Multiple sequence alignment - TraesCS6A01G093500

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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 TraesCS6A01G093500 chr6A 100.000 2935 0 0 1 2935 61184437 61187371 0.000000e+00 5421
1 TraesCS6A01G093500 chr6A 87.223 1174 100 22 1041 2190 61136493 61137640 0.000000e+00 1291
2 TraesCS6A01G093500 chr6D 92.976 1025 38 13 1041 2053 53850410 53849408 0.000000e+00 1463
3 TraesCS6A01G093500 chr6D 92.019 639 32 9 2031 2653 53848953 53848318 0.000000e+00 880
4 TraesCS6A01G093500 chr1D 86.765 1020 102 14 1 1003 349711160 349712163 0.000000e+00 1105
5 TraesCS6A01G093500 chr1D 89.033 848 82 8 63 907 24039950 24040789 0.000000e+00 1040
6 TraesCS6A01G093500 chr6B 87.692 910 93 15 1 907 579092576 579091683 0.000000e+00 1042
7 TraesCS6A01G093500 chr6B 92.535 710 38 8 1041 1747 117630531 117631228 0.000000e+00 1003
8 TraesCS6A01G093500 chr6B 88.970 825 52 14 1926 2732 117631400 117632203 0.000000e+00 983
9 TraesCS6A01G093500 chr6B 88.083 772 48 17 1867 2627 117541703 117542441 0.000000e+00 876
10 TraesCS6A01G093500 chr6B 86.685 721 48 21 1043 1746 117588663 117589352 0.000000e+00 756
11 TraesCS6A01G093500 chr6B 87.685 609 52 8 1146 1747 117541035 117541627 0.000000e+00 688
12 TraesCS6A01G093500 chr5A 86.748 898 99 11 1 895 459764320 459765200 0.000000e+00 981
13 TraesCS6A01G093500 chr5A 92.105 114 7 1 2747 2858 495925316 495925203 3.030000e-35 159
14 TraesCS6A01G093500 chr5D 86.192 898 107 10 1 896 446262478 446261596 0.000000e+00 955
15 TraesCS6A01G093500 chr7B 83.842 1015 129 21 1 994 704787541 704786541 0.000000e+00 933
16 TraesCS6A01G093500 chr7B 90.000 120 10 2 2739 2858 66320198 66320315 1.410000e-33 154
17 TraesCS6A01G093500 chr2B 86.171 875 107 10 6 876 51954576 51955440 0.000000e+00 933
18 TraesCS6A01G093500 chr2D 85.844 883 107 9 26 907 644102110 644101245 0.000000e+00 922
19 TraesCS6A01G093500 chr2D 84.828 903 113 17 1 898 194066651 194067534 0.000000e+00 887
20 TraesCS6A01G093500 chr2D 90.323 124 8 2 2739 2860 613987123 613987244 3.030000e-35 159
21 TraesCS6A01G093500 chr2D 87.692 130 13 3 2739 2865 586157609 586157738 6.550000e-32 148
22 TraesCS6A01G093500 chr3A 90.551 127 11 1 2739 2864 743689712 743689586 1.810000e-37 167
23 TraesCS6A01G093500 chr3A 87.692 130 14 2 2740 2867 740079677 740079548 1.820000e-32 150
24 TraesCS6A01G093500 chr1A 88.148 135 12 3 2740 2870 49000238 49000372 1.090000e-34 158
25 TraesCS6A01G093500 chr7A 92.593 108 6 1 2753 2858 685390857 685390750 1.410000e-33 154
26 TraesCS6A01G093500 chr2A 87.786 131 12 4 2739 2866 581965746 581965617 1.820000e-32 150


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 TraesCS6A01G093500 chr6A 61184437 61187371 2934 False 5421.0 5421 100.0000 1 2935 1 chr6A.!!$F2 2934
1 TraesCS6A01G093500 chr6A 61136493 61137640 1147 False 1291.0 1291 87.2230 1041 2190 1 chr6A.!!$F1 1149
2 TraesCS6A01G093500 chr6D 53848318 53850410 2092 True 1171.5 1463 92.4975 1041 2653 2 chr6D.!!$R1 1612
3 TraesCS6A01G093500 chr1D 349711160 349712163 1003 False 1105.0 1105 86.7650 1 1003 1 chr1D.!!$F2 1002
4 TraesCS6A01G093500 chr1D 24039950 24040789 839 False 1040.0 1040 89.0330 63 907 1 chr1D.!!$F1 844
5 TraesCS6A01G093500 chr6B 579091683 579092576 893 True 1042.0 1042 87.6920 1 907 1 chr6B.!!$R1 906
6 TraesCS6A01G093500 chr6B 117630531 117632203 1672 False 993.0 1003 90.7525 1041 2732 2 chr6B.!!$F3 1691
7 TraesCS6A01G093500 chr6B 117541035 117542441 1406 False 782.0 876 87.8840 1146 2627 2 chr6B.!!$F2 1481
8 TraesCS6A01G093500 chr6B 117588663 117589352 689 False 756.0 756 86.6850 1043 1746 1 chr6B.!!$F1 703
9 TraesCS6A01G093500 chr5A 459764320 459765200 880 False 981.0 981 86.7480 1 895 1 chr5A.!!$F1 894
10 TraesCS6A01G093500 chr5D 446261596 446262478 882 True 955.0 955 86.1920 1 896 1 chr5D.!!$R1 895
11 TraesCS6A01G093500 chr7B 704786541 704787541 1000 True 933.0 933 83.8420 1 994 1 chr7B.!!$R1 993
12 TraesCS6A01G093500 chr2B 51954576 51955440 864 False 933.0 933 86.1710 6 876 1 chr2B.!!$F1 870
13 TraesCS6A01G093500 chr2D 644101245 644102110 865 True 922.0 922 85.8440 26 907 1 chr2D.!!$R1 881
14 TraesCS6A01G093500 chr2D 194066651 194067534 883 False 887.0 887 84.8280 1 898 1 chr2D.!!$F1 897

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
932 970 0.039527 AGCATTTTTCACGCGAACCC 60.04 50.0 15.93 0.0 0.0 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2578 3218 0.17668 CAGGACAGGTAAGCGCAGAT 59.823 55.0 11.47 0.0 0.0 2.9 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
76 78 3.648067 ACCTCCTTCACTTCATCTTCACA 59.352 43.478 0.00 0.00 0.00 3.58
99 101 2.203209 GATCATCCACGCCACCCC 60.203 66.667 0.00 0.00 0.00 4.95
190 192 0.107410 TTCACGAACTTGGCAGTGGT 60.107 50.000 4.28 0.00 35.50 4.16
245 248 1.893137 AGTCACGAGCTACCACAATGA 59.107 47.619 0.00 0.00 0.00 2.57
291 297 4.262207 GGATCGAAGATGCATACCTTCTGA 60.262 45.833 20.05 18.32 45.12 3.27
320 326 4.250305 AACACCTCGCCTGCGGTT 62.250 61.111 12.06 4.97 40.25 4.44
366 373 2.674754 GGGAACATCTTGCCGGGA 59.325 61.111 2.18 0.00 0.00 5.14
685 694 4.179579 GCTTCCATGGCGGCGAAC 62.180 66.667 12.98 2.36 33.14 3.95
768 788 4.097361 GGAGGGGAGCGGGAACAC 62.097 72.222 0.00 0.00 0.00 3.32
837 863 4.458829 TCGGATCGGCCTCCCACT 62.459 66.667 0.00 0.00 31.04 4.00
838 864 2.520982 CGGATCGGCCTCCCACTA 60.521 66.667 0.00 0.00 31.04 2.74
850 876 4.042187 GGCCTCCCACTATGTGAATCTAAT 59.958 45.833 0.00 0.00 35.23 1.73
851 877 5.248477 GGCCTCCCACTATGTGAATCTAATA 59.752 44.000 0.00 0.00 35.23 0.98
859 885 8.642432 CCACTATGTGAATCTAATAGTTGAGGA 58.358 37.037 5.92 0.00 35.45 3.71
877 903 2.054140 GACGAACTTTTGCCGCACCA 62.054 55.000 0.00 0.00 0.00 4.17
921 959 0.955905 ACGTTACGGGCAGCATTTTT 59.044 45.000 10.20 0.00 0.00 1.94
927 965 2.088178 GGGCAGCATTTTTCACGCG 61.088 57.895 3.53 3.53 0.00 6.01
932 970 0.039527 AGCATTTTTCACGCGAACCC 60.040 50.000 15.93 0.00 0.00 4.11
940 978 2.360553 TCACGCGAACCCGTATTTTA 57.639 45.000 15.93 0.00 39.83 1.52
942 980 3.260740 TCACGCGAACCCGTATTTTAAT 58.739 40.909 15.93 0.00 39.83 1.40
943 981 4.428209 TCACGCGAACCCGTATTTTAATA 58.572 39.130 15.93 0.00 39.83 0.98
951 989 9.373750 GCGAACCCGTATTTTAATAGTTATTTC 57.626 33.333 0.00 0.00 38.24 2.17
971 1009 1.445942 CGGGTCACGGCATTATCCT 59.554 57.895 0.00 0.00 39.42 3.24
974 1012 0.180406 GGTCACGGCATTATCCTGGT 59.820 55.000 0.00 0.00 0.00 4.00
975 1013 1.414919 GGTCACGGCATTATCCTGGTA 59.585 52.381 0.00 0.00 0.00 3.25
976 1014 2.158871 GGTCACGGCATTATCCTGGTAA 60.159 50.000 0.00 0.00 0.00 2.85
988 1026 7.845037 CATTATCCTGGTAATGCTAGAGATGA 58.155 38.462 12.72 0.00 35.84 2.92
994 1032 7.395772 TCCTGGTAATGCTAGAGATGATCTAAG 59.604 40.741 0.00 0.00 40.06 2.18
996 1034 7.013220 TGGTAATGCTAGAGATGATCTAAGGT 58.987 38.462 0.00 0.00 40.06 3.50
1003 1041 4.798882 AGAGATGATCTAAGGTTCCGAGT 58.201 43.478 0.00 0.00 36.10 4.18
1004 1042 5.942961 AGAGATGATCTAAGGTTCCGAGTA 58.057 41.667 0.00 0.00 36.10 2.59
1005 1043 6.366340 AGAGATGATCTAAGGTTCCGAGTAA 58.634 40.000 0.00 0.00 36.10 2.24
1006 1044 6.834451 AGAGATGATCTAAGGTTCCGAGTAAA 59.166 38.462 0.00 0.00 36.10 2.01
1007 1045 7.342284 AGAGATGATCTAAGGTTCCGAGTAAAA 59.658 37.037 0.00 0.00 36.10 1.52
1008 1046 7.493367 AGATGATCTAAGGTTCCGAGTAAAAG 58.507 38.462 0.00 0.00 0.00 2.27
1009 1047 5.416947 TGATCTAAGGTTCCGAGTAAAAGC 58.583 41.667 0.00 0.00 0.00 3.51
1010 1048 4.198028 TCTAAGGTTCCGAGTAAAAGCC 57.802 45.455 0.00 0.00 0.00 4.35
1011 1049 2.195741 AAGGTTCCGAGTAAAAGCCC 57.804 50.000 0.00 0.00 0.00 5.19
1012 1050 0.036671 AGGTTCCGAGTAAAAGCCCG 60.037 55.000 0.00 0.00 0.00 6.13
1013 1051 0.321034 GGTTCCGAGTAAAAGCCCGT 60.321 55.000 0.00 0.00 0.00 5.28
1014 1052 0.794473 GTTCCGAGTAAAAGCCCGTG 59.206 55.000 0.00 0.00 0.00 4.94
1015 1053 0.680618 TTCCGAGTAAAAGCCCGTGA 59.319 50.000 0.00 0.00 0.00 4.35
1016 1054 0.899720 TCCGAGTAAAAGCCCGTGAT 59.100 50.000 0.00 0.00 0.00 3.06
1017 1055 1.134907 TCCGAGTAAAAGCCCGTGATC 60.135 52.381 0.00 0.00 0.00 2.92
1018 1056 1.404986 CCGAGTAAAAGCCCGTGATCA 60.405 52.381 0.00 0.00 0.00 2.92
1019 1057 2.550978 CGAGTAAAAGCCCGTGATCAT 58.449 47.619 0.00 0.00 0.00 2.45
1020 1058 2.285220 CGAGTAAAAGCCCGTGATCATG 59.715 50.000 8.03 8.03 0.00 3.07
1021 1059 3.270877 GAGTAAAAGCCCGTGATCATGT 58.729 45.455 13.81 0.00 0.00 3.21
1022 1060 3.009723 AGTAAAAGCCCGTGATCATGTG 58.990 45.455 13.81 3.50 0.00 3.21
1023 1061 1.909700 AAAAGCCCGTGATCATGTGT 58.090 45.000 13.81 0.00 0.00 3.72
1024 1062 1.167851 AAAGCCCGTGATCATGTGTG 58.832 50.000 13.81 3.48 0.00 3.82
1025 1063 1.308069 AAGCCCGTGATCATGTGTGC 61.308 55.000 13.81 12.43 0.00 4.57
1026 1064 3.092403 CCCGTGATCATGTGTGCG 58.908 61.111 13.81 4.28 0.00 5.34
1027 1065 1.741401 CCCGTGATCATGTGTGCGT 60.741 57.895 13.81 0.00 0.00 5.24
1028 1066 1.421093 CCGTGATCATGTGTGCGTG 59.579 57.895 13.81 0.00 0.00 5.34
1029 1067 1.291184 CCGTGATCATGTGTGCGTGT 61.291 55.000 13.81 0.00 33.51 4.49
1030 1068 1.345410 CGTGATCATGTGTGCGTGTA 58.655 50.000 6.77 0.00 33.51 2.90
1031 1069 1.321445 CGTGATCATGTGTGCGTGTAG 59.679 52.381 6.77 0.00 33.51 2.74
1079 1117 2.200899 CAAAGGTTTGTTTGGCTTCGG 58.799 47.619 0.00 0.00 34.34 4.30
1117 1155 4.624015 AGACAACAATGCCATTCAGTTTG 58.376 39.130 0.00 0.00 0.00 2.93
1266 1333 2.549282 CGCCACTTTTCGGTCGTG 59.451 61.111 0.00 0.00 0.00 4.35
1406 1473 2.601067 TCGTTGGCCCGTCTACCA 60.601 61.111 0.00 0.00 0.00 3.25
1498 1568 2.438583 GACTCGGACGTCTACGAATTG 58.561 52.381 16.46 7.79 43.02 2.32
1843 1978 1.062002 CAATTGATACGGCGGTGTGTC 59.938 52.381 13.24 0.00 0.00 3.67
1846 1981 1.226888 GATACGGCGGTGTGTCTCC 60.227 63.158 13.24 0.00 0.00 3.71
2004 2145 6.991531 ACACATGTTGGCAATGTAAATTTCTT 59.008 30.769 1.92 0.00 0.00 2.52
2005 2146 7.498570 ACACATGTTGGCAATGTAAATTTCTTT 59.501 29.630 1.92 0.00 0.00 2.52
2097 2718 6.779539 CCTTAATTTGATCTGGCTTCCCTTAT 59.220 38.462 0.00 0.00 0.00 1.73
2104 2725 4.938575 TCTGGCTTCCCTTATTTAACCA 57.061 40.909 0.00 0.00 0.00 3.67
2186 2807 2.697363 CGACTTGCGTATGATTTGCTG 58.303 47.619 0.00 0.00 34.64 4.41
2209 2841 3.363970 CCGTCAGAAATTCAGAAACCACG 60.364 47.826 0.00 0.00 0.00 4.94
2211 2843 4.260620 CGTCAGAAATTCAGAAACCACGTT 60.261 41.667 0.00 0.00 0.00 3.99
2257 2890 4.767255 GGAGGCTGCTCACGTGGG 62.767 72.222 17.00 14.73 0.00 4.61
2653 3293 7.004086 TGTTCCTCTATCTTTTGTTGATTGGT 58.996 34.615 0.00 0.00 0.00 3.67
2656 3296 8.477419 TCCTCTATCTTTTGTTGATTGGTTTT 57.523 30.769 0.00 0.00 0.00 2.43
2692 3332 6.825944 TCATATTTCGTTGATTGGTTTGGA 57.174 33.333 0.00 0.00 0.00 3.53
2788 3428 5.895636 AAATATCCACGCAAATCTCAACA 57.104 34.783 0.00 0.00 0.00 3.33
2789 3429 6.455360 AAATATCCACGCAAATCTCAACAT 57.545 33.333 0.00 0.00 0.00 2.71
2790 3430 7.566760 AAATATCCACGCAAATCTCAACATA 57.433 32.000 0.00 0.00 0.00 2.29
2791 3431 7.566760 AATATCCACGCAAATCTCAACATAA 57.433 32.000 0.00 0.00 0.00 1.90
2792 3432 4.944962 TCCACGCAAATCTCAACATAAG 57.055 40.909 0.00 0.00 0.00 1.73
2793 3433 4.574892 TCCACGCAAATCTCAACATAAGA 58.425 39.130 0.00 0.00 0.00 2.10
2794 3434 5.185454 TCCACGCAAATCTCAACATAAGAT 58.815 37.500 0.00 0.00 34.96 2.40
2795 3435 5.647658 TCCACGCAAATCTCAACATAAGATT 59.352 36.000 0.00 0.00 43.58 2.40
2796 3436 6.821160 TCCACGCAAATCTCAACATAAGATTA 59.179 34.615 0.00 0.00 41.47 1.75
2797 3437 7.335673 TCCACGCAAATCTCAACATAAGATTAA 59.664 33.333 0.00 0.00 41.47 1.40
2798 3438 8.131100 CCACGCAAATCTCAACATAAGATTAAT 58.869 33.333 0.00 0.00 41.47 1.40
2799 3439 8.950961 CACGCAAATCTCAACATAAGATTAATG 58.049 33.333 0.00 0.00 41.47 1.90
2800 3440 8.892723 ACGCAAATCTCAACATAAGATTAATGA 58.107 29.630 0.00 0.00 41.47 2.57
2801 3441 9.720667 CGCAAATCTCAACATAAGATTAATGAA 57.279 29.630 0.00 0.00 41.47 2.57
2824 3464 9.890629 TGAAATAAGACTTAGATGTGCAATACT 57.109 29.630 0.73 0.00 0.00 2.12
2829 3469 8.668510 AAGACTTAGATGTGCAATACTTATGG 57.331 34.615 0.00 0.00 0.00 2.74
2830 3470 6.708054 AGACTTAGATGTGCAATACTTATGGC 59.292 38.462 0.00 0.00 33.16 4.40
2831 3471 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
2836 3476 3.260475 TGCAATACTTATGGCACGTCT 57.740 42.857 0.00 0.00 37.70 4.18
2837 3477 4.394439 TGCAATACTTATGGCACGTCTA 57.606 40.909 0.00 0.00 37.70 2.59
2838 3478 4.368315 TGCAATACTTATGGCACGTCTAG 58.632 43.478 0.00 0.00 37.70 2.43
2839 3479 4.098807 TGCAATACTTATGGCACGTCTAGA 59.901 41.667 0.00 0.00 37.70 2.43
2840 3480 5.221441 TGCAATACTTATGGCACGTCTAGAT 60.221 40.000 0.00 0.00 37.70 1.98
2841 3481 5.119279 GCAATACTTATGGCACGTCTAGATG 59.881 44.000 10.54 10.54 32.79 2.90
2842 3482 6.216569 CAATACTTATGGCACGTCTAGATGT 58.783 40.000 11.99 11.99 0.00 3.06
2912 3552 2.365582 ACAAATCATGTAAGGACCGGC 58.634 47.619 0.00 0.00 41.63 6.13
2913 3553 2.290641 ACAAATCATGTAAGGACCGGCA 60.291 45.455 0.00 0.00 41.63 5.69
2914 3554 2.951642 CAAATCATGTAAGGACCGGCAT 59.048 45.455 0.00 0.00 0.00 4.40
2915 3555 2.260844 ATCATGTAAGGACCGGCATG 57.739 50.000 0.00 6.23 39.81 4.06
2916 3556 1.199615 TCATGTAAGGACCGGCATGA 58.800 50.000 18.29 18.29 43.44 3.07
2917 3557 1.134521 TCATGTAAGGACCGGCATGAC 60.135 52.381 18.29 0.00 41.60 3.06
2918 3558 0.908910 ATGTAAGGACCGGCATGACA 59.091 50.000 0.00 1.76 0.00 3.58
2919 3559 0.687920 TGTAAGGACCGGCATGACAA 59.312 50.000 0.00 0.00 0.00 3.18
2920 3560 1.072489 TGTAAGGACCGGCATGACAAA 59.928 47.619 0.00 0.00 0.00 2.83
2921 3561 2.290641 TGTAAGGACCGGCATGACAAAT 60.291 45.455 0.00 0.00 0.00 2.32
2922 3562 1.923356 AAGGACCGGCATGACAAATT 58.077 45.000 0.00 0.00 0.00 1.82
2923 3563 1.463674 AGGACCGGCATGACAAATTC 58.536 50.000 0.00 0.00 0.00 2.17
2924 3564 1.173043 GGACCGGCATGACAAATTCA 58.827 50.000 0.00 0.00 39.11 2.57
2925 3565 1.543802 GGACCGGCATGACAAATTCAA 59.456 47.619 0.00 0.00 37.92 2.69
2926 3566 2.029470 GGACCGGCATGACAAATTCAAA 60.029 45.455 0.00 0.00 37.92 2.69
2927 3567 3.553922 GGACCGGCATGACAAATTCAAAA 60.554 43.478 0.00 0.00 37.92 2.44
2928 3568 3.652274 ACCGGCATGACAAATTCAAAAG 58.348 40.909 0.00 0.00 37.92 2.27
2929 3569 2.995258 CCGGCATGACAAATTCAAAAGG 59.005 45.455 0.00 0.00 37.92 3.11
2930 3570 3.554752 CCGGCATGACAAATTCAAAAGGT 60.555 43.478 0.00 0.00 37.92 3.50
2931 3571 4.321601 CCGGCATGACAAATTCAAAAGGTA 60.322 41.667 0.00 0.00 37.92 3.08
2932 3572 4.858692 CGGCATGACAAATTCAAAAGGTAG 59.141 41.667 0.00 0.00 37.92 3.18
2933 3573 4.627035 GGCATGACAAATTCAAAAGGTAGC 59.373 41.667 0.00 0.00 37.92 3.58
2934 3574 5.229423 GCATGACAAATTCAAAAGGTAGCA 58.771 37.500 0.00 0.00 37.92 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.124736 GGGGCGTATGAGCAAGCA 60.125 61.111 0.00 0.00 39.27 3.91
76 78 0.255604 TGGCGTGGATGATCATGGTT 59.744 50.000 14.30 0.00 0.00 3.67
102 104 6.095440 ACTGATTTCGATTACAATTGAAGGGG 59.905 38.462 13.59 0.00 39.34 4.79
103 105 6.968904 CACTGATTTCGATTACAATTGAAGGG 59.031 38.462 13.59 0.00 39.34 3.95
104 106 7.751732 TCACTGATTTCGATTACAATTGAAGG 58.248 34.615 13.59 0.00 39.34 3.46
105 107 9.055248 GTTCACTGATTTCGATTACAATTGAAG 57.945 33.333 13.59 0.00 39.34 3.02
107 109 7.233689 CGTTCACTGATTTCGATTACAATTGA 58.766 34.615 13.59 0.00 0.00 2.57
108 110 6.465781 CCGTTCACTGATTTCGATTACAATTG 59.534 38.462 3.24 3.24 0.00 2.32
109 111 6.403200 CCCGTTCACTGATTTCGATTACAATT 60.403 38.462 0.00 0.00 0.00 2.32
181 183 2.147958 GTTCGAACAATACCACTGCCA 58.852 47.619 23.12 0.00 0.00 4.92
190 192 3.530265 ATAGCGGTGGTTCGAACAATA 57.470 42.857 28.24 12.21 0.00 1.90
245 248 2.206750 TGTACTTGCTTCGCTTTTCGT 58.793 42.857 0.00 0.00 39.67 3.85
320 326 2.590291 TTCAACGGCGCTGCTTCA 60.590 55.556 18.15 0.00 0.00 3.02
366 373 0.978146 CCTTCATCCACTCCCTCCGT 60.978 60.000 0.00 0.00 0.00 4.69
399 406 2.027192 TGAAGCGCAAGAAGGTTCCTAT 60.027 45.455 11.47 0.00 43.21 2.57
426 434 1.704641 GAGAAGGTGGGCAAGGTTTT 58.295 50.000 0.00 0.00 0.00 2.43
655 664 3.157949 GAAGCCTCCTAGCCGCCT 61.158 66.667 0.00 0.00 0.00 5.52
663 672 3.801997 CCGCCATGGAAGCCTCCT 61.802 66.667 18.40 0.00 42.94 3.69
685 694 1.829533 CCATCTTCCCCGGCCATTG 60.830 63.158 2.24 0.00 0.00 2.82
837 863 8.459911 TCGTCCTCAACTATTAGATTCACATA 57.540 34.615 0.00 0.00 0.00 2.29
838 864 7.348080 TCGTCCTCAACTATTAGATTCACAT 57.652 36.000 0.00 0.00 0.00 3.21
850 876 3.135994 GGCAAAAGTTCGTCCTCAACTA 58.864 45.455 0.00 0.00 32.71 2.24
851 877 1.947456 GGCAAAAGTTCGTCCTCAACT 59.053 47.619 0.00 0.00 35.51 3.16
859 885 1.452145 ATGGTGCGGCAAAAGTTCGT 61.452 50.000 3.23 0.00 0.00 3.85
898 924 0.887387 ATGCTGCCCGTAACGTGTTT 60.887 50.000 0.00 0.00 0.00 2.83
899 925 0.887387 AATGCTGCCCGTAACGTGTT 60.887 50.000 0.00 0.00 0.00 3.32
907 933 1.285641 CGTGAAAAATGCTGCCCGT 59.714 52.632 0.00 0.00 0.00 5.28
921 959 2.360553 TAAAATACGGGTTCGCGTGA 57.639 45.000 21.44 0.00 40.63 4.35
932 970 9.853921 GACCCGTGAAATAACTATTAAAATACG 57.146 33.333 0.00 0.00 0.00 3.06
940 978 4.186159 CCGTGACCCGTGAAATAACTATT 58.814 43.478 0.00 0.00 33.66 1.73
942 980 2.674747 GCCGTGACCCGTGAAATAACTA 60.675 50.000 0.00 0.00 33.66 2.24
943 981 1.942586 GCCGTGACCCGTGAAATAACT 60.943 52.381 0.00 0.00 33.66 2.24
951 989 1.157870 GGATAATGCCGTGACCCGTG 61.158 60.000 0.00 0.00 33.66 4.94
964 1002 8.621126 ATCATCTCTAGCATTACCAGGATAAT 57.379 34.615 0.00 0.00 0.00 1.28
969 1007 5.999205 AGATCATCTCTAGCATTACCAGG 57.001 43.478 0.00 0.00 30.26 4.45
971 1009 7.013220 ACCTTAGATCATCTCTAGCATTACCA 58.987 38.462 0.00 0.00 37.75 3.25
974 1012 7.094162 CGGAACCTTAGATCATCTCTAGCATTA 60.094 40.741 0.00 0.00 37.75 1.90
975 1013 6.295011 CGGAACCTTAGATCATCTCTAGCATT 60.295 42.308 0.00 0.00 37.75 3.56
976 1014 5.184864 CGGAACCTTAGATCATCTCTAGCAT 59.815 44.000 0.00 0.00 37.75 3.79
988 1026 4.383880 GGGCTTTTACTCGGAACCTTAGAT 60.384 45.833 0.00 0.00 0.00 1.98
994 1032 0.321034 ACGGGCTTTTACTCGGAACC 60.321 55.000 0.00 0.00 0.00 3.62
996 1034 0.680618 TCACGGGCTTTTACTCGGAA 59.319 50.000 0.00 0.00 0.00 4.30
1003 1041 2.746904 CACACATGATCACGGGCTTTTA 59.253 45.455 0.00 0.00 0.00 1.52
1004 1042 1.541147 CACACATGATCACGGGCTTTT 59.459 47.619 0.00 0.00 0.00 2.27
1005 1043 1.167851 CACACATGATCACGGGCTTT 58.832 50.000 0.00 0.00 0.00 3.51
1006 1044 1.308069 GCACACATGATCACGGGCTT 61.308 55.000 0.00 0.00 0.00 4.35
1007 1045 1.746615 GCACACATGATCACGGGCT 60.747 57.895 0.00 0.00 0.00 5.19
1008 1046 2.793946 GCACACATGATCACGGGC 59.206 61.111 0.00 0.00 0.00 6.13
1009 1047 1.741401 ACGCACACATGATCACGGG 60.741 57.895 0.00 0.00 0.00 5.28
1010 1048 1.291184 ACACGCACACATGATCACGG 61.291 55.000 0.00 0.00 0.00 4.94
1011 1049 1.321445 CTACACGCACACATGATCACG 59.679 52.381 0.00 0.00 0.00 4.35
1012 1050 1.061131 GCTACACGCACACATGATCAC 59.939 52.381 0.00 0.00 38.92 3.06
1013 1051 1.337635 TGCTACACGCACACATGATCA 60.338 47.619 0.00 0.00 45.47 2.92
1014 1052 1.358877 TGCTACACGCACACATGATC 58.641 50.000 0.00 0.00 45.47 2.92
1015 1053 3.531073 TGCTACACGCACACATGAT 57.469 47.368 0.00 0.00 45.47 2.45
1024 1062 1.416434 GTCGAGCTTTGCTACACGC 59.584 57.895 0.00 0.00 39.88 5.34
1025 1063 1.696644 CGTCGAGCTTTGCTACACG 59.303 57.895 7.90 7.90 39.88 4.49
1026 1064 1.416434 GCGTCGAGCTTTGCTACAC 59.584 57.895 0.00 0.00 39.88 2.90
1027 1065 3.856508 GCGTCGAGCTTTGCTACA 58.143 55.556 0.00 0.00 39.88 2.74
1038 1076 2.693762 ATTTCGGACTCGGCGTCGA 61.694 57.895 13.29 13.29 43.79 4.20
1039 1077 2.202570 ATTTCGGACTCGGCGTCG 60.203 61.111 1.15 1.15 43.79 5.12
1079 1117 2.876645 CTCGAGGCTTGCGACGAC 60.877 66.667 3.91 0.00 33.71 4.34
1117 1155 0.036294 CCTGGAGTTTCCCGAGTTCC 60.036 60.000 0.00 0.00 35.03 3.62
1266 1333 2.356818 CTGGCCGGAGATCGACTTCC 62.357 65.000 5.28 6.91 42.43 3.46
1292 1359 0.108138 ACGAGCAGGCAGAACATACC 60.108 55.000 0.00 0.00 0.00 2.73
1294 1361 0.608130 ACACGAGCAGGCAGAACATA 59.392 50.000 0.00 0.00 0.00 2.29
1498 1568 4.400109 TGCTGCGTCGTCGTCTCC 62.400 66.667 3.66 0.00 39.49 3.71
1751 1883 4.391830 TCTTCACATTATTCCACGCTTGTC 59.608 41.667 0.00 0.00 0.00 3.18
1847 1982 3.240134 TTGAGTGAGCCGGACTGCC 62.240 63.158 5.05 0.00 0.00 4.85
1848 1983 1.739562 CTTGAGTGAGCCGGACTGC 60.740 63.158 5.05 0.00 0.00 4.40
1849 1984 1.668294 ACTTGAGTGAGCCGGACTG 59.332 57.895 5.05 0.00 0.00 3.51
1850 1985 4.199804 ACTTGAGTGAGCCGGACT 57.800 55.556 5.05 0.00 0.00 3.85
2004 2145 2.469274 TACGCATACGGGTTTTCCAA 57.531 45.000 0.00 0.00 46.04 3.53
2005 2146 2.695127 ATACGCATACGGGTTTTCCA 57.305 45.000 0.00 0.00 46.04 3.53
2186 2807 2.552315 TGGTTTCTGAATTTCTGACGGC 59.448 45.455 5.57 0.00 0.00 5.68
2209 2841 2.485122 CATCGCGAGGGCCAAAAC 59.515 61.111 16.66 0.00 35.02 2.43
2578 3218 0.176680 CAGGACAGGTAAGCGCAGAT 59.823 55.000 11.47 0.00 0.00 2.90
2662 3302 7.923888 ACCAATCAACGAAATATGATTCTCAG 58.076 34.615 0.00 0.00 42.72 3.35
2664 3304 9.013490 CAAACCAATCAACGAAATATGATTCTC 57.987 33.333 0.00 0.00 42.72 2.87
2673 3313 4.262420 CCCTTCCAAACCAATCAACGAAAT 60.262 41.667 0.00 0.00 0.00 2.17
2677 3317 1.336795 GCCCTTCCAAACCAATCAACG 60.337 52.381 0.00 0.00 0.00 4.10
2764 3404 6.686630 TGTTGAGATTTGCGTGGATATTTTT 58.313 32.000 0.00 0.00 0.00 1.94
2765 3405 6.266168 TGTTGAGATTTGCGTGGATATTTT 57.734 33.333 0.00 0.00 0.00 1.82
2766 3406 5.895636 TGTTGAGATTTGCGTGGATATTT 57.104 34.783 0.00 0.00 0.00 1.40
2767 3407 7.498900 TCTTATGTTGAGATTTGCGTGGATATT 59.501 33.333 0.00 0.00 0.00 1.28
2768 3408 6.992123 TCTTATGTTGAGATTTGCGTGGATAT 59.008 34.615 0.00 0.00 0.00 1.63
2769 3409 6.345298 TCTTATGTTGAGATTTGCGTGGATA 58.655 36.000 0.00 0.00 0.00 2.59
2770 3410 5.185454 TCTTATGTTGAGATTTGCGTGGAT 58.815 37.500 0.00 0.00 0.00 3.41
2771 3411 4.574892 TCTTATGTTGAGATTTGCGTGGA 58.425 39.130 0.00 0.00 0.00 4.02
2772 3412 4.944962 TCTTATGTTGAGATTTGCGTGG 57.055 40.909 0.00 0.00 0.00 4.94
2773 3413 8.950961 CATTAATCTTATGTTGAGATTTGCGTG 58.049 33.333 4.86 0.00 42.30 5.34
2774 3414 8.892723 TCATTAATCTTATGTTGAGATTTGCGT 58.107 29.630 4.86 0.00 42.30 5.24
2775 3415 9.720667 TTCATTAATCTTATGTTGAGATTTGCG 57.279 29.630 4.86 0.00 42.30 4.85
2798 3438 9.890629 AGTATTGCACATCTAAGTCTTATTTCA 57.109 29.630 0.00 0.00 0.00 2.69
2803 3443 9.764363 CCATAAGTATTGCACATCTAAGTCTTA 57.236 33.333 0.00 0.00 0.00 2.10
2804 3444 7.227512 GCCATAAGTATTGCACATCTAAGTCTT 59.772 37.037 0.00 0.00 0.00 3.01
2805 3445 6.708054 GCCATAAGTATTGCACATCTAAGTCT 59.292 38.462 0.00 0.00 0.00 3.24
2806 3446 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
2807 3447 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
2808 3448 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
2811 3451 8.797958 AGACGTGCCATAAGTATTGCACATCT 62.798 42.308 20.94 18.57 46.22 2.90
2815 3455 2.936498 AGACGTGCCATAAGTATTGCAC 59.064 45.455 14.49 14.49 46.12 4.57
2816 3456 3.260475 AGACGTGCCATAAGTATTGCA 57.740 42.857 0.00 0.00 32.69 4.08
2817 3457 4.617959 TCTAGACGTGCCATAAGTATTGC 58.382 43.478 0.00 0.00 0.00 3.56
2818 3458 6.144563 CACATCTAGACGTGCCATAAGTATTG 59.855 42.308 5.94 0.00 0.00 1.90
2819 3459 6.216569 CACATCTAGACGTGCCATAAGTATT 58.783 40.000 5.94 0.00 0.00 1.89
2820 3460 5.773575 CACATCTAGACGTGCCATAAGTAT 58.226 41.667 5.94 0.00 0.00 2.12
2821 3461 5.183014 CACATCTAGACGTGCCATAAGTA 57.817 43.478 5.94 0.00 0.00 2.24
2822 3462 4.046938 CACATCTAGACGTGCCATAAGT 57.953 45.455 5.94 0.00 0.00 2.24
2883 3523 9.125026 GGTCCTTACATGATTTGTATTTGATCT 57.875 33.333 0.00 0.00 40.46 2.75
2884 3524 8.070171 CGGTCCTTACATGATTTGTATTTGATC 58.930 37.037 0.00 0.00 40.46 2.92
2885 3525 7.013274 CCGGTCCTTACATGATTTGTATTTGAT 59.987 37.037 0.00 0.00 40.46 2.57
2886 3526 6.317642 CCGGTCCTTACATGATTTGTATTTGA 59.682 38.462 0.00 0.00 40.46 2.69
2887 3527 6.494842 CCGGTCCTTACATGATTTGTATTTG 58.505 40.000 0.00 0.00 40.46 2.32
2888 3528 5.067283 GCCGGTCCTTACATGATTTGTATTT 59.933 40.000 1.90 0.00 40.46 1.40
2889 3529 4.578928 GCCGGTCCTTACATGATTTGTATT 59.421 41.667 1.90 0.00 40.46 1.89
2890 3530 4.134563 GCCGGTCCTTACATGATTTGTAT 58.865 43.478 1.90 0.00 40.46 2.29
2891 3531 3.055021 TGCCGGTCCTTACATGATTTGTA 60.055 43.478 1.90 0.00 39.87 2.41
2892 3532 2.290641 TGCCGGTCCTTACATGATTTGT 60.291 45.455 1.90 0.00 42.62 2.83
2893 3533 2.364632 TGCCGGTCCTTACATGATTTG 58.635 47.619 1.90 0.00 0.00 2.32
2894 3534 2.799126 TGCCGGTCCTTACATGATTT 57.201 45.000 1.90 0.00 0.00 2.17
2895 3535 2.172505 TCATGCCGGTCCTTACATGATT 59.827 45.455 14.01 0.00 42.86 2.57
2896 3536 1.768275 TCATGCCGGTCCTTACATGAT 59.232 47.619 14.01 0.00 42.86 2.45
2897 3537 1.134521 GTCATGCCGGTCCTTACATGA 60.135 52.381 14.01 14.01 44.86 3.07
2898 3538 1.299541 GTCATGCCGGTCCTTACATG 58.700 55.000 1.90 7.25 40.97 3.21
2899 3539 0.908910 TGTCATGCCGGTCCTTACAT 59.091 50.000 1.90 0.00 0.00 2.29
2900 3540 0.687920 TTGTCATGCCGGTCCTTACA 59.312 50.000 1.90 0.00 0.00 2.41
2901 3541 1.816074 TTTGTCATGCCGGTCCTTAC 58.184 50.000 1.90 0.00 0.00 2.34
2902 3542 2.799126 ATTTGTCATGCCGGTCCTTA 57.201 45.000 1.90 0.00 0.00 2.69
2903 3543 1.818674 GAATTTGTCATGCCGGTCCTT 59.181 47.619 1.90 0.00 0.00 3.36
2904 3544 1.271871 TGAATTTGTCATGCCGGTCCT 60.272 47.619 1.90 0.00 0.00 3.85
2905 3545 1.173043 TGAATTTGTCATGCCGGTCC 58.827 50.000 1.90 0.00 0.00 4.46
2906 3546 3.296322 TTTGAATTTGTCATGCCGGTC 57.704 42.857 1.90 0.00 35.70 4.79
2907 3547 3.554752 CCTTTTGAATTTGTCATGCCGGT 60.555 43.478 1.90 0.00 35.70 5.28
2908 3548 2.995258 CCTTTTGAATTTGTCATGCCGG 59.005 45.455 0.00 0.00 35.70 6.13
2909 3549 3.652274 ACCTTTTGAATTTGTCATGCCG 58.348 40.909 0.00 0.00 35.70 5.69
2910 3550 4.627035 GCTACCTTTTGAATTTGTCATGCC 59.373 41.667 0.00 0.00 35.70 4.40
2911 3551 5.229423 TGCTACCTTTTGAATTTGTCATGC 58.771 37.500 0.00 0.00 35.70 4.06


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

AutoCloner maintained by Alex Coulton.