Multiple sequence alignment - TraesCS2B01G574700

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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 TraesCS2B01G574700 chr2B 100.000 4863 0 0 1 4863 763903352 763898490 0.000000e+00 8981
1 TraesCS2B01G574700 chr2B 95.343 816 34 3 4052 4863 53013234 53014049 0.000000e+00 1293
2 TraesCS2B01G574700 chr2B 95.343 816 34 3 4052 4863 369693286 369694101 0.000000e+00 1293
3 TraesCS2B01G574700 chr2B 95.098 816 36 3 4052 4863 364805925 364805110 0.000000e+00 1282
4 TraesCS2B01G574700 chr2B 74.259 1383 323 28 1592 2953 20317479 20316109 7.110000e-153 551
5 TraesCS2B01G574700 chr2B 77.656 913 116 41 3081 3953 163569059 163568195 4.400000e-130 475
6 TraesCS2B01G574700 chr2B 90.270 185 17 1 3878 4062 240317886 240318069 1.750000e-59 241
7 TraesCS2B01G574700 chr5A 96.650 3851 116 11 76 3920 239953898 239950055 0.000000e+00 6384
8 TraesCS2B01G574700 chr5A 96.573 2976 93 6 76 3047 174058971 174061941 0.000000e+00 4922
9 TraesCS2B01G574700 chr5A 95.224 984 41 3 3073 4056 174099238 174100215 0.000000e+00 1552
10 TraesCS2B01G574700 chr6A 97.846 2971 58 5 1088 4055 19370920 19367953 0.000000e+00 5127
11 TraesCS2B01G574700 chr6A 96.418 977 27 6 76 1048 19371994 19371022 0.000000e+00 1604
12 TraesCS2B01G574700 chr6A 84.615 988 96 28 76 1039 290807958 290807003 0.000000e+00 931
13 TraesCS2B01G574700 chr4B 97.379 1450 34 4 2608 4055 383136738 383138185 0.000000e+00 2464
14 TraesCS2B01G574700 chr4B 95.343 816 34 3 4052 4863 341638173 341638988 0.000000e+00 1293
15 TraesCS2B01G574700 chr4B 96.032 126 5 0 81 206 383136745 383136620 6.380000e-49 206
16 TraesCS2B01G574700 chr4B 98.667 75 1 0 1 75 1036905 1036979 3.050000e-27 134
17 TraesCS2B01G574700 chr4B 97.436 78 2 0 1 78 324379575 324379498 3.050000e-27 134
18 TraesCS2B01G574700 chr4B 97.436 78 2 0 1 78 489835029 489834952 3.050000e-27 134
19 TraesCS2B01G574700 chr4B 98.667 75 1 0 1 75 497624724 497624798 3.050000e-27 134
20 TraesCS2B01G574700 chr7B 95.466 816 33 3 4052 4863 653975172 653975987 0.000000e+00 1299
21 TraesCS2B01G574700 chr7B 82.969 229 36 2 75 303 346998925 346998700 2.290000e-48 204
22 TraesCS2B01G574700 chr4A 95.221 816 35 3 4052 4863 653107756 653106941 0.000000e+00 1288
23 TraesCS2B01G574700 chr4A 98.667 75 1 0 1 75 712508232 712508306 3.050000e-27 134
24 TraesCS2B01G574700 chr6B 95.098 816 36 3 4052 4863 645836994 645837809 0.000000e+00 1282
25 TraesCS2B01G574700 chr3B 94.853 816 38 3 4052 4863 310956782 310955967 0.000000e+00 1271
26 TraesCS2B01G574700 chr3B 74.224 1385 320 30 1592 2953 191574104 191575474 3.310000e-151 545
27 TraesCS2B01G574700 chr1B 94.730 816 39 3 4052 4863 38098157 38098972 0.000000e+00 1266
28 TraesCS2B01G574700 chr1B 77.661 573 128 0 1592 2164 12840993 12841565 2.790000e-92 350
29 TraesCS2B01G574700 chr5B 92.443 794 53 5 3265 4055 147658895 147659684 0.000000e+00 1127
30 TraesCS2B01G574700 chr5B 90.669 493 38 4 379 869 147658413 147658899 0.000000e+00 649
31 TraesCS2B01G574700 chr5B 74.003 1154 256 35 1829 2953 590385028 590386166 3.480000e-116 429
32 TraesCS2B01G574700 chr5B 91.061 179 16 0 3878 4056 611566486 611566308 4.860000e-60 243
33 TraesCS2B01G574700 chr5B 98.667 75 1 0 1 75 53725278 53725352 3.050000e-27 134
34 TraesCS2B01G574700 chr5B 97.436 78 2 0 1 78 369294135 369294058 3.050000e-27 134
35 TraesCS2B01G574700 chr5B 97.436 78 2 0 1 78 485476855 485476778 3.050000e-27 134
36 TraesCS2B01G574700 chr5B 97.436 78 2 0 1 78 505919312 505919235 3.050000e-27 134
37 TraesCS2B01G574700 chr6D 93.041 388 27 0 3672 4059 233778712 233778325 7.060000e-158 568
38 TraesCS2B01G574700 chr6D 92.029 276 21 1 76 350 233779011 233778736 2.120000e-103 387
39 TraesCS2B01G574700 chr3D 73.612 1387 326 33 1592 2953 212267945 212269316 9.400000e-137 497
40 TraesCS2B01G574700 chr3D 74.933 742 173 10 1867 2604 553176157 553175425 1.310000e-85 327
41 TraesCS2B01G574700 chr2A 77.741 903 122 33 3083 3953 114674846 114675701 9.470000e-132 481
42 TraesCS2B01G574700 chr7D 89.340 197 21 0 76 272 465869245 465869441 1.050000e-61 248
43 TraesCS2B01G574700 chr1A 92.045 176 14 0 3880 4055 139542183 139542008 1.050000e-61 248
44 TraesCS2B01G574700 chr1A 91.209 182 14 2 3880 4060 559715513 559715333 3.760000e-61 246
45 TraesCS2B01G574700 chr3A 86.000 200 28 0 73 272 388977028 388977227 1.060000e-51 215


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 TraesCS2B01G574700 chr2B 763898490 763903352 4862 True 8981.0 8981 100.000 1 4863 1 chr2B.!!$R4 4862
1 TraesCS2B01G574700 chr2B 53013234 53014049 815 False 1293.0 1293 95.343 4052 4863 1 chr2B.!!$F1 811
2 TraesCS2B01G574700 chr2B 369693286 369694101 815 False 1293.0 1293 95.343 4052 4863 1 chr2B.!!$F3 811
3 TraesCS2B01G574700 chr2B 364805110 364805925 815 True 1282.0 1282 95.098 4052 4863 1 chr2B.!!$R3 811
4 TraesCS2B01G574700 chr2B 20316109 20317479 1370 True 551.0 551 74.259 1592 2953 1 chr2B.!!$R1 1361
5 TraesCS2B01G574700 chr2B 163568195 163569059 864 True 475.0 475 77.656 3081 3953 1 chr2B.!!$R2 872
6 TraesCS2B01G574700 chr5A 239950055 239953898 3843 True 6384.0 6384 96.650 76 3920 1 chr5A.!!$R1 3844
7 TraesCS2B01G574700 chr5A 174058971 174061941 2970 False 4922.0 4922 96.573 76 3047 1 chr5A.!!$F1 2971
8 TraesCS2B01G574700 chr5A 174099238 174100215 977 False 1552.0 1552 95.224 3073 4056 1 chr5A.!!$F2 983
9 TraesCS2B01G574700 chr6A 19367953 19371994 4041 True 3365.5 5127 97.132 76 4055 2 chr6A.!!$R2 3979
10 TraesCS2B01G574700 chr6A 290807003 290807958 955 True 931.0 931 84.615 76 1039 1 chr6A.!!$R1 963
11 TraesCS2B01G574700 chr4B 383136738 383138185 1447 False 2464.0 2464 97.379 2608 4055 1 chr4B.!!$F3 1447
12 TraesCS2B01G574700 chr4B 341638173 341638988 815 False 1293.0 1293 95.343 4052 4863 1 chr4B.!!$F2 811
13 TraesCS2B01G574700 chr7B 653975172 653975987 815 False 1299.0 1299 95.466 4052 4863 1 chr7B.!!$F1 811
14 TraesCS2B01G574700 chr4A 653106941 653107756 815 True 1288.0 1288 95.221 4052 4863 1 chr4A.!!$R1 811
15 TraesCS2B01G574700 chr6B 645836994 645837809 815 False 1282.0 1282 95.098 4052 4863 1 chr6B.!!$F1 811
16 TraesCS2B01G574700 chr3B 310955967 310956782 815 True 1271.0 1271 94.853 4052 4863 1 chr3B.!!$R1 811
17 TraesCS2B01G574700 chr3B 191574104 191575474 1370 False 545.0 545 74.224 1592 2953 1 chr3B.!!$F1 1361
18 TraesCS2B01G574700 chr1B 38098157 38098972 815 False 1266.0 1266 94.730 4052 4863 1 chr1B.!!$F2 811
19 TraesCS2B01G574700 chr1B 12840993 12841565 572 False 350.0 350 77.661 1592 2164 1 chr1B.!!$F1 572
20 TraesCS2B01G574700 chr5B 147658413 147659684 1271 False 888.0 1127 91.556 379 4055 2 chr5B.!!$F3 3676
21 TraesCS2B01G574700 chr5B 590385028 590386166 1138 False 429.0 429 74.003 1829 2953 1 chr5B.!!$F2 1124
22 TraesCS2B01G574700 chr6D 233778325 233779011 686 True 477.5 568 92.535 76 4059 2 chr6D.!!$R1 3983
23 TraesCS2B01G574700 chr3D 212267945 212269316 1371 False 497.0 497 73.612 1592 2953 1 chr3D.!!$F1 1361
24 TraesCS2B01G574700 chr3D 553175425 553176157 732 True 327.0 327 74.933 1867 2604 1 chr3D.!!$R1 737
25 TraesCS2B01G574700 chr2A 114674846 114675701 855 False 481.0 481 77.741 3083 3953 1 chr2A.!!$F1 870

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
64 65 0.034477 CCCTTGTAACCCGGCATCTT 60.034 55.000 0.00 0.0 0.0 2.40 F
465 470 0.107410 TGAACGTGAGGTGGCTTGTT 60.107 50.000 0.00 0.0 0.0 2.83 F
468 473 0.108585 ACGTGAGGTGGCTTGTTGAT 59.891 50.000 0.00 0.0 0.0 2.57 F
1582 1671 1.200948 GAACTGCTCAAGGAACCATGC 59.799 52.381 0.00 0.0 0.0 4.06 F
2073 2163 5.620738 AAGCAGCTGGTGATCTCTTAATA 57.379 39.130 20.97 0.0 0.0 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1671 5.588648 TCTCTTCCTTTTTGTAGTGTTGGTG 59.411 40.000 0.0 0.0 0.00 4.17 R
2646 2768 7.980742 AAAATCGGTGAAACAAAGAAAGTAC 57.019 32.000 0.0 0.0 39.98 2.73 R
2841 2965 6.833416 CCCTTTCATTTACATCAGGAACCATA 59.167 38.462 0.0 0.0 0.00 2.74 R
3794 3936 2.023598 TCATCCCCATTATTGTTGGCCA 60.024 45.455 0.0 0.0 32.60 5.36 R
4085 4245 2.096909 CGACCGGCTTATGCTAAATTCG 60.097 50.000 0.0 0.0 39.59 3.34 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
17 18 4.841441 TCACATTCCAAGGCCACC 57.159 55.556 5.01 0.00 0.00 4.61
18 19 2.163454 TCACATTCCAAGGCCACCT 58.837 52.632 5.01 0.00 33.87 4.00
19 20 0.482446 TCACATTCCAAGGCCACCTT 59.518 50.000 5.01 0.00 45.88 3.50
20 21 1.133199 TCACATTCCAAGGCCACCTTT 60.133 47.619 5.01 0.00 41.69 3.11
21 22 1.273327 CACATTCCAAGGCCACCTTTC 59.727 52.381 5.01 0.00 41.69 2.62
22 23 1.133199 ACATTCCAAGGCCACCTTTCA 60.133 47.619 5.01 0.00 41.69 2.69
23 24 1.969923 CATTCCAAGGCCACCTTTCAA 59.030 47.619 5.01 0.00 41.69 2.69
24 25 1.408969 TTCCAAGGCCACCTTTCAAC 58.591 50.000 5.01 0.00 41.69 3.18
25 26 0.555769 TCCAAGGCCACCTTTCAACT 59.444 50.000 5.01 0.00 41.69 3.16
26 27 0.961753 CCAAGGCCACCTTTCAACTC 59.038 55.000 5.01 0.00 41.69 3.01
27 28 0.961753 CAAGGCCACCTTTCAACTCC 59.038 55.000 5.01 0.00 41.69 3.85
28 29 0.178961 AAGGCCACCTTTCAACTCCC 60.179 55.000 5.01 0.00 41.69 4.30
29 30 1.152830 GGCCACCTTTCAACTCCCA 59.847 57.895 0.00 0.00 0.00 4.37
30 31 0.251787 GGCCACCTTTCAACTCCCAT 60.252 55.000 0.00 0.00 0.00 4.00
31 32 0.890683 GCCACCTTTCAACTCCCATG 59.109 55.000 0.00 0.00 0.00 3.66
32 33 0.890683 CCACCTTTCAACTCCCATGC 59.109 55.000 0.00 0.00 0.00 4.06
33 34 1.619654 CACCTTTCAACTCCCATGCA 58.380 50.000 0.00 0.00 0.00 3.96
34 35 1.270550 CACCTTTCAACTCCCATGCAC 59.729 52.381 0.00 0.00 0.00 4.57
35 36 1.133513 ACCTTTCAACTCCCATGCACA 60.134 47.619 0.00 0.00 0.00 4.57
36 37 1.542915 CCTTTCAACTCCCATGCACAG 59.457 52.381 0.00 0.00 0.00 3.66
37 38 2.233271 CTTTCAACTCCCATGCACAGT 58.767 47.619 0.00 0.00 0.00 3.55
38 39 1.608055 TTCAACTCCCATGCACAGTG 58.392 50.000 0.00 0.00 0.00 3.66
39 40 0.764271 TCAACTCCCATGCACAGTGA 59.236 50.000 4.15 0.00 0.00 3.41
40 41 1.352017 TCAACTCCCATGCACAGTGAT 59.648 47.619 4.15 0.00 0.00 3.06
41 42 1.471287 CAACTCCCATGCACAGTGATG 59.529 52.381 4.15 5.46 0.00 3.07
42 43 0.034767 ACTCCCATGCACAGTGATGG 60.035 55.000 18.35 18.35 39.18 3.51
43 44 0.034767 CTCCCATGCACAGTGATGGT 60.035 55.000 21.28 0.00 37.96 3.55
44 45 0.322726 TCCCATGCACAGTGATGGTG 60.323 55.000 21.28 15.76 37.96 4.17
49 50 4.828409 CACAGTGATGGTGCCCTT 57.172 55.556 0.00 0.00 0.00 3.95
50 51 2.260247 CACAGTGATGGTGCCCTTG 58.740 57.895 0.00 0.00 0.00 3.61
51 52 0.538057 CACAGTGATGGTGCCCTTGT 60.538 55.000 0.00 0.00 0.00 3.16
52 53 1.064003 ACAGTGATGGTGCCCTTGTA 58.936 50.000 0.00 0.00 0.00 2.41
53 54 1.423541 ACAGTGATGGTGCCCTTGTAA 59.576 47.619 0.00 0.00 0.00 2.41
54 55 1.812571 CAGTGATGGTGCCCTTGTAAC 59.187 52.381 0.00 0.00 0.00 2.50
55 56 1.173913 GTGATGGTGCCCTTGTAACC 58.826 55.000 0.00 0.00 34.38 2.85
56 57 0.039035 TGATGGTGCCCTTGTAACCC 59.961 55.000 0.00 0.00 32.70 4.11
57 58 1.001393 ATGGTGCCCTTGTAACCCG 60.001 57.895 0.00 0.00 32.70 5.28
58 59 2.360726 GGTGCCCTTGTAACCCGG 60.361 66.667 0.00 0.00 0.00 5.73
59 60 3.060000 GTGCCCTTGTAACCCGGC 61.060 66.667 0.00 0.00 41.99 6.13
61 62 2.044352 GCCCTTGTAACCCGGCAT 60.044 61.111 0.00 0.00 41.25 4.40
62 63 2.119029 GCCCTTGTAACCCGGCATC 61.119 63.158 0.00 0.00 41.25 3.91
63 64 1.607612 CCCTTGTAACCCGGCATCT 59.392 57.895 0.00 0.00 0.00 2.90
64 65 0.034477 CCCTTGTAACCCGGCATCTT 60.034 55.000 0.00 0.00 0.00 2.40
65 66 1.094785 CCTTGTAACCCGGCATCTTG 58.905 55.000 0.00 0.00 0.00 3.02
66 67 1.339631 CCTTGTAACCCGGCATCTTGA 60.340 52.381 0.00 0.00 0.00 3.02
67 68 2.009774 CTTGTAACCCGGCATCTTGAG 58.990 52.381 0.00 0.00 0.00 3.02
68 69 0.392461 TGTAACCCGGCATCTTGAGC 60.392 55.000 0.00 0.00 0.00 4.26
69 70 0.107654 GTAACCCGGCATCTTGAGCT 60.108 55.000 0.00 0.00 0.00 4.09
70 71 0.107703 TAACCCGGCATCTTGAGCTG 60.108 55.000 0.00 0.00 38.10 4.24
71 72 2.129555 AACCCGGCATCTTGAGCTGT 62.130 55.000 0.00 0.00 36.64 4.40
72 73 1.264749 ACCCGGCATCTTGAGCTGTA 61.265 55.000 0.00 0.00 36.64 2.74
73 74 0.107703 CCCGGCATCTTGAGCTGTAA 60.108 55.000 0.00 0.00 36.64 2.41
74 75 1.293924 CCGGCATCTTGAGCTGTAAG 58.706 55.000 0.00 0.00 36.64 2.34
131 132 4.201657 TCCTACGATTTCACGATCCTACA 58.798 43.478 0.00 0.00 37.03 2.74
143 144 2.748605 GATCCTACAGAAGCATGTCGG 58.251 52.381 0.00 2.10 37.37 4.79
303 304 6.573725 GCCGTTCGTTTAATTCTAGCATAATG 59.426 38.462 0.00 0.00 0.00 1.90
457 460 2.838202 ACCCATAGATTGAACGTGAGGT 59.162 45.455 0.00 0.00 0.00 3.85
458 461 3.198068 CCCATAGATTGAACGTGAGGTG 58.802 50.000 0.00 0.00 0.00 4.00
465 470 0.107410 TGAACGTGAGGTGGCTTGTT 60.107 50.000 0.00 0.00 0.00 2.83
468 473 0.108585 ACGTGAGGTGGCTTGTTGAT 59.891 50.000 0.00 0.00 0.00 2.57
566 571 4.397730 TGTAGGTAATTGCGTGCATTGAAT 59.602 37.500 3.14 0.00 0.00 2.57
643 648 5.815581 ACATAGTAGGCCAGTGATGAAAAA 58.184 37.500 5.01 0.00 0.00 1.94
1005 1032 1.890489 GGCCGGGAGTTTTGTAACAAT 59.110 47.619 2.18 0.00 36.70 2.71
1013 1040 5.278315 GGGAGTTTTGTAACAATGTGAGGAC 60.278 44.000 0.00 0.00 36.70 3.85
1317 1406 6.491403 AGTTTTGCAATGAAACTAGATCTGGT 59.509 34.615 12.26 5.80 43.46 4.00
1363 1452 3.660970 TGGCTGGCACTAAATTCCATA 57.339 42.857 0.00 0.00 0.00 2.74
1582 1671 1.200948 GAACTGCTCAAGGAACCATGC 59.799 52.381 0.00 0.00 0.00 4.06
2073 2163 5.620738 AAGCAGCTGGTGATCTCTTAATA 57.379 39.130 20.97 0.00 0.00 0.98
2841 2965 8.049721 AGTAGAGCTTATAATTGCCTGAAAAGT 58.950 33.333 0.00 0.00 0.00 2.66
2895 3019 6.881065 AGATAGACTTGCAGCTTGATTTGTTA 59.119 34.615 0.00 0.00 0.00 2.41
3794 3936 3.861840 CACATCCTTCAACCTCGTACAT 58.138 45.455 0.00 0.00 0.00 2.29
4023 4183 6.034591 TCGATTCTGTCTAAGGAAAATCGAC 58.965 40.000 12.39 0.00 45.36 4.20
4407 4570 1.078426 CAAGGCTAACTGACCCGGG 60.078 63.158 22.25 22.25 0.00 5.73
4469 4632 1.815003 GGGCTGTTTTGACCATCTCAG 59.185 52.381 0.00 0.00 34.56 3.35
4546 4709 4.449743 GGTCACGTTTGCATAAACTAGTGA 59.550 41.667 0.00 7.50 43.13 3.41
4554 4717 8.012809 CGTTTGCATAAACTAGTGATAAACACA 58.987 33.333 0.00 0.00 45.41 3.72
4575 4738 1.915489 TGATACTGCCCACCACTCAAT 59.085 47.619 0.00 0.00 0.00 2.57
4611 4774 0.108138 GATAACCCGACTGCTGCTGT 60.108 55.000 12.15 12.15 0.00 4.40
4689 4852 1.241315 CGGAATTTGAACCACCGCCT 61.241 55.000 0.00 0.00 37.32 5.52
4736 4899 2.592861 GCCGCCAGATCCATGACC 60.593 66.667 0.00 0.00 0.00 4.02
4847 5010 0.255890 GGGCAGGGCTCATTGAGTAA 59.744 55.000 14.90 0.00 31.39 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.273327 GAAAGGTGGCCTTGGAATGTG 59.727 52.381 3.32 0.00 43.92 3.21
3 4 1.631405 TGAAAGGTGGCCTTGGAATG 58.369 50.000 3.32 0.00 43.92 2.67
5 6 1.063266 AGTTGAAAGGTGGCCTTGGAA 60.063 47.619 3.32 0.00 43.92 3.53
6 7 0.555769 AGTTGAAAGGTGGCCTTGGA 59.444 50.000 3.32 0.00 43.92 3.53
7 8 0.961753 GAGTTGAAAGGTGGCCTTGG 59.038 55.000 3.32 0.00 43.92 3.61
8 9 0.961753 GGAGTTGAAAGGTGGCCTTG 59.038 55.000 3.32 0.00 43.92 3.61
10 11 1.360393 TGGGAGTTGAAAGGTGGCCT 61.360 55.000 3.32 0.00 33.87 5.19
11 12 0.251787 ATGGGAGTTGAAAGGTGGCC 60.252 55.000 0.00 0.00 0.00 5.36
12 13 0.890683 CATGGGAGTTGAAAGGTGGC 59.109 55.000 0.00 0.00 0.00 5.01
13 14 0.890683 GCATGGGAGTTGAAAGGTGG 59.109 55.000 0.00 0.00 0.00 4.61
14 15 1.270550 GTGCATGGGAGTTGAAAGGTG 59.729 52.381 0.00 0.00 0.00 4.00
15 16 1.133513 TGTGCATGGGAGTTGAAAGGT 60.134 47.619 0.00 0.00 0.00 3.50
16 17 1.542915 CTGTGCATGGGAGTTGAAAGG 59.457 52.381 0.00 0.00 0.00 3.11
17 18 2.030540 CACTGTGCATGGGAGTTGAAAG 60.031 50.000 0.00 0.00 0.00 2.62
18 19 1.955778 CACTGTGCATGGGAGTTGAAA 59.044 47.619 0.00 0.00 0.00 2.69
19 20 1.142667 TCACTGTGCATGGGAGTTGAA 59.857 47.619 2.12 0.00 0.00 2.69
20 21 0.764271 TCACTGTGCATGGGAGTTGA 59.236 50.000 2.12 0.00 0.00 3.18
21 22 1.471287 CATCACTGTGCATGGGAGTTG 59.529 52.381 2.12 0.00 0.00 3.16
22 23 1.615116 CCATCACTGTGCATGGGAGTT 60.615 52.381 21.56 0.00 36.62 3.01
23 24 0.034767 CCATCACTGTGCATGGGAGT 60.035 55.000 21.56 0.00 36.62 3.85
24 25 0.034767 ACCATCACTGTGCATGGGAG 60.035 55.000 27.49 13.74 43.59 4.30
25 26 0.322726 CACCATCACTGTGCATGGGA 60.323 55.000 27.49 2.08 43.59 4.37
26 27 2.186155 CACCATCACTGTGCATGGG 58.814 57.895 27.49 18.08 43.59 4.00
42 43 3.060000 GCCGGGTTACAAGGGCAC 61.060 66.667 2.18 0.00 44.91 5.01
44 45 2.044352 ATGCCGGGTTACAAGGGC 60.044 61.111 2.18 4.06 45.76 5.19
45 46 0.034477 AAGATGCCGGGTTACAAGGG 60.034 55.000 2.18 0.00 0.00 3.95
46 47 1.094785 CAAGATGCCGGGTTACAAGG 58.905 55.000 2.18 0.00 0.00 3.61
47 48 2.009774 CTCAAGATGCCGGGTTACAAG 58.990 52.381 2.18 0.00 0.00 3.16
48 49 1.948611 GCTCAAGATGCCGGGTTACAA 60.949 52.381 2.18 0.00 0.00 2.41
49 50 0.392461 GCTCAAGATGCCGGGTTACA 60.392 55.000 2.18 0.00 0.00 2.41
50 51 0.107654 AGCTCAAGATGCCGGGTTAC 60.108 55.000 2.18 0.00 0.00 2.50
51 52 0.107703 CAGCTCAAGATGCCGGGTTA 60.108 55.000 2.18 0.00 0.00 2.85
52 53 1.377725 CAGCTCAAGATGCCGGGTT 60.378 57.895 2.18 0.00 0.00 4.11
53 54 1.264749 TACAGCTCAAGATGCCGGGT 61.265 55.000 2.18 0.00 34.24 5.28
54 55 0.107703 TTACAGCTCAAGATGCCGGG 60.108 55.000 2.18 0.00 34.24 5.73
55 56 1.293924 CTTACAGCTCAAGATGCCGG 58.706 55.000 0.00 0.00 34.24 6.13
56 57 0.654683 GCTTACAGCTCAAGATGCCG 59.345 55.000 8.48 0.00 38.45 5.69
57 58 1.742761 TGCTTACAGCTCAAGATGCC 58.257 50.000 8.48 0.00 42.97 4.40
58 59 2.097142 CCTTGCTTACAGCTCAAGATGC 59.903 50.000 12.40 0.79 42.97 3.91
59 60 3.341823 ACCTTGCTTACAGCTCAAGATG 58.658 45.455 12.40 0.00 42.97 2.90
60 61 3.710209 ACCTTGCTTACAGCTCAAGAT 57.290 42.857 12.40 0.00 42.97 2.40
61 62 3.578716 ACTACCTTGCTTACAGCTCAAGA 59.421 43.478 12.40 0.00 42.97 3.02
62 63 3.929610 GACTACCTTGCTTACAGCTCAAG 59.070 47.826 5.36 5.36 42.97 3.02
63 64 3.323691 TGACTACCTTGCTTACAGCTCAA 59.676 43.478 0.00 0.00 42.97 3.02
64 65 2.897326 TGACTACCTTGCTTACAGCTCA 59.103 45.455 0.00 0.00 42.97 4.26
65 66 3.193691 TCTGACTACCTTGCTTACAGCTC 59.806 47.826 0.00 0.00 42.97 4.09
66 67 3.165875 TCTGACTACCTTGCTTACAGCT 58.834 45.455 0.00 0.00 42.97 4.24
67 68 3.056465 ACTCTGACTACCTTGCTTACAGC 60.056 47.826 0.00 0.00 42.82 4.40
68 69 4.673061 CGACTCTGACTACCTTGCTTACAG 60.673 50.000 0.00 0.00 0.00 2.74
69 70 3.190744 CGACTCTGACTACCTTGCTTACA 59.809 47.826 0.00 0.00 0.00 2.41
70 71 3.760537 CGACTCTGACTACCTTGCTTAC 58.239 50.000 0.00 0.00 0.00 2.34
71 72 2.163815 GCGACTCTGACTACCTTGCTTA 59.836 50.000 0.00 0.00 0.00 3.09
72 73 1.067495 GCGACTCTGACTACCTTGCTT 60.067 52.381 0.00 0.00 0.00 3.91
73 74 0.528470 GCGACTCTGACTACCTTGCT 59.472 55.000 0.00 0.00 0.00 3.91
74 75 0.798771 CGCGACTCTGACTACCTTGC 60.799 60.000 0.00 0.00 0.00 4.01
131 132 0.687354 ACTTGGACCGACATGCTTCT 59.313 50.000 0.00 0.00 0.00 2.85
143 144 3.741388 CGGATTCATAGTGGGACTTGGAC 60.741 52.174 0.00 0.00 0.00 4.02
206 207 6.373495 GGATTCTACCGTTTTGTACAGGATTT 59.627 38.462 5.91 0.00 0.00 2.17
457 460 4.646040 CCAATTCCATCTATCAACAAGCCA 59.354 41.667 0.00 0.00 0.00 4.75
458 461 4.646492 ACCAATTCCATCTATCAACAAGCC 59.354 41.667 0.00 0.00 0.00 4.35
465 470 7.632861 TCTTCTCAAACCAATTCCATCTATCA 58.367 34.615 0.00 0.00 0.00 2.15
468 473 6.886459 CCTTCTTCTCAAACCAATTCCATCTA 59.114 38.462 0.00 0.00 0.00 1.98
643 648 4.080356 TCAATGCTGGCTATACTCCACTTT 60.080 41.667 0.00 0.00 0.00 2.66
1005 1032 6.929625 TGATTTTCTTGTTTTTGTCCTCACA 58.070 32.000 0.00 0.00 0.00 3.58
1317 1406 5.623169 TGATGCTTCAATCTGTATATGCCA 58.377 37.500 0.00 0.00 0.00 4.92
1582 1671 5.588648 TCTCTTCCTTTTTGTAGTGTTGGTG 59.411 40.000 0.00 0.00 0.00 4.17
2646 2768 7.980742 AAAATCGGTGAAACAAAGAAAGTAC 57.019 32.000 0.00 0.00 39.98 2.73
2841 2965 6.833416 CCCTTTCATTTACATCAGGAACCATA 59.167 38.462 0.00 0.00 0.00 2.74
3119 3243 2.408565 TCCTTTCACACCCTGAAGAGT 58.591 47.619 0.00 0.00 40.12 3.24
3794 3936 2.023598 TCATCCCCATTATTGTTGGCCA 60.024 45.455 0.00 0.00 32.60 5.36
4023 4183 2.831742 TCGGGATTCGGAGTCGGG 60.832 66.667 0.00 0.00 39.77 5.14
4085 4245 2.096909 CGACCGGCTTATGCTAAATTCG 60.097 50.000 0.00 0.00 39.59 3.34
4457 4620 4.278310 TCCTCGTTATCTGAGATGGTCAA 58.722 43.478 4.96 0.00 35.43 3.18
4469 4632 0.586802 GCCGGCAATTCCTCGTTATC 59.413 55.000 24.80 0.00 0.00 1.75
4546 4709 4.207165 GGTGGGCAGTATCATGTGTTTAT 58.793 43.478 0.00 0.00 0.00 1.40
4554 4717 1.583556 TGAGTGGTGGGCAGTATCAT 58.416 50.000 0.00 0.00 0.00 2.45
4575 4738 5.546526 GGTTATCAAAGCCATCCAAAACAA 58.453 37.500 0.00 0.00 0.00 2.83
4611 4774 0.178992 CTGGTCAAGGAGGGCAACAA 60.179 55.000 0.00 0.00 39.74 2.83
4689 4852 2.994417 GGCGGTTTTCATGGCCCA 60.994 61.111 0.00 0.00 39.67 5.36


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

AutoCloner maintained by Alex Coulton.