Multiple sequence alignment - TraesCS7B01G393000

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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 TraesCS7B01G393000 chr7B 100.000 3064 0 0 1 3064 659655515 659652452 0.000000e+00 5659
1 TraesCS7B01G393000 chr7B 82.917 480 60 13 778 1252 659938620 659938158 2.200000e-111 412
2 TraesCS7B01G393000 chr7A 88.065 2698 208 60 444 3064 679820678 679818018 0.000000e+00 3094
3 TraesCS7B01G393000 chr7A 83.453 417 18 17 1 407 679821040 679820665 1.050000e-89 340
4 TraesCS7B01G393000 chr7D 91.706 1061 44 15 1414 2447 587851743 587850700 0.000000e+00 1432
5 TraesCS7B01G393000 chr7D 84.694 1470 107 58 1 1414 587853185 587851778 0.000000e+00 1360
6 TraesCS7B01G393000 chr7D 83.570 633 84 12 2447 3064 587850649 587850022 2.650000e-160 575
7 TraesCS7B01G393000 chr2B 87.875 734 55 18 628 1351 124151089 124151798 0.000000e+00 832
8 TraesCS7B01G393000 chr2B 86.706 504 34 15 295 772 124150684 124151180 2.090000e-146 529
9 TraesCS7B01G393000 chr5B 92.123 584 31 7 777 1351 16395397 16394820 0.000000e+00 809
10 TraesCS7B01G393000 chr5B 88.578 464 26 10 295 732 16405323 16404861 3.480000e-149 538


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 TraesCS7B01G393000 chr7B 659652452 659655515 3063 True 5659.000000 5659 100.000000 1 3064 1 chr7B.!!$R1 3063
1 TraesCS7B01G393000 chr7A 679818018 679821040 3022 True 1717.000000 3094 85.759000 1 3064 2 chr7A.!!$R1 3063
2 TraesCS7B01G393000 chr7D 587850022 587853185 3163 True 1122.333333 1432 86.656667 1 3064 3 chr7D.!!$R1 3063
3 TraesCS7B01G393000 chr2B 124150684 124151798 1114 False 680.500000 832 87.290500 295 1351 2 chr2B.!!$F1 1056
4 TraesCS7B01G393000 chr5B 16394820 16395397 577 True 809.000000 809 92.123000 777 1351 1 chr5B.!!$R1 574

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
572 661 0.940126 CGACATGGATAGTGGCAAGC 59.060 55.000 0.00 0.0 0.0 4.01 F
1067 1222 1.574428 CAAACGTTTCCCTCTGCCG 59.426 57.895 11.37 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1830 1.254954 ACTCCCTGTACGGTCTGAAC 58.745 55.0 0.0 0.0 0.00 3.18 R
2934 3255 0.174162 GGCAAATGAGCATGGTGACC 59.826 55.0 0.0 0.0 35.83 4.02 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
22 23 4.426313 CCGAACCCAAGCCCCCTC 62.426 72.222 0.00 0.00 0.00 4.30
23 24 3.330720 CGAACCCAAGCCCCCTCT 61.331 66.667 0.00 0.00 0.00 3.69
24 25 2.677848 GAACCCAAGCCCCCTCTC 59.322 66.667 0.00 0.00 0.00 3.20
25 26 2.941583 AACCCAAGCCCCCTCTCC 60.942 66.667 0.00 0.00 0.00 3.71
61 62 2.283676 TCGCTTTCCCCTCGGACT 60.284 61.111 0.00 0.00 38.14 3.85
67 68 1.812113 TTTCCCCTCGGACTCCTCCT 61.812 60.000 0.00 0.00 38.14 3.69
74 81 2.277404 GGACTCCTCCTCTCCGCT 59.723 66.667 0.00 0.00 33.07 5.52
214 221 3.321497 CTCCTTCTTGGTTTCGTCTCTG 58.679 50.000 0.00 0.00 37.07 3.35
224 231 2.125753 CGTCTCTGGTGCCTCTGC 60.126 66.667 0.00 0.00 38.26 4.26
265 272 3.197664 CAAGATTGCCCCCTTCTCC 57.802 57.895 0.00 0.00 0.00 3.71
268 275 1.452108 GATTGCCCCCTTCTCCGTG 60.452 63.158 0.00 0.00 0.00 4.94
269 276 3.645268 ATTGCCCCCTTCTCCGTGC 62.645 63.158 0.00 0.00 0.00 5.34
349 373 3.454573 CGTAGGTGTGGCGGGCTA 61.455 66.667 2.38 0.00 0.00 3.93
350 374 2.499685 GTAGGTGTGGCGGGCTAG 59.500 66.667 2.38 0.00 0.00 3.42
351 375 2.762459 TAGGTGTGGCGGGCTAGG 60.762 66.667 2.38 0.00 0.00 3.02
431 504 2.416972 GGTGGTCGACAGTTAGATGGAC 60.417 54.545 18.91 0.00 0.00 4.02
450 523 3.984749 GGATCTCCGAGCGAGGGC 61.985 72.222 0.00 0.00 39.30 5.19
469 555 2.489722 GGCTTCATGGTTTCTGAAGGTC 59.510 50.000 13.26 0.35 46.27 3.85
529 615 3.881089 TCTTTCTGGGAAAAAGACGGTTC 59.119 43.478 0.00 0.00 37.72 3.62
572 661 0.940126 CGACATGGATAGTGGCAAGC 59.060 55.000 0.00 0.00 0.00 4.01
582 673 2.834638 AGTGGCAAGCCCAGATATTT 57.165 45.000 8.89 0.00 46.54 1.40
629 720 3.239464 TGCTGGGTCACTGAAGCA 58.761 55.556 0.52 0.52 43.10 3.91
633 724 1.815408 GCTGGGTCACTGAAGCAGAAA 60.815 52.381 0.82 0.00 35.69 2.52
652 743 8.773762 GCAGAAATAATTGTAGTTATGCAGAC 57.226 34.615 8.22 0.00 46.46 3.51
670 761 3.260884 CAGACTAACTGGGGCAGAACTAA 59.739 47.826 0.00 0.00 42.39 2.24
768 898 7.798596 ACTGAAGCATAATTACTGAATCAGG 57.201 36.000 15.38 0.00 35.51 3.86
773 911 9.547753 GAAGCATAATTACTGAATCAGGACTTA 57.452 33.333 15.38 11.17 35.51 2.24
775 913 9.331282 AGCATAATTACTGAATCAGGACTTAAC 57.669 33.333 15.38 7.78 35.51 2.01
803 946 7.434897 GTGTACAACATGCTCAAAGAATTTCAA 59.565 33.333 0.00 0.00 35.03 2.69
1053 1204 3.686016 TCCTTCATCAGGTTAGCCAAAC 58.314 45.455 0.00 0.00 44.37 2.93
1067 1222 1.574428 CAAACGTTTCCCTCTGCCG 59.426 57.895 11.37 0.00 0.00 5.69
1079 1234 2.693591 CCCTCTGCCGATACAGTTTCTA 59.306 50.000 0.00 0.00 38.84 2.10
1089 1244 5.347093 CCGATACAGTTTCTATGCATAGCAG 59.653 44.000 26.05 15.86 43.65 4.24
1287 1454 4.773323 AAGCAGCAGGTATTTTCTCAAC 57.227 40.909 0.00 0.00 0.00 3.18
1321 1488 7.811236 TCAACTAGAATTTACTACGGTTCACAG 59.189 37.037 0.00 0.00 0.00 3.66
1347 1516 6.603599 TCTGCATCTTGTATGTACTAGTCAGT 59.396 38.462 0.00 0.00 38.91 3.41
1373 1543 7.648770 AGTTATATAAACCCACCATGGTCTTT 58.351 34.615 16.53 14.65 37.76 2.52
1571 1782 9.741647 AAGTTGATCAGATTTTCTTTTGAGTTC 57.258 29.630 0.00 0.00 0.00 3.01
1617 1830 9.962783 AAGACTCATGATTTTTCTTCTTCTTTG 57.037 29.630 0.00 0.00 0.00 2.77
1694 1907 2.300152 TGGTGAGCAAGGTTAGTCTCTG 59.700 50.000 0.00 0.00 0.00 3.35
1710 1927 4.404073 AGTCTCTGTCTCTCTCTCTCTCTC 59.596 50.000 0.00 0.00 0.00 3.20
1711 1928 4.404073 GTCTCTGTCTCTCTCTCTCTCTCT 59.596 50.000 0.00 0.00 0.00 3.10
1712 1929 4.646945 TCTCTGTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
1713 1930 4.614475 TCTGTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
1714 1931 4.646945 TCTGTCTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
1716 1933 4.646945 TGTCTCTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
1717 1934 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
1718 1935 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
1719 1936 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1720 1937 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
1721 1938 4.871822 TCTCTCTCTCTCTCTCTCTCTGA 58.128 47.826 0.00 0.00 0.00 3.27
1722 1939 5.462240 TCTCTCTCTCTCTCTCTCTCTGAT 58.538 45.833 0.00 0.00 0.00 2.90
1723 1940 5.303845 TCTCTCTCTCTCTCTCTCTCTGATG 59.696 48.000 0.00 0.00 0.00 3.07
1724 1941 4.964897 TCTCTCTCTCTCTCTCTCTGATGT 59.035 45.833 0.00 0.00 0.00 3.06
1725 1942 5.426509 TCTCTCTCTCTCTCTCTCTGATGTT 59.573 44.000 0.00 0.00 0.00 2.71
1726 1943 5.674525 TCTCTCTCTCTCTCTCTGATGTTC 58.325 45.833 0.00 0.00 0.00 3.18
1727 1944 4.441792 TCTCTCTCTCTCTCTGATGTTCG 58.558 47.826 0.00 0.00 0.00 3.95
1728 1945 4.161377 TCTCTCTCTCTCTCTGATGTTCGA 59.839 45.833 0.00 0.00 0.00 3.71
1767 1984 7.933577 CACTTTCCAGTCATAGGCTATTTCATA 59.066 37.037 3.76 0.00 0.00 2.15
1956 2197 1.896220 TGTCAATGACAGGCAGTTCC 58.104 50.000 12.63 0.00 37.67 3.62
1988 2229 2.987149 AGTACAAAGCGTTGATGAGTCG 59.013 45.455 19.51 0.00 38.20 4.18
2019 2260 2.690840 CTATACCAACCAGGGGCTACT 58.309 52.381 0.00 0.00 43.89 2.57
2049 2290 1.497286 ACAACAAAAGGGCAGGGTCTA 59.503 47.619 0.00 0.00 0.00 2.59
2060 2301 2.025898 GCAGGGTCTACTACAGAGGAC 58.974 57.143 0.00 0.00 32.51 3.85
2282 2525 3.817647 ACTCTGTTGTTGAGAATTGAGGC 59.182 43.478 0.00 0.00 35.66 4.70
2334 2581 5.456822 GCATTTCTTTAGCTTCTAATTGCCG 59.543 40.000 0.00 0.00 0.00 5.69
2359 2606 5.411361 TGTTAATCTGTGCTGGATGTGTTAC 59.589 40.000 0.00 0.00 0.00 2.50
2361 2608 3.319137 TCTGTGCTGGATGTGTTACTC 57.681 47.619 0.00 0.00 0.00 2.59
2376 2623 3.192633 TGTTACTCGCTGTTATGAGCTGA 59.807 43.478 0.00 0.00 36.77 4.26
2449 2752 6.832384 AGCAAGATCAGGATCATGTTTTGTAT 59.168 34.615 7.33 0.00 38.41 2.29
2496 2799 8.668353 TGATACATACATTTCACAGAAGCTTTC 58.332 33.333 0.00 0.00 0.00 2.62
2513 2816 4.580855 CTTTCTGAAGCTTCACATCTCG 57.419 45.455 25.16 14.23 32.90 4.04
2523 2826 3.665871 GCTTCACATCTCGTTTGCTTTTC 59.334 43.478 0.00 0.00 0.00 2.29
2528 2831 2.748461 TCTCGTTTGCTTTTCAACCG 57.252 45.000 0.00 0.00 41.19 4.44
2530 2833 2.875933 TCTCGTTTGCTTTTCAACCGAT 59.124 40.909 0.00 0.00 46.01 4.18
2532 2835 3.367607 TCGTTTGCTTTTCAACCGATTG 58.632 40.909 0.00 0.00 43.15 2.67
2533 2836 2.097444 CGTTTGCTTTTCAACCGATTGC 60.097 45.455 0.00 0.00 42.22 3.56
2546 2849 2.819608 ACCGATTGCTGTAACATTTGCT 59.180 40.909 0.00 0.00 0.00 3.91
2548 2851 3.127548 CCGATTGCTGTAACATTTGCTCT 59.872 43.478 0.00 0.00 0.00 4.09
2551 2854 6.202762 CCGATTGCTGTAACATTTGCTCTATA 59.797 38.462 0.00 0.00 0.00 1.31
2555 2858 5.997746 TGCTGTAACATTTGCTCTATATCCC 59.002 40.000 0.00 0.00 0.00 3.85
2566 2869 4.586421 TGCTCTATATCCCACTGACTCTTG 59.414 45.833 0.00 0.00 0.00 3.02
2569 2872 6.014669 GCTCTATATCCCACTGACTCTTGATT 60.015 42.308 0.00 0.00 0.00 2.57
2570 2873 7.295322 TCTATATCCCACTGACTCTTGATTG 57.705 40.000 0.00 0.00 0.00 2.67
2579 2882 7.448420 CCACTGACTCTTGATTGATGGTATAT 58.552 38.462 0.00 0.00 0.00 0.86
2708 3015 3.521560 GACGACCTGCTTGATGTATGAA 58.478 45.455 0.00 0.00 0.00 2.57
2723 3030 0.251341 ATGAAGCGCCTGGGAAGTTT 60.251 50.000 2.29 0.00 0.00 2.66
2738 3045 3.891977 GGAAGTTTCTCCTTTCCTTTGCT 59.108 43.478 0.00 0.00 37.86 3.91
2741 3048 4.075682 AGTTTCTCCTTTCCTTTGCTAGC 58.924 43.478 8.10 8.10 0.00 3.42
2744 3051 2.003301 CTCCTTTCCTTTGCTAGCGAC 58.997 52.381 10.77 0.00 0.00 5.19
2747 3054 0.672401 TTTCCTTTGCTAGCGACCGG 60.672 55.000 10.77 11.31 0.00 5.28
2753 3060 4.273257 GCTAGCGACCGGAGCTCC 62.273 72.222 26.91 23.79 44.79 4.70
2776 3083 2.596904 AGCCAGTACGCGACATATTT 57.403 45.000 15.93 0.00 0.00 1.40
2780 3087 1.071502 CAGTACGCGACATATTTGCCG 60.072 52.381 15.93 0.00 0.00 5.69
2792 3099 1.935933 ATTTGCCGTCAGGATCGTAC 58.064 50.000 0.00 0.00 41.02 3.67
2824 3131 2.628178 ACAGAGGAATGTTCACTCGTGA 59.372 45.455 0.00 0.00 36.40 4.35
2829 3136 3.511540 AGGAATGTTCACTCGTGATCAGA 59.488 43.478 14.06 0.00 41.07 3.27
2830 3137 3.614616 GGAATGTTCACTCGTGATCAGAC 59.385 47.826 14.06 10.65 41.07 3.51
2835 3146 4.082733 TGTTCACTCGTGATCAGACTAAGG 60.083 45.833 0.00 0.00 39.64 2.69
2847 3158 9.339850 GTGATCAGACTAAGGTATGAGTAGTAA 57.660 37.037 0.00 0.00 45.12 2.24
2866 3177 1.981256 AAAAACCACCGTGCTCTGAT 58.019 45.000 0.00 0.00 0.00 2.90
2869 3180 3.350219 AAACCACCGTGCTCTGATATT 57.650 42.857 0.00 0.00 0.00 1.28
2871 3182 4.481368 AACCACCGTGCTCTGATATTAA 57.519 40.909 0.00 0.00 0.00 1.40
2872 3183 4.060038 ACCACCGTGCTCTGATATTAAG 57.940 45.455 0.00 0.00 0.00 1.85
2879 3190 7.540400 CACCGTGCTCTGATATTAAGATCTTAG 59.460 40.741 14.63 9.08 0.00 2.18
2891 3208 3.708236 AGATCTTAGGGTTAGGAGGCA 57.292 47.619 0.00 0.00 0.00 4.75
2895 3212 5.544562 AGATCTTAGGGTTAGGAGGCAATAC 59.455 44.000 0.00 0.00 0.00 1.89
2896 3213 4.627015 TCTTAGGGTTAGGAGGCAATACA 58.373 43.478 0.00 0.00 0.00 2.29
2897 3214 5.224441 TCTTAGGGTTAGGAGGCAATACAT 58.776 41.667 0.00 0.00 0.00 2.29
2907 3224 3.633525 GGAGGCAATACATTGATGCTCAA 59.366 43.478 6.13 1.85 41.09 3.02
2910 3227 5.413499 AGGCAATACATTGATGCTCAAAAC 58.587 37.500 6.13 0.00 40.12 2.43
2911 3228 4.567959 GGCAATACATTGATGCTCAAAACC 59.432 41.667 6.13 0.00 40.12 3.27
2912 3229 5.413499 GCAATACATTGATGCTCAAAACCT 58.587 37.500 6.13 0.00 40.12 3.50
2913 3230 6.405731 GGCAATACATTGATGCTCAAAACCTA 60.406 38.462 6.13 0.00 40.12 3.08
2914 3231 6.473455 GCAATACATTGATGCTCAAAACCTAC 59.527 38.462 6.13 0.00 40.12 3.18
2916 3233 5.376854 ACATTGATGCTCAAAACCTACAC 57.623 39.130 3.27 0.00 40.12 2.90
2918 3235 5.536161 ACATTGATGCTCAAAACCTACACTT 59.464 36.000 3.27 0.00 40.12 3.16
2920 3237 5.689383 TGATGCTCAAAACCTACACTTTC 57.311 39.130 0.00 0.00 0.00 2.62
2923 3240 5.437289 TGCTCAAAACCTACACTTTCATG 57.563 39.130 0.00 0.00 0.00 3.07
2924 3241 4.278170 TGCTCAAAACCTACACTTTCATGG 59.722 41.667 0.00 0.00 0.00 3.66
2934 3255 6.710744 ACCTACACTTTCATGGTTGTTCTTAG 59.289 38.462 0.00 0.00 0.00 2.18
2938 3259 5.530915 CACTTTCATGGTTGTTCTTAGGTCA 59.469 40.000 0.00 0.00 0.00 4.02
2940 3261 4.015872 TCATGGTTGTTCTTAGGTCACC 57.984 45.455 0.00 0.00 0.00 4.02
2948 3269 3.264193 TGTTCTTAGGTCACCATGCTCAT 59.736 43.478 0.00 0.00 0.00 2.90
2953 3274 0.174162 GGTCACCATGCTCATTTGCC 59.826 55.000 0.00 0.00 0.00 4.52
2954 3275 0.889994 GTCACCATGCTCATTTGCCA 59.110 50.000 0.00 0.00 0.00 4.92
2957 3278 3.130869 GTCACCATGCTCATTTGCCAATA 59.869 43.478 0.00 0.00 0.00 1.90
2958 3279 3.130869 TCACCATGCTCATTTGCCAATAC 59.869 43.478 0.00 0.00 0.00 1.89
2959 3280 2.099592 ACCATGCTCATTTGCCAATACG 59.900 45.455 0.00 0.00 0.00 3.06
2960 3281 2.121786 CATGCTCATTTGCCAATACGC 58.878 47.619 0.00 0.00 0.00 4.42
2961 3282 1.462616 TGCTCATTTGCCAATACGCT 58.537 45.000 5.28 0.00 0.00 5.07
2962 3283 2.637947 TGCTCATTTGCCAATACGCTA 58.362 42.857 5.28 0.00 0.00 4.26
2963 3284 2.613595 TGCTCATTTGCCAATACGCTAG 59.386 45.455 5.28 0.00 0.00 3.42
2964 3285 2.603173 GCTCATTTGCCAATACGCTAGC 60.603 50.000 4.06 4.06 0.00 3.42
2965 3286 2.874701 CTCATTTGCCAATACGCTAGCT 59.125 45.455 13.93 2.46 0.00 3.32
2966 3287 4.058124 CTCATTTGCCAATACGCTAGCTA 58.942 43.478 13.93 4.80 0.00 3.32
2969 3290 2.455674 TGCCAATACGCTAGCTATGG 57.544 50.000 13.93 15.34 0.00 2.74
2976 3297 2.781681 ACGCTAGCTATGGTGGTTTT 57.218 45.000 13.93 0.00 0.00 2.43
2977 3298 2.356135 ACGCTAGCTATGGTGGTTTTG 58.644 47.619 13.93 0.00 0.00 2.44
2983 3304 2.647802 AGCTATGGTGGTTTTGGGTAGT 59.352 45.455 0.00 0.00 0.00 2.73
2990 3311 5.013547 TGGTGGTTTTGGGTAGTATGATTG 58.986 41.667 0.00 0.00 0.00 2.67
2995 3316 5.357032 GGTTTTGGGTAGTATGATTGACTGG 59.643 44.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.197324 CGGAGAGGAGGGGAGAGG 59.803 72.222 0.00 0.00 0.00 3.69
21 22 4.144727 GCCGGAGAGGAGGGGAGA 62.145 72.222 5.05 0.00 45.00 3.71
192 199 2.300437 AGAGACGAAACCAAGAAGGAGG 59.700 50.000 0.00 0.00 41.22 4.30
214 221 2.512515 CCGCTAAGCAGAGGCACC 60.513 66.667 0.00 0.00 44.61 5.01
224 231 1.278127 TCCTCCAAAGAACCCGCTAAG 59.722 52.381 0.00 0.00 0.00 2.18
256 263 3.787001 GGGAGCACGGAGAAGGGG 61.787 72.222 0.00 0.00 0.00 4.79
260 267 1.258445 GGAGAAGGGAGCACGGAGAA 61.258 60.000 0.00 0.00 0.00 2.87
261 268 1.682684 GGAGAAGGGAGCACGGAGA 60.683 63.158 0.00 0.00 0.00 3.71
262 269 2.896443 GGAGAAGGGAGCACGGAG 59.104 66.667 0.00 0.00 0.00 4.63
263 270 3.068691 CGGAGAAGGGAGCACGGA 61.069 66.667 0.00 0.00 0.00 4.69
265 272 4.821589 GGCGGAGAAGGGAGCACG 62.822 72.222 0.00 0.00 0.00 5.34
268 275 4.516195 GACGGCGGAGAAGGGAGC 62.516 72.222 13.24 0.00 0.00 4.70
269 276 4.194720 CGACGGCGGAGAAGGGAG 62.195 72.222 13.24 0.00 0.00 4.30
333 357 2.499685 CTAGCCCGCCACACCTAC 59.500 66.667 0.00 0.00 0.00 3.18
334 358 2.762459 CCTAGCCCGCCACACCTA 60.762 66.667 0.00 0.00 0.00 3.08
337 361 4.840005 GAGCCTAGCCCGCCACAC 62.840 72.222 0.00 0.00 0.00 3.82
338 362 3.672338 TAGAGCCTAGCCCGCCACA 62.672 63.158 0.00 0.00 0.00 4.17
339 363 2.838225 TAGAGCCTAGCCCGCCAC 60.838 66.667 0.00 0.00 0.00 5.01
340 364 2.521950 CTAGAGCCTAGCCCGCCA 60.522 66.667 0.00 0.00 0.00 5.69
341 365 3.307108 CCTAGAGCCTAGCCCGCC 61.307 72.222 0.00 0.00 0.00 6.13
342 366 3.307108 CCCTAGAGCCTAGCCCGC 61.307 72.222 0.00 0.00 0.00 6.13
343 367 2.601966 CCCCTAGAGCCTAGCCCG 60.602 72.222 0.00 0.00 0.00 6.13
344 368 0.694783 AAACCCCTAGAGCCTAGCCC 60.695 60.000 0.00 0.00 0.00 5.19
345 369 2.098618 TAAACCCCTAGAGCCTAGCC 57.901 55.000 0.00 0.00 0.00 3.93
346 370 4.348461 AGATTTAAACCCCTAGAGCCTAGC 59.652 45.833 0.00 0.00 0.00 3.42
347 371 5.367060 ACAGATTTAAACCCCTAGAGCCTAG 59.633 44.000 0.00 3.06 0.00 3.02
348 372 5.286221 ACAGATTTAAACCCCTAGAGCCTA 58.714 41.667 0.00 0.00 0.00 3.93
349 373 4.112331 ACAGATTTAAACCCCTAGAGCCT 58.888 43.478 0.00 0.00 0.00 4.58
350 374 4.164413 AGACAGATTTAAACCCCTAGAGCC 59.836 45.833 0.00 0.00 0.00 4.70
351 375 5.119694 CAGACAGATTTAAACCCCTAGAGC 58.880 45.833 0.00 0.00 0.00 4.09
352 376 6.109359 CACAGACAGATTTAAACCCCTAGAG 58.891 44.000 0.00 0.00 0.00 2.43
353 377 5.570844 GCACAGACAGATTTAAACCCCTAGA 60.571 44.000 0.00 0.00 0.00 2.43
469 555 4.085363 CGACTGATACGCATCTTAGCAAAG 60.085 45.833 0.00 0.00 31.93 2.77
529 615 6.624917 CGACATGCTACAGAATCGTAAAATTG 59.375 38.462 0.00 0.00 0.00 2.32
582 673 6.935240 TCCCAGACTTCTCTTCTTGATAAA 57.065 37.500 0.00 0.00 0.00 1.40
633 724 9.547753 CCAGTTAGTCTGCATAACTACAATTAT 57.452 33.333 10.16 0.00 40.61 1.28
652 743 4.589908 ACAATTAGTTCTGCCCCAGTTAG 58.410 43.478 0.00 0.00 32.61 2.34
734 831 9.347240 AGTAATTATGCTTCAGTTATTCTGCAT 57.653 29.630 0.00 0.00 43.32 3.96
745 842 7.714377 AGTCCTGATTCAGTAATTATGCTTCAG 59.286 37.037 12.54 4.85 0.00 3.02
768 898 5.465390 TGAGCATGTTGTACACAGTTAAGTC 59.535 40.000 0.00 0.00 39.40 3.01
773 911 4.881273 TCTTTGAGCATGTTGTACACAGTT 59.119 37.500 0.00 0.00 39.40 3.16
775 913 5.422666 TTCTTTGAGCATGTTGTACACAG 57.577 39.130 0.00 0.00 39.40 3.66
1053 1204 0.174845 TGTATCGGCAGAGGGAAACG 59.825 55.000 0.00 0.00 0.00 3.60
1067 1222 7.116090 CAGTCTGCTATGCATAGAAACTGTATC 59.884 40.741 33.10 14.76 38.13 2.24
1079 1234 2.498885 TCAGTCACAGTCTGCTATGCAT 59.501 45.455 3.79 3.79 38.13 3.96
1089 1244 7.702772 CCTATGTACAAATAGTCAGTCACAGTC 59.297 40.741 0.00 0.00 0.00 3.51
1287 1454 7.911205 CGTAGTAAATTCTAGTTGACCAGAGAG 59.089 40.741 0.00 0.00 0.00 3.20
1321 1488 6.796426 TGACTAGTACATACAAGATGCAGAC 58.204 40.000 0.00 0.00 0.00 3.51
1347 1516 7.941053 AGACCATGGTGGGTTTATATAACTA 57.059 36.000 25.52 0.00 43.37 2.24
1403 1573 6.875076 TGGGACAACTCTAGAAAATAGCTAC 58.125 40.000 0.00 0.00 31.92 3.58
1617 1830 1.254954 ACTCCCTGTACGGTCTGAAC 58.745 55.000 0.00 0.00 0.00 3.18
1694 1907 4.892934 AGAGAGAGAGAGAGAGAGAGAGAC 59.107 50.000 0.00 0.00 0.00 3.36
1710 1927 5.559427 TTTCTCGAACATCAGAGAGAGAG 57.441 43.478 0.00 0.00 43.42 3.20
1711 1928 5.417266 ACATTTCTCGAACATCAGAGAGAGA 59.583 40.000 0.00 0.00 43.42 3.10
1712 1929 5.515982 CACATTTCTCGAACATCAGAGAGAG 59.484 44.000 0.00 0.00 43.42 3.20
1713 1930 5.405797 CACATTTCTCGAACATCAGAGAGA 58.594 41.667 0.00 0.00 43.42 3.10
1714 1931 4.032672 GCACATTTCTCGAACATCAGAGAG 59.967 45.833 0.00 0.00 43.42 3.20
1716 1933 3.931468 AGCACATTTCTCGAACATCAGAG 59.069 43.478 0.00 0.00 35.91 3.35
1717 1934 3.930336 AGCACATTTCTCGAACATCAGA 58.070 40.909 0.00 0.00 0.00 3.27
1718 1935 4.400845 CAAGCACATTTCTCGAACATCAG 58.599 43.478 0.00 0.00 0.00 2.90
1719 1936 3.365264 GCAAGCACATTTCTCGAACATCA 60.365 43.478 0.00 0.00 0.00 3.07
1720 1937 3.166657 GCAAGCACATTTCTCGAACATC 58.833 45.455 0.00 0.00 0.00 3.06
1721 1938 2.553602 TGCAAGCACATTTCTCGAACAT 59.446 40.909 0.00 0.00 0.00 2.71
1722 1939 1.946081 TGCAAGCACATTTCTCGAACA 59.054 42.857 0.00 0.00 0.00 3.18
1723 1940 2.310577 GTGCAAGCACATTTCTCGAAC 58.689 47.619 19.47 0.00 45.53 3.95
1724 1941 2.686558 GTGCAAGCACATTTCTCGAA 57.313 45.000 19.47 0.00 45.53 3.71
1787 2028 5.070001 AGCTGTGCTAACAATTTACTCCAA 58.930 37.500 0.00 0.00 36.99 3.53
1862 2103 3.820467 CCTGCAGATTGTCAAACCAACTA 59.180 43.478 17.39 0.00 0.00 2.24
1956 2197 2.650608 GCTTTGTACTTTCCAAGCACG 58.349 47.619 0.00 0.00 0.00 5.34
1988 2229 2.143925 GTTGGTATAGGAATGCCGAGC 58.856 52.381 0.00 0.00 40.57 5.03
2041 2282 3.054287 TCAGTCCTCTGTAGTAGACCCTG 60.054 52.174 0.00 0.00 41.91 4.45
2049 2290 4.035612 TGTAGCTTCAGTCCTCTGTAGT 57.964 45.455 0.00 0.00 39.94 2.73
2060 2301 8.886719 TCATGAAACTGATAAATGTAGCTTCAG 58.113 33.333 7.60 7.60 39.70 3.02
2167 2409 2.030007 ACCGATGACATGCCACAAAAAG 60.030 45.455 0.00 0.00 0.00 2.27
2282 2525 8.764287 GTCATTTCCATTAAACCTGAACAAAAG 58.236 33.333 0.00 0.00 0.00 2.27
2322 2565 6.250819 CACAGATTAACACGGCAATTAGAAG 58.749 40.000 0.00 0.00 0.00 2.85
2334 2581 3.753272 ACACATCCAGCACAGATTAACAC 59.247 43.478 0.00 0.00 0.00 3.32
2359 2606 4.871993 AAAATCAGCTCATAACAGCGAG 57.128 40.909 0.00 0.00 44.82 5.03
2382 2629 2.147958 GTTCCAGCAATAACCGTGACA 58.852 47.619 0.00 0.00 0.00 3.58
2389 2636 3.763897 AGTCAATGGGTTCCAGCAATAAC 59.236 43.478 0.00 0.00 36.75 1.89
2391 2638 3.245229 ACAGTCAATGGGTTCCAGCAATA 60.245 43.478 0.00 0.00 36.75 1.90
2395 2642 1.270550 CAACAGTCAATGGGTTCCAGC 59.729 52.381 0.00 0.00 36.75 4.85
2419 2669 3.827008 TGATCCTGATCTTGCTGTACC 57.173 47.619 8.50 0.00 38.60 3.34
2449 2752 2.435805 AGTGACAAGGTGAGCTCAGAAA 59.564 45.455 18.89 0.00 0.00 2.52
2496 2799 3.666374 GCAAACGAGATGTGAAGCTTCAG 60.666 47.826 29.13 18.05 37.98 3.02
2501 2804 2.977405 AAGCAAACGAGATGTGAAGC 57.023 45.000 0.00 0.00 0.00 3.86
2513 2816 3.060339 CAGCAATCGGTTGAAAAGCAAAC 60.060 43.478 13.85 0.00 46.59 2.93
2523 2826 3.364621 GCAAATGTTACAGCAATCGGTTG 59.635 43.478 3.38 3.38 38.39 3.77
2528 2831 8.233190 GGATATAGAGCAAATGTTACAGCAATC 58.767 37.037 0.00 0.00 0.00 2.67
2530 2833 6.486657 GGGATATAGAGCAAATGTTACAGCAA 59.513 38.462 0.00 0.00 0.00 3.91
2532 2835 5.997746 TGGGATATAGAGCAAATGTTACAGC 59.002 40.000 0.00 0.00 0.00 4.40
2533 2836 7.172190 CAGTGGGATATAGAGCAAATGTTACAG 59.828 40.741 0.00 0.00 0.00 2.74
2546 2849 7.069344 TCAATCAAGAGTCAGTGGGATATAGA 58.931 38.462 0.00 0.00 0.00 1.98
2548 2851 7.256439 CCATCAATCAAGAGTCAGTGGGATATA 60.256 40.741 0.00 0.00 0.00 0.86
2551 2854 4.384978 CCATCAATCAAGAGTCAGTGGGAT 60.385 45.833 0.00 0.00 0.00 3.85
2595 2898 9.515020 GAACATTTACAGAAGACAAAAATGACA 57.485 29.630 11.76 0.00 38.99 3.58
2596 2899 9.736023 AGAACATTTACAGAAGACAAAAATGAC 57.264 29.630 11.76 6.54 38.99 3.06
2600 2903 9.364989 CCAAAGAACATTTACAGAAGACAAAAA 57.635 29.630 0.00 0.00 0.00 1.94
2618 2925 3.873805 GCAGACAAGGCCAAAGAAC 57.126 52.632 5.01 0.00 0.00 3.01
2678 2985 1.374758 GCAGGTCGTCCCACTGAAG 60.375 63.158 0.00 0.00 34.21 3.02
2708 3015 1.003233 GAGAAACTTCCCAGGCGCT 60.003 57.895 7.64 0.00 0.00 5.92
2711 3018 2.163509 GAAAGGAGAAACTTCCCAGGC 58.836 52.381 0.00 0.00 38.02 4.85
2723 3030 1.899814 TCGCTAGCAAAGGAAAGGAGA 59.100 47.619 16.45 0.00 0.00 3.71
2753 3060 2.277756 GTCGCGTACTGGCTACCG 60.278 66.667 5.77 0.00 0.00 4.02
2758 3065 1.332904 GCAAATATGTCGCGTACTGGC 60.333 52.381 5.77 0.00 0.00 4.85
2776 3083 1.985447 GACGTACGATCCTGACGGCA 61.985 60.000 24.41 0.00 44.14 5.69
2780 3087 1.798079 GCCAAGACGTACGATCCTGAC 60.798 57.143 24.41 4.79 0.00 3.51
2792 3099 0.895530 TTCCTCTGTAGGCCAAGACG 59.104 55.000 5.01 0.00 43.31 4.18
2821 3128 7.811117 ACTACTCATACCTTAGTCTGATCAC 57.189 40.000 0.00 0.00 29.64 3.06
2847 3158 1.981256 ATCAGAGCACGGTGGTTTTT 58.019 45.000 14.71 0.95 0.00 1.94
2849 3160 3.350219 AATATCAGAGCACGGTGGTTT 57.650 42.857 14.71 5.86 0.00 3.27
2850 3161 4.161565 TCTTAATATCAGAGCACGGTGGTT 59.838 41.667 14.71 0.76 0.00 3.67
2852 3163 4.322080 TCTTAATATCAGAGCACGGTGG 57.678 45.455 10.60 0.00 0.00 4.61
2857 3168 7.902087 ACCCTAAGATCTTAATATCAGAGCAC 58.098 38.462 15.85 0.00 0.00 4.40
2866 3177 7.310634 TGCCTCCTAACCCTAAGATCTTAATA 58.689 38.462 15.85 6.69 0.00 0.98
2869 3180 5.152306 TGCCTCCTAACCCTAAGATCTTA 57.848 43.478 14.42 14.42 0.00 2.10
2871 3182 3.708236 TGCCTCCTAACCCTAAGATCT 57.292 47.619 0.00 0.00 0.00 2.75
2872 3183 4.984146 ATTGCCTCCTAACCCTAAGATC 57.016 45.455 0.00 0.00 0.00 2.75
2879 3190 4.164843 TCAATGTATTGCCTCCTAACCC 57.835 45.455 0.00 0.00 37.68 4.11
2885 3196 3.216800 TGAGCATCAATGTATTGCCTCC 58.783 45.455 0.00 0.00 45.97 4.30
2907 3224 5.891551 AGAACAACCATGAAAGTGTAGGTTT 59.108 36.000 0.00 0.00 40.39 3.27
2910 3227 6.149474 CCTAAGAACAACCATGAAAGTGTAGG 59.851 42.308 0.00 0.00 0.00 3.18
2911 3228 6.710744 ACCTAAGAACAACCATGAAAGTGTAG 59.289 38.462 0.00 0.00 0.00 2.74
2912 3229 6.597562 ACCTAAGAACAACCATGAAAGTGTA 58.402 36.000 0.00 0.00 0.00 2.90
2913 3230 5.445964 ACCTAAGAACAACCATGAAAGTGT 58.554 37.500 0.00 0.00 0.00 3.55
2914 3231 5.530915 TGACCTAAGAACAACCATGAAAGTG 59.469 40.000 0.00 0.00 0.00 3.16
2916 3233 5.048713 GGTGACCTAAGAACAACCATGAAAG 60.049 44.000 0.00 0.00 0.00 2.62
2918 3235 4.141367 TGGTGACCTAAGAACAACCATGAA 60.141 41.667 2.11 0.00 0.00 2.57
2920 3237 3.750371 TGGTGACCTAAGAACAACCATG 58.250 45.455 2.11 0.00 0.00 3.66
2923 3240 2.488153 GCATGGTGACCTAAGAACAACC 59.512 50.000 2.11 0.00 0.00 3.77
2924 3241 3.412386 AGCATGGTGACCTAAGAACAAC 58.588 45.455 2.11 0.00 0.00 3.32
2934 3255 0.174162 GGCAAATGAGCATGGTGACC 59.826 55.000 0.00 0.00 35.83 4.02
2938 3259 2.099592 CGTATTGGCAAATGAGCATGGT 59.900 45.455 3.01 0.00 35.83 3.55
2940 3261 2.121786 GCGTATTGGCAAATGAGCATG 58.878 47.619 3.01 0.00 35.83 4.06
2948 3269 3.138304 CCATAGCTAGCGTATTGGCAAA 58.862 45.455 9.55 0.00 34.64 3.68
2953 3274 3.386768 ACCACCATAGCTAGCGTATTG 57.613 47.619 9.55 5.73 0.00 1.90
2954 3275 4.417426 AAACCACCATAGCTAGCGTATT 57.583 40.909 9.55 0.00 0.00 1.89
2957 3278 2.356135 CAAAACCACCATAGCTAGCGT 58.644 47.619 9.55 0.00 0.00 5.07
2958 3279 1.670811 CCAAAACCACCATAGCTAGCG 59.329 52.381 9.55 0.00 0.00 4.26
2959 3280 2.024414 CCCAAAACCACCATAGCTAGC 58.976 52.381 6.62 6.62 0.00 3.42
2960 3281 3.366052 ACCCAAAACCACCATAGCTAG 57.634 47.619 0.00 0.00 0.00 3.42
2961 3282 3.847780 ACTACCCAAAACCACCATAGCTA 59.152 43.478 0.00 0.00 0.00 3.32
2962 3283 2.647802 ACTACCCAAAACCACCATAGCT 59.352 45.455 0.00 0.00 0.00 3.32
2963 3284 3.081710 ACTACCCAAAACCACCATAGC 57.918 47.619 0.00 0.00 0.00 2.97
2964 3285 5.996644 TCATACTACCCAAAACCACCATAG 58.003 41.667 0.00 0.00 0.00 2.23
2965 3286 6.584471 ATCATACTACCCAAAACCACCATA 57.416 37.500 0.00 0.00 0.00 2.74
2966 3287 4.938575 TCATACTACCCAAAACCACCAT 57.061 40.909 0.00 0.00 0.00 3.55
2969 3290 5.944007 AGTCAATCATACTACCCAAAACCAC 59.056 40.000 0.00 0.00 0.00 4.16
2976 3297 4.620723 ACTCCAGTCAATCATACTACCCA 58.379 43.478 0.00 0.00 0.00 4.51
2977 3298 5.128827 TGAACTCCAGTCAATCATACTACCC 59.871 44.000 0.00 0.00 0.00 3.69
3007 3328 9.743057 CACCAACATCTGAATACTTGTTTTTAA 57.257 29.630 0.00 0.00 30.23 1.52


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

AutoCloner maintained by Alex Coulton.