Multiple sequence alignment - TraesCS1D01G110600

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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 TraesCS1D01G110600 chr1D 100.000 2857 0 0 1 2857 104542585 104545441 0.000000e+00 5276.0
1 TraesCS1D01G110600 chr1D 96.081 791 28 3 1 790 375707677 375706889 0.000000e+00 1286.0
2 TraesCS1D01G110600 chr1D 95.944 789 32 0 1 789 316167174 316167962 0.000000e+00 1280.0
3 TraesCS1D01G110600 chr1D 91.429 105 9 0 2566 2670 447257617 447257721 8.250000e-31 145.0
4 TraesCS1D01G110600 chr1A 93.720 1672 48 27 836 2458 107485846 107484183 0.000000e+00 2453.0
5 TraesCS1D01G110600 chr1A 90.761 184 15 2 2675 2857 107484037 107483855 7.910000e-61 244.0
6 TraesCS1D01G110600 chr1A 94.286 140 6 2 2441 2579 107484175 107484037 2.230000e-51 213.0
7 TraesCS1D01G110600 chr1B 91.795 1682 73 33 790 2437 162006506 162004856 0.000000e+00 2281.0
8 TraesCS1D01G110600 chr1B 93.836 146 8 1 2435 2579 162004618 162004473 4.790000e-53 219.0
9 TraesCS1D01G110600 chr1B 86.911 191 16 3 2675 2857 162004473 162004284 3.730000e-49 206.0
10 TraesCS1D01G110600 chr1B 91.589 107 8 1 2575 2680 553897833 553897727 2.290000e-31 147.0
11 TraesCS1D01G110600 chr2D 96.324 789 29 0 1 789 323538830 323539618 0.000000e+00 1297.0
12 TraesCS1D01G110600 chr2D 96.081 791 31 0 1 791 450505899 450506689 0.000000e+00 1290.0
13 TraesCS1D01G110600 chr2D 95.833 792 27 4 1 790 444401475 444400688 0.000000e+00 1275.0
14 TraesCS1D01G110600 chr7D 95.990 798 30 2 1 796 311303783 311304580 0.000000e+00 1295.0
15 TraesCS1D01G110600 chr7D 82.482 137 22 2 1090 1225 446920018 446919883 5.000000e-23 119.0
16 TraesCS1D01G110600 chr5D 96.071 789 31 0 1 789 337191667 337190879 0.000000e+00 1286.0
17 TraesCS1D01G110600 chr5D 95.876 97 4 0 2574 2670 379575720 379575624 1.060000e-34 158.0
18 TraesCS1D01G110600 chr3D 96.071 789 31 0 1 789 288272169 288272957 0.000000e+00 1286.0
19 TraesCS1D01G110600 chr3D 85.135 74 9 2 1153 1225 600424409 600424337 1.100000e-09 75.0
20 TraesCS1D01G110600 chr4D 95.949 790 30 2 1 789 164989105 164988317 0.000000e+00 1280.0
21 TraesCS1D01G110600 chr2A 77.340 406 67 21 1315 1703 94157945 94158342 1.720000e-52 217.0
22 TraesCS1D01G110600 chr2A 87.234 94 12 0 1393 1486 598642203 598642110 1.080000e-19 108.0
23 TraesCS1D01G110600 chr5A 95.833 96 4 0 2575 2670 680655880 680655785 3.810000e-34 156.0
24 TraesCS1D01G110600 chr5A 95.789 95 4 0 2576 2670 510559778 510559684 1.370000e-33 154.0
25 TraesCS1D01G110600 chr5A 77.073 205 41 6 1307 1508 463765752 463765551 2.330000e-21 113.0
26 TraesCS1D01G110600 chr7B 74.447 407 79 19 1314 1703 535614588 535614986 4.930000e-33 152.0
27 TraesCS1D01G110600 chr7B 75.248 202 42 6 1312 1510 610737459 610737263 3.920000e-14 89.8
28 TraesCS1D01G110600 chr6D 95.745 94 4 0 2576 2669 50771931 50772024 4.930000e-33 152.0
29 TraesCS1D01G110600 chr6D 90.435 115 10 1 2572 2686 349035520 349035407 1.770000e-32 150.0
30 TraesCS1D01G110600 chr6B 94.059 101 5 1 2571 2670 36774417 36774517 4.930000e-33 152.0
31 TraesCS1D01G110600 chr6B 88.793 116 9 4 2565 2680 526103186 526103297 3.840000e-29 139.0
32 TraesCS1D01G110600 chr7A 73.723 411 79 22 1312 1703 574754115 574754515 1.790000e-27 134.0
33 TraesCS1D01G110600 chr7A 82.482 137 22 2 1090 1225 497776183 497776318 5.000000e-23 119.0
34 TraesCS1D01G110600 chr5B 76.585 205 42 6 1307 1508 428963019 428962818 1.080000e-19 108.0
35 TraesCS1D01G110600 chrUn 84.932 73 9 2 1153 1224 195649516 195649445 3.950000e-09 73.1
36 TraesCS1D01G110600 chrUn 84.932 73 9 2 1153 1224 195664747 195664676 3.950000e-09 73.1
37 TraesCS1D01G110600 chrUn 84.932 73 9 2 1153 1224 226785679 226785608 3.950000e-09 73.1
38 TraesCS1D01G110600 chrUn 84.932 73 9 2 1153 1224 269606485 269606556 3.950000e-09 73.1


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 TraesCS1D01G110600 chr1D 104542585 104545441 2856 False 5276 5276 100.000000 1 2857 1 chr1D.!!$F1 2856
1 TraesCS1D01G110600 chr1D 375706889 375707677 788 True 1286 1286 96.081000 1 790 1 chr1D.!!$R1 789
2 TraesCS1D01G110600 chr1D 316167174 316167962 788 False 1280 1280 95.944000 1 789 1 chr1D.!!$F2 788
3 TraesCS1D01G110600 chr1A 107483855 107485846 1991 True 970 2453 92.922333 836 2857 3 chr1A.!!$R1 2021
4 TraesCS1D01G110600 chr1B 162004284 162006506 2222 True 902 2281 90.847333 790 2857 3 chr1B.!!$R2 2067
5 TraesCS1D01G110600 chr2D 323538830 323539618 788 False 1297 1297 96.324000 1 789 1 chr2D.!!$F1 788
6 TraesCS1D01G110600 chr2D 450505899 450506689 790 False 1290 1290 96.081000 1 791 1 chr2D.!!$F2 790
7 TraesCS1D01G110600 chr2D 444400688 444401475 787 True 1275 1275 95.833000 1 790 1 chr2D.!!$R1 789
8 TraesCS1D01G110600 chr7D 311303783 311304580 797 False 1295 1295 95.990000 1 796 1 chr7D.!!$F1 795
9 TraesCS1D01G110600 chr5D 337190879 337191667 788 True 1286 1286 96.071000 1 789 1 chr5D.!!$R1 788
10 TraesCS1D01G110600 chr3D 288272169 288272957 788 False 1286 1286 96.071000 1 789 1 chr3D.!!$F1 788
11 TraesCS1D01G110600 chr4D 164988317 164989105 788 True 1280 1280 95.949000 1 789 1 chr4D.!!$R1 788

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
223 224 0.035343 GCCCTTCGAAGCTACCCTTT 60.035 55.0 19.99 0.0 32.78 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2249 0.24912 AAGATGATGGTGAACGGCGA 59.751 50.0 16.62 0.0 0.0 5.54 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
217 218 0.537188 CCTTGAGCCCTTCGAAGCTA 59.463 55.000 19.99 0.95 40.11 3.32
223 224 0.035343 GCCCTTCGAAGCTACCCTTT 60.035 55.000 19.99 0.00 32.78 3.11
409 411 3.244665 CCCCTTACGGTGAAGGTAAAAGT 60.245 47.826 10.90 0.00 44.02 2.66
442 444 5.424573 AGTTGAGGTGGTATTACTTAGGGTC 59.575 44.000 0.00 0.00 0.00 4.46
466 469 1.568504 TGACCAGGGAGCTTAATCGT 58.431 50.000 0.00 0.00 0.00 3.73
496 499 2.223479 GCTCTCGATCTGTTGTCTCTCC 60.223 54.545 0.00 0.00 0.00 3.71
497 500 3.013219 CTCTCGATCTGTTGTCTCTCCA 58.987 50.000 0.00 0.00 0.00 3.86
498 501 3.625853 TCTCGATCTGTTGTCTCTCCAT 58.374 45.455 0.00 0.00 0.00 3.41
541 544 8.010697 TCATCCCTTTATATAGAGAGGTTGACA 58.989 37.037 3.48 0.00 0.00 3.58
652 658 1.068585 GGCGGGTTATCACTACGGG 59.931 63.158 0.00 0.00 0.00 5.28
708 714 0.690192 TCCGCCATCCTCAAACTTGA 59.310 50.000 0.00 0.00 35.57 3.02
735 741 3.248602 GGGCTTCACGTGATGATCATTAC 59.751 47.826 29.54 18.24 37.11 1.89
736 742 3.871006 GGCTTCACGTGATGATCATTACA 59.129 43.478 29.54 11.39 37.11 2.41
801 807 4.842531 TCCTCAACAGAAGGAATATGCA 57.157 40.909 0.00 0.00 39.99 3.96
806 812 6.238676 CCTCAACAGAAGGAATATGCAGATTG 60.239 42.308 12.07 0.00 35.83 2.67
807 813 6.417258 TCAACAGAAGGAATATGCAGATTGA 58.583 36.000 12.07 0.00 0.00 2.57
834 840 7.039714 GGATAATGGATCAAATTAACTGGTCCC 60.040 40.741 13.65 1.62 42.57 4.46
880 886 1.091537 GCCTGCGGTTAGTAATGCAA 58.908 50.000 12.18 0.64 36.82 4.08
921 927 3.589951 AGTTCTACCCAGCGTCCTATA 57.410 47.619 0.00 0.00 0.00 1.31
932 938 2.997986 AGCGTCCTATAAAAACCACACG 59.002 45.455 0.00 0.00 0.00 4.49
941 947 1.595466 AAAACCACACGCCACGAATA 58.405 45.000 0.00 0.00 0.00 1.75
942 948 1.153353 AAACCACACGCCACGAATAG 58.847 50.000 0.00 0.00 0.00 1.73
943 949 0.672401 AACCACACGCCACGAATAGG 60.672 55.000 0.00 0.00 0.00 2.57
944 950 1.216977 CCACACGCCACGAATAGGA 59.783 57.895 0.00 0.00 0.00 2.94
945 951 0.806102 CCACACGCCACGAATAGGAG 60.806 60.000 0.00 0.00 0.00 3.69
946 952 0.172578 CACACGCCACGAATAGGAGA 59.827 55.000 0.00 0.00 0.00 3.71
947 953 0.456221 ACACGCCACGAATAGGAGAG 59.544 55.000 0.00 0.00 0.00 3.20
948 954 0.456221 CACGCCACGAATAGGAGAGT 59.544 55.000 0.00 0.00 0.00 3.24
949 955 1.674441 CACGCCACGAATAGGAGAGTA 59.326 52.381 0.00 0.00 0.00 2.59
950 956 2.293677 CACGCCACGAATAGGAGAGTAT 59.706 50.000 0.00 0.00 0.00 2.12
951 957 2.957006 ACGCCACGAATAGGAGAGTATT 59.043 45.455 0.00 0.00 0.00 1.89
952 958 4.023450 CACGCCACGAATAGGAGAGTATTA 60.023 45.833 0.00 0.00 0.00 0.98
953 959 4.765856 ACGCCACGAATAGGAGAGTATTAT 59.234 41.667 0.00 0.00 0.00 1.28
954 960 5.106237 ACGCCACGAATAGGAGAGTATTATC 60.106 44.000 0.00 0.00 0.00 1.75
955 961 5.652518 GCCACGAATAGGAGAGTATTATCC 58.347 45.833 0.00 0.00 35.71 2.59
956 962 5.185249 GCCACGAATAGGAGAGTATTATCCA 59.815 44.000 1.42 0.00 38.12 3.41
957 963 6.622549 CCACGAATAGGAGAGTATTATCCAC 58.377 44.000 1.42 0.00 38.12 4.02
958 964 6.315551 CACGAATAGGAGAGTATTATCCACG 58.684 44.000 1.42 4.48 38.12 4.94
959 965 6.148976 CACGAATAGGAGAGTATTATCCACGA 59.851 42.308 1.42 0.00 38.12 4.35
960 966 6.713903 ACGAATAGGAGAGTATTATCCACGAA 59.286 38.462 1.42 0.00 38.12 3.85
961 967 7.094720 ACGAATAGGAGAGTATTATCCACGAAG 60.095 40.741 1.42 0.00 38.12 3.79
962 968 4.857509 AGGAGAGTATTATCCACGAAGC 57.142 45.455 1.42 0.00 38.12 3.86
963 969 4.475345 AGGAGAGTATTATCCACGAAGCT 58.525 43.478 1.42 0.00 38.12 3.74
964 970 4.279671 AGGAGAGTATTATCCACGAAGCTG 59.720 45.833 1.42 0.00 38.12 4.24
965 971 3.983741 AGAGTATTATCCACGAAGCTGC 58.016 45.455 0.00 0.00 0.00 5.25
966 972 3.384789 AGAGTATTATCCACGAAGCTGCA 59.615 43.478 1.02 0.00 0.00 4.41
967 973 4.119862 GAGTATTATCCACGAAGCTGCAA 58.880 43.478 1.02 0.00 0.00 4.08
1106 1146 0.731855 GACGTGGGCTTCTACGACAC 60.732 60.000 9.09 0.00 42.54 3.67
1237 1277 1.065418 TCAAGGTAAGCCAAGCTAGCC 60.065 52.381 12.13 0.00 38.25 3.93
1239 1279 0.543749 AGGTAAGCCAAGCTAGCCAG 59.456 55.000 12.13 3.84 38.25 4.85
1305 1349 1.800586 CATATACTCACATGCACGGGC 59.199 52.381 0.34 0.34 41.68 6.13
1568 1612 3.041940 GCCGTGTGTCCACCGAAG 61.042 66.667 9.03 0.00 38.41 3.79
1749 1794 1.969200 TTCCCAACACAACCGACGGA 61.969 55.000 23.38 0.00 0.00 4.69
1810 1857 2.293122 TGGAATTTTGAGCAGTCAACGG 59.707 45.455 0.00 0.00 42.60 4.44
1902 1949 3.499737 CATCTGCCCGCCGAACAC 61.500 66.667 0.00 0.00 0.00 3.32
2114 2169 0.685131 CCATGCTCAAGATGGGGCAA 60.685 55.000 0.00 0.00 37.33 4.52
2133 2188 2.856039 AATCGAGGTGCTCTCCGGGA 62.856 60.000 0.00 0.00 39.30 5.14
2194 2249 1.006571 CCAACGTCACTAGTGCCGT 60.007 57.895 24.92 24.92 0.00 5.68
2220 2275 1.123077 TCACCATCATCTTCTCCCCG 58.877 55.000 0.00 0.00 0.00 5.73
2262 2332 2.271800 CAAGCTGATTAGTCGGTGGTC 58.728 52.381 0.00 0.00 33.06 4.02
2263 2333 1.557099 AGCTGATTAGTCGGTGGTCA 58.443 50.000 0.00 0.00 33.06 4.02
2329 2412 8.562052 TGCTCTAGTGTGATGCAATAAATTATG 58.438 33.333 0.00 0.00 0.00 1.90
2385 2469 2.223144 CGAGCGTTTGAAATGAACCAGA 59.777 45.455 0.48 0.00 0.00 3.86
2407 2495 7.201767 CCAGATCCAAAATGTTCCTATGAGAAC 60.202 40.741 3.41 3.41 45.24 3.01
2548 2879 6.152154 ACCCTTACTTTTGTTTAATCCATCCG 59.848 38.462 0.00 0.00 0.00 4.18
2579 2910 9.350951 ACCCAATTTGCCTACTAATTAATACTC 57.649 33.333 0.00 0.00 31.33 2.59
2580 2911 8.793592 CCCAATTTGCCTACTAATTAATACTCC 58.206 37.037 0.00 0.00 31.33 3.85
2581 2912 8.793592 CCAATTTGCCTACTAATTAATACTCCC 58.206 37.037 0.00 0.00 31.33 4.30
2582 2913 9.574516 CAATTTGCCTACTAATTAATACTCCCT 57.425 33.333 0.00 0.00 31.33 4.20
2583 2914 9.794719 AATTTGCCTACTAATTAATACTCCCTC 57.205 33.333 0.00 0.00 30.84 4.30
2584 2915 6.930068 TGCCTACTAATTAATACTCCCTCC 57.070 41.667 0.00 0.00 0.00 4.30
2585 2916 6.387127 TGCCTACTAATTAATACTCCCTCCA 58.613 40.000 0.00 0.00 0.00 3.86
2586 2917 7.023120 TGCCTACTAATTAATACTCCCTCCAT 58.977 38.462 0.00 0.00 0.00 3.41
2587 2918 7.516209 TGCCTACTAATTAATACTCCCTCCATT 59.484 37.037 0.00 0.00 0.00 3.16
2588 2919 8.041919 GCCTACTAATTAATACTCCCTCCATTC 58.958 40.741 0.00 0.00 0.00 2.67
2589 2920 9.327731 CCTACTAATTAATACTCCCTCCATTCT 57.672 37.037 0.00 0.00 0.00 2.40
2600 2931 7.937700 ACTCCCTCCATTCTAAAATAGATGA 57.062 36.000 0.00 0.00 34.22 2.92
2601 2932 7.740805 ACTCCCTCCATTCTAAAATAGATGAC 58.259 38.462 0.00 0.00 34.22 3.06
2602 2933 7.079451 TCCCTCCATTCTAAAATAGATGACC 57.921 40.000 0.00 0.00 34.22 4.02
2603 2934 6.044404 TCCCTCCATTCTAAAATAGATGACCC 59.956 42.308 0.00 0.00 34.22 4.46
2604 2935 6.183361 CCCTCCATTCTAAAATAGATGACCCA 60.183 42.308 0.00 0.00 34.22 4.51
2605 2936 7.290061 CCTCCATTCTAAAATAGATGACCCAA 58.710 38.462 0.00 0.00 34.22 4.12
2606 2937 7.229506 CCTCCATTCTAAAATAGATGACCCAAC 59.770 40.741 0.00 0.00 34.22 3.77
2607 2938 7.872138 TCCATTCTAAAATAGATGACCCAACT 58.128 34.615 0.00 0.00 34.22 3.16
2608 2939 8.336235 TCCATTCTAAAATAGATGACCCAACTT 58.664 33.333 0.00 0.00 34.22 2.66
2609 2940 8.971073 CCATTCTAAAATAGATGACCCAACTTT 58.029 33.333 0.00 0.00 34.22 2.66
2663 2994 7.133891 AGTTGAGTCATCTATTTTGAAACGG 57.866 36.000 1.70 0.00 0.00 4.44
2664 2995 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
2665 2996 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
2666 2997 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
2667 2998 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
2668 2999 5.045869 AGTCATCTATTTTGAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
2669 3000 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
2670 3001 4.216411 TCTATTTTGAAACGGAGGGAGG 57.784 45.455 0.00 0.00 0.00 4.30
2671 3002 2.215942 ATTTTGAAACGGAGGGAGGG 57.784 50.000 0.00 0.00 0.00 4.30
2672 3003 1.142060 TTTTGAAACGGAGGGAGGGA 58.858 50.000 0.00 0.00 0.00 4.20
2673 3004 0.690762 TTTGAAACGGAGGGAGGGAG 59.309 55.000 0.00 0.00 0.00 4.30
2674 3005 0.473117 TTGAAACGGAGGGAGGGAGT 60.473 55.000 0.00 0.00 0.00 3.85
2679 3010 1.212934 ACGGAGGGAGGGAGTACTCA 61.213 60.000 23.91 0.00 39.27 3.41
2680 3011 0.466555 CGGAGGGAGGGAGTACTCAG 60.467 65.000 23.91 0.68 39.27 3.35
2684 3015 0.827368 GGGAGGGAGTACTCAGCAAG 59.173 60.000 23.91 0.00 39.27 4.01
2700 3031 6.493458 ACTCAGCAAGGTACCACATTTATTTT 59.507 34.615 15.94 0.00 0.00 1.82
2709 3040 8.603304 AGGTACCACATTTATTTTGTCTAGTCT 58.397 33.333 15.94 0.00 0.00 3.24
2760 3092 9.653516 TGAACCCATCAACCATATATGTTAAAT 57.346 29.630 11.73 0.00 34.30 1.40
2791 3123 3.857052 TCGTCCTGAATGTTATGGTGAC 58.143 45.455 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 218 5.077564 GGTGGATTTGAGTTCTTAAAGGGT 58.922 41.667 0.00 0.00 0.00 4.34
223 224 3.071479 GCACGGTGGATTTGAGTTCTTA 58.929 45.455 10.60 0.00 0.00 2.10
312 314 2.107750 CTGCGATGGCTCCACGAT 59.892 61.111 0.15 0.00 40.82 3.73
347 349 2.433436 GTGTTCCTTGTCCCGCTTAAT 58.567 47.619 0.00 0.00 0.00 1.40
409 411 1.254026 CCACCTCAACTGGACGTAGA 58.746 55.000 0.00 0.00 0.00 2.59
442 444 1.403814 TAAGCTCCCTGGTCATCGAG 58.596 55.000 0.00 0.00 0.00 4.04
466 469 1.342496 CAGATCGAGAGCCAGGCATAA 59.658 52.381 15.80 0.00 0.00 1.90
602 606 6.293955 GCAAGACTTGTAATGTAAGGCAAGAA 60.294 38.462 16.39 0.00 40.30 2.52
708 714 1.831106 TCATCACGTGAAGCCCAGTAT 59.169 47.619 24.13 0.00 32.78 2.12
735 741 3.963687 GAGGGGCCGGGTTACGTTG 62.964 68.421 2.18 0.00 42.24 4.10
736 742 3.709633 GAGGGGCCGGGTTACGTT 61.710 66.667 2.18 0.00 42.24 3.99
806 812 8.697507 ACCAGTTAATTTGATCCATTATCCTC 57.302 34.615 0.00 0.00 33.22 3.71
807 813 7.725844 GGACCAGTTAATTTGATCCATTATCCT 59.274 37.037 0.00 0.00 33.22 3.24
863 869 3.000041 TCACTTGCATTACTAACCGCAG 59.000 45.455 0.00 0.00 35.47 5.18
880 886 1.425066 TGGAAGGGCATTTCTGTCACT 59.575 47.619 0.00 0.00 0.00 3.41
921 927 0.741915 ATTCGTGGCGTGTGGTTTTT 59.258 45.000 0.00 0.00 0.00 1.94
932 938 5.185249 TGGATAATACTCTCCTATTCGTGGC 59.815 44.000 0.00 0.00 32.47 5.01
941 947 4.279671 CAGCTTCGTGGATAATACTCTCCT 59.720 45.833 0.00 0.00 32.47 3.69
942 948 4.551388 CAGCTTCGTGGATAATACTCTCC 58.449 47.826 0.00 0.00 0.00 3.71
943 949 3.984633 GCAGCTTCGTGGATAATACTCTC 59.015 47.826 0.00 0.00 0.00 3.20
944 950 3.384789 TGCAGCTTCGTGGATAATACTCT 59.615 43.478 0.00 0.00 0.00 3.24
945 951 3.717707 TGCAGCTTCGTGGATAATACTC 58.282 45.455 0.00 0.00 0.00 2.59
946 952 3.819564 TGCAGCTTCGTGGATAATACT 57.180 42.857 0.00 0.00 0.00 2.12
947 953 4.786609 GCTTTGCAGCTTCGTGGATAATAC 60.787 45.833 0.00 0.00 43.51 1.89
948 954 3.312421 GCTTTGCAGCTTCGTGGATAATA 59.688 43.478 0.00 0.00 43.51 0.98
949 955 2.098117 GCTTTGCAGCTTCGTGGATAAT 59.902 45.455 0.00 0.00 43.51 1.28
950 956 1.468520 GCTTTGCAGCTTCGTGGATAA 59.531 47.619 0.00 0.00 43.51 1.75
951 957 1.086696 GCTTTGCAGCTTCGTGGATA 58.913 50.000 0.00 0.00 43.51 2.59
952 958 1.878775 GCTTTGCAGCTTCGTGGAT 59.121 52.632 0.00 0.00 43.51 3.41
953 959 3.343972 GCTTTGCAGCTTCGTGGA 58.656 55.556 0.00 0.00 43.51 4.02
962 968 2.026445 TGCGCTGTTGCTTTGCAG 59.974 55.556 9.73 0.00 40.61 4.41
963 969 2.278726 GTGCGCTGTTGCTTTGCA 60.279 55.556 9.73 0.00 36.47 4.08
964 970 1.611592 GATGTGCGCTGTTGCTTTGC 61.612 55.000 9.73 0.00 36.97 3.68
965 971 0.318022 TGATGTGCGCTGTTGCTTTG 60.318 50.000 9.73 0.00 36.97 2.77
966 972 0.039798 CTGATGTGCGCTGTTGCTTT 60.040 50.000 9.73 0.00 36.97 3.51
967 973 0.886043 TCTGATGTGCGCTGTTGCTT 60.886 50.000 9.73 0.00 36.97 3.91
1305 1349 2.259204 CGCACCCCTGCAACAATG 59.741 61.111 0.00 0.00 44.50 2.82
1749 1794 9.013229 TGTTGAAGAATTATGCAAGTCATTACT 57.987 29.630 0.00 0.00 36.63 2.24
1756 1801 6.804677 TGTGTTGTTGAAGAATTATGCAAGT 58.195 32.000 0.00 0.00 0.00 3.16
1757 1802 7.595875 TGATGTGTTGTTGAAGAATTATGCAAG 59.404 33.333 0.00 0.00 0.00 4.01
1758 1803 7.432059 TGATGTGTTGTTGAAGAATTATGCAA 58.568 30.769 0.00 0.00 0.00 4.08
1759 1804 6.979465 TGATGTGTTGTTGAAGAATTATGCA 58.021 32.000 0.00 0.00 0.00 3.96
1760 1805 7.872163 TTGATGTGTTGTTGAAGAATTATGC 57.128 32.000 0.00 0.00 0.00 3.14
1801 1848 6.737254 ACAAATAATTAGGACCGTTGACTG 57.263 37.500 0.00 0.00 0.00 3.51
2114 2169 2.427245 CCCGGAGAGCACCTCGATT 61.427 63.158 0.73 0.00 42.89 3.34
2194 2249 0.249120 AAGATGATGGTGAACGGCGA 59.751 50.000 16.62 0.00 0.00 5.54
2220 2275 1.609783 CCACCTGGTTGGATCCTCC 59.390 63.158 14.23 15.44 39.24 4.30
2255 2325 4.038042 ACACATATCTCTACATGACCACCG 59.962 45.833 0.00 0.00 0.00 4.94
2262 2332 5.519722 TGCACGTACACATATCTCTACATG 58.480 41.667 0.00 0.00 0.00 3.21
2263 2333 5.299531 ACTGCACGTACACATATCTCTACAT 59.700 40.000 0.00 0.00 0.00 2.29
2329 2412 4.034048 ACAGACGTTCAGACAAAACATCAC 59.966 41.667 0.00 0.00 0.00 3.06
2385 2469 9.401058 CTTAGTTCTCATAGGAACATTTTGGAT 57.599 33.333 9.50 0.00 45.52 3.41
2407 2495 6.910536 ACTTGAGAAACCGAATATGCTTAG 57.089 37.500 0.00 0.00 0.00 2.18
2468 2799 3.071479 GGCGTCTTGGTCAAATACAGAA 58.929 45.455 0.00 0.00 0.00 3.02
2474 2805 1.169661 TTGCGGCGTCTTGGTCAAAT 61.170 50.000 9.37 0.00 0.00 2.32
2548 2879 6.715347 ATTAGTAGGCAAATTGGGTCAATC 57.285 37.500 0.00 0.00 32.43 2.67
2579 2910 6.183361 TGGGTCATCTATTTTAGAATGGAGGG 60.183 42.308 4.57 0.00 36.39 4.30
2580 2911 6.841601 TGGGTCATCTATTTTAGAATGGAGG 58.158 40.000 0.00 0.00 36.39 4.30
2581 2912 7.995488 AGTTGGGTCATCTATTTTAGAATGGAG 59.005 37.037 0.00 0.00 36.39 3.86
2582 2913 7.872138 AGTTGGGTCATCTATTTTAGAATGGA 58.128 34.615 0.00 0.00 38.50 3.41
2583 2914 8.525290 AAGTTGGGTCATCTATTTTAGAATGG 57.475 34.615 0.00 0.00 38.50 3.16
2637 2968 8.076178 CCGTTTCAAAATAGATGACTCAACTTT 58.924 33.333 0.00 0.00 0.00 2.66
2638 2969 7.444183 TCCGTTTCAAAATAGATGACTCAACTT 59.556 33.333 0.00 0.00 0.00 2.66
2639 2970 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
2640 2971 7.129109 TCCGTTTCAAAATAGATGACTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
2641 2972 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
2642 2973 5.874810 CCTCCGTTTCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
2643 2974 5.294552 CCCTCCGTTTCAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
2644 2975 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
2645 2976 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
2646 2977 5.428253 CTCCCTCCGTTTCAAAATAGATGA 58.572 41.667 0.00 0.00 0.00 2.92
2647 2978 4.576463 CCTCCCTCCGTTTCAAAATAGATG 59.424 45.833 0.00 0.00 0.00 2.90
2648 2979 4.385310 CCCTCCCTCCGTTTCAAAATAGAT 60.385 45.833 0.00 0.00 0.00 1.98
2649 2980 3.054655 CCCTCCCTCCGTTTCAAAATAGA 60.055 47.826 0.00 0.00 0.00 1.98
2650 2981 3.054655 TCCCTCCCTCCGTTTCAAAATAG 60.055 47.826 0.00 0.00 0.00 1.73
2651 2982 2.914278 TCCCTCCCTCCGTTTCAAAATA 59.086 45.455 0.00 0.00 0.00 1.40
2652 2983 1.708551 TCCCTCCCTCCGTTTCAAAAT 59.291 47.619 0.00 0.00 0.00 1.82
2653 2984 1.073284 CTCCCTCCCTCCGTTTCAAAA 59.927 52.381 0.00 0.00 0.00 2.44
2654 2985 0.690762 CTCCCTCCCTCCGTTTCAAA 59.309 55.000 0.00 0.00 0.00 2.69
2655 2986 0.473117 ACTCCCTCCCTCCGTTTCAA 60.473 55.000 0.00 0.00 0.00 2.69
2656 2987 0.410663 TACTCCCTCCCTCCGTTTCA 59.589 55.000 0.00 0.00 0.00 2.69
2657 2988 0.822811 GTACTCCCTCCCTCCGTTTC 59.177 60.000 0.00 0.00 0.00 2.78
2658 2989 0.412640 AGTACTCCCTCCCTCCGTTT 59.587 55.000 0.00 0.00 0.00 3.60
2659 2990 0.033306 GAGTACTCCCTCCCTCCGTT 60.033 60.000 12.13 0.00 0.00 4.44
2660 2991 1.212934 TGAGTACTCCCTCCCTCCGT 61.213 60.000 20.11 0.00 0.00 4.69
2661 2992 0.466555 CTGAGTACTCCCTCCCTCCG 60.467 65.000 20.11 0.00 0.00 4.63
2662 2993 0.757561 GCTGAGTACTCCCTCCCTCC 60.758 65.000 20.11 0.00 0.00 4.30
2663 2994 0.033011 TGCTGAGTACTCCCTCCCTC 60.033 60.000 20.11 2.49 0.00 4.30
2664 2995 0.413832 TTGCTGAGTACTCCCTCCCT 59.586 55.000 20.11 0.00 0.00 4.20
2665 2996 0.827368 CTTGCTGAGTACTCCCTCCC 59.173 60.000 20.11 4.69 0.00 4.30
2666 2997 0.827368 CCTTGCTGAGTACTCCCTCC 59.173 60.000 20.11 6.36 0.00 4.30
2667 2998 1.562783 ACCTTGCTGAGTACTCCCTC 58.437 55.000 20.11 9.40 0.00 4.30
2668 2999 2.458620 GTACCTTGCTGAGTACTCCCT 58.541 52.381 20.11 0.00 36.69 4.20
2669 3000 1.481363 GGTACCTTGCTGAGTACTCCC 59.519 57.143 20.11 11.47 39.07 4.30
2670 3001 2.094130 GTGGTACCTTGCTGAGTACTCC 60.094 54.545 20.11 6.32 39.07 3.85
2671 3002 2.561419 TGTGGTACCTTGCTGAGTACTC 59.439 50.000 16.32 16.32 39.07 2.59
2672 3003 2.605257 TGTGGTACCTTGCTGAGTACT 58.395 47.619 14.36 0.00 39.07 2.73
2673 3004 3.611766 ATGTGGTACCTTGCTGAGTAC 57.388 47.619 14.36 0.00 38.49 2.73
2674 3005 4.634012 AAATGTGGTACCTTGCTGAGTA 57.366 40.909 14.36 0.00 0.00 2.59
2679 3010 6.493458 AGACAAAATAAATGTGGTACCTTGCT 59.507 34.615 14.36 5.00 0.00 3.91
2680 3011 6.687604 AGACAAAATAAATGTGGTACCTTGC 58.312 36.000 14.36 4.15 0.00 4.01
2684 3015 8.788325 AGACTAGACAAAATAAATGTGGTACC 57.212 34.615 4.43 4.43 0.00 3.34
2718 3049 7.505585 TGATGGGTTCAGTTCTGTAAAGAAAAT 59.494 33.333 0.00 0.00 0.00 1.82
2728 3059 2.862541 TGGTTGATGGGTTCAGTTCTG 58.137 47.619 0.00 0.00 35.27 3.02
2765 3097 8.035394 GTCACCATAACATTCAGGACGATATAT 58.965 37.037 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.