Multiple sequence alignment - TraesCS3B01G327900

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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 TraesCS3B01G327900 chr3B 100.000 3986 0 0 1 3986 528503542 528499557 0 7361
1 TraesCS3B01G327900 chr3D 93.088 3964 167 38 89 3984 402781937 402778013 0 5703
2 TraesCS3B01G327900 chr3A 94.515 2607 112 7 549 3124 523734052 523731446 0 3993
3 TraesCS3B01G327900 chr3A 97.090 859 21 3 3129 3986 523731358 523730503 0 1445


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 TraesCS3B01G327900 chr3B 528499557 528503542 3985 True 7361 7361 100.0000 1 3986 1 chr3B.!!$R1 3985
1 TraesCS3B01G327900 chr3D 402778013 402781937 3924 True 5703 5703 93.0880 89 3984 1 chr3D.!!$R1 3895
2 TraesCS3B01G327900 chr3A 523730503 523734052 3549 True 2719 3993 95.8025 549 3986 2 chr3A.!!$R1 3437

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
33 34 0.035881 CTGAGAGTGGCCTTGCAAGA 59.964 55.000 28.05 4.99 0.00 3.02 F
1440 1493 0.034670 ATGGCTTGTCTGAAGGCTCC 60.035 55.000 9.12 0.00 42.57 4.70 F
1468 1521 1.008079 GTCTTGCCTGCACTTGTGC 60.008 57.895 17.73 17.73 0.00 4.57 F
1668 1721 1.205055 GGAGTAACTTCCCAGGGAGG 58.795 60.000 16.37 16.37 34.79 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 1521 1.377202 CATGAACTGGGTCCGGTGG 60.377 63.158 0.0 0.0 35.44 4.61 R
2455 2508 0.698238 TGCACCAGCCTACCAAGAAT 59.302 50.000 0.0 0.0 41.13 2.40 R
2678 2731 0.758123 AGCAGCCTCTTCCATAGCTC 59.242 55.000 0.0 0.0 31.93 4.09 R
2995 3048 2.070573 ACCCACCTCCATTGTTTACCT 58.929 47.619 0.0 0.0 0.00 3.08 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 3.686760 CACCACGAGAGGAGCTGA 58.313 61.111 0.00 0.00 0.00 4.26
18 19 1.510383 CACCACGAGAGGAGCTGAG 59.490 63.158 0.00 0.00 0.00 3.35
19 20 0.962855 CACCACGAGAGGAGCTGAGA 60.963 60.000 0.00 0.00 0.00 3.27
20 21 0.679640 ACCACGAGAGGAGCTGAGAG 60.680 60.000 0.00 0.00 0.00 3.20
21 22 0.679640 CCACGAGAGGAGCTGAGAGT 60.680 60.000 0.00 0.00 0.00 3.24
22 23 0.451383 CACGAGAGGAGCTGAGAGTG 59.549 60.000 0.00 0.00 0.00 3.51
23 24 0.679640 ACGAGAGGAGCTGAGAGTGG 60.680 60.000 0.00 0.00 0.00 4.00
24 25 1.815866 GAGAGGAGCTGAGAGTGGC 59.184 63.158 0.00 0.00 0.00 5.01
25 26 1.675720 GAGAGGAGCTGAGAGTGGCC 61.676 65.000 0.00 0.00 0.00 5.36
26 27 1.685421 GAGGAGCTGAGAGTGGCCT 60.685 63.158 3.32 0.00 0.00 5.19
27 28 1.229464 AGGAGCTGAGAGTGGCCTT 60.229 57.895 3.32 0.00 0.00 4.35
28 29 1.078567 GGAGCTGAGAGTGGCCTTG 60.079 63.158 3.32 0.00 0.00 3.61
29 30 1.744741 GAGCTGAGAGTGGCCTTGC 60.745 63.158 3.32 0.00 0.00 4.01
30 31 2.033141 GCTGAGAGTGGCCTTGCA 59.967 61.111 3.32 0.00 0.00 4.08
31 32 1.601759 GCTGAGAGTGGCCTTGCAA 60.602 57.895 3.32 0.00 0.00 4.08
32 33 1.584380 GCTGAGAGTGGCCTTGCAAG 61.584 60.000 19.93 19.93 0.00 4.01
33 34 0.035881 CTGAGAGTGGCCTTGCAAGA 59.964 55.000 28.05 4.99 0.00 3.02
34 35 0.473755 TGAGAGTGGCCTTGCAAGAA 59.526 50.000 28.05 10.04 0.00 2.52
35 36 1.163554 GAGAGTGGCCTTGCAAGAAG 58.836 55.000 28.05 12.99 0.00 2.85
36 37 0.475906 AGAGTGGCCTTGCAAGAAGT 59.524 50.000 28.05 14.82 0.00 3.01
37 38 1.699634 AGAGTGGCCTTGCAAGAAGTA 59.300 47.619 28.05 8.18 0.00 2.24
38 39 1.807142 GAGTGGCCTTGCAAGAAGTAC 59.193 52.381 28.05 18.61 0.00 2.73
39 40 0.881796 GTGGCCTTGCAAGAAGTACC 59.118 55.000 28.05 18.80 0.00 3.34
40 41 0.251165 TGGCCTTGCAAGAAGTACCC 60.251 55.000 28.05 16.14 0.00 3.69
41 42 0.965866 GGCCTTGCAAGAAGTACCCC 60.966 60.000 28.05 11.34 0.00 4.95
42 43 0.038310 GCCTTGCAAGAAGTACCCCT 59.962 55.000 28.05 0.00 0.00 4.79
43 44 1.547901 GCCTTGCAAGAAGTACCCCTT 60.548 52.381 28.05 0.00 35.59 3.95
44 45 2.290705 GCCTTGCAAGAAGTACCCCTTA 60.291 50.000 28.05 0.00 32.03 2.69
45 46 3.812882 GCCTTGCAAGAAGTACCCCTTAA 60.813 47.826 28.05 0.00 32.03 1.85
46 47 3.756963 CCTTGCAAGAAGTACCCCTTAAC 59.243 47.826 28.05 0.00 32.03 2.01
47 48 4.506802 CCTTGCAAGAAGTACCCCTTAACT 60.507 45.833 28.05 0.00 32.03 2.24
48 49 5.280317 CCTTGCAAGAAGTACCCCTTAACTA 60.280 44.000 28.05 0.00 32.03 2.24
49 50 5.416271 TGCAAGAAGTACCCCTTAACTAG 57.584 43.478 0.00 0.00 32.03 2.57
50 51 4.842380 TGCAAGAAGTACCCCTTAACTAGT 59.158 41.667 0.00 0.00 32.03 2.57
51 52 5.176592 GCAAGAAGTACCCCTTAACTAGTG 58.823 45.833 0.00 0.00 32.03 2.74
52 53 5.046807 GCAAGAAGTACCCCTTAACTAGTGA 60.047 44.000 0.00 0.00 32.03 3.41
53 54 6.351966 GCAAGAAGTACCCCTTAACTAGTGAT 60.352 42.308 0.00 0.00 32.03 3.06
54 55 7.621796 CAAGAAGTACCCCTTAACTAGTGATT 58.378 38.462 0.00 0.00 32.03 2.57
55 56 7.809880 AGAAGTACCCCTTAACTAGTGATTT 57.190 36.000 0.00 0.00 32.03 2.17
56 57 8.215954 AGAAGTACCCCTTAACTAGTGATTTT 57.784 34.615 0.00 0.00 32.03 1.82
57 58 9.330220 AGAAGTACCCCTTAACTAGTGATTTTA 57.670 33.333 0.00 0.00 32.03 1.52
58 59 9.597170 GAAGTACCCCTTAACTAGTGATTTTAG 57.403 37.037 0.00 0.00 32.03 1.85
59 60 8.676397 AGTACCCCTTAACTAGTGATTTTAGT 57.324 34.615 0.00 0.00 32.90 2.24
60 61 9.109246 AGTACCCCTTAACTAGTGATTTTAGTT 57.891 33.333 0.00 3.50 42.38 2.24
61 62 9.730705 GTACCCCTTAACTAGTGATTTTAGTTT 57.269 33.333 0.00 0.00 40.69 2.66
103 104 6.705825 GCACAAATGTTAAAGAAATTGGGTCT 59.294 34.615 0.00 0.00 0.00 3.85
106 107 8.919145 ACAAATGTTAAAGAAATTGGGTCTACA 58.081 29.630 0.00 0.00 0.00 2.74
149 150 1.145531 CCAACATGGGGATAGGATGCA 59.854 52.381 0.00 0.00 32.67 3.96
175 176 3.188880 TGGCCTCCAAAATCCAAAGAT 57.811 42.857 3.32 0.00 0.00 2.40
195 196 6.365970 AGATACACCATAGTCATTGGGATC 57.634 41.667 0.00 0.00 38.64 3.36
206 207 2.535485 ATTGGGATCGCGGTTCTGCA 62.535 55.000 6.13 0.00 34.15 4.41
209 210 2.401195 GATCGCGGTTCTGCAAGC 59.599 61.111 6.13 0.00 34.15 4.01
231 232 1.534595 CCTGTTTGATGCTTATGGCGC 60.535 52.381 0.00 0.00 45.43 6.53
232 233 0.455410 TGTTTGATGCTTATGGCGCC 59.545 50.000 22.73 22.73 45.43 6.53
245 246 2.709475 GCGCCTGAATTGTAGCCG 59.291 61.111 0.00 0.00 0.00 5.52
280 281 2.356125 GCCTCTCCAGCCAACAGATAAA 60.356 50.000 0.00 0.00 0.00 1.40
282 283 3.881688 CCTCTCCAGCCAACAGATAAATG 59.118 47.826 0.00 0.00 0.00 2.32
287 288 6.267471 TCTCCAGCCAACAGATAAATGTTTTT 59.733 34.615 0.00 0.00 41.41 1.94
316 318 9.979270 TTAGTTAGAAATCTTCGTACGTTAGAG 57.021 33.333 16.05 9.37 34.02 2.43
319 321 9.334693 GTTAGAAATCTTCGTACGTTAGAGAAA 57.665 33.333 16.05 0.00 34.02 2.52
326 328 8.752766 TCTTCGTACGTTAGAGAAAATGAATT 57.247 30.769 16.05 0.00 0.00 2.17
331 333 9.250986 CGTACGTTAGAGAAAATGAATTTGAAG 57.749 33.333 7.22 0.00 0.00 3.02
370 394 3.486043 GGAAAACGTGCGCCAAAATTTTT 60.486 39.130 4.18 1.90 0.00 1.94
375 399 4.827601 ACGTGCGCCAAAATTTTTAAAAG 58.172 34.783 4.18 0.00 0.00 2.27
459 483 9.102757 TCATCAAATGGAAAAATGTTCGAAAAA 57.897 25.926 0.00 0.00 0.00 1.94
460 484 9.881529 CATCAAATGGAAAAATGTTCGAAAAAT 57.118 25.926 0.00 0.00 0.00 1.82
462 486 9.102757 TCAAATGGAAAAATGTTCGAAAAATCA 57.897 25.926 0.00 0.00 0.00 2.57
463 487 9.881529 CAAATGGAAAAATGTTCGAAAAATCAT 57.118 25.926 0.00 0.00 0.00 2.45
464 488 9.881529 AAATGGAAAAATGTTCGAAAAATCATG 57.118 25.926 0.00 0.00 0.00 3.07
465 489 8.830201 ATGGAAAAATGTTCGAAAAATCATGA 57.170 26.923 0.00 0.00 0.00 3.07
798 829 1.930567 ATACCATTTTCCGACGGTCG 58.069 50.000 22.88 22.88 40.07 4.79
866 897 1.318576 CCAACTTCCACCACCTTGTC 58.681 55.000 0.00 0.00 0.00 3.18
959 1012 3.515286 GCCTCGGTCGATCGGTCA 61.515 66.667 19.53 0.00 0.00 4.02
1051 1104 2.045047 TCCCTCTTCAACTCCCTCATCT 59.955 50.000 0.00 0.00 0.00 2.90
1155 1208 2.831742 ACCTTCGCGCCGATCCTA 60.832 61.111 0.00 0.00 35.23 2.94
1164 1217 1.979693 GCCGATCCTATCCTCGCCT 60.980 63.158 0.00 0.00 33.63 5.52
1173 1226 0.968901 TATCCTCGCCTTCCGTGTGT 60.969 55.000 0.00 0.00 38.35 3.72
1218 1271 3.197790 CACATCCTCAAGCGCGGG 61.198 66.667 8.83 0.00 0.00 6.13
1242 1295 2.341101 CCACAGCGACCCGTACTCT 61.341 63.158 0.00 0.00 0.00 3.24
1362 1415 0.110328 GTCTCGTCTCTTCGTTCGCA 60.110 55.000 0.00 0.00 0.00 5.10
1440 1493 0.034670 ATGGCTTGTCTGAAGGCTCC 60.035 55.000 9.12 0.00 42.57 4.70
1468 1521 1.008079 GTCTTGCCTGCACTTGTGC 60.008 57.895 17.73 17.73 0.00 4.57
1521 1574 1.281867 ACCGCAATGGATTCCTTCTCA 59.718 47.619 3.95 0.00 42.00 3.27
1599 1652 4.036144 GCAGAGAAGCTATTTGATGGGTTC 59.964 45.833 7.78 7.78 45.09 3.62
1646 1699 5.490139 AATACAATGATCACTGCTTTCGG 57.510 39.130 3.61 0.00 0.00 4.30
1668 1721 1.205055 GGAGTAACTTCCCAGGGAGG 58.795 60.000 16.37 16.37 34.79 4.30
1744 1797 8.514330 AACTACATTTTCCAGTGTTCTTTACA 57.486 30.769 0.00 0.00 0.00 2.41
1970 2023 4.156739 GTCAGATGGTGATTTTCCAACTCC 59.843 45.833 0.00 0.00 36.25 3.85
2195 2248 4.452455 GGCTTATGGAGTTACATTGGATCG 59.548 45.833 0.00 0.00 32.39 3.69
2203 2256 3.513912 AGTTACATTGGATCGTGACTCCA 59.486 43.478 0.00 0.00 41.03 3.86
2295 2348 5.233263 GCTACTCTTACATCAGCAAACTAGC 59.767 44.000 0.00 0.00 32.46 3.42
2613 2666 5.434352 TGGAAGATAGGAACGTAATCTCG 57.566 43.478 0.00 0.00 0.00 4.04
2678 2731 0.324645 AAGGCCCTGGCATGGTTTAG 60.325 55.000 10.86 0.00 44.11 1.85
2995 3048 6.436218 TCAAGTGTTTAGCTAGTGATGGTCTA 59.564 38.462 0.00 0.00 0.00 2.59
3302 3448 0.553333 TGGTGGTTCATTGTGGGTCA 59.447 50.000 0.00 0.00 0.00 4.02
3365 3511 6.813649 GCTTTGTGTTCTGTCATCATCTAGTA 59.186 38.462 0.00 0.00 0.00 1.82
3434 3580 3.476552 CAAACTAGCAAGAGGTGTTCCA 58.523 45.455 0.00 0.00 35.89 3.53
3436 3582 2.047061 ACTAGCAAGAGGTGTTCCACA 58.953 47.619 0.00 0.00 35.86 4.17
3494 3650 1.561542 TGGAGGAGGAGAAAAGGATGC 59.438 52.381 0.00 0.00 0.00 3.91
3771 3928 8.292444 TGGCATAAAGTTTATTGAGCATTAGT 57.708 30.769 14.76 0.00 0.00 2.24
3831 3988 3.698539 TGAAATGTTTCAGTTCACAGGCA 59.301 39.130 8.22 0.00 42.20 4.75
3879 4036 5.508200 TGTTGTCAAAATACCAAGGTGTC 57.492 39.130 1.07 0.00 0.00 3.67
3923 4080 5.599732 CAAATGTGGAAAATGACTGGAACA 58.400 37.500 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.962855 TCTCAGCTCCTCTCGTGGTG 60.963 60.000 0.00 0.00 35.32 4.17
2 3 0.679640 ACTCTCAGCTCCTCTCGTGG 60.680 60.000 0.00 0.00 0.00 4.94
3 4 0.451383 CACTCTCAGCTCCTCTCGTG 59.549 60.000 0.00 0.00 0.00 4.35
4 5 0.679640 CCACTCTCAGCTCCTCTCGT 60.680 60.000 0.00 0.00 0.00 4.18
5 6 2.003658 GCCACTCTCAGCTCCTCTCG 62.004 65.000 0.00 0.00 0.00 4.04
6 7 1.675720 GGCCACTCTCAGCTCCTCTC 61.676 65.000 0.00 0.00 0.00 3.20
7 8 1.685421 GGCCACTCTCAGCTCCTCT 60.685 63.158 0.00 0.00 0.00 3.69
8 9 1.264045 AAGGCCACTCTCAGCTCCTC 61.264 60.000 5.01 0.00 0.00 3.71
9 10 1.229464 AAGGCCACTCTCAGCTCCT 60.229 57.895 5.01 0.00 0.00 3.69
10 11 1.078567 CAAGGCCACTCTCAGCTCC 60.079 63.158 5.01 0.00 0.00 4.70
11 12 1.744741 GCAAGGCCACTCTCAGCTC 60.745 63.158 5.01 0.00 0.00 4.09
12 13 2.060567 TTGCAAGGCCACTCTCAGCT 62.061 55.000 5.01 0.00 0.00 4.24
13 14 1.584380 CTTGCAAGGCCACTCTCAGC 61.584 60.000 19.14 0.00 0.00 4.26
14 15 0.035881 TCTTGCAAGGCCACTCTCAG 59.964 55.000 25.73 0.00 0.00 3.35
15 16 0.473755 TTCTTGCAAGGCCACTCTCA 59.526 50.000 25.73 0.31 0.00 3.27
16 17 1.163554 CTTCTTGCAAGGCCACTCTC 58.836 55.000 25.73 0.00 0.00 3.20
17 18 0.475906 ACTTCTTGCAAGGCCACTCT 59.524 50.000 25.73 0.00 0.00 3.24
18 19 1.807142 GTACTTCTTGCAAGGCCACTC 59.193 52.381 25.73 9.18 0.00 3.51
19 20 1.545651 GGTACTTCTTGCAAGGCCACT 60.546 52.381 25.73 7.33 0.00 4.00
20 21 0.881796 GGTACTTCTTGCAAGGCCAC 59.118 55.000 25.73 17.04 0.00 5.01
21 22 0.251165 GGGTACTTCTTGCAAGGCCA 60.251 55.000 25.73 9.82 0.00 5.36
22 23 0.965866 GGGGTACTTCTTGCAAGGCC 60.966 60.000 25.73 18.05 0.00 5.19
23 24 0.038310 AGGGGTACTTCTTGCAAGGC 59.962 55.000 25.73 11.03 0.00 4.35
24 25 2.586648 AAGGGGTACTTCTTGCAAGG 57.413 50.000 25.73 13.43 32.85 3.61
25 26 4.652822 AGTTAAGGGGTACTTCTTGCAAG 58.347 43.478 20.81 20.81 40.64 4.01
26 27 4.717279 AGTTAAGGGGTACTTCTTGCAA 57.283 40.909 0.00 0.00 40.64 4.08
27 28 4.842380 ACTAGTTAAGGGGTACTTCTTGCA 59.158 41.667 10.15 0.00 40.64 4.08
28 29 5.046807 TCACTAGTTAAGGGGTACTTCTTGC 60.047 44.000 0.00 5.07 40.64 4.01
29 30 6.600882 TCACTAGTTAAGGGGTACTTCTTG 57.399 41.667 0.00 0.00 40.64 3.02
30 31 7.809880 AATCACTAGTTAAGGGGTACTTCTT 57.190 36.000 0.00 0.00 40.64 2.52
31 32 7.809880 AAATCACTAGTTAAGGGGTACTTCT 57.190 36.000 0.00 0.00 40.64 2.85
32 33 9.597170 CTAAAATCACTAGTTAAGGGGTACTTC 57.403 37.037 0.00 0.00 40.64 3.01
33 34 9.109246 ACTAAAATCACTAGTTAAGGGGTACTT 57.891 33.333 0.00 0.00 43.28 2.24
34 35 8.676397 ACTAAAATCACTAGTTAAGGGGTACT 57.324 34.615 0.00 0.00 0.00 2.73
35 36 9.730705 AAACTAAAATCACTAGTTAAGGGGTAC 57.269 33.333 0.00 0.00 38.38 3.34
66 67 9.935682 CTTTAACATTTGTGCGATGATATACTT 57.064 29.630 0.00 0.00 0.00 2.24
67 68 9.325198 TCTTTAACATTTGTGCGATGATATACT 57.675 29.630 0.00 0.00 0.00 2.12
68 69 9.929722 TTCTTTAACATTTGTGCGATGATATAC 57.070 29.630 0.00 0.00 0.00 1.47
71 72 9.853555 AATTTCTTTAACATTTGTGCGATGATA 57.146 25.926 0.00 0.00 0.00 2.15
72 73 8.649841 CAATTTCTTTAACATTTGTGCGATGAT 58.350 29.630 0.00 0.00 0.00 2.45
73 74 7.116090 CCAATTTCTTTAACATTTGTGCGATGA 59.884 33.333 0.00 0.00 0.00 2.92
74 75 7.228840 CCAATTTCTTTAACATTTGTGCGATG 58.771 34.615 0.00 0.00 0.00 3.84
75 76 6.368516 CCCAATTTCTTTAACATTTGTGCGAT 59.631 34.615 0.00 0.00 0.00 4.58
76 77 5.694006 CCCAATTTCTTTAACATTTGTGCGA 59.306 36.000 0.00 0.00 0.00 5.10
77 78 5.465056 ACCCAATTTCTTTAACATTTGTGCG 59.535 36.000 0.00 0.00 0.00 5.34
78 79 6.705825 AGACCCAATTTCTTTAACATTTGTGC 59.294 34.615 0.00 0.00 0.00 4.57
79 80 9.191995 GTAGACCCAATTTCTTTAACATTTGTG 57.808 33.333 0.00 0.00 0.00 3.33
80 81 8.919145 TGTAGACCCAATTTCTTTAACATTTGT 58.081 29.630 0.00 0.00 0.00 2.83
81 82 9.410556 CTGTAGACCCAATTTCTTTAACATTTG 57.589 33.333 0.00 0.00 0.00 2.32
82 83 8.088365 GCTGTAGACCCAATTTCTTTAACATTT 58.912 33.333 0.00 0.00 0.00 2.32
83 84 7.309805 GGCTGTAGACCCAATTTCTTTAACATT 60.310 37.037 0.00 0.00 0.00 2.71
84 85 6.152831 GGCTGTAGACCCAATTTCTTTAACAT 59.847 38.462 0.00 0.00 0.00 2.71
85 86 5.475564 GGCTGTAGACCCAATTTCTTTAACA 59.524 40.000 0.00 0.00 0.00 2.41
86 87 5.710567 AGGCTGTAGACCCAATTTCTTTAAC 59.289 40.000 0.00 0.00 0.00 2.01
87 88 5.710099 CAGGCTGTAGACCCAATTTCTTTAA 59.290 40.000 6.28 0.00 0.00 1.52
103 104 0.114168 ATTTGTTGGGCCAGGCTGTA 59.886 50.000 12.43 0.00 0.00 2.74
106 107 1.077005 TCTAATTTGTTGGGCCAGGCT 59.923 47.619 12.43 0.00 0.00 4.58
146 147 0.252148 TTTGGAGGCCAATGGATGCA 60.252 50.000 5.01 0.00 43.55 3.96
149 150 2.293051 TGGATTTTGGAGGCCAATGGAT 60.293 45.455 5.01 0.00 43.55 3.41
155 156 2.692709 TCTTTGGATTTTGGAGGCCA 57.307 45.000 5.01 0.00 0.00 5.36
166 167 7.000472 CCAATGACTATGGTGTATCTTTGGAT 59.000 38.462 10.63 0.00 43.79 3.41
175 176 3.244078 GCGATCCCAATGACTATGGTGTA 60.244 47.826 0.00 0.00 36.14 2.90
195 196 3.793144 GGAGCTTGCAGAACCGCG 61.793 66.667 0.00 0.00 33.35 6.46
206 207 3.698040 CCATAAGCATCAAACAGGAGCTT 59.302 43.478 0.00 0.00 46.23 3.74
209 210 2.032550 CGCCATAAGCATCAAACAGGAG 59.967 50.000 0.00 0.00 44.04 3.69
231 232 2.823829 GCGCCGGCTACAATTCAGG 61.824 63.158 26.68 5.48 35.83 3.86
232 233 2.709475 GCGCCGGCTACAATTCAG 59.291 61.111 26.68 6.32 35.83 3.02
290 291 9.979270 CTCTAACGTACGAAGATTTCTAACTAA 57.021 33.333 24.41 0.00 0.00 2.24
291 292 9.371136 TCTCTAACGTACGAAGATTTCTAACTA 57.629 33.333 24.41 0.00 0.00 2.24
292 293 8.261492 TCTCTAACGTACGAAGATTTCTAACT 57.739 34.615 24.41 0.00 0.00 2.24
293 294 8.886816 TTCTCTAACGTACGAAGATTTCTAAC 57.113 34.615 24.41 0.00 0.00 2.34
301 303 8.752766 AATTCATTTTCTCTAACGTACGAAGA 57.247 30.769 24.41 21.03 0.00 2.87
346 349 1.668101 TTTTGGCGCACGTTTTCCCT 61.668 50.000 10.83 0.00 0.00 4.20
347 350 0.598942 ATTTTGGCGCACGTTTTCCC 60.599 50.000 10.83 0.00 0.00 3.97
348 351 1.213491 AATTTTGGCGCACGTTTTCC 58.787 45.000 10.83 0.00 0.00 3.13
349 352 3.311788 AAAATTTTGGCGCACGTTTTC 57.688 38.095 10.83 0.00 0.00 2.29
354 378 4.827601 ACTTTTAAAAATTTTGGCGCACG 58.172 34.783 10.83 0.00 0.00 5.34
375 399 8.547069 TCGTCAAAATTTTCCAAATTCATGAAC 58.453 29.630 11.07 0.00 0.00 3.18
432 456 8.654230 TTTCGAACATTTTTCCATTTGATGAA 57.346 26.923 0.00 0.00 0.00 2.57
434 458 9.881529 ATTTTTCGAACATTTTTCCATTTGATG 57.118 25.926 0.00 0.00 0.00 3.07
437 461 9.881529 ATGATTTTTCGAACATTTTTCCATTTG 57.118 25.926 0.00 0.00 0.00 2.32
440 464 8.830201 TCATGATTTTTCGAACATTTTTCCAT 57.170 26.923 0.00 0.00 0.00 3.41
490 514 8.655651 TTTTCCCAACATTCAAACATTTCTAC 57.344 30.769 0.00 0.00 0.00 2.59
493 517 7.552458 ACTTTTCCCAACATTCAAACATTTC 57.448 32.000 0.00 0.00 0.00 2.17
501 525 6.537453 TTCAAGAACTTTTCCCAACATTCA 57.463 33.333 0.00 0.00 0.00 2.57
505 529 6.940739 TCAAATTCAAGAACTTTTCCCAACA 58.059 32.000 0.00 0.00 0.00 3.33
506 530 7.841915 TTCAAATTCAAGAACTTTTCCCAAC 57.158 32.000 0.00 0.00 0.00 3.77
681 712 9.771534 TTTTTCTGTTTCTTTCTTTCCTTTTCA 57.228 25.926 0.00 0.00 0.00 2.69
708 739 5.070047 TGGGCCGGTTTTGTTCTTTTTATTA 59.930 36.000 1.90 0.00 0.00 0.98
782 813 1.356527 GGACGACCGTCGGAAAATGG 61.357 60.000 24.03 0.00 45.59 3.16
1081 1134 2.490217 GAGCAGCGAGAAGGCGTA 59.510 61.111 0.00 0.00 38.18 4.42
1155 1208 2.227089 GACACACGGAAGGCGAGGAT 62.227 60.000 0.00 0.00 0.00 3.24
1335 1388 2.666069 CGAAGAGACGAGACAGTTCCAC 60.666 54.545 0.00 0.00 35.09 4.02
1362 1415 1.379443 CTGGACATGCCCATGCTGT 60.379 57.895 0.00 0.00 42.39 4.40
1440 1493 1.898574 AGGCAAGACCGCAACAAGG 60.899 57.895 0.00 0.00 46.52 3.61
1443 1496 3.286751 GCAGGCAAGACCGCAACA 61.287 61.111 0.00 0.00 46.52 3.33
1468 1521 1.377202 CATGAACTGGGTCCGGTGG 60.377 63.158 0.00 0.00 35.44 4.61
1574 1627 3.548770 CCATCAAATAGCTTCTCTGCCA 58.451 45.455 0.00 0.00 0.00 4.92
1599 1652 2.306341 AGACCGCATCTCTGAACATG 57.694 50.000 0.00 0.00 28.16 3.21
1646 1699 3.032459 CTCCCTGGGAAGTTACTCCTAC 58.968 54.545 17.81 0.00 35.63 3.18
1970 2023 8.219769 GCAACATATCTCTCAGAATCATAAACG 58.780 37.037 0.00 0.00 0.00 3.60
2151 2204 3.820595 GGCATCAGAAACAAAGCCC 57.179 52.632 0.00 0.00 36.17 5.19
2295 2348 9.809096 ATAAGTATGCTCCATGAAATAGTATCG 57.191 33.333 0.00 0.00 0.00 2.92
2455 2508 0.698238 TGCACCAGCCTACCAAGAAT 59.302 50.000 0.00 0.00 41.13 2.40
2613 2666 1.808945 CCTGAAATCACAGCTGTCCAC 59.191 52.381 18.64 7.66 36.67 4.02
2678 2731 0.758123 AGCAGCCTCTTCCATAGCTC 59.242 55.000 0.00 0.00 31.93 4.09
2995 3048 2.070573 ACCCACCTCCATTGTTTACCT 58.929 47.619 0.00 0.00 0.00 3.08
3233 3379 4.261994 CGTTTCCAATCAACACCCTTCATT 60.262 41.667 0.00 0.00 0.00 2.57
3365 3511 4.944317 GGCATTTTCCTTCTGTAGTTAGCT 59.056 41.667 0.00 0.00 0.00 3.32
3434 3580 5.902613 CATGAAGGTAACAACATGGATGT 57.097 39.130 0.00 0.00 43.55 3.06
3771 3928 4.351407 TCAACCACCAAACCCAGTAGATTA 59.649 41.667 0.00 0.00 0.00 1.75
3821 3978 2.952310 ACTCTCCTTTTTGCCTGTGAAC 59.048 45.455 0.00 0.00 0.00 3.18
3831 3988 6.265649 GCCTTTCTCCTTTTACTCTCCTTTTT 59.734 38.462 0.00 0.00 0.00 1.94
3879 4036 0.179073 ATAGGCTGCAAGTGGCTACG 60.179 55.000 9.50 0.00 43.60 3.51
3900 4057 5.599732 TGTTCCAGTCATTTTCCACATTTG 58.400 37.500 0.00 0.00 0.00 2.32
3923 4080 4.014273 AGGAGGGGATCTTACTGAACAT 57.986 45.455 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.