Multiple sequence alignment - TraesCS4A01G138100

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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 TraesCS4A01G138100 chr4A 100.000 3170 0 0 1 3170 202223267 202220098 0.000000e+00 5854.0
1 TraesCS4A01G138100 chr4A 90.144 832 76 3 1 832 106365606 106366431 0.000000e+00 1077.0
2 TraesCS4A01G138100 chr4A 89.474 57 6 0 2690 2746 37805054 37805110 4.390000e-09 73.1
3 TraesCS4A01G138100 chr4D 97.066 1295 32 4 936 2227 259155518 259156809 0.000000e+00 2176.0
4 TraesCS4A01G138100 chr4D 92.063 189 9 3 2643 2828 259157531 259157716 8.720000e-66 261.0
5 TraesCS4A01G138100 chr4D 99.194 124 1 0 2449 2572 259157408 259157531 1.140000e-54 224.0
6 TraesCS4A01G138100 chr4D 93.333 150 6 1 2244 2389 259156796 259156945 5.320000e-53 219.0
7 TraesCS4A01G138100 chr4D 91.011 89 8 0 3082 3170 259158124 259158212 1.540000e-23 121.0
8 TraesCS4A01G138100 chr4D 95.890 73 3 0 2830 2902 259157955 259158027 5.550000e-23 119.0
9 TraesCS4A01G138100 chr4D 97.561 41 1 0 2706 2746 53760120 53760080 1.580000e-08 71.3
10 TraesCS4A01G138100 chr4B 95.277 1334 51 5 889 2216 310166312 310164985 0.000000e+00 2104.0
11 TraesCS4A01G138100 chr4B 92.778 360 17 4 2448 2803 310164695 310164341 2.180000e-141 512.0
12 TraesCS4A01G138100 chr4B 94.156 154 5 1 2250 2399 310164987 310164834 6.840000e-57 231.0
13 TraesCS4A01G138100 chr4B 86.154 65 7 1 2690 2754 526929260 526929322 5.670000e-08 69.4
14 TraesCS4A01G138100 chr6A 90.056 895 75 9 1 895 505352509 505353389 0.000000e+00 1147.0
15 TraesCS4A01G138100 chr2A 89.521 897 78 10 1 895 734514010 734514892 0.000000e+00 1122.0
16 TraesCS4A01G138100 chr2A 89.085 907 77 11 2 896 78503551 78502655 0.000000e+00 1107.0
17 TraesCS4A01G138100 chr2A 88.058 829 74 10 75 881 232414814 232415639 0.000000e+00 959.0
18 TraesCS4A01G138100 chr2A 87.963 324 37 2 1214 1536 99788562 99788240 6.420000e-102 381.0
19 TraesCS4A01G138100 chr3A 89.049 904 87 6 1 898 737794086 737793189 0.000000e+00 1110.0
20 TraesCS4A01G138100 chr3A 87.832 904 71 22 1 895 711370111 711369238 0.000000e+00 1024.0
21 TraesCS4A01G138100 chr3A 89.855 69 6 1 2679 2746 724371530 724371598 1.570000e-13 87.9
22 TraesCS4A01G138100 chr1A 88.398 905 93 8 1 898 341156863 341157762 0.000000e+00 1079.0
23 TraesCS4A01G138100 chr1A 88.737 879 84 5 1 869 551882731 551881858 0.000000e+00 1061.0
24 TraesCS4A01G138100 chr5A 89.043 867 69 14 51 897 589022667 589021807 0.000000e+00 1051.0
25 TraesCS4A01G138100 chr5A 86.364 66 8 1 2681 2745 613478060 613478125 1.580000e-08 71.3
26 TraesCS4A01G138100 chr7D 90.212 756 51 14 17 762 244448466 244449208 0.000000e+00 965.0
27 TraesCS4A01G138100 chr2D 88.272 324 36 2 1214 1536 100185660 100185338 1.380000e-103 387.0
28 TraesCS4A01G138100 chr2B 88.272 324 36 2 1214 1536 151904232 151903910 1.380000e-103 387.0
29 TraesCS4A01G138100 chr3D 91.429 70 5 1 2679 2747 593106479 593106548 9.360000e-16 95.3
30 TraesCS4A01G138100 chr5B 85.714 70 9 1 2681 2749 605786421 605786490 4.390000e-09 73.1
31 TraesCS4A01G138100 chr1B 100.000 28 0 0 2801 2828 678247814 678247841 6.000000e-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 TraesCS4A01G138100 chr4A 202220098 202223267 3169 True 5854 5854 100.000000 1 3170 1 chr4A.!!$R1 3169
1 TraesCS4A01G138100 chr4A 106365606 106366431 825 False 1077 1077 90.144000 1 832 1 chr4A.!!$F2 831
2 TraesCS4A01G138100 chr4D 259155518 259158212 2694 False 520 2176 94.759500 936 3170 6 chr4D.!!$F1 2234
3 TraesCS4A01G138100 chr4B 310164341 310166312 1971 True 949 2104 94.070333 889 2803 3 chr4B.!!$R1 1914
4 TraesCS4A01G138100 chr6A 505352509 505353389 880 False 1147 1147 90.056000 1 895 1 chr6A.!!$F1 894
5 TraesCS4A01G138100 chr2A 734514010 734514892 882 False 1122 1122 89.521000 1 895 1 chr2A.!!$F2 894
6 TraesCS4A01G138100 chr2A 78502655 78503551 896 True 1107 1107 89.085000 2 896 1 chr2A.!!$R1 894
7 TraesCS4A01G138100 chr2A 232414814 232415639 825 False 959 959 88.058000 75 881 1 chr2A.!!$F1 806
8 TraesCS4A01G138100 chr3A 737793189 737794086 897 True 1110 1110 89.049000 1 898 1 chr3A.!!$R2 897
9 TraesCS4A01G138100 chr3A 711369238 711370111 873 True 1024 1024 87.832000 1 895 1 chr3A.!!$R1 894
10 TraesCS4A01G138100 chr1A 341156863 341157762 899 False 1079 1079 88.398000 1 898 1 chr1A.!!$F1 897
11 TraesCS4A01G138100 chr1A 551881858 551882731 873 True 1061 1061 88.737000 1 869 1 chr1A.!!$R1 868
12 TraesCS4A01G138100 chr5A 589021807 589022667 860 True 1051 1051 89.043000 51 897 1 chr5A.!!$R1 846
13 TraesCS4A01G138100 chr7D 244448466 244449208 742 False 965 965 90.212000 17 762 1 chr7D.!!$F1 745

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
832 936 0.111617 CGTCTTCAACGCGCGTTTTA 60.112 50.0 42.41 30.54 45.76 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2435 2909 0.902984 ATGGCTGGGACGTCTACACA 60.903 55.0 16.46 10.34 0.0 3.72 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
27 28 4.779733 TCCCTGCCGTCCCTCTCC 62.780 72.222 0.00 0.00 0.00 3.71
96 97 3.677284 CTCCTCCTCGTCCGGTCGA 62.677 68.421 22.09 22.09 38.19 4.20
113 114 1.228184 GATCGACCGGCTCTCCCTA 60.228 63.158 0.00 0.00 0.00 3.53
236 292 4.194720 GCGCCTCATCCTCGTCGT 62.195 66.667 0.00 0.00 0.00 4.34
258 314 1.376037 CAAACCGGAGCCCAGTCTC 60.376 63.158 9.46 0.00 0.00 3.36
284 340 2.572209 GGAGTACGAGGAGATAGCCT 57.428 55.000 0.00 0.00 42.17 4.58
574 656 1.198637 GACTACACGCGGTTCTACAGT 59.801 52.381 12.47 5.47 0.00 3.55
595 677 1.478510 CTCCTCGGCATGTAGAACTGT 59.521 52.381 0.00 0.00 0.00 3.55
599 681 3.130516 CCTCGGCATGTAGAACTGTAAGA 59.869 47.826 0.00 0.00 37.43 2.10
708 812 0.246910 TATGAGCGGGCGTGTTTGTA 59.753 50.000 0.00 0.00 0.00 2.41
710 814 1.666872 GAGCGGGCGTGTTTGTACT 60.667 57.895 0.00 0.00 0.00 2.73
767 871 0.793861 GCATGAACTCGCCGTGTTTA 59.206 50.000 5.98 2.44 0.00 2.01
798 902 3.870633 AAAAATTTTATGGGCGCCGTA 57.129 38.095 22.54 12.99 0.00 4.02
817 921 0.615331 AACTGGATGGCATCACGTCT 59.385 50.000 27.39 11.71 0.00 4.18
832 936 0.111617 CGTCTTCAACGCGCGTTTTA 60.112 50.000 42.41 30.54 45.76 1.52
842 946 0.994263 GCGCGTTTTACATCGGTACT 59.006 50.000 8.43 0.00 0.00 2.73
883 992 1.450312 CTCATGGAGGCCAACGACC 60.450 63.158 5.01 0.35 36.95 4.79
898 1007 0.317103 CGACCGGAGATGCTCTTACG 60.317 60.000 9.46 0.00 0.00 3.18
899 1008 0.739561 GACCGGAGATGCTCTTACGT 59.260 55.000 9.46 0.00 0.00 3.57
902 1011 1.405821 CCGGAGATGCTCTTACGTTCT 59.594 52.381 0.00 0.00 0.00 3.01
904 1013 2.854777 CGGAGATGCTCTTACGTTCTTG 59.145 50.000 0.00 0.00 0.00 3.02
923 1032 1.336440 TGGCACAAATCCAGAAACACG 59.664 47.619 0.00 0.00 31.92 4.49
944 1053 0.462047 GGTGCGATGACTAACCAGGG 60.462 60.000 0.00 0.00 32.69 4.45
951 1060 1.327690 TGACTAACCAGGGCCGCTAG 61.328 60.000 0.00 0.20 0.00 3.42
1136 1252 1.407258 GGGGACTCTGAAGACATCGAG 59.593 57.143 0.00 0.00 35.88 4.04
1160 1276 2.423373 CCCAGTCGATCCAATTCCCAAT 60.423 50.000 0.00 0.00 0.00 3.16
1171 1287 3.560105 CAATTCCCAATCCTCCCTTCTC 58.440 50.000 0.00 0.00 0.00 2.87
1172 1288 1.596496 TTCCCAATCCTCCCTTCTCC 58.404 55.000 0.00 0.00 0.00 3.71
1173 1289 0.725133 TCCCAATCCTCCCTTCTCCT 59.275 55.000 0.00 0.00 0.00 3.69
1262 1378 1.465200 GGCTATGGACGGAGGAGGAC 61.465 65.000 0.00 0.00 0.00 3.85
1367 1483 2.515290 TACGAGGAGATGCGCCGA 60.515 61.111 4.18 0.00 0.00 5.54
1600 1716 3.487202 CGACGCCACAATCACCGG 61.487 66.667 0.00 0.00 0.00 5.28
1778 1894 0.677731 TGCCGGCATTCTTTCCTCAG 60.678 55.000 29.03 0.00 0.00 3.35
1941 2057 2.743928 GGGAGCAACCGTCTGCAG 60.744 66.667 7.63 7.63 45.18 4.41
1979 2095 0.178891 AGGGAGAGAAGTGGAGGCAA 60.179 55.000 0.00 0.00 0.00 4.52
2078 2194 0.889638 TAAAATCCACGCCGCCAACA 60.890 50.000 0.00 0.00 0.00 3.33
2338 2459 6.319405 AGTTAATTTACGTGGTTCAGGTTGTT 59.681 34.615 0.00 0.00 34.30 2.83
2389 2510 5.123344 AGCTGTTTTTCTCGTGTTACTGTTT 59.877 36.000 0.00 0.00 0.00 2.83
2391 2512 6.307077 GCTGTTTTTCTCGTGTTACTGTTTTT 59.693 34.615 0.00 0.00 0.00 1.94
2562 3086 9.739276 CAGGAAGGCAAAATATATACTCCAATA 57.261 33.333 0.00 0.00 0.00 1.90
2605 3129 5.243954 TGCGTATAATGATAAGCTGAGGAGT 59.756 40.000 9.14 0.00 41.85 3.85
2607 3131 6.970043 GCGTATAATGATAAGCTGAGGAGTAG 59.030 42.308 1.00 0.00 39.23 2.57
2608 3132 7.362229 GCGTATAATGATAAGCTGAGGAGTAGT 60.362 40.741 1.00 0.00 39.23 2.73
2609 3133 9.163899 CGTATAATGATAAGCTGAGGAGTAGTA 57.836 37.037 0.00 0.00 0.00 1.82
2611 3135 8.941995 ATAATGATAAGCTGAGGAGTAGTACA 57.058 34.615 2.52 0.00 0.00 2.90
2612 3136 7.847711 AATGATAAGCTGAGGAGTAGTACAT 57.152 36.000 2.52 0.00 0.00 2.29
2613 3137 8.941995 AATGATAAGCTGAGGAGTAGTACATA 57.058 34.615 2.52 0.00 0.00 2.29
2614 3138 7.747155 TGATAAGCTGAGGAGTAGTACATAC 57.253 40.000 2.52 0.00 34.30 2.39
2615 3139 6.427242 TGATAAGCTGAGGAGTAGTACATACG 59.573 42.308 2.52 0.00 39.55 3.06
2616 3140 4.153673 AGCTGAGGAGTAGTACATACGT 57.846 45.455 2.52 0.00 39.55 3.57
2623 3147 6.207221 TGAGGAGTAGTACATACGTGACAAAA 59.793 38.462 0.00 0.00 39.55 2.44
2696 3220 6.719370 TCCAAGTTTGCTAACAAATATCACCT 59.281 34.615 13.46 0.00 46.93 4.00
2697 3221 7.232534 TCCAAGTTTGCTAACAAATATCACCTT 59.767 33.333 13.46 0.00 46.93 3.50
2698 3222 7.329226 CCAAGTTTGCTAACAAATATCACCTTG 59.671 37.037 13.46 9.01 46.93 3.61
2699 3223 6.924111 AGTTTGCTAACAAATATCACCTTGG 58.076 36.000 13.46 0.00 46.93 3.61
2701 3225 6.909550 TTGCTAACAAATATCACCTTGGTT 57.090 33.333 0.00 0.00 31.21 3.67
2722 3249 9.703892 TTGGTTGTGAATTATAAGATGTTTTGG 57.296 29.630 0.00 0.00 0.00 3.28
2893 3657 0.320771 TCCAAAGCGAACTCAGAGCC 60.321 55.000 0.00 0.00 0.00 4.70
2898 3662 1.375268 GCGAACTCAGAGCCAGCTT 60.375 57.895 0.00 0.00 0.00 3.74
2902 3666 2.006169 GAACTCAGAGCCAGCTTTAGC 58.994 52.381 0.00 0.00 42.49 3.09
2908 3672 1.427592 GAGCCAGCTTTAGCGCTCTG 61.428 60.000 16.34 15.51 45.09 3.35
2912 3676 2.124942 GCTTTAGCGCTCTGGCCT 60.125 61.111 16.34 0.00 34.44 5.19
2913 3677 2.176926 GCTTTAGCGCTCTGGCCTC 61.177 63.158 16.34 0.00 34.44 4.70
2914 3678 1.880340 CTTTAGCGCTCTGGCCTCG 60.880 63.158 16.34 3.47 34.44 4.63
2915 3679 2.284798 CTTTAGCGCTCTGGCCTCGA 62.285 60.000 16.34 0.00 34.44 4.04
2916 3680 2.558554 TTTAGCGCTCTGGCCTCGAC 62.559 60.000 16.34 0.00 34.44 4.20
2919 3683 4.504916 CGCTCTGGCCTCGACCTG 62.505 72.222 3.32 0.00 34.44 4.00
2920 3684 4.154347 GCTCTGGCCTCGACCTGG 62.154 72.222 3.32 0.00 0.00 4.45
2921 3685 2.363018 CTCTGGCCTCGACCTGGA 60.363 66.667 3.32 0.00 0.00 3.86
2922 3686 2.680352 TCTGGCCTCGACCTGGAC 60.680 66.667 3.32 0.00 0.00 4.02
2923 3687 2.997315 CTGGCCTCGACCTGGACA 60.997 66.667 3.32 0.00 40.92 4.02
2924 3688 2.525629 TGGCCTCGACCTGGACAA 60.526 61.111 3.32 0.00 40.11 3.18
2925 3689 2.111999 CTGGCCTCGACCTGGACAAA 62.112 60.000 3.32 0.00 42.85 2.83
2926 3690 1.072505 GGCCTCGACCTGGACAAAA 59.927 57.895 0.00 0.00 31.53 2.44
2927 3691 1.235281 GGCCTCGACCTGGACAAAAC 61.235 60.000 0.00 0.00 31.53 2.43
2928 3692 0.534203 GCCTCGACCTGGACAAAACA 60.534 55.000 0.00 0.00 0.00 2.83
2929 3693 1.882352 GCCTCGACCTGGACAAAACAT 60.882 52.381 0.00 0.00 0.00 2.71
2930 3694 2.076863 CCTCGACCTGGACAAAACATC 58.923 52.381 0.00 0.00 0.00 3.06
2931 3695 2.289694 CCTCGACCTGGACAAAACATCT 60.290 50.000 0.00 0.00 0.00 2.90
2932 3696 3.403038 CTCGACCTGGACAAAACATCTT 58.597 45.455 0.00 0.00 0.00 2.40
2933 3697 4.562757 CCTCGACCTGGACAAAACATCTTA 60.563 45.833 0.00 0.00 0.00 2.10
2934 3698 4.566004 TCGACCTGGACAAAACATCTTAG 58.434 43.478 0.00 0.00 0.00 2.18
2935 3699 3.684788 CGACCTGGACAAAACATCTTAGG 59.315 47.826 0.00 0.00 0.00 2.69
2936 3700 3.421844 ACCTGGACAAAACATCTTAGGC 58.578 45.455 0.00 0.00 0.00 3.93
2937 3701 2.755103 CCTGGACAAAACATCTTAGGCC 59.245 50.000 0.00 0.00 0.00 5.19
2938 3702 3.420893 CTGGACAAAACATCTTAGGCCA 58.579 45.455 5.01 0.00 0.00 5.36
2939 3703 3.420893 TGGACAAAACATCTTAGGCCAG 58.579 45.455 5.01 0.00 0.00 4.85
2940 3704 3.181434 TGGACAAAACATCTTAGGCCAGT 60.181 43.478 5.01 0.00 0.00 4.00
2941 3705 3.826729 GGACAAAACATCTTAGGCCAGTT 59.173 43.478 5.01 0.00 0.00 3.16
2942 3706 4.082733 GGACAAAACATCTTAGGCCAGTTC 60.083 45.833 5.01 0.00 0.00 3.01
2943 3707 4.729868 ACAAAACATCTTAGGCCAGTTCT 58.270 39.130 5.01 0.00 0.00 3.01
2970 3734 2.292845 GCTGGCTTCTGGAATAAGATGC 59.707 50.000 4.07 4.07 43.26 3.91
2973 3737 3.220674 GCTTCTGGAATAAGATGCCCT 57.779 47.619 1.71 0.00 39.98 5.19
3024 3796 8.788325 TTATTCTCTTAAAAGCCTAGTGGTTC 57.212 34.615 0.00 0.00 32.32 3.62
3025 3797 5.161943 TCTCTTAAAAGCCTAGTGGTTCC 57.838 43.478 0.00 0.00 32.32 3.62
3026 3798 4.019591 TCTCTTAAAAGCCTAGTGGTTCCC 60.020 45.833 0.00 0.00 32.32 3.97
3027 3799 3.009805 TCTTAAAAGCCTAGTGGTTCCCC 59.990 47.826 0.00 0.00 32.32 4.81
3028 3800 0.037734 AAAAGCCTAGTGGTTCCCCG 59.962 55.000 0.00 0.00 32.32 5.73
3029 3801 2.479820 AAAGCCTAGTGGTTCCCCGC 62.480 60.000 0.00 0.00 41.87 6.13
3030 3802 3.712907 GCCTAGTGGTTCCCCGCA 61.713 66.667 0.00 0.00 44.14 5.69
3031 3803 3.074281 CCTAGTGGTTCCCCGCAA 58.926 61.111 0.00 0.00 44.14 4.85
3032 3804 1.377229 CCTAGTGGTTCCCCGCAAA 59.623 57.895 0.00 0.00 44.14 3.68
3033 3805 0.250989 CCTAGTGGTTCCCCGCAAAA 60.251 55.000 0.00 0.00 44.14 2.44
3034 3806 1.611519 CTAGTGGTTCCCCGCAAAAA 58.388 50.000 0.00 0.00 44.14 1.94
3077 3849 3.332706 TTTTTGGCGGGTCTAGTGG 57.667 52.632 0.00 0.00 0.00 4.00
3078 3850 0.475044 TTTTTGGCGGGTCTAGTGGT 59.525 50.000 0.00 0.00 0.00 4.16
3079 3851 0.475044 TTTTGGCGGGTCTAGTGGTT 59.525 50.000 0.00 0.00 0.00 3.67
3080 3852 1.350071 TTTGGCGGGTCTAGTGGTTA 58.650 50.000 0.00 0.00 0.00 2.85
3081 3853 1.350071 TTGGCGGGTCTAGTGGTTAA 58.650 50.000 0.00 0.00 0.00 2.01
3082 3854 1.350071 TGGCGGGTCTAGTGGTTAAA 58.650 50.000 0.00 0.00 0.00 1.52
3083 3855 1.276989 TGGCGGGTCTAGTGGTTAAAG 59.723 52.381 0.00 0.00 0.00 1.85
3084 3856 1.277273 GGCGGGTCTAGTGGTTAAAGT 59.723 52.381 0.00 0.00 0.00 2.66
3085 3857 2.289882 GGCGGGTCTAGTGGTTAAAGTT 60.290 50.000 0.00 0.00 0.00 2.66
3124 3896 8.950007 TTCTAGAAAGATAAATTTGGTTGGGT 57.050 30.769 1.68 0.00 0.00 4.51
3130 3902 9.549078 GAAAGATAAATTTGGTTGGGTTTACAA 57.451 29.630 0.00 0.00 0.00 2.41
3139 3911 5.848406 TGGTTGGGTTTACAAAATAAGCTG 58.152 37.500 0.00 0.00 31.17 4.24
3143 3915 4.525100 TGGGTTTACAAAATAAGCTGGGTC 59.475 41.667 0.00 0.00 0.00 4.46
3144 3916 4.081862 GGGTTTACAAAATAAGCTGGGTCC 60.082 45.833 0.00 0.00 0.00 4.46
3147 3919 1.102978 CAAAATAAGCTGGGTCCCGG 58.897 55.000 13.08 13.08 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 1.528776 GTAGGGAGAGCCGGTCGAT 60.529 63.158 1.90 0.00 33.83 3.59
365 421 1.828660 CGGCGATCTCCTACAGGGT 60.829 63.158 0.00 0.00 36.25 4.34
574 656 1.751351 CAGTTCTACATGCCGAGGAGA 59.249 52.381 0.00 0.00 0.00 3.71
708 812 3.020984 ACCAAATTCGACCAAACACAGT 58.979 40.909 0.00 0.00 0.00 3.55
710 814 4.082190 TCAAACCAAATTCGACCAAACACA 60.082 37.500 0.00 0.00 0.00 3.72
786 890 1.404479 ATCCAGTTACGGCGCCCATA 61.404 55.000 23.46 11.31 0.00 2.74
798 902 0.615331 AGACGTGATGCCATCCAGTT 59.385 50.000 1.49 0.00 0.00 3.16
817 921 1.718983 CGATGTAAAACGCGCGTTGAA 60.719 47.619 44.28 32.33 38.47 2.69
832 936 2.100989 GTCTCTGGGAAGTACCGATGT 58.899 52.381 0.00 0.00 40.11 3.06
842 946 3.259064 CGCTAAAAATCGTCTCTGGGAA 58.741 45.455 0.00 0.00 0.00 3.97
898 1007 4.051237 GTTTCTGGATTTGTGCCAAGAAC 58.949 43.478 0.00 0.00 34.44 3.01
899 1008 3.703556 TGTTTCTGGATTTGTGCCAAGAA 59.296 39.130 0.00 0.00 34.44 2.52
902 1011 2.223688 CGTGTTTCTGGATTTGTGCCAA 60.224 45.455 0.00 0.00 34.44 4.52
904 1013 1.335872 CCGTGTTTCTGGATTTGTGCC 60.336 52.381 0.00 0.00 0.00 5.01
913 1022 3.353836 CGCACCCCGTGTTTCTGG 61.354 66.667 0.00 0.00 35.75 3.86
914 1023 1.671054 ATCGCACCCCGTGTTTCTG 60.671 57.895 0.00 0.00 35.75 3.02
919 1028 1.537814 TTAGTCATCGCACCCCGTGT 61.538 55.000 0.00 0.00 35.75 4.49
920 1029 1.082117 GTTAGTCATCGCACCCCGTG 61.082 60.000 0.00 0.00 38.35 4.94
923 1032 0.462047 CTGGTTAGTCATCGCACCCC 60.462 60.000 0.00 0.00 0.00 4.95
975 1084 2.338620 GGTTGGGGTTTTCGCTGC 59.661 61.111 0.00 0.00 0.00 5.25
1136 1252 2.289565 GGAATTGGATCGACTGGGAAC 58.710 52.381 0.00 0.00 0.00 3.62
1160 1276 0.633921 CAGAGGAGGAGAAGGGAGGA 59.366 60.000 0.00 0.00 0.00 3.71
1171 1287 3.522731 CGACGGGAGCAGAGGAGG 61.523 72.222 0.00 0.00 0.00 4.30
1172 1288 4.200283 GCGACGGGAGCAGAGGAG 62.200 72.222 0.00 0.00 34.19 3.69
1262 1378 0.451299 CGCGTAGGATCACGATCTCG 60.451 60.000 9.56 10.00 44.69 4.04
1600 1716 3.271706 TTGGCTGCAGCATTCGTGC 62.272 57.895 37.63 20.06 44.36 5.34
1676 1792 2.047274 GCAGCCAAGTCAGCCGTA 60.047 61.111 0.00 0.00 0.00 4.02
1778 1894 2.125106 GCACCGTCCATGGAGACC 60.125 66.667 16.81 2.19 32.91 3.85
1924 2040 2.743928 CTGCAGACGGTTGCTCCC 60.744 66.667 8.42 0.00 44.38 4.30
1964 2080 1.622811 CTCTGTTGCCTCCACTTCTCT 59.377 52.381 0.00 0.00 0.00 3.10
1979 2095 1.202330 CCAGCTCCAGAATCCTCTGT 58.798 55.000 1.74 0.00 46.71 3.41
2078 2194 2.574006 ATAGCGGCCACAATCATCAT 57.426 45.000 2.24 0.00 0.00 2.45
2185 2302 2.678336 GACAAGGGCAATTCCTACGAAG 59.322 50.000 0.00 0.00 35.80 3.79
2247 2364 9.864034 GTCGCGCTGCAAATTTTATATATATAT 57.136 29.630 5.56 10.10 0.00 0.86
2257 2374 3.827524 CGTCGCGCTGCAAATTTT 58.172 50.000 5.56 0.00 0.00 1.82
2338 2459 5.872617 CCGACAGTCAGAACCACATAAATTA 59.127 40.000 0.41 0.00 0.00 1.40
2399 2520 6.630444 AACTCCATGCTTATTCATGATCAC 57.370 37.500 0.00 0.00 44.94 3.06
2401 2522 7.144000 GGAAAACTCCATGCTTATTCATGATC 58.856 38.462 0.00 0.00 44.94 2.92
2402 2523 6.608405 TGGAAAACTCCATGCTTATTCATGAT 59.392 34.615 0.00 0.00 44.94 2.45
2403 2524 5.951148 TGGAAAACTCCATGCTTATTCATGA 59.049 36.000 5.41 0.00 44.94 3.07
2404 2525 6.211587 TGGAAAACTCCATGCTTATTCATG 57.788 37.500 0.00 0.00 42.53 3.07
2435 2909 0.902984 ATGGCTGGGACGTCTACACA 60.903 55.000 16.46 10.34 0.00 3.72
2605 3129 7.780253 CGTAACTTTTGTCACGTATGTACTA 57.220 36.000 0.00 0.00 39.13 1.82
2616 3140 3.486841 GCTACGTGACGTAACTTTTGTCA 59.513 43.478 19.00 0.00 41.82 3.58
2623 3147 4.860907 CCTTTTATGCTACGTGACGTAACT 59.139 41.667 19.00 8.81 41.82 2.24
2666 3190 8.986477 ATATTTGTTAGCAAACTTGGATGAAC 57.014 30.769 6.91 0.00 45.99 3.18
2696 3220 9.703892 CCAAAACATCTTATAATTCACAACCAA 57.296 29.630 0.00 0.00 0.00 3.67
2697 3221 9.083422 TCCAAAACATCTTATAATTCACAACCA 57.917 29.630 0.00 0.00 0.00 3.67
2885 3649 1.427592 GCGCTAAAGCTGGCTCTGAG 61.428 60.000 0.00 0.00 39.32 3.35
2898 3662 2.754254 TCGAGGCCAGAGCGCTAA 60.754 61.111 11.50 0.00 41.24 3.09
2902 3666 4.504916 CAGGTCGAGGCCAGAGCG 62.505 72.222 19.90 11.68 41.24 5.03
2903 3667 4.154347 CCAGGTCGAGGCCAGAGC 62.154 72.222 18.90 18.90 36.46 4.09
2905 3669 2.680352 GTCCAGGTCGAGGCCAGA 60.680 66.667 5.01 0.00 0.00 3.86
2906 3670 2.111999 TTTGTCCAGGTCGAGGCCAG 62.112 60.000 5.01 0.00 0.00 4.85
2908 3672 1.072505 TTTTGTCCAGGTCGAGGCC 59.927 57.895 0.00 0.00 0.00 5.19
2909 3673 0.534203 TGTTTTGTCCAGGTCGAGGC 60.534 55.000 0.00 0.00 0.00 4.70
2910 3674 2.076863 GATGTTTTGTCCAGGTCGAGG 58.923 52.381 0.00 0.00 0.00 4.63
2911 3675 3.045601 AGATGTTTTGTCCAGGTCGAG 57.954 47.619 0.00 0.00 0.00 4.04
2912 3676 3.485463 AAGATGTTTTGTCCAGGTCGA 57.515 42.857 0.00 0.00 0.00 4.20
2913 3677 3.684788 CCTAAGATGTTTTGTCCAGGTCG 59.315 47.826 0.00 0.00 0.00 4.79
2914 3678 3.440522 GCCTAAGATGTTTTGTCCAGGTC 59.559 47.826 0.00 0.00 0.00 3.85
2915 3679 3.421844 GCCTAAGATGTTTTGTCCAGGT 58.578 45.455 0.00 0.00 0.00 4.00
2916 3680 2.755103 GGCCTAAGATGTTTTGTCCAGG 59.245 50.000 0.00 0.00 0.00 4.45
2917 3681 3.420893 TGGCCTAAGATGTTTTGTCCAG 58.579 45.455 3.32 0.00 0.00 3.86
2918 3682 3.181434 ACTGGCCTAAGATGTTTTGTCCA 60.181 43.478 3.32 0.00 0.00 4.02
2919 3683 3.421844 ACTGGCCTAAGATGTTTTGTCC 58.578 45.455 3.32 0.00 0.00 4.02
2920 3684 4.762251 AGAACTGGCCTAAGATGTTTTGTC 59.238 41.667 3.32 0.00 0.00 3.18
2921 3685 4.729868 AGAACTGGCCTAAGATGTTTTGT 58.270 39.130 3.32 0.00 0.00 2.83
2922 3686 5.712152 AAGAACTGGCCTAAGATGTTTTG 57.288 39.130 3.32 0.00 0.00 2.44
2923 3687 6.731292 AAAAGAACTGGCCTAAGATGTTTT 57.269 33.333 3.32 3.38 0.00 2.43
2924 3688 6.731292 AAAAAGAACTGGCCTAAGATGTTT 57.269 33.333 3.32 0.00 0.00 2.83
2970 3734 2.461695 TGAGCTTTCAGAGGTAGAGGG 58.538 52.381 0.00 0.00 35.91 4.30
2973 3737 5.745312 TTGATTGAGCTTTCAGAGGTAGA 57.255 39.130 0.00 0.00 35.91 2.59
3059 3831 0.475044 ACCACTAGACCCGCCAAAAA 59.525 50.000 0.00 0.00 0.00 1.94
3060 3832 0.475044 AACCACTAGACCCGCCAAAA 59.525 50.000 0.00 0.00 0.00 2.44
3061 3833 1.350071 TAACCACTAGACCCGCCAAA 58.650 50.000 0.00 0.00 0.00 3.28
3062 3834 1.350071 TTAACCACTAGACCCGCCAA 58.650 50.000 0.00 0.00 0.00 4.52
3063 3835 1.276989 CTTTAACCACTAGACCCGCCA 59.723 52.381 0.00 0.00 0.00 5.69
3064 3836 1.277273 ACTTTAACCACTAGACCCGCC 59.723 52.381 0.00 0.00 0.00 6.13
3065 3837 2.756840 ACTTTAACCACTAGACCCGC 57.243 50.000 0.00 0.00 0.00 6.13
3066 3838 7.677454 ATTAAAACTTTAACCACTAGACCCG 57.323 36.000 0.00 0.00 35.65 5.28
3124 3896 3.759618 CGGGACCCAGCTTATTTTGTAAA 59.240 43.478 12.15 0.00 0.00 2.01
3128 3900 1.102978 CCGGGACCCAGCTTATTTTG 58.897 55.000 12.15 0.00 0.00 2.44
3130 3902 1.076995 GCCGGGACCCAGCTTATTT 60.077 57.895 11.84 0.00 0.00 1.40
3139 3911 4.185286 ATTAAGCCGCCGGGACCC 62.185 66.667 4.77 0.00 34.06 4.46
3143 3915 0.391597 TTCTAGATTAAGCCGCCGGG 59.608 55.000 4.77 0.00 0.00 5.73
3144 3916 1.784525 CTTCTAGATTAAGCCGCCGG 58.215 55.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.