83.200 1250 193 12 705 1941 66923635 66924880 0.000000e+00 1129.0
5 TraesCS1A01G064700 chr1B 85.885 503 28 17 1 464 66962282 66961784 2.030000e-136 496.0
6 TraesCS1A01G064700 chr1B 100.000 41 0 0 2893 2933 618904020 618903980 3.130000e-10 76.8
7 TraesCS1A01G064700 chr1D 95.903 952 39 0 656 1607 46645293 46644342 0.000000e+00 1543.0
8 TraesCS1A01G064700 chr1D 93.199 647 19 12 1 631 46670263 46669626 0.000000e+00 928.0
9 TraesCS1A01G064700 chr1D 86.765 816 98 6 711 1518 46628784 46627971 0.000000e+00 900.0
10 TraesCS1A01G064700 chr1D 92.400 500 35 3 1650 2147 46644347 46643849 0.000000e+00 710.0
11 TraesCS1A01G064700 chr1D 84.035 689 88 18 2155 2835 95660176 95660850 0.000000e+00 643.0
12 TraesCS1A01G064700 chr1D 95.455 44 2 0 2890 2933 141800460 141800503 1.460000e-08 71.3
13 TraesCS1A01G064700 chr2D 87.415 588 65 9 2156 2741 651518624 651519204 0.000000e+00 667.0
14 TraesCS1A01G064700 chr2D 87.130 575 66 7 2156 2723 295349403 295348830 0.000000e+00 645.0
15 TraesCS1A01G064700 chr2D 83.384 662 92 18 2156 2806 22682726 22683380 5.410000e-167 597.0
16 TraesCS1A01G064700 chr2D 92.000 50 3 1 2884 2933 129062671 129062623 5.250000e-08 69.4
17 TraesCS1A01G064700 chr3D 84.545 660 79 19 2152 2802 229181409 229180764 1.480000e-177 632.0
18 TraesCS1A01G064700 chr3D 97.561 41 1 0 2890 2930 471154593 471154633 1.460000e-08 71.3
19 TraesCS1A01G064700 chr7D 83.780 672 92 17 2155 2817 215211347 215212010 3.210000e-174 621.0
20 TraesCS1A01G064700 chr7D 84.375 640 89 11 2163 2797 585761557 585760924 4.150000e-173 617.0
21 TraesCS1A01G064700 chr7D 83.560 663 96 12 2154 2810 585858060 585857405 2.500000e-170 608.0
22 TraesCS1A01G064700 chr7D 95.556 45 2 0 2889 2933 516768369 516768325 4.050000e-09 73.1
23 TraesCS1A01G064700 chr4A 84.018 657 87 14 2155 2799 373550972 373550322 1.490000e-172 616.0
24 TraesCS1A01G064700 chr4A 95.455 44 2 0 2890 2933 582727288 582727331 1.460000e-08 71.3
25 TraesCS1A01G064700 chr7A 84.677 124 15 3 1 121 124143726 124143848 1.430000e-23 121.0
26 TraesCS1A01G064700 chr7A 95.455 44 2 0 2890 2933 202191748 202191791 1.460000e-08 71.3
27 TraesCS1A01G064700 chr6D 100.000 41 0 0 2893 2933 319893380 319893340 3.130000e-10 76.8


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 TraesCS1A01G064700 chr1A 46440846 46443778 2932 False 5417.0 5417 100.0000 1 2933 1 chr1A.!!$F1 2932
1 TraesCS1A01G064700 chr1B 66942250 66943664 1414 True 2176.0 2176 94.3740 532 1953 1 chr1B.!!$R1 1421
2 TraesCS1A01G064700 chr1B 66923635 66924880 1245 False 1129.0 1129 83.2000 705 1941 1 chr1B.!!$F1 1236
3 TraesCS1A01G064700 chr1D 46643849 46645293 1444 True 1126.5 1543 94.1515 656 2147 2 chr1D.!!$R3 1491
4 TraesCS1A01G064700 chr1D 46669626 46670263 637 True 928.0 928 93.1990 1 631 1 chr1D.!!$R2 630
5 TraesCS1A01G064700 chr1D 46627971 46628784 813 True 900.0 900 86.7650 711 1518 1 chr1D.!!$R1 807
6 TraesCS1A01G064700 chr1D 95660176 95660850 674 False 643.0 643 84.0350 2155 2835 1 chr1D.!!$F1 680
7 TraesCS1A01G064700 chr2D 651518624 651519204 580 False 667.0 667 87.4150 2156 2741 1 chr2D.!!$F2 585
8 TraesCS1A01G064700 chr2D 295348830 295349403 573 True 645.0 645 87.1300 2156 2723 1 chr2D.!!$R2 567
9 TraesCS1A01G064700 chr2D 22682726 22683380 654 False 597.0 597 83.3840 2156 2806 1 chr2D.!!$F1 650
10 TraesCS1A01G064700 chr3D 229180764 229181409 645 True 632.0 632 84.5450 2152 2802 1 chr3D.!!$R1 650
11 TraesCS1A01G064700 chr7D 215211347 215212010 663 False 621.0 621 83.7800 2155 2817 1 chr7D.!!$F1 662
12 TraesCS1A01G064700 chr7D 585760924 585761557 633 True 617.0 617 84.3750 2163 2797 1 chr7D.!!$R2 634
13 TraesCS1A01G064700 chr7D 585857405 585858060 655 True 608.0 608 83.5600 2154 2810 1 chr7D.!!$R3 656
14 TraesCS1A01G064700 chr4A 373550322 373550972 650 True 616.0 616 84.0180 2155 2799 1 chr4A.!!$R1 644

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
422 429 0.866061 CCGATGCGAACGAGACGATT 60.866 55.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 2180 0.035439 ACTCGGGGCATTACACCTTG 60.035 55.0 0.0 0.0 0.0 3.61 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
37 38 6.373774 TGCTTTGAAATTTGTTTTGTCATGGT 59.626 30.769 0.00 0.00 0.00 3.55
49 50 4.700268 TTGTCATGGTGATTACATGTGC 57.300 40.909 9.11 0.00 44.57 4.57
55 56 5.997129 TCATGGTGATTACATGTGCGATATT 59.003 36.000 9.11 0.00 44.57 1.28
212 213 8.184304 ACCATGGCATTTTTACACTAAACTAA 57.816 30.769 13.04 0.00 0.00 2.24
420 427 2.099638 CCGATGCGAACGAGACGA 59.900 61.111 0.00 0.00 0.00 4.20
422 429 0.866061 CCGATGCGAACGAGACGATT 60.866 55.000 0.00 0.00 0.00 3.34
486 502 4.469657 TCTTTTTGCTGGGACTGTTGTAT 58.530 39.130 0.00 0.00 0.00 2.29
501 517 4.373527 TGTTGTATGTATATGTGCCGGAC 58.626 43.478 5.05 0.46 0.00 4.79
561 577 8.842358 TTAAACCGTGATTAGTTTGAGATCTT 57.158 30.769 0.00 0.00 36.85 2.40
633 649 6.073765 CGCATCTCCAAAACCTACACATATAC 60.074 42.308 0.00 0.00 0.00 1.47
635 651 7.041780 GCATCTCCAAAACCTACACATATACAG 60.042 40.741 0.00 0.00 0.00 2.74
636 652 7.490657 TCTCCAAAACCTACACATATACAGT 57.509 36.000 0.00 0.00 0.00 3.55
637 653 8.598202 TCTCCAAAACCTACACATATACAGTA 57.402 34.615 0.00 0.00 0.00 2.74
638 654 8.472413 TCTCCAAAACCTACACATATACAGTAC 58.528 37.037 0.00 0.00 0.00 2.73
639 655 8.370266 TCCAAAACCTACACATATACAGTACT 57.630 34.615 0.00 0.00 0.00 2.73
757 773 3.649277 CTCCTTGCCACCGTCCTCG 62.649 68.421 0.00 0.00 0.00 4.63
1047 1066 2.123683 CCTCTCCCCGAGCTAGCA 60.124 66.667 18.83 0.00 38.49 3.49
1059 1078 1.145598 GCTAGCAGCTCTCATGGCA 59.854 57.895 10.63 0.00 38.45 4.92
1145 1164 1.604378 CCTCGGTGGAGCTGGAATT 59.396 57.895 0.00 0.00 39.06 2.17
1200 1219 2.125350 CTTCTCTCCACCTGCCGC 60.125 66.667 0.00 0.00 0.00 6.53
1245 1264 1.067071 GTAGCGCTGGACCAGTACTTT 60.067 52.381 22.90 7.25 33.43 2.66
1292 1311 5.480205 GTTCTTTCAAGGGAAGATCTACGT 58.520 41.667 0.00 0.00 33.82 3.57
1384 1403 0.179100 ACCATCTTGCATCGAGGTCG 60.179 55.000 0.00 0.00 41.45 4.79
1425 1447 2.107953 GCGATGACAGAGGAGCCC 59.892 66.667 0.00 0.00 0.00 5.19
1479 1501 2.895372 GTTGCGGGGCGGTATCTG 60.895 66.667 0.00 0.00 0.00 2.90
1515 1537 2.580815 CTGCTCATGGTCAGGCGA 59.419 61.111 7.09 0.00 0.00 5.54
1550 1572 8.352942 CAAACCTTTGATGAGCTTTAGTTACTT 58.647 33.333 0.00 0.00 40.55 2.24
1716 1744 4.081185 TCGCGATGCTCCAAGGCA 62.081 61.111 3.71 0.00 46.63 4.75
1718 1746 2.437359 GCGATGCTCCAAGGCAGT 60.437 61.111 0.00 0.00 45.75 4.40
1905 1933 2.589157 ATGGAGCCGACGGTTTCCA 61.589 57.895 31.09 31.09 40.69 3.53
1945 1973 9.981114 CTATGGAAGTTTAATTTGGTTTCAGTT 57.019 29.630 0.00 0.00 0.00 3.16
1974 2002 9.520204 CATATTGATTTGTTCTCAATTGGTACC 57.480 33.333 4.43 4.43 42.03 3.34
1985 2013 9.933723 GTTCTCAATTGGTACCTACTAGTTTTA 57.066 33.333 14.36 0.00 0.00 1.52
2016 2044 5.385198 AGGTGTGTTTCTTGTATCCATGTT 58.615 37.500 0.00 0.00 0.00 2.71
2022 2050 5.163764 TGTTTCTTGTATCCATGTTCGCATC 60.164 40.000 0.00 0.00 35.23 3.91
2056 2086 7.969387 TTTTCTATGAAATTGTAAGATGCGC 57.031 32.000 0.00 0.00 0.00 6.09
2086 2116 5.163814 GCGCACTCTCAAAGAAGATTGTAAT 60.164 40.000 0.30 0.00 30.78 1.89
2088 2118 7.254590 GCGCACTCTCAAAGAAGATTGTAATAT 60.255 37.037 0.30 0.00 30.78 1.28
2123 2153 7.815840 TTGAATATGTCTGGTGAAAACTTGA 57.184 32.000 0.00 0.00 0.00 3.02
2147 2177 4.493350 GCGATGAATCAAGAACATTGAACG 59.507 41.667 0.00 0.00 31.55 3.95
2148 2178 5.671082 GCGATGAATCAAGAACATTGAACGA 60.671 40.000 0.00 0.00 31.55 3.85
2149 2179 6.481134 CGATGAATCAAGAACATTGAACGAT 58.519 36.000 0.00 0.00 31.55 3.73
2150 2180 6.626488 CGATGAATCAAGAACATTGAACGATC 59.374 38.462 0.00 0.00 31.55 3.69
2186 2216 4.015406 TCCGATGCGCCAGGTGTT 62.015 61.111 4.18 0.00 0.00 3.32
2205 2235 4.024387 GTGTTTTCCAGTTATTCGCTGTCA 60.024 41.667 0.00 0.00 32.41 3.58
2209 2239 3.937814 TCCAGTTATTCGCTGTCATTGT 58.062 40.909 0.00 0.00 32.41 2.71
2334 2366 1.170442 TTCCGATACTCTCACACGCA 58.830 50.000 0.00 0.00 0.00 5.24
2362 2394 2.158475 TGCACCTCCCAGATCTTGTTTT 60.158 45.455 0.00 0.00 0.00 2.43
2369 2401 5.178096 TCCCAGATCTTGTTTTATGAGCA 57.822 39.130 0.00 0.00 0.00 4.26
2372 2404 4.337555 CCAGATCTTGTTTTATGAGCAGGG 59.662 45.833 0.00 0.00 0.00 4.45
2389 2421 2.477754 CAGGGTAAAAACGTTCTCGGAC 59.522 50.000 0.00 0.00 41.85 4.79
2420 2454 0.034337 TTGTCGAGTGGCCTTGGTAC 59.966 55.000 3.32 0.00 0.00 3.34
2436 2470 2.097825 GGTACATCACCGGTAGACTGT 58.902 52.381 6.87 11.10 37.63 3.55
2641 2680 2.578940 GCCTCTCCTAGCTCCCTCTATA 59.421 54.545 0.00 0.00 0.00 1.31
2662 2701 9.417561 TCTATATATAAATTAGTCACCTCCCCG 57.582 37.037 0.00 0.00 0.00 5.73
2666 2705 4.586306 AAATTAGTCACCTCCCCGAAAT 57.414 40.909 0.00 0.00 0.00 2.17
2696 2744 0.269173 CCCTAGATCAACCCCCTCCT 59.731 60.000 0.00 0.00 0.00 3.69
2699 2748 1.023719 TAGATCAACCCCCTCCTCCA 58.976 55.000 0.00 0.00 0.00 3.86
2741 2792 4.345962 CGTACGTGTCCACCGCCA 62.346 66.667 7.22 0.00 0.00 5.69
2777 2828 2.440796 CCAATCAGTGGCCGCCAT 60.441 61.111 16.96 2.07 41.72 4.40
2827 2879 4.783621 GCTGCCACATCGCCTCCA 62.784 66.667 0.00 0.00 0.00 3.86
2828 2880 2.513204 CTGCCACATCGCCTCCAG 60.513 66.667 0.00 0.00 0.00 3.86
2831 2883 3.790437 CCACATCGCCTCCAGCCT 61.790 66.667 0.00 0.00 38.78 4.58
2833 2885 3.474570 ACATCGCCTCCAGCCTCC 61.475 66.667 0.00 0.00 38.78 4.30
2834 2886 3.473647 CATCGCCTCCAGCCTCCA 61.474 66.667 0.00 0.00 38.78 3.86
2835 2887 3.474570 ATCGCCTCCAGCCTCCAC 61.475 66.667 0.00 0.00 38.78 4.02
2838 2890 3.791586 GCCTCCAGCCTCCACCTC 61.792 72.222 0.00 0.00 34.35 3.85
2839 2891 3.086600 CCTCCAGCCTCCACCTCC 61.087 72.222 0.00 0.00 0.00 4.30
2840 2892 2.284921 CTCCAGCCTCCACCTCCA 60.285 66.667 0.00 0.00 0.00 3.86
2841 2893 2.607750 TCCAGCCTCCACCTCCAC 60.608 66.667 0.00 0.00 0.00 4.02
2842 2894 2.608988 CCAGCCTCCACCTCCACT 60.609 66.667 0.00 0.00 0.00 4.00
2843 2895 2.667418 CAGCCTCCACCTCCACTG 59.333 66.667 0.00 0.00 0.00 3.66
2844 2896 3.325753 AGCCTCCACCTCCACTGC 61.326 66.667 0.00 0.00 0.00 4.40
2845 2897 4.767255 GCCTCCACCTCCACTGCG 62.767 72.222 0.00 0.00 0.00 5.18
2846 2898 4.767255 CCTCCACCTCCACTGCGC 62.767 72.222 0.00 0.00 0.00 6.09
2847 2899 4.007644 CTCCACCTCCACTGCGCA 62.008 66.667 10.98 10.98 0.00 6.09
2848 2900 3.947132 CTCCACCTCCACTGCGCAG 62.947 68.421 34.89 34.89 0.00 5.18
2896 2948 4.154347 GCCCGAGACCCTGCTGAG 62.154 72.222 0.00 0.00 0.00 3.35
2897 2949 3.465403 CCCGAGACCCTGCTGAGG 61.465 72.222 0.00 0.00 39.42 3.86
2905 2957 3.307445 CCTGCTGAGGGAGTCCTG 58.693 66.667 9.58 0.00 45.05 3.86
2906 2958 2.365586 CCTGCTGAGGGAGTCCTGG 61.366 68.421 9.58 0.00 45.05 4.45
2907 2959 1.305633 CTGCTGAGGGAGTCCTGGA 60.306 63.158 9.58 0.00 45.05 3.86
2908 2960 0.690411 CTGCTGAGGGAGTCCTGGAT 60.690 60.000 9.58 0.00 45.05 3.41
2909 2961 0.252881 TGCTGAGGGAGTCCTGGATT 60.253 55.000 9.58 0.00 45.05 3.01
2910 2962 1.008327 TGCTGAGGGAGTCCTGGATTA 59.992 52.381 9.58 0.00 45.05 1.75
2911 2963 1.691434 GCTGAGGGAGTCCTGGATTAG 59.309 57.143 9.58 0.93 45.05 1.73
2912 2964 2.324541 CTGAGGGAGTCCTGGATTAGG 58.675 57.143 9.58 0.00 45.05 2.69
2920 2972 2.442056 CCTGGATTAGGGGTCCTCG 58.558 63.158 0.00 0.00 43.33 4.63
2921 2973 1.122019 CCTGGATTAGGGGTCCTCGG 61.122 65.000 0.00 0.00 43.33 4.63
2922 2974 1.074775 TGGATTAGGGGTCCTCGGG 60.075 63.158 0.00 0.00 36.68 5.14
2923 2975 2.517798 GGATTAGGGGTCCTCGGGC 61.518 68.421 0.00 0.00 34.61 6.13
2924 2976 2.842936 ATTAGGGGTCCTCGGGCG 60.843 66.667 0.00 0.00 34.61 6.13
2925 2977 3.691297 ATTAGGGGTCCTCGGGCGT 62.691 63.158 0.00 0.00 34.61 5.68
2926 2978 4.828296 TAGGGGTCCTCGGGCGTC 62.828 72.222 0.00 0.00 34.61 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
287 294 2.561478 TTACTGGGCCTCTTGTCAAC 57.439 50.000 4.53 0.00 0.00 3.18
465 481 4.037923 ACATACAACAGTCCCAGCAAAAAG 59.962 41.667 0.00 0.00 0.00 2.27
466 482 3.957497 ACATACAACAGTCCCAGCAAAAA 59.043 39.130 0.00 0.00 0.00 1.94
467 483 3.561143 ACATACAACAGTCCCAGCAAAA 58.439 40.909 0.00 0.00 0.00 2.44
468 484 3.222173 ACATACAACAGTCCCAGCAAA 57.778 42.857 0.00 0.00 0.00 3.68
469 485 2.949177 ACATACAACAGTCCCAGCAA 57.051 45.000 0.00 0.00 0.00 3.91
470 486 5.130311 ACATATACATACAACAGTCCCAGCA 59.870 40.000 0.00 0.00 0.00 4.41
486 502 0.671796 CGGAGTCCGGCACATATACA 59.328 55.000 24.39 0.00 44.15 2.29
501 517 1.959042 ATGCTGCTGGTTTATCGGAG 58.041 50.000 0.00 0.00 0.00 4.63
561 577 6.371271 TGCCGTAAGCTATACGTATACACATA 59.629 38.462 11.27 2.21 44.23 2.29
573 589 3.744238 TCTTGCATGCCGTAAGCTATA 57.256 42.857 16.68 0.00 44.23 1.31
574 590 2.620251 TCTTGCATGCCGTAAGCTAT 57.380 45.000 16.68 0.00 44.23 2.97
679 695 0.994995 CGTTCTGAAGACGCCATGAG 59.005 55.000 0.00 0.00 0.00 2.90
994 1013 2.514824 GAAGGCGTCCATCAGGGC 60.515 66.667 0.00 0.00 36.21 5.19
1054 1073 1.454572 TTCACGTTGCAAGCTGCCAT 61.455 50.000 0.00 0.00 44.23 4.40
1059 1078 1.286880 GGCATTCACGTTGCAAGCT 59.713 52.632 12.42 0.00 41.95 3.74
1133 1152 2.272146 GGCGGAATTCCAGCTCCA 59.728 61.111 28.20 0.00 36.36 3.86
1177 1196 2.637947 GCAGGTGGAGAGAAGGAATTC 58.362 52.381 0.00 0.00 0.00 2.17
1239 1258 3.001330 CGGCGATGGAGAATTCAAAGTAC 59.999 47.826 0.00 0.00 0.00 2.73
1245 1264 0.534873 TGTCGGCGATGGAGAATTCA 59.465 50.000 14.79 0.00 0.00 2.57
1292 1311 2.231478 GTCTCGTTGATCTTGGACAGGA 59.769 50.000 0.00 0.00 0.00 3.86
1322 1341 1.833630 AGCCATTGTTGAGATCGAGGA 59.166 47.619 0.00 0.00 0.00 3.71
1384 1403 1.065928 CGGACCTCACTCCGCATAC 59.934 63.158 0.00 0.00 46.47 2.39
1425 1447 2.364324 CCATGGATCCTTTTGCAGATGG 59.636 50.000 14.23 10.94 0.00 3.51
1479 1501 2.017049 AGCTTGCCATTACATTCGACC 58.983 47.619 0.00 0.00 0.00 4.79
1515 1537 2.203773 AAAGGTTTGCGGGCCCAT 60.204 55.556 24.92 0.00 0.00 4.00
1635 1657 2.194056 CGGCCATGGCTCATCCTT 59.806 61.111 34.70 0.00 41.60 3.36
1716 1744 1.171308 CATGGCTTGCTGCAGTTACT 58.829 50.000 16.64 0.00 45.15 2.24
1718 1746 0.038021 TCCATGGCTTGCTGCAGTTA 59.962 50.000 16.64 1.73 45.15 2.24
1872 1900 3.129502 CATGGCAGTGACCCAGCG 61.130 66.667 0.00 0.00 35.48 5.18
1881 1909 4.457496 CGTCGGCTCCATGGCAGT 62.457 66.667 6.96 0.00 41.89 4.40
1923 1951 9.157104 TGAAAACTGAAACCAAATTAAACTTCC 57.843 29.630 0.00 0.00 0.00 3.46
1974 2002 7.817962 ACACACCTAGCACAATAAAACTAGTAG 59.182 37.037 0.00 0.00 32.03 2.57
1985 2013 4.207165 ACAAGAAACACACCTAGCACAAT 58.793 39.130 0.00 0.00 0.00 2.71
2040 2070 4.676924 GCTAATGGCGCATCTTACAATTTC 59.323 41.667 10.83 0.00 0.00 2.17
2043 2073 3.904136 GCTAATGGCGCATCTTACAAT 57.096 42.857 10.83 0.00 0.00 2.71
2055 2085 1.063174 CTTTGAGAGTGCGCTAATGGC 59.937 52.381 9.73 0.00 37.64 4.40
2056 2086 2.621338 TCTTTGAGAGTGCGCTAATGG 58.379 47.619 9.73 0.00 0.00 3.16
2086 2116 9.914131 CCAGACATATTCAATCGAGACTTTATA 57.086 33.333 0.00 0.00 0.00 0.98
2088 2118 7.706607 CACCAGACATATTCAATCGAGACTTTA 59.293 37.037 0.00 0.00 0.00 1.85
2095 2125 6.878923 AGTTTTCACCAGACATATTCAATCGA 59.121 34.615 0.00 0.00 0.00 3.59
2109 2139 2.807967 TCATCGCTCAAGTTTTCACCAG 59.192 45.455 0.00 0.00 0.00 4.00
2123 2153 5.634896 GTTCAATGTTCTTGATTCATCGCT 58.365 37.500 0.00 0.00 0.00 4.93
2140 2170 4.096382 GGCATTACACCTTGATCGTTCAAT 59.904 41.667 9.26 0.00 40.95 2.57
2147 2177 1.134220 TCGGGGCATTACACCTTGATC 60.134 52.381 0.00 0.00 0.00 2.92
2148 2178 0.916086 TCGGGGCATTACACCTTGAT 59.084 50.000 0.00 0.00 0.00 2.57
2149 2179 0.251916 CTCGGGGCATTACACCTTGA 59.748 55.000 0.00 0.00 0.00 3.02
2150 2180 0.035439 ACTCGGGGCATTACACCTTG 60.035 55.000 0.00 0.00 0.00 3.61
2186 2216 4.759693 ACAATGACAGCGAATAACTGGAAA 59.240 37.500 0.00 0.00 39.55 3.13
2205 2235 1.402968 GCAAGCGGATGACATGACAAT 59.597 47.619 0.00 0.00 0.00 2.71
2209 2239 1.079197 ACGCAAGCGGATGACATGA 60.079 52.632 19.30 0.00 44.69 3.07
2315 2347 1.170442 TGCGTGTGAGAGTATCGGAA 58.830 50.000 0.00 0.00 42.67 4.30
2321 2353 1.287815 CGGGTTGCGTGTGAGAGTA 59.712 57.895 0.00 0.00 0.00 2.59
2334 2366 3.491598 CTGGGAGGTGCAACGGGTT 62.492 63.158 0.00 0.00 38.12 4.11
2362 2394 4.901868 AGAACGTTTTTACCCTGCTCATA 58.098 39.130 0.46 0.00 0.00 2.15
2369 2401 2.366590 AGTCCGAGAACGTTTTTACCCT 59.633 45.455 0.46 0.00 37.88 4.34
2372 2404 2.477754 CCCAGTCCGAGAACGTTTTTAC 59.522 50.000 0.46 0.00 37.88 2.01
2389 2421 1.202533 ACTCGACAAATATCGGCCCAG 60.203 52.381 0.00 0.00 42.50 4.45
2398 2430 1.349688 ACCAAGGCCACTCGACAAATA 59.650 47.619 5.01 0.00 0.00 1.40
2420 2454 1.819288 ACAGACAGTCTACCGGTGATG 59.181 52.381 19.93 12.70 0.00 3.07
2434 2468 8.637099 TCCATATGAAACAAAATTTGACAGACA 58.363 29.630 13.19 5.70 0.00 3.41
2436 2470 8.306038 CCTCCATATGAAACAAAATTTGACAGA 58.694 33.333 13.19 7.28 0.00 3.41
2452 2486 4.401022 GGCATCAAATGACCTCCATATGA 58.599 43.478 3.65 0.00 34.45 2.15
2501 2538 0.884514 GCTGCAAAGAGAAAGGGGTC 59.115 55.000 0.00 0.00 0.00 4.46
2641 2680 7.383156 TTTCGGGGAGGTGACTAATTTATAT 57.617 36.000 0.00 0.00 44.43 0.86
2662 2701 1.749063 CTAGGGGTTGCCCGAAATTTC 59.251 52.381 8.20 8.20 46.66 2.17
2666 2705 0.544697 GATCTAGGGGTTGCCCGAAA 59.455 55.000 0.00 0.00 46.66 3.46
2671 2710 0.106669 GGGTTGATCTAGGGGTTGCC 60.107 60.000 0.00 0.00 0.00 4.52
2673 2712 0.551396 GGGGGTTGATCTAGGGGTTG 59.449 60.000 0.00 0.00 0.00 3.77
2818 2870 3.474570 GTGGAGGCTGGAGGCGAT 61.475 66.667 0.00 0.00 46.23 4.58
2821 2873 3.791586 GAGGTGGAGGCTGGAGGC 61.792 72.222 0.00 0.00 41.43 4.70
2824 2876 2.607750 GTGGAGGTGGAGGCTGGA 60.608 66.667 0.00 0.00 0.00 3.86
2827 2879 3.325753 GCAGTGGAGGTGGAGGCT 61.326 66.667 0.00 0.00 0.00 4.58
2828 2880 4.767255 CGCAGTGGAGGTGGAGGC 62.767 72.222 0.00 0.00 0.00 4.70
2830 2882 3.947132 CTGCGCAGTGGAGGTGGAG 62.947 68.421 29.24 0.00 31.26 3.86
2831 2883 4.007644 CTGCGCAGTGGAGGTGGA 62.008 66.667 29.24 0.00 31.26 4.02
2879 2931 4.154347 CTCAGCAGGGTCTCGGGC 62.154 72.222 0.00 0.00 0.00 6.13
2880 2932 3.465403 CCTCAGCAGGGTCTCGGG 61.465 72.222 0.00 0.00 35.89 5.14
2888 2940 2.365586 CCAGGACTCCCTCAGCAGG 61.366 68.421 0.00 0.00 42.02 4.85
2889 2941 0.690411 ATCCAGGACTCCCTCAGCAG 60.690 60.000 0.00 0.00 42.02 4.24
2890 2942 0.252881 AATCCAGGACTCCCTCAGCA 60.253 55.000 0.00 0.00 42.02 4.41
2891 2943 1.691434 CTAATCCAGGACTCCCTCAGC 59.309 57.143 0.00 0.00 42.02 4.26
2902 2954 1.122019 CCGAGGACCCCTAATCCAGG 61.122 65.000 0.00 0.00 45.07 4.45
2903 2955 1.122019 CCCGAGGACCCCTAATCCAG 61.122 65.000 0.00 0.00 38.86 3.86
2904 2956 1.074775 CCCGAGGACCCCTAATCCA 60.075 63.158 0.00 0.00 38.86 3.41
2905 2957 2.517798 GCCCGAGGACCCCTAATCC 61.518 68.421 0.00 0.00 31.76 3.01
2906 2958 2.868986 CGCCCGAGGACCCCTAATC 61.869 68.421 0.00 0.00 31.76 1.75
2907 2959 2.842936 CGCCCGAGGACCCCTAAT 60.843 66.667 0.00 0.00 31.76 1.73
2908 2960 4.387343 ACGCCCGAGGACCCCTAA 62.387 66.667 0.00 0.00 31.76 2.69
2909 2961 4.828296 GACGCCCGAGGACCCCTA 62.828 72.222 0.00 0.00 31.76 3.53


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

AutoCloner maintained by Alex Coulton.