Multiple sequence alignment - TraesCS3D01G456200

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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 TraesCS3D01G456200 chr3D 100.000 2223 0 0 1 2223 562347087 562349309 0.000000e+00 4106
1 TraesCS3D01G456200 chr3D 100.000 1684 0 0 2426 4109 562349512 562351195 0.000000e+00 3110
2 TraesCS3D01G456200 chr3D 92.491 1891 101 6 1 1888 562432197 562434049 0.000000e+00 2667
3 TraesCS3D01G456200 chr3D 98.743 955 10 2 3156 4109 129451609 129450656 0.000000e+00 1696
4 TraesCS3D01G456200 chr3D 93.997 733 16 4 2426 3158 562436177 562436881 0.000000e+00 1085
5 TraesCS3D01G456200 chr3D 80.769 1092 189 16 1021 2105 561456376 561455299 0.000000e+00 833
6 TraesCS3D01G456200 chr3D 77.882 1275 212 38 970 2209 561711686 561710447 0.000000e+00 728
7 TraesCS3D01G456200 chr3D 78.228 1208 195 37 922 2104 562504126 562505290 0.000000e+00 712
8 TraesCS3D01G456200 chr3D 78.335 1177 192 40 948 2101 562545103 562546239 0.000000e+00 702
9 TraesCS3D01G456200 chr3D 96.232 345 12 1 1879 2223 562435810 562436153 7.710000e-157 564
10 TraesCS3D01G456200 chr3D 82.275 378 46 12 2649 3010 562385454 562385826 1.430000e-79 307
11 TraesCS3D01G456200 chr3D 77.579 504 73 24 2460 2938 562460849 562461337 6.770000e-68 268
12 TraesCS3D01G456200 chr3B 92.868 1304 78 4 924 2220 749648189 749649484 0.000000e+00 1879
13 TraesCS3D01G456200 chr3B 96.757 740 17 2 2426 3158 749649511 749650250 0.000000e+00 1227
14 TraesCS3D01G456200 chr3B 81.104 1196 181 21 1026 2204 749680333 749681500 0.000000e+00 915
15 TraesCS3D01G456200 chr3B 83.769 918 140 8 1025 1941 748779472 748778563 0.000000e+00 861
16 TraesCS3D01G456200 chr3B 79.917 1205 187 36 925 2104 749725701 749726875 0.000000e+00 833
17 TraesCS3D01G456200 chr3B 77.829 1290 215 38 962 2209 749025855 749024595 0.000000e+00 732
18 TraesCS3D01G456200 chr3B 77.825 1186 196 41 948 2101 749979287 749980437 0.000000e+00 671
19 TraesCS3D01G456200 chr3B 81.212 165 25 5 718 880 749647722 749647882 1.200000e-25 128
20 TraesCS3D01G456200 chr3B 91.765 85 7 0 2125 2209 749682070 749682154 7.220000e-23 119
21 TraesCS3D01G456200 chr3B 80.392 153 27 2 580 729 749725392 749725544 3.360000e-21 113
22 TraesCS3D01G456200 chr5D 98.849 956 9 2 3155 4109 293149126 293150080 0.000000e+00 1703
23 TraesCS3D01G456200 chr5D 98.848 955 8 3 3156 4109 179923938 179924890 0.000000e+00 1700
24 TraesCS3D01G456200 chr5D 98.846 953 8 3 3158 4109 214177740 214176790 0.000000e+00 1696
25 TraesCS3D01G456200 chr5D 98.845 952 8 3 3159 4109 342160291 342161240 0.000000e+00 1694
26 TraesCS3D01G456200 chr1D 98.847 954 9 2 3157 4109 204293845 204292893 0.000000e+00 1700
27 TraesCS3D01G456200 chr6D 98.846 953 8 3 3158 4109 68362820 68363770 0.000000e+00 1696
28 TraesCS3D01G456200 chr6D 98.846 953 8 3 3158 4109 433658409 433657459 0.000000e+00 1696
29 TraesCS3D01G456200 chrUn 98.845 952 8 3 3159 4109 90088877 90087928 0.000000e+00 1694
30 TraesCS3D01G456200 chr3A 81.835 1090 179 13 1022 2105 697391430 697390354 0.000000e+00 898
31 TraesCS3D01G456200 chr3A 78.051 1303 212 43 944 2209 697457515 697456250 0.000000e+00 754
32 TraesCS3D01G456200 chr3A 79.317 1054 165 29 1026 2068 697567791 697568802 0.000000e+00 689
33 TraesCS3D01G456200 chr3A 78.061 1176 193 39 948 2101 697679895 697681027 0.000000e+00 682
34 TraesCS3D01G456200 chr3A 77.403 770 132 29 1190 1946 697617717 697618457 1.770000e-113 420
35 TraesCS3D01G456200 chr3A 76.822 535 78 29 2428 2937 697569393 697569906 4.070000e-65 259
36 TraesCS3D01G456200 chr3A 87.624 202 22 2 696 896 697617444 697617643 8.880000e-57 231


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 TraesCS3D01G456200 chr3D 562347087 562351195 4108 False 3608.000000 4106 100.0000 1 4109 2 chr3D.!!$F5 4108
1 TraesCS3D01G456200 chr3D 129450656 129451609 953 True 1696.000000 1696 98.7430 3156 4109 1 chr3D.!!$R1 953
2 TraesCS3D01G456200 chr3D 562432197 562436881 4684 False 1438.666667 2667 94.2400 1 3158 3 chr3D.!!$F6 3157
3 TraesCS3D01G456200 chr3D 561455299 561456376 1077 True 833.000000 833 80.7690 1021 2105 1 chr3D.!!$R2 1084
4 TraesCS3D01G456200 chr3D 561710447 561711686 1239 True 728.000000 728 77.8820 970 2209 1 chr3D.!!$R3 1239
5 TraesCS3D01G456200 chr3D 562504126 562505290 1164 False 712.000000 712 78.2280 922 2104 1 chr3D.!!$F3 1182
6 TraesCS3D01G456200 chr3D 562545103 562546239 1136 False 702.000000 702 78.3350 948 2101 1 chr3D.!!$F4 1153
7 TraesCS3D01G456200 chr3B 749647722 749650250 2528 False 1078.000000 1879 90.2790 718 3158 3 chr3B.!!$F2 2440
8 TraesCS3D01G456200 chr3B 748778563 748779472 909 True 861.000000 861 83.7690 1025 1941 1 chr3B.!!$R1 916
9 TraesCS3D01G456200 chr3B 749024595 749025855 1260 True 732.000000 732 77.8290 962 2209 1 chr3B.!!$R2 1247
10 TraesCS3D01G456200 chr3B 749979287 749980437 1150 False 671.000000 671 77.8250 948 2101 1 chr3B.!!$F1 1153
11 TraesCS3D01G456200 chr3B 749680333 749682154 1821 False 517.000000 915 86.4345 1026 2209 2 chr3B.!!$F3 1183
12 TraesCS3D01G456200 chr3B 749725392 749726875 1483 False 473.000000 833 80.1545 580 2104 2 chr3B.!!$F4 1524
13 TraesCS3D01G456200 chr5D 293149126 293150080 954 False 1703.000000 1703 98.8490 3155 4109 1 chr5D.!!$F2 954
14 TraesCS3D01G456200 chr5D 179923938 179924890 952 False 1700.000000 1700 98.8480 3156 4109 1 chr5D.!!$F1 953
15 TraesCS3D01G456200 chr5D 214176790 214177740 950 True 1696.000000 1696 98.8460 3158 4109 1 chr5D.!!$R1 951
16 TraesCS3D01G456200 chr5D 342160291 342161240 949 False 1694.000000 1694 98.8450 3159 4109 1 chr5D.!!$F3 950
17 TraesCS3D01G456200 chr1D 204292893 204293845 952 True 1700.000000 1700 98.8470 3157 4109 1 chr1D.!!$R1 952
18 TraesCS3D01G456200 chr6D 68362820 68363770 950 False 1696.000000 1696 98.8460 3158 4109 1 chr6D.!!$F1 951
19 TraesCS3D01G456200 chr6D 433657459 433658409 950 True 1696.000000 1696 98.8460 3158 4109 1 chr6D.!!$R1 951
20 TraesCS3D01G456200 chrUn 90087928 90088877 949 True 1694.000000 1694 98.8450 3159 4109 1 chrUn.!!$R1 950
21 TraesCS3D01G456200 chr3A 697390354 697391430 1076 True 898.000000 898 81.8350 1022 2105 1 chr3A.!!$R1 1083
22 TraesCS3D01G456200 chr3A 697456250 697457515 1265 True 754.000000 754 78.0510 944 2209 1 chr3A.!!$R2 1265
23 TraesCS3D01G456200 chr3A 697679895 697681027 1132 False 682.000000 682 78.0610 948 2101 1 chr3A.!!$F1 1153
24 TraesCS3D01G456200 chr3A 697567791 697569906 2115 False 474.000000 689 78.0695 1026 2937 2 chr3A.!!$F2 1911
25 TraesCS3D01G456200 chr3A 697617444 697618457 1013 False 325.500000 420 82.5135 696 1946 2 chr3A.!!$F3 1250

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
957 1170 0.179001 CACCGAAACCCCTCCAAACT 60.179 55.000 0.00 0.00 0.0 2.66 F
1262 1519 0.685097 TACAAGTTCCTGCCGCTTCT 59.315 50.000 0.00 0.00 0.0 2.85 F
2016 4096 1.153269 TTGGTGTTGCTGCAGTCGA 60.153 52.632 16.64 4.76 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2710 5232 1.355005 TGTACGACATGGCATGAACG 58.645 50.000 32.74 31.99 38.58 3.95 R
3046 5570 3.181440 GGTGGCCAGATCATCATAAAGGA 60.181 47.826 5.11 0.00 0.00 3.36 R
3351 5875 0.752743 CCATGGATGGCGGTGTGATT 60.753 55.000 5.56 0.00 41.75 2.57 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
44 45 2.255252 GCCGTGTTGCCACATGAC 59.745 61.111 11.56 0.00 41.91 3.06
45 46 2.555782 CCGTGTTGCCACATGACG 59.444 61.111 11.56 2.33 41.91 4.35
46 47 2.555782 CGTGTTGCCACATGACGG 59.444 61.111 4.10 0.00 41.91 4.79
47 48 2.953821 GTGTTGCCACATGACGGG 59.046 61.111 0.00 0.00 41.44 5.28
68 69 1.361668 CGATGGTTTGACTGAGCCCG 61.362 60.000 0.00 0.00 0.00 6.13
125 126 9.454859 AGAATGTTTTAGTAGGAGAATTTGGAG 57.545 33.333 0.00 0.00 0.00 3.86
135 136 5.946486 AGGAGAATTTGGAGAAAGTGAAGT 58.054 37.500 0.00 0.00 0.00 3.01
137 138 7.518188 AGGAGAATTTGGAGAAAGTGAAGTAA 58.482 34.615 0.00 0.00 0.00 2.24
147 148 6.305693 AGAAAGTGAAGTAACATGCAAGAC 57.694 37.500 0.00 0.00 0.00 3.01
186 187 3.579151 AGAAAACTTTCCCTCTCGCTAGT 59.421 43.478 0.00 0.00 37.92 2.57
190 191 2.231721 ACTTTCCCTCTCGCTAGTGTTC 59.768 50.000 2.66 0.00 0.00 3.18
192 193 3.361281 TTCCCTCTCGCTAGTGTTCTA 57.639 47.619 2.66 0.00 0.00 2.10
209 210 2.724454 TCTAGTCCTCACAGGTGCTAC 58.276 52.381 0.00 0.00 36.53 3.58
255 256 2.588877 GGTGGGCGACGATGATGG 60.589 66.667 0.00 0.00 0.00 3.51
281 282 3.372554 GAGGCGGACTGGTGGCTAC 62.373 68.421 0.00 0.00 41.57 3.58
295 296 3.279434 GTGGCTACGATTCCCTTTTGAT 58.721 45.455 0.00 0.00 0.00 2.57
333 334 2.566010 CGGGGTTTGCAACGATGG 59.434 61.111 0.00 0.00 0.00 3.51
378 379 3.321396 GTCCTAGGGTCCTACTATGCAAC 59.679 52.174 9.46 0.00 0.00 4.17
434 435 1.859427 CGTTGGTGCTTGCTCATGCT 61.859 55.000 8.80 0.00 40.48 3.79
483 484 5.071923 TGATGAAGAGAGGATGAGATGCAAT 59.928 40.000 0.00 0.00 0.00 3.56
563 564 5.347907 AGTGTCCTAATCGAACGATGAAAAC 59.652 40.000 10.40 7.90 34.70 2.43
581 582 4.853924 AAACTGGACTGGCAAATTACTG 57.146 40.909 0.00 0.00 0.00 2.74
620 621 4.863131 GTGTTAGACGAAGATGGTGTAAGG 59.137 45.833 0.00 0.00 0.00 2.69
627 628 3.458189 GAAGATGGTGTAAGGGATGACG 58.542 50.000 0.00 0.00 0.00 4.35
628 629 2.467880 AGATGGTGTAAGGGATGACGT 58.532 47.619 0.00 0.00 0.00 4.34
629 630 2.168521 AGATGGTGTAAGGGATGACGTG 59.831 50.000 0.00 0.00 0.00 4.49
652 653 3.018149 GGGCACAATCCAACCGTTATTA 58.982 45.455 0.00 0.00 0.00 0.98
653 654 3.444388 GGGCACAATCCAACCGTTATTAA 59.556 43.478 0.00 0.00 0.00 1.40
654 655 4.098807 GGGCACAATCCAACCGTTATTAAT 59.901 41.667 0.00 0.00 0.00 1.40
670 671 7.011669 CCGTTATTAATGTTCTAATCCAACGGT 59.988 37.037 17.56 0.00 42.19 4.83
676 677 6.642707 ATGTTCTAATCCAACGGTGAAAAA 57.357 33.333 0.00 0.00 0.00 1.94
677 678 6.642707 TGTTCTAATCCAACGGTGAAAAAT 57.357 33.333 0.00 0.00 0.00 1.82
679 680 5.637006 TCTAATCCAACGGTGAAAAATGG 57.363 39.130 0.00 0.00 0.00 3.16
680 681 5.317808 TCTAATCCAACGGTGAAAAATGGA 58.682 37.500 0.00 0.00 43.79 3.41
681 682 3.934457 ATCCAACGGTGAAAAATGGAC 57.066 42.857 0.00 0.00 42.57 4.02
682 683 2.938838 TCCAACGGTGAAAAATGGACT 58.061 42.857 0.00 0.00 35.33 3.85
684 685 2.288152 CCAACGGTGAAAAATGGACTGG 60.288 50.000 0.00 0.00 32.82 4.00
685 686 0.958822 ACGGTGAAAAATGGACTGGC 59.041 50.000 0.00 0.00 0.00 4.85
686 687 0.958091 CGGTGAAAAATGGACTGGCA 59.042 50.000 0.00 0.00 0.00 4.92
687 688 1.068333 CGGTGAAAAATGGACTGGCAG 60.068 52.381 14.16 14.16 0.00 4.85
689 690 2.627699 GGTGAAAAATGGACTGGCAGAA 59.372 45.455 23.66 6.63 0.00 3.02
690 691 3.259123 GGTGAAAAATGGACTGGCAGAAT 59.741 43.478 23.66 8.84 0.00 2.40
692 693 5.402398 GTGAAAAATGGACTGGCAGAATAC 58.598 41.667 23.66 8.42 0.00 1.89
693 694 5.183904 GTGAAAAATGGACTGGCAGAATACT 59.816 40.000 23.66 0.00 0.00 2.12
694 695 5.774690 TGAAAAATGGACTGGCAGAATACTT 59.225 36.000 23.66 5.82 0.00 2.24
695 696 5.649782 AAAATGGACTGGCAGAATACTTG 57.350 39.130 23.66 0.00 0.00 3.16
696 697 4.574674 AATGGACTGGCAGAATACTTGA 57.425 40.909 23.66 0.00 0.00 3.02
698 699 2.237143 TGGACTGGCAGAATACTTGAGG 59.763 50.000 23.66 0.00 0.00 3.86
699 700 2.501723 GGACTGGCAGAATACTTGAGGA 59.498 50.000 23.66 0.00 0.00 3.71
700 701 3.135530 GGACTGGCAGAATACTTGAGGAT 59.864 47.826 23.66 0.00 0.00 3.24
701 702 4.125703 GACTGGCAGAATACTTGAGGATG 58.874 47.826 23.66 0.00 0.00 3.51
702 703 3.776969 ACTGGCAGAATACTTGAGGATGA 59.223 43.478 23.66 0.00 0.00 2.92
703 704 4.141756 ACTGGCAGAATACTTGAGGATGAG 60.142 45.833 23.66 0.00 0.00 2.90
704 705 4.033009 TGGCAGAATACTTGAGGATGAGA 58.967 43.478 0.00 0.00 0.00 3.27
705 706 4.657504 TGGCAGAATACTTGAGGATGAGAT 59.342 41.667 0.00 0.00 0.00 2.75
706 707 4.996122 GGCAGAATACTTGAGGATGAGATG 59.004 45.833 0.00 0.00 0.00 2.90
707 708 4.451774 GCAGAATACTTGAGGATGAGATGC 59.548 45.833 0.00 0.00 0.00 3.91
708 709 5.608449 CAGAATACTTGAGGATGAGATGCA 58.392 41.667 0.00 0.00 0.00 3.96
709 710 5.466058 CAGAATACTTGAGGATGAGATGCAC 59.534 44.000 0.00 0.00 0.00 4.57
715 716 0.897621 AGGATGAGATGCACGTGTGA 59.102 50.000 18.38 4.51 0.00 3.58
746 747 1.153229 GTAAGGGATGACGTGGGGC 60.153 63.158 0.00 0.00 0.00 5.80
759 760 3.068064 GGGGCCACAATCCAACCG 61.068 66.667 4.39 0.00 0.00 4.44
865 983 2.740714 GATGACGCGAGGGCACAAC 61.741 63.158 15.93 0.00 39.92 3.32
895 1015 8.975295 ACCCCGTTATTAGTGTCCTATATAATC 58.025 37.037 0.00 0.00 0.00 1.75
896 1016 8.133627 CCCCGTTATTAGTGTCCTATATAATCG 58.866 40.741 0.00 0.00 0.00 3.34
897 1017 7.646922 CCCGTTATTAGTGTCCTATATAATCGC 59.353 40.741 0.00 0.00 0.00 4.58
898 1018 8.186163 CCGTTATTAGTGTCCTATATAATCGCA 58.814 37.037 0.00 0.00 0.00 5.10
899 1019 9.007252 CGTTATTAGTGTCCTATATAATCGCAC 57.993 37.037 0.00 0.00 0.00 5.34
900 1020 9.007252 GTTATTAGTGTCCTATATAATCGCACG 57.993 37.037 0.00 0.00 0.00 5.34
901 1021 4.436242 AGTGTCCTATATAATCGCACGG 57.564 45.455 0.00 0.00 0.00 4.94
957 1170 0.179001 CACCGAAACCCCTCCAAACT 60.179 55.000 0.00 0.00 0.00 2.66
994 1226 2.339712 CCAAACTTTGGCTGGCCG 59.660 61.111 7.63 0.00 45.17 6.13
1188 1442 2.920912 TTCCTCCGCCACTTCCGT 60.921 61.111 0.00 0.00 0.00 4.69
1262 1519 0.685097 TACAAGTTCCTGCCGCTTCT 59.315 50.000 0.00 0.00 0.00 2.85
1498 1784 4.529219 CGCAGGCCGGCTCATACA 62.529 66.667 28.56 0.00 0.00 2.29
1767 2059 3.071479 GTCTAGATTTGGCCACGTCAAA 58.929 45.455 3.88 0.00 41.40 2.69
1847 2139 2.973406 GAGGGTTCCGGGATCTATCTTT 59.027 50.000 0.00 0.00 0.00 2.52
2016 4096 1.153269 TTGGTGTTGCTGCAGTCGA 60.153 52.632 16.64 4.76 0.00 4.20
2192 4686 1.758440 TATGATGACCTGGCCGCCTC 61.758 60.000 11.61 0.06 0.00 4.70
2633 5133 1.542915 ACTCTGCAATCAACACATGCC 59.457 47.619 0.00 0.00 39.31 4.40
2868 5392 3.965379 TCTAAGATTAACCGTGGTGCA 57.035 42.857 0.00 0.00 0.00 4.57
2887 5411 9.613428 GTGGTGCATATAAGATATTGCCTATAA 57.387 33.333 0.00 0.00 34.20 0.98
3008 5532 5.346281 GCTTGACGGCAGTGTATTAGATATC 59.654 44.000 0.00 0.00 0.00 1.63
3159 5683 9.920946 ATAATATTGTCACTGGGTATGACTTTT 57.079 29.630 6.68 0.00 45.58 2.27
3160 5684 8.650143 AATATTGTCACTGGGTATGACTTTTT 57.350 30.769 6.68 0.00 45.58 1.94
3337 5861 0.755698 TCCAGCCTAAGGAGCGGTAG 60.756 60.000 0.00 0.00 34.64 3.18
3351 5875 3.755378 GAGCGGTAGATCCTATCCGTAAA 59.245 47.826 13.89 0.00 44.07 2.01
3695 6219 2.351276 CCGTAGCCCAAACTGCCT 59.649 61.111 0.00 0.00 0.00 4.75
3867 6392 5.949952 TCTTAGGGGAATTTTTAGCTTCCAC 59.050 40.000 0.00 0.00 43.94 4.02
3868 6393 3.503827 GGGGAATTTTTAGCTTCCACG 57.496 47.619 0.00 0.00 42.29 4.94
4021 6546 5.070446 AGGCGAGTGAGTAATTCATTCCATA 59.930 40.000 0.00 0.00 38.85 2.74
4058 6583 3.308188 CCCAAAAGATCCCTACGGAAAGT 60.308 47.826 0.00 0.00 43.10 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.312052 GCAACACGGCCCATTAGA 57.688 55.556 0.00 0.00 0.00 2.10
44 45 2.046314 AGTCAAACCATCGCCCCG 60.046 61.111 0.00 0.00 0.00 5.73
45 46 1.002624 TCAGTCAAACCATCGCCCC 60.003 57.895 0.00 0.00 0.00 5.80
46 47 1.648467 GCTCAGTCAAACCATCGCCC 61.648 60.000 0.00 0.00 0.00 6.13
47 48 1.648467 GGCTCAGTCAAACCATCGCC 61.648 60.000 0.00 0.00 0.00 5.54
49 50 1.361668 CGGGCTCAGTCAAACCATCG 61.362 60.000 0.00 0.00 0.00 3.84
96 97 8.936864 CAAATTCTCCTACTAAAACATTCTCGT 58.063 33.333 0.00 0.00 0.00 4.18
98 99 9.449719 TCCAAATTCTCCTACTAAAACATTCTC 57.550 33.333 0.00 0.00 0.00 2.87
125 126 6.060028 TGTCTTGCATGTTACTTCACTTTC 57.940 37.500 0.00 0.00 0.00 2.62
147 148 1.229428 TCTTTCTCCGCAGCAAGTTG 58.771 50.000 0.00 0.00 0.00 3.16
186 187 1.618837 GCACCTGTGAGGACTAGAACA 59.381 52.381 0.51 0.00 37.67 3.18
190 191 1.402259 CGTAGCACCTGTGAGGACTAG 59.598 57.143 0.51 0.00 37.67 2.57
192 193 0.251209 TCGTAGCACCTGTGAGGACT 60.251 55.000 0.51 0.00 37.67 3.85
240 241 2.178876 AACACCATCATCGTCGCCCA 62.179 55.000 0.00 0.00 0.00 5.36
245 246 3.448686 CCTCTACAACACCATCATCGTC 58.551 50.000 0.00 0.00 0.00 4.20
255 256 0.389948 CCAGTCCGCCTCTACAACAC 60.390 60.000 0.00 0.00 0.00 3.32
281 282 3.546815 GCATCGTCATCAAAAGGGAATCG 60.547 47.826 0.00 0.00 0.00 3.34
295 296 2.942879 GCCGTGTTTGCATCGTCA 59.057 55.556 0.00 0.00 0.00 4.35
330 331 0.175073 GCGTAGAAGGTCGTTCCCAT 59.825 55.000 1.67 0.00 35.51 4.00
333 334 1.659098 CATTGCGTAGAAGGTCGTTCC 59.341 52.381 1.67 0.00 35.51 3.62
360 361 2.954318 GTCGTTGCATAGTAGGACCCTA 59.046 50.000 0.00 0.00 0.00 3.53
434 435 2.492088 CACACGGACATCTCAACCTCTA 59.508 50.000 0.00 0.00 0.00 2.43
483 484 3.942130 ACGTCATCTTCATCTCACACA 57.058 42.857 0.00 0.00 0.00 3.72
507 508 2.098934 GGATTGTGCCAATGCGTCATTA 59.901 45.455 5.31 0.00 41.78 1.90
508 509 1.135024 GGATTGTGCCAATGCGTCATT 60.135 47.619 5.31 0.09 41.78 2.57
563 564 4.326826 TCTTCAGTAATTTGCCAGTCCAG 58.673 43.478 0.00 0.00 0.00 3.86
581 582 4.923871 TCTAACACGTGCTTCTCATTCTTC 59.076 41.667 17.22 0.00 0.00 2.87
613 614 0.107848 CCCCACGTCATCCCTTACAC 60.108 60.000 0.00 0.00 0.00 2.90
620 621 2.837031 ATTGTGCCCCCACGTCATCC 62.837 60.000 0.00 0.00 45.04 3.51
627 628 2.282783 GGTTGGATTGTGCCCCCAC 61.283 63.158 0.00 0.00 42.40 4.61
628 629 2.119391 GGTTGGATTGTGCCCCCA 59.881 61.111 0.00 0.00 0.00 4.96
629 630 3.068064 CGGTTGGATTGTGCCCCC 61.068 66.667 0.00 0.00 0.00 5.40
652 653 6.642707 TTTTCACCGTTGGATTAGAACATT 57.357 33.333 0.00 0.00 0.00 2.71
653 654 6.642707 TTTTTCACCGTTGGATTAGAACAT 57.357 33.333 0.00 0.00 0.00 2.71
654 655 6.442952 CATTTTTCACCGTTGGATTAGAACA 58.557 36.000 0.00 0.00 0.00 3.18
670 671 5.324409 AGTATTCTGCCAGTCCATTTTTCA 58.676 37.500 0.00 0.00 0.00 2.69
676 677 3.118112 CCTCAAGTATTCTGCCAGTCCAT 60.118 47.826 0.00 0.00 0.00 3.41
677 678 2.237143 CCTCAAGTATTCTGCCAGTCCA 59.763 50.000 0.00 0.00 0.00 4.02
679 680 3.895232 TCCTCAAGTATTCTGCCAGTC 57.105 47.619 0.00 0.00 0.00 3.51
680 681 3.776969 TCATCCTCAAGTATTCTGCCAGT 59.223 43.478 0.00 0.00 0.00 4.00
681 682 4.100653 TCTCATCCTCAAGTATTCTGCCAG 59.899 45.833 0.00 0.00 0.00 4.85
682 683 4.033009 TCTCATCCTCAAGTATTCTGCCA 58.967 43.478 0.00 0.00 0.00 4.92
684 685 4.451774 GCATCTCATCCTCAAGTATTCTGC 59.548 45.833 0.00 0.00 0.00 4.26
685 686 5.466058 GTGCATCTCATCCTCAAGTATTCTG 59.534 44.000 0.00 0.00 0.00 3.02
686 687 5.609423 GTGCATCTCATCCTCAAGTATTCT 58.391 41.667 0.00 0.00 0.00 2.40
687 688 4.447054 CGTGCATCTCATCCTCAAGTATTC 59.553 45.833 0.00 0.00 0.00 1.75
689 690 3.386078 ACGTGCATCTCATCCTCAAGTAT 59.614 43.478 0.00 0.00 0.00 2.12
690 691 2.760650 ACGTGCATCTCATCCTCAAGTA 59.239 45.455 0.00 0.00 0.00 2.24
692 693 1.931841 CACGTGCATCTCATCCTCAAG 59.068 52.381 0.82 0.00 0.00 3.02
693 694 1.276138 ACACGTGCATCTCATCCTCAA 59.724 47.619 17.22 0.00 0.00 3.02
694 695 0.897621 ACACGTGCATCTCATCCTCA 59.102 50.000 17.22 0.00 0.00 3.86
695 696 1.134995 TCACACGTGCATCTCATCCTC 60.135 52.381 17.22 0.00 0.00 3.71
696 697 0.897621 TCACACGTGCATCTCATCCT 59.102 50.000 17.22 0.00 0.00 3.24
698 699 1.923204 GTCTCACACGTGCATCTCATC 59.077 52.381 17.22 0.00 0.00 2.92
699 700 1.733718 CGTCTCACACGTGCATCTCAT 60.734 52.381 17.22 0.00 44.07 2.90
700 701 0.387239 CGTCTCACACGTGCATCTCA 60.387 55.000 17.22 0.00 44.07 3.27
701 702 2.353807 CGTCTCACACGTGCATCTC 58.646 57.895 17.22 3.02 44.07 2.75
702 703 4.559835 CGTCTCACACGTGCATCT 57.440 55.556 17.22 0.00 44.07 2.90
715 716 2.719739 TCCCTTACGTCATCTTCGTCT 58.280 47.619 0.00 0.00 41.72 4.18
746 747 4.698304 ACACTAATAACGGTTGGATTGTGG 59.302 41.667 3.07 0.00 0.00 4.17
865 983 2.635714 GACACTAATAACGGGGTTGGG 58.364 52.381 0.00 0.00 0.00 4.12
895 1015 1.801913 CTTCCTCTTCGACCGTGCG 60.802 63.158 0.00 0.00 0.00 5.34
896 1016 1.446272 CCTTCCTCTTCGACCGTGC 60.446 63.158 0.00 0.00 0.00 5.34
897 1017 0.601558 TTCCTTCCTCTTCGACCGTG 59.398 55.000 0.00 0.00 0.00 4.94
898 1018 1.000618 GTTTCCTTCCTCTTCGACCGT 59.999 52.381 0.00 0.00 0.00 4.83
899 1019 1.711206 GTTTCCTTCCTCTTCGACCG 58.289 55.000 0.00 0.00 0.00 4.79
900 1020 1.711206 CGTTTCCTTCCTCTTCGACC 58.289 55.000 0.00 0.00 0.00 4.79
901 1021 1.069255 GCGTTTCCTTCCTCTTCGAC 58.931 55.000 0.00 0.00 0.00 4.20
957 1170 1.568118 GGGATTTTCCGGTGGGAGGA 61.568 60.000 0.00 0.00 44.98 3.71
994 1226 1.136305 TCGATCTCCGTCCATGGTTTC 59.864 52.381 12.58 3.06 39.75 2.78
1066 1319 4.421479 CTCGCGCAGGAGGTCGTT 62.421 66.667 8.75 0.00 0.00 3.85
1485 1771 1.819632 CCTTGTGTATGAGCCGGCC 60.820 63.158 26.15 15.80 0.00 6.13
1486 1772 1.819632 CCCTTGTGTATGAGCCGGC 60.820 63.158 21.89 21.89 0.00 6.13
1487 1773 1.153168 CCCCTTGTGTATGAGCCGG 60.153 63.158 0.00 0.00 0.00 6.13
1488 1774 0.828022 TACCCCTTGTGTATGAGCCG 59.172 55.000 0.00 0.00 0.00 5.52
1495 1781 4.710375 GTCTGAGAGAATACCCCTTGTGTA 59.290 45.833 0.00 0.00 0.00 2.90
1498 1784 4.067944 AGTCTGAGAGAATACCCCTTGT 57.932 45.455 0.00 0.00 0.00 3.16
1767 2059 2.303311 GGTAGCTCAAGGGTGAAGAAGT 59.697 50.000 0.00 0.00 31.88 3.01
1847 2139 2.655090 TGAAACCCATCTGCACTGAA 57.345 45.000 0.00 0.00 0.00 3.02
2016 4096 5.564550 AGAATACAAACTCAGCATTGTCCT 58.435 37.500 0.00 0.00 40.14 3.85
2123 4617 5.130350 ACCCGGACGAATAAAATGATGATT 58.870 37.500 0.73 0.00 0.00 2.57
2181 4675 2.751837 GGAAAAGAGGCGGCCAGG 60.752 66.667 23.09 0.00 0.00 4.45
2192 4686 2.951642 TGTTCTTCAGTGCAGGGAAAAG 59.048 45.455 0.00 0.00 0.00 2.27
2633 5133 1.659098 GCCTATCGAACAAACAGGACG 59.341 52.381 0.00 0.00 0.00 4.79
2710 5232 1.355005 TGTACGACATGGCATGAACG 58.645 50.000 32.74 31.99 38.58 3.95
2887 5411 8.606830 ACCTACTGTTTCAGGAAGAGAAATAAT 58.393 33.333 2.19 0.00 37.33 1.28
3008 5532 3.719173 TCAAAACAAGGTAAAAGGGCG 57.281 42.857 0.00 0.00 0.00 6.13
3046 5570 3.181440 GGTGGCCAGATCATCATAAAGGA 60.181 47.826 5.11 0.00 0.00 3.36
3159 5683 8.580720 TCAATGAAATGTCCTTTATCGGAAAAA 58.419 29.630 0.00 0.00 34.20 1.94
3160 5684 8.116651 TCAATGAAATGTCCTTTATCGGAAAA 57.883 30.769 0.00 0.00 34.20 2.29
3161 5685 7.695480 TCAATGAAATGTCCTTTATCGGAAA 57.305 32.000 0.00 0.00 34.20 3.13
3162 5686 7.695480 TTCAATGAAATGTCCTTTATCGGAA 57.305 32.000 0.00 0.00 34.20 4.30
3163 5687 7.880160 ATTCAATGAAATGTCCTTTATCGGA 57.120 32.000 0.00 0.00 0.00 4.55
3164 5688 9.056005 TCTATTCAATGAAATGTCCTTTATCGG 57.944 33.333 0.00 0.00 0.00 4.18
3337 5861 4.684703 CGGTGTGATTTTACGGATAGGATC 59.315 45.833 0.00 0.00 0.00 3.36
3351 5875 0.752743 CCATGGATGGCGGTGTGATT 60.753 55.000 5.56 0.00 41.75 2.57
3405 5929 6.017109 GGACATTTTTATGATGGCGTCTACAT 60.017 38.462 8.40 5.11 33.17 2.29
4021 6546 1.399744 TTGGGCACTCGTCTGACAGT 61.400 55.000 8.73 7.69 0.00 3.55
4058 6583 4.042174 AGGACAGGAAAACCCCGATATTA 58.958 43.478 0.00 0.00 34.66 0.98


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

AutoCloner maintained by Alex Coulton.