Multiple sequence alignment - TraesCS7A01G497600

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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 TraesCS7A01G497600 chr7A 100.000 3323 0 0 1 3323 688315248 688311926 0.000000e+00 6137.0
1 TraesCS7A01G497600 chr7D 92.487 2356 127 27 996 3323 595328930 595326597 0.000000e+00 3325.0
2 TraesCS7A01G497600 chr7D 93.953 893 45 7 1 886 595329880 595328990 0.000000e+00 1341.0
3 TraesCS7A01G497600 chr7B 93.964 1690 78 8 996 2661 672765491 672763802 0.000000e+00 2534.0
4 TraesCS7A01G497600 chr7B 94.118 340 15 3 552 886 672765902 672765563 2.290000e-141 512.0
5 TraesCS7A01G497600 chr7B 90.523 306 25 4 3020 3323 672763493 672763190 5.160000e-108 401.0
6 TraesCS7A01G497600 chr7B 86.957 253 30 3 2784 3035 672763795 672763545 7.020000e-72 281.0
7 TraesCS7A01G497600 chr7B 86.096 187 22 4 246 430 705325564 705325380 7.270000e-47 198.0
8 TraesCS7A01G497600 chr5B 86.702 188 21 4 246 430 626351929 626351743 4.350000e-49 206.0
9 TraesCS7A01G497600 chr5B 78.906 128 23 4 1113 1238 504833499 504833374 2.120000e-12 84.2
10 TraesCS7A01G497600 chr5B 91.667 48 4 0 1535 1582 586358586 586358539 2.140000e-07 67.6
11 TraesCS7A01G497600 chr5D 86.702 188 20 5 246 430 558062044 558061859 1.560000e-48 204.0
12 TraesCS7A01G497600 chr5D 93.750 48 2 1 1535 1582 478595148 478595194 1.650000e-08 71.3
13 TraesCS7A01G497600 chr2B 86.885 183 20 3 250 430 386503198 386503378 5.620000e-48 202.0
14 TraesCS7A01G497600 chr2B 84.694 196 25 4 238 430 479991195 479991388 1.220000e-44 191.0
15 TraesCS7A01G497600 chr2B 95.238 42 2 0 1541 1582 551639222 551639263 2.140000e-07 67.6
16 TraesCS7A01G497600 chr1B 86.667 180 22 2 252 430 311430464 311430642 7.270000e-47 198.0
17 TraesCS7A01G497600 chr3B 85.204 196 24 3 238 429 655624165 655624359 2.620000e-46 196.0
18 TraesCS7A01G497600 chr3B 81.061 132 19 6 15 144 808968209 808968082 2.110000e-17 100.0
19 TraesCS7A01G497600 chr3D 85.638 188 22 5 246 430 285767429 285767244 3.380000e-45 193.0
20 TraesCS7A01G497600 chr5A 83.529 85 11 3 1156 1238 531083356 531083273 3.550000e-10 76.8
21 TraesCS7A01G497600 chr5A 87.143 70 6 3 1516 1582 597686871 597686802 3.550000e-10 76.8
22 TraesCS7A01G497600 chr2D 95.238 42 2 0 1541 1582 472471866 472471907 2.140000e-07 67.6
23 TraesCS7A01G497600 chr2A 95.238 42 2 0 1541 1582 613992872 613992913 2.140000e-07 67.6


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 TraesCS7A01G497600 chr7A 688311926 688315248 3322 True 6137 6137 100.0000 1 3323 1 chr7A.!!$R1 3322
1 TraesCS7A01G497600 chr7D 595326597 595329880 3283 True 2333 3325 93.2200 1 3323 2 chr7D.!!$R1 3322
2 TraesCS7A01G497600 chr7B 672763190 672765902 2712 True 932 2534 91.3905 552 3323 4 chr7B.!!$R2 2771

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
110 111 0.037697 TGTTTACGCGAGAGGCACAT 60.038 50.0 15.93 0.0 43.84 3.21 F
977 985 0.249531 TAAACAGCGTTGCACCGAGA 60.250 50.0 8.22 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2125 0.738975 CGCTGTTCTCCGTCTCCATA 59.261 55.0 0.0 0.0 0.0 2.74 R
2857 2921 0.110823 CTTGTGGTGCTACGAAACGC 60.111 55.0 0.0 0.0 0.0 4.84 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
74 75 3.304659 CGCAAGAGGCACACATTTACTTT 60.305 43.478 0.00 0.00 45.17 2.66
80 81 5.047802 AGAGGCACACATTTACTTTTCATGG 60.048 40.000 0.00 0.00 0.00 3.66
96 97 5.697473 TTCATGGAGCACGAATTTGTTTA 57.303 34.783 0.00 0.00 0.00 2.01
100 101 1.896193 GAGCACGAATTTGTTTACGCG 59.104 47.619 3.53 3.53 0.00 6.01
109 110 0.249531 TTGTTTACGCGAGAGGCACA 60.250 50.000 15.93 3.54 43.84 4.57
110 111 0.037697 TGTTTACGCGAGAGGCACAT 60.038 50.000 15.93 0.00 43.84 3.21
156 157 6.421377 ACACTTGTTTTCAAATTTGCTTCC 57.579 33.333 13.54 2.56 39.47 3.46
226 227 2.047061 GGAAAGGGGAAAAAGGTGCTT 58.953 47.619 0.00 0.00 0.00 3.91
244 245 2.169561 GCTTCTGGTTTGGGTTTTTCCA 59.830 45.455 0.00 0.00 38.11 3.53
354 357 1.983605 GTTTTGAAGATCTCGACGCGA 59.016 47.619 15.93 0.00 0.00 5.87
377 380 1.444212 CCCAACGGCGAAAATGCTG 60.444 57.895 16.62 0.00 46.83 4.41
391 394 3.411415 AATGCTGCAAGATTTAGTCGC 57.589 42.857 6.36 0.00 34.07 5.19
452 455 0.537371 AAGGCGGGAGTGTTCTTTGG 60.537 55.000 0.00 0.00 0.00 3.28
456 459 1.523758 CGGGAGTGTTCTTTGGAAGG 58.476 55.000 0.00 0.00 31.46 3.46
463 466 5.454897 GGAGTGTTCTTTGGAAGGAGTACTT 60.455 44.000 0.00 0.00 43.65 2.24
488 491 6.813649 TCTCAATTACTGATTTGGAAGAGACG 59.186 38.462 0.00 0.00 32.14 4.18
490 493 2.770164 ACTGATTTGGAAGAGACGGG 57.230 50.000 0.00 0.00 0.00 5.28
531 534 1.555967 TTTAACTTCATGCTGGGCCC 58.444 50.000 17.59 17.59 0.00 5.80
621 625 0.539051 AGTGCGGATCCCTTTCTCTG 59.461 55.000 6.06 0.00 0.00 3.35
741 745 1.362224 ACTACCAGGTCAACCAGCAT 58.638 50.000 0.00 0.00 38.89 3.79
843 851 4.181578 CCATAAGTACCTTCTTCACACCG 58.818 47.826 0.00 0.00 0.00 4.94
877 885 4.845580 CGCTCCAAGCCGCATCCT 62.846 66.667 0.00 0.00 38.18 3.24
886 894 1.228367 GCCGCATCCTTCCATCCAT 60.228 57.895 0.00 0.00 0.00 3.41
887 895 1.239968 GCCGCATCCTTCCATCCATC 61.240 60.000 0.00 0.00 0.00 3.51
891 899 2.444421 GCATCCTTCCATCCATCCATC 58.556 52.381 0.00 0.00 0.00 3.51
892 900 2.883058 GCATCCTTCCATCCATCCATCC 60.883 54.545 0.00 0.00 0.00 3.51
893 901 2.520188 TCCTTCCATCCATCCATCCT 57.480 50.000 0.00 0.00 0.00 3.24
894 902 2.793017 TCCTTCCATCCATCCATCCTT 58.207 47.619 0.00 0.00 0.00 3.36
895 903 2.713167 TCCTTCCATCCATCCATCCTTC 59.287 50.000 0.00 0.00 0.00 3.46
896 904 2.224967 CCTTCCATCCATCCATCCTTCC 60.225 54.545 0.00 0.00 0.00 3.46
897 905 1.449271 TCCATCCATCCATCCTTCCC 58.551 55.000 0.00 0.00 0.00 3.97
898 906 1.151760 CCATCCATCCATCCTTCCCA 58.848 55.000 0.00 0.00 0.00 4.37
899 907 1.075050 CCATCCATCCATCCTTCCCAG 59.925 57.143 0.00 0.00 0.00 4.45
900 908 0.776176 ATCCATCCATCCTTCCCAGC 59.224 55.000 0.00 0.00 0.00 4.85
901 909 0.624206 TCCATCCATCCTTCCCAGCA 60.624 55.000 0.00 0.00 0.00 4.41
902 910 0.466922 CCATCCATCCTTCCCAGCAC 60.467 60.000 0.00 0.00 0.00 4.40
903 911 0.816825 CATCCATCCTTCCCAGCACG 60.817 60.000 0.00 0.00 0.00 5.34
904 912 2.615227 ATCCATCCTTCCCAGCACGC 62.615 60.000 0.00 0.00 0.00 5.34
905 913 2.046023 CATCCTTCCCAGCACGCA 60.046 61.111 0.00 0.00 0.00 5.24
906 914 2.110967 CATCCTTCCCAGCACGCAG 61.111 63.158 0.00 0.00 0.00 5.18
907 915 3.984193 ATCCTTCCCAGCACGCAGC 62.984 63.158 0.00 0.00 46.19 5.25
915 923 4.405671 AGCACGCAGCCAGCTGAT 62.406 61.111 23.40 7.40 46.30 2.90
916 924 3.873883 GCACGCAGCCAGCTGATC 61.874 66.667 23.40 6.56 46.30 2.92
917 925 3.561213 CACGCAGCCAGCTGATCG 61.561 66.667 23.40 18.75 46.30 3.69
918 926 3.763356 ACGCAGCCAGCTGATCGA 61.763 61.111 23.40 0.00 46.30 3.59
919 927 2.960659 CGCAGCCAGCTGATCGAG 60.961 66.667 23.40 0.00 46.30 4.04
935 943 1.971418 GAGCTCATCGATCCCTCCC 59.029 63.158 9.40 0.00 0.00 4.30
936 944 1.535202 AGCTCATCGATCCCTCCCC 60.535 63.158 0.00 0.00 0.00 4.81
937 945 2.588201 GCTCATCGATCCCTCCCCC 61.588 68.421 0.00 0.00 0.00 5.40
938 946 1.157276 CTCATCGATCCCTCCCCCT 59.843 63.158 0.00 0.00 0.00 4.79
939 947 0.902516 CTCATCGATCCCTCCCCCTC 60.903 65.000 0.00 0.00 0.00 4.30
940 948 1.915769 CATCGATCCCTCCCCCTCC 60.916 68.421 0.00 0.00 0.00 4.30
941 949 2.100983 ATCGATCCCTCCCCCTCCT 61.101 63.158 0.00 0.00 0.00 3.69
942 950 2.100525 ATCGATCCCTCCCCCTCCTC 62.101 65.000 0.00 0.00 0.00 3.71
943 951 2.205749 GATCCCTCCCCCTCCTCC 59.794 72.222 0.00 0.00 0.00 4.30
944 952 2.289979 ATCCCTCCCCCTCCTCCT 60.290 66.667 0.00 0.00 0.00 3.69
945 953 2.395180 GATCCCTCCCCCTCCTCCTC 62.395 70.000 0.00 0.00 0.00 3.71
946 954 4.179599 CCCTCCCCCTCCTCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
947 955 3.039526 CCTCCCCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
949 957 3.036959 TCCCCCTCCTCCTCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
953 961 2.018086 CCCTCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
958 966 0.338120 CCTCCTCCTCCTCCTCTGTT 59.662 60.000 0.00 0.00 0.00 3.16
959 967 1.571457 CCTCCTCCTCCTCCTCTGTTA 59.429 57.143 0.00 0.00 0.00 2.41
962 970 3.442076 TCCTCCTCCTCCTCTGTTAAAC 58.558 50.000 0.00 0.00 0.00 2.01
963 971 3.173965 CCTCCTCCTCCTCTGTTAAACA 58.826 50.000 0.00 0.00 0.00 2.83
965 973 2.567615 TCCTCCTCCTCTGTTAAACAGC 59.432 50.000 0.00 0.00 45.54 4.40
971 979 1.601903 CCTCTGTTAAACAGCGTTGCA 59.398 47.619 0.00 0.00 45.54 4.08
977 985 0.249531 TAAACAGCGTTGCACCGAGA 60.250 50.000 8.22 0.00 0.00 4.04
978 986 1.498865 AAACAGCGTTGCACCGAGAG 61.499 55.000 8.22 0.00 0.00 3.20
982 990 2.089349 GCGTTGCACCGAGAGAGAC 61.089 63.158 8.22 0.00 0.00 3.36
983 991 1.285950 CGTTGCACCGAGAGAGACA 59.714 57.895 0.00 0.00 0.00 3.41
984 992 0.730834 CGTTGCACCGAGAGAGACAG 60.731 60.000 0.00 0.00 0.00 3.51
985 993 0.598562 GTTGCACCGAGAGAGACAGA 59.401 55.000 0.00 0.00 0.00 3.41
986 994 1.203523 GTTGCACCGAGAGAGACAGAT 59.796 52.381 0.00 0.00 0.00 2.90
987 995 2.420058 TGCACCGAGAGAGACAGATA 57.580 50.000 0.00 0.00 0.00 1.98
988 996 2.017782 TGCACCGAGAGAGACAGATAC 58.982 52.381 0.00 0.00 0.00 2.24
990 998 2.644676 CACCGAGAGAGACAGATACCA 58.355 52.381 0.00 0.00 0.00 3.25
991 999 2.616376 CACCGAGAGAGACAGATACCAG 59.384 54.545 0.00 0.00 0.00 4.00
993 1001 3.138304 CCGAGAGAGACAGATACCAGAG 58.862 54.545 0.00 0.00 0.00 3.35
994 1002 3.138304 CGAGAGAGACAGATACCAGAGG 58.862 54.545 0.00 0.00 0.00 3.69
1005 1030 4.864334 CCAGAGGCGTCCATGGGC 62.864 72.222 13.02 9.73 31.56 5.36
1545 1573 2.203252 CCCAGCATCATCCACCGG 60.203 66.667 0.00 0.00 0.00 5.28
1710 1738 1.379044 CATGTGGGGCAAGGTCTCC 60.379 63.158 0.00 0.00 0.00 3.71
2097 2125 1.045407 TCAAGTACGCAGACCACCTT 58.955 50.000 0.00 0.00 0.00 3.50
2307 2335 2.290323 CGTCAGGAGGTTTGGAGGAAAT 60.290 50.000 0.00 0.00 0.00 2.17
2324 2352 6.114187 AGGAAATGGCGTCAAGATATGATA 57.886 37.500 0.00 0.00 40.97 2.15
2329 2357 6.732531 ATGGCGTCAAGATATGATAATGTG 57.267 37.500 0.00 0.00 40.97 3.21
2355 2384 1.586028 ATTGTGTGACAATGCCGGC 59.414 52.632 22.73 22.73 46.18 6.13
2509 2549 8.668353 GTTCTTGTACATGCTATCTTTGAATGA 58.332 33.333 0.00 0.00 0.00 2.57
2523 2563 3.688475 AATGAGCGCGCATGTTGGC 62.688 57.895 35.10 13.03 0.00 4.52
2543 2583 1.684983 CCTAGCCCATTTGCTTGATGG 59.315 52.381 6.59 6.59 42.75 3.51
2559 2616 0.043334 ATGGTCTACAGTGGGAGCCT 59.957 55.000 12.64 3.40 0.00 4.58
2560 2617 0.614979 TGGTCTACAGTGGGAGCCTC 60.615 60.000 12.64 0.00 0.00 4.70
2564 2621 0.467384 CTACAGTGGGAGCCTCATGG 59.533 60.000 0.00 0.00 0.00 3.66
2567 2624 1.229625 AGTGGGAGCCTCATGGTGA 60.230 57.895 0.00 0.00 35.27 4.02
2569 2626 2.191641 GGGAGCCTCATGGTGAGC 59.808 66.667 1.46 0.00 42.98 4.26
2572 2629 0.034670 GGAGCCTCATGGTGAGCTTT 60.035 55.000 1.46 0.00 42.98 3.51
2575 2632 2.169352 GAGCCTCATGGTGAGCTTTCTA 59.831 50.000 1.46 0.00 42.98 2.10
2582 2639 2.244695 TGGTGAGCTTTCTACGAGGAA 58.755 47.619 0.00 0.00 0.00 3.36
2596 2653 3.665190 ACGAGGAAACCAAGAAGATGAC 58.335 45.455 0.00 0.00 0.00 3.06
2610 2674 7.413877 CCAAGAAGATGACTAGAGATTTTGTGC 60.414 40.741 0.00 0.00 0.00 4.57
2714 2778 2.420022 CCTTCTTTTACCTGATGTGCCG 59.580 50.000 0.00 0.00 0.00 5.69
2747 2811 2.119457 CTTGAAACACGAGGCAAAAGC 58.881 47.619 0.00 0.00 0.00 3.51
2753 2817 0.031178 CACGAGGCAAAAGCTTTGCT 59.969 50.000 23.53 14.58 44.36 3.91
2769 2833 8.452989 AAGCTTTGCTCGTTTCATTAATTAAG 57.547 30.769 3.94 0.00 38.25 1.85
2776 2840 9.214957 TGCTCGTTTCATTAATTAAGAAGAAGA 57.785 29.630 3.94 7.33 0.00 2.87
2819 2883 4.932268 TCGGGTGAAAATCGATACAAAC 57.068 40.909 0.00 0.00 0.00 2.93
2840 2904 4.660938 GCCAAGCCCCCACTCGTT 62.661 66.667 0.00 0.00 0.00 3.85
2846 2910 0.907704 AGCCCCCACTCGTTACATGA 60.908 55.000 0.00 0.00 0.00 3.07
2847 2911 0.035820 GCCCCCACTCGTTACATGAA 60.036 55.000 0.00 0.00 0.00 2.57
2856 2920 4.072131 ACTCGTTACATGAACAAGCCAAT 58.928 39.130 0.00 0.00 37.99 3.16
2857 2921 4.083324 ACTCGTTACATGAACAAGCCAATG 60.083 41.667 0.00 0.00 37.99 2.82
2866 2931 1.231221 ACAAGCCAATGCGTTTCGTA 58.769 45.000 0.00 0.00 44.33 3.43
2878 2943 0.237498 GTTTCGTAGCACCACAAGGC 59.763 55.000 0.00 0.00 39.06 4.35
2885 2950 2.123939 CACCACAAGGCCACACCA 60.124 61.111 5.01 0.00 43.14 4.17
2904 2969 1.917303 CAAAACTTGCCAACGACACAC 59.083 47.619 0.00 0.00 0.00 3.82
2918 2984 2.290367 CGACACACCACAAACATCACAT 59.710 45.455 0.00 0.00 0.00 3.21
2932 2998 2.078849 TCACATGAGCACACTAACCG 57.921 50.000 0.00 0.00 0.00 4.44
2973 3039 2.171341 GGTTGCCGAAGAGAAGAAGT 57.829 50.000 0.00 0.00 0.00 3.01
2975 3041 1.721926 GTTGCCGAAGAGAAGAAGTCG 59.278 52.381 0.00 0.00 0.00 4.18
2989 3055 4.112341 GTCGCGACTGCTACGGGT 62.112 66.667 31.12 0.00 42.58 5.28
3015 3081 1.457831 ACCCGGGACTCTCCTATGC 60.458 63.158 32.02 0.00 36.57 3.14
3024 3090 1.381191 TCTCCTATGCGCCACAGGA 60.381 57.895 17.67 17.67 36.97 3.86
3059 3192 2.195727 TCATGCCTGATGTAACCCAGA 58.804 47.619 0.00 0.00 33.29 3.86
3093 3227 2.110753 AGAGCTCCCTTTATCCTCCC 57.889 55.000 10.93 0.00 0.00 4.30
3134 3269 1.884579 AGCAACATCTGGCAGTTGAAG 59.115 47.619 27.55 19.80 46.01 3.02
3136 3271 2.035066 GCAACATCTGGCAGTTGAAGTT 59.965 45.455 27.55 16.39 46.01 2.66
3231 3366 7.231317 ACATACATGTTCTCCTTTGTCAAACAT 59.769 33.333 2.30 0.00 40.25 2.71
3301 3437 1.414181 AGTGACAGTGACTCCTGTTGG 59.586 52.381 0.00 0.00 45.46 3.77
3304 3440 2.628178 TGACAGTGACTCCTGTTGGTAG 59.372 50.000 0.00 0.00 45.46 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.804151 GTAAATGTGTGCCTCTTGCGA 59.196 47.619 0.00 0.00 45.60 5.10
64 65 4.759693 TCGTGCTCCATGAAAAGTAAATGT 59.240 37.500 0.00 0.00 0.00 2.71
74 75 4.582701 AAACAAATTCGTGCTCCATGAA 57.417 36.364 0.00 2.70 42.45 2.57
80 81 1.896193 CGCGTAAACAAATTCGTGCTC 59.104 47.619 0.00 0.00 0.00 4.26
109 110 0.392193 CCTTTCTGAGAGGCACGCAT 60.392 55.000 0.78 0.00 0.00 4.73
110 111 1.004560 CCTTTCTGAGAGGCACGCA 60.005 57.895 0.78 0.00 0.00 5.24
113 114 0.693049 TTCCCCTTTCTGAGAGGCAC 59.307 55.000 8.69 0.00 32.74 5.01
116 117 2.373502 AGTGTTTCCCCTTTCTGAGAGG 59.626 50.000 7.26 7.26 0.00 3.69
122 123 4.775253 TGAAAACAAGTGTTTCCCCTTTCT 59.225 37.500 9.73 0.00 46.47 2.52
137 138 6.315891 CCTCTTGGAAGCAAATTTGAAAACAA 59.684 34.615 22.31 17.18 34.57 2.83
142 143 3.387374 TGCCTCTTGGAAGCAAATTTGAA 59.613 39.130 22.31 5.78 32.56 2.69
144 145 3.389925 TGCCTCTTGGAAGCAAATTTG 57.610 42.857 14.03 14.03 32.56 2.32
146 147 3.167485 TCATGCCTCTTGGAAGCAAATT 58.833 40.909 0.00 0.00 40.46 1.82
354 357 2.420466 ATTTTCGCCGTTGGGTCCCT 62.420 55.000 10.00 0.00 34.97 4.20
362 365 0.664166 CTTGCAGCATTTTCGCCGTT 60.664 50.000 0.00 0.00 0.00 4.44
377 380 3.764885 AACCATGCGACTAAATCTTGC 57.235 42.857 0.00 0.00 0.00 4.01
411 414 7.979537 GCCTTCCCAGATTCGTTTATTTAAAAT 59.020 33.333 0.00 0.00 0.00 1.82
416 419 3.377172 CGCCTTCCCAGATTCGTTTATTT 59.623 43.478 0.00 0.00 0.00 1.40
456 459 9.436957 TTCCAAATCAGTAATTGAGAAGTACTC 57.563 33.333 0.00 0.00 40.00 2.59
463 466 6.813649 CGTCTCTTCCAAATCAGTAATTGAGA 59.186 38.462 0.00 0.00 39.68 3.27
472 475 2.770164 ACCCGTCTCTTCCAAATCAG 57.230 50.000 0.00 0.00 0.00 2.90
488 491 4.564110 GCACGGCCCATCCTACCC 62.564 72.222 0.00 0.00 0.00 3.69
490 493 2.109181 GAGCACGGCCCATCCTAC 59.891 66.667 0.00 0.00 0.00 3.18
531 534 3.705638 CGCTGGTGCTGTGACACG 61.706 66.667 0.22 0.00 41.65 4.49
568 571 0.947180 GAACCGGTCAAGCGCAGTAA 60.947 55.000 8.04 0.00 0.00 2.24
685 689 2.671070 CGCCTCCATGTGGAAGGT 59.329 61.111 14.75 0.00 44.91 3.50
741 745 0.909133 TATGCTGTGGCCTGTGGAGA 60.909 55.000 3.32 0.00 37.74 3.71
799 807 4.980903 GTTGGCAGTTGGCGTGCG 62.981 66.667 1.08 0.00 46.16 5.34
843 851 2.681591 GGGTGAAGGGGCCTAACC 59.318 66.667 0.84 6.21 34.18 2.85
876 884 2.224967 GGGAAGGATGGATGGATGGAAG 60.225 54.545 0.00 0.00 0.00 3.46
877 885 1.782752 GGGAAGGATGGATGGATGGAA 59.217 52.381 0.00 0.00 0.00 3.53
886 894 2.989639 CGTGCTGGGAAGGATGGA 59.010 61.111 0.00 0.00 0.00 3.41
887 895 2.825836 GCGTGCTGGGAAGGATGG 60.826 66.667 0.00 0.00 0.00 3.51
903 911 3.270839 GCTCGATCAGCTGGCTGC 61.271 66.667 15.13 8.47 45.83 5.25
917 925 1.540435 GGGGAGGGATCGATGAGCTC 61.540 65.000 6.82 6.82 0.00 4.09
918 926 1.535202 GGGGAGGGATCGATGAGCT 60.535 63.158 0.54 0.00 0.00 4.09
919 927 2.588201 GGGGGAGGGATCGATGAGC 61.588 68.421 0.54 0.00 0.00 4.26
920 928 0.902516 GAGGGGGAGGGATCGATGAG 60.903 65.000 0.54 0.00 0.00 2.90
921 929 1.156330 GAGGGGGAGGGATCGATGA 59.844 63.158 0.54 0.00 0.00 2.92
922 930 1.915769 GGAGGGGGAGGGATCGATG 60.916 68.421 0.54 0.00 0.00 3.84
923 931 2.100525 GAGGAGGGGGAGGGATCGAT 62.101 65.000 0.00 0.00 0.00 3.59
924 932 2.704198 AGGAGGGGGAGGGATCGA 60.704 66.667 0.00 0.00 0.00 3.59
925 933 2.203714 GAGGAGGGGGAGGGATCG 60.204 72.222 0.00 0.00 0.00 3.69
926 934 2.205749 GGAGGAGGGGGAGGGATC 59.794 72.222 0.00 0.00 0.00 3.36
927 935 2.289979 AGGAGGAGGGGGAGGGAT 60.290 66.667 0.00 0.00 0.00 3.85
928 936 3.036959 GAGGAGGAGGGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
929 937 4.179599 GGAGGAGGAGGGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
930 938 3.039526 AGGAGGAGGAGGGGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
931 939 2.612251 GAGGAGGAGGAGGGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
932 940 3.036959 GGAGGAGGAGGAGGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
933 941 3.039526 AGGAGGAGGAGGAGGGGG 61.040 72.222 0.00 0.00 0.00 5.40
934 942 2.612251 GAGGAGGAGGAGGAGGGG 59.388 72.222 0.00 0.00 0.00 4.79
935 943 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
936 944 0.998945 AGAGGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
937 945 0.185901 CAGAGGAGGAGGAGGAGGAG 59.814 65.000 0.00 0.00 0.00 3.69
938 946 0.553862 ACAGAGGAGGAGGAGGAGGA 60.554 60.000 0.00 0.00 0.00 3.71
939 947 0.338120 AACAGAGGAGGAGGAGGAGG 59.662 60.000 0.00 0.00 0.00 4.30
940 948 3.390175 TTAACAGAGGAGGAGGAGGAG 57.610 52.381 0.00 0.00 0.00 3.69
941 949 3.181410 TGTTTAACAGAGGAGGAGGAGGA 60.181 47.826 0.00 0.00 0.00 3.71
942 950 3.173965 TGTTTAACAGAGGAGGAGGAGG 58.826 50.000 0.00 0.00 0.00 4.30
958 966 0.249531 TCTCGGTGCAACGCTGTTTA 60.250 50.000 21.87 0.00 38.12 2.01
959 967 1.498865 CTCTCGGTGCAACGCTGTTT 61.499 55.000 21.87 0.00 38.12 2.83
962 970 2.049156 TCTCTCGGTGCAACGCTG 60.049 61.111 21.87 14.97 38.12 5.18
963 971 2.259818 CTCTCTCGGTGCAACGCT 59.740 61.111 21.87 0.00 38.12 5.07
964 972 2.089349 GTCTCTCTCGGTGCAACGC 61.089 63.158 21.87 0.00 38.12 4.84
965 973 0.730834 CTGTCTCTCTCGGTGCAACG 60.731 60.000 20.47 20.47 38.12 4.10
971 979 2.506231 TCTGGTATCTGTCTCTCTCGGT 59.494 50.000 0.00 0.00 0.00 4.69
977 985 1.064314 ACGCCTCTGGTATCTGTCTCT 60.064 52.381 0.00 0.00 0.00 3.10
978 986 1.335496 GACGCCTCTGGTATCTGTCTC 59.665 57.143 0.00 0.00 0.00 3.36
982 990 1.043816 ATGGACGCCTCTGGTATCTG 58.956 55.000 0.00 0.00 0.00 2.90
983 991 1.043816 CATGGACGCCTCTGGTATCT 58.956 55.000 0.00 0.00 0.00 1.98
984 992 0.034059 CCATGGACGCCTCTGGTATC 59.966 60.000 5.56 0.00 0.00 2.24
985 993 1.410850 CCCATGGACGCCTCTGGTAT 61.411 60.000 15.22 0.00 0.00 2.73
986 994 2.063979 CCCATGGACGCCTCTGGTA 61.064 63.158 15.22 0.00 0.00 3.25
987 995 3.402681 CCCATGGACGCCTCTGGT 61.403 66.667 15.22 0.00 0.00 4.00
988 996 4.864334 GCCCATGGACGCCTCTGG 62.864 72.222 15.22 0.00 0.00 3.86
990 998 3.474570 GAGCCCATGGACGCCTCT 61.475 66.667 15.22 0.00 0.00 3.69
991 999 4.554036 GGAGCCCATGGACGCCTC 62.554 72.222 15.22 12.53 0.00 4.70
1108 1136 2.299521 GTAGCTGTAGATCCTCCACGT 58.700 52.381 0.00 0.00 0.00 4.49
1470 1498 4.885270 CCAACGGCCACACCCACA 62.885 66.667 2.24 0.00 33.26 4.17
1503 1531 3.157949 TCGTGGTGGAGGTGCACA 61.158 61.111 20.43 0.00 0.00 4.57
1545 1573 1.885871 GTTGCTGGCCTTGATGTCC 59.114 57.895 3.32 0.00 0.00 4.02
1716 1744 1.773496 GAAGCTGTACACGTCGCAC 59.227 57.895 7.48 0.00 0.00 5.34
2097 2125 0.738975 CGCTGTTCTCCGTCTCCATA 59.261 55.000 0.00 0.00 0.00 2.74
2147 2175 0.747283 GGCCTCCTTCTCGTCGTCTA 60.747 60.000 0.00 0.00 0.00 2.59
2307 2335 4.452114 GCACATTATCATATCTTGACGCCA 59.548 41.667 0.00 0.00 37.11 5.69
2324 2352 7.686438 TTGTCACACAATAGAATAGCACATT 57.314 32.000 0.00 0.00 32.34 2.71
2329 2357 5.514279 GGCATTGTCACACAATAGAATAGC 58.486 41.667 1.60 1.09 46.22 2.97
2509 2549 4.776322 TAGGCCAACATGCGCGCT 62.776 61.111 33.29 15.19 0.00 5.92
2523 2563 1.684983 CCATCAAGCAAATGGGCTAGG 59.315 52.381 4.54 0.00 45.07 3.02
2543 2583 1.137872 CATGAGGCTCCCACTGTAGAC 59.862 57.143 12.86 0.00 0.00 2.59
2559 2616 2.166459 CCTCGTAGAAAGCTCACCATGA 59.834 50.000 0.00 0.00 34.09 3.07
2560 2617 2.166459 TCCTCGTAGAAAGCTCACCATG 59.834 50.000 0.00 0.00 34.09 3.66
2564 2621 2.994578 GGTTTCCTCGTAGAAAGCTCAC 59.005 50.000 18.33 3.81 46.03 3.51
2569 2626 5.539048 TCTTCTTGGTTTCCTCGTAGAAAG 58.461 41.667 3.41 0.00 36.45 2.62
2572 2629 4.770531 TCATCTTCTTGGTTTCCTCGTAGA 59.229 41.667 0.00 0.00 0.00 2.59
2575 2632 3.325135 AGTCATCTTCTTGGTTTCCTCGT 59.675 43.478 0.00 0.00 0.00 4.18
2582 2639 8.160106 ACAAAATCTCTAGTCATCTTCTTGGTT 58.840 33.333 0.00 0.00 0.00 3.67
2610 2674 0.244450 ATTTTGGTCACGCAGCATGG 59.756 50.000 0.00 0.00 35.86 3.66
2675 2739 4.017037 AGAAGGAAGTCTCCATGGACTCTA 60.017 45.833 11.44 0.00 44.67 2.43
2682 2746 5.645497 CAGGTAAAAGAAGGAAGTCTCCATG 59.355 44.000 0.00 0.00 45.24 3.66
2721 2785 3.275143 TGCCTCGTGTTTCAAGAGAAAA 58.725 40.909 12.63 0.00 44.75 2.29
2747 2811 9.825972 TCTTCTTAATTAATGAAACGAGCAAAG 57.174 29.630 0.00 0.00 0.00 2.77
2776 2840 7.706179 CCCGATTTTCATAATTAACTGTGCAAT 59.294 33.333 0.00 0.00 0.00 3.56
2781 2845 7.931578 TCACCCGATTTTCATAATTAACTGT 57.068 32.000 0.00 0.00 0.00 3.55
2798 2862 3.368539 CGTTTGTATCGATTTTCACCCGA 59.631 43.478 1.71 0.00 36.72 5.14
2809 2873 0.391927 CTTGGCCCCGTTTGTATCGA 60.392 55.000 0.00 0.00 0.00 3.59
2840 2904 2.158559 ACGCATTGGCTTGTTCATGTA 58.841 42.857 0.00 0.00 38.10 2.29
2846 2910 0.383949 ACGAAACGCATTGGCTTGTT 59.616 45.000 0.00 0.00 38.10 2.83
2847 2911 1.196808 CTACGAAACGCATTGGCTTGT 59.803 47.619 0.00 0.00 38.10 3.16
2856 2920 0.810426 TTGTGGTGCTACGAAACGCA 60.810 50.000 0.00 0.00 0.00 5.24
2857 2921 0.110823 CTTGTGGTGCTACGAAACGC 60.111 55.000 0.00 0.00 0.00 4.84
2866 2931 2.519302 GTGTGGCCTTGTGGTGCT 60.519 61.111 3.32 0.00 35.27 4.40
2878 2943 1.650825 GTTGGCAAGTTTTGGTGTGG 58.349 50.000 0.00 0.00 0.00 4.17
2885 2950 1.135228 GGTGTGTCGTTGGCAAGTTTT 60.135 47.619 0.00 0.00 0.00 2.43
2904 2969 2.293955 TGTGCTCATGTGATGTTTGTGG 59.706 45.455 0.00 0.00 0.00 4.17
2918 2984 1.663388 CGTGCGGTTAGTGTGCTCA 60.663 57.895 0.00 0.00 0.00 4.26
2932 2998 3.702555 GTCGGTCTGTGTGCGTGC 61.703 66.667 0.00 0.00 0.00 5.34
2973 3039 4.111016 CACCCGTAGCAGTCGCGA 62.111 66.667 3.71 3.71 45.49 5.87
2975 3041 3.701604 CTCCACCCGTAGCAGTCGC 62.702 68.421 0.00 0.00 38.99 5.19
2989 3055 4.316823 AGTCCCGGGTCTGCTCCA 62.317 66.667 22.86 0.00 0.00 3.86
3015 3081 2.030007 ACATGTTTCAAATCCTGTGGCG 60.030 45.455 0.00 0.00 0.00 5.69
3124 3259 0.389025 CACCCCAAACTTCAACTGCC 59.611 55.000 0.00 0.00 0.00 4.85
3134 3269 2.878089 AAATGGCGGCACCCCAAAC 61.878 57.895 16.34 0.00 37.83 2.93
3136 3271 2.715181 TACAAATGGCGGCACCCCAA 62.715 55.000 16.34 0.00 37.83 4.12


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

AutoCloner maintained by Alex Coulton.