Multiple sequence alignment - TraesCS3A01G324000

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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 TraesCS3A01G324000 chr3A 100.000 3931 0 0 1 3931 568447332 568443402 0.000000e+00 7260
1 TraesCS3A01G324000 chr3B 93.257 2432 99 27 696 3078 562777750 562775335 0.000000e+00 3522
2 TraesCS3A01G324000 chr3B 86.270 488 56 6 95 580 562778633 562778155 1.620000e-143 520
3 TraesCS3A01G324000 chr3B 90.265 113 7 3 3 113 810596316 810596206 1.140000e-30 145
4 TraesCS3A01G324000 chr3D 94.374 2293 78 15 824 3078 430361035 430358756 0.000000e+00 3472
5 TraesCS3A01G324000 chr3D 94.262 488 27 1 104 590 430370573 430370086 0.000000e+00 745
6 TraesCS3A01G324000 chr3D 98.361 244 2 1 585 826 430369496 430369253 1.010000e-115 427
7 TraesCS3A01G324000 chr7B 96.429 868 18 3 3077 3931 965203 966070 0.000000e+00 1419
8 TraesCS3A01G324000 chr5A 96.301 865 20 3 3078 3931 691680839 691681702 0.000000e+00 1410
9 TraesCS3A01G324000 chr5A 95.789 95 4 0 1 95 471789606 471789700 1.890000e-33 154
10 TraesCS3A01G324000 chr5A 95.789 95 4 0 1 95 578911251 578911157 1.890000e-33 154
11 TraesCS3A01G324000 chr5A 93.137 102 7 0 1 102 597664907 597664806 2.450000e-32 150
12 TraesCS3A01G324000 chr1A 96.078 867 24 2 3075 3931 1600692 1601558 0.000000e+00 1404
13 TraesCS3A01G324000 chr1A 95.963 867 25 2 3075 3931 1534375 1535241 0.000000e+00 1399
14 TraesCS3A01G324000 chrUn 96.176 863 24 2 3078 3931 194117163 194116301 0.000000e+00 1402
15 TraesCS3A01G324000 chr6A 95.771 875 28 2 3066 3931 575521320 575520446 0.000000e+00 1402
16 TraesCS3A01G324000 chr7A 95.455 880 29 3 3062 3931 77073204 77072326 0.000000e+00 1393
17 TraesCS3A01G324000 chr7A 94.949 99 5 0 1 99 91801528 91801430 5.260000e-34 156
18 TraesCS3A01G324000 chr4B 95.652 874 27 4 3069 3931 575730037 575730910 0.000000e+00 1393
19 TraesCS3A01G324000 chr5B 95.647 873 26 4 3068 3931 127772116 127772985 0.000000e+00 1391
20 TraesCS3A01G324000 chr6B 93.269 104 6 1 1 104 10579973 10580075 6.800000e-33 152
21 TraesCS3A01G324000 chr1B 91.743 109 8 1 1 109 151551393 151551500 2.450000e-32 150
22 TraesCS3A01G324000 chr2D 90.909 110 9 1 1 110 310380765 310380873 3.170000e-31 147
23 TraesCS3A01G324000 chr1D 87.023 131 10 5 1 127 403234872 403234745 1.470000e-29 141


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 TraesCS3A01G324000 chr3A 568443402 568447332 3930 True 7260 7260 100.0000 1 3931 1 chr3A.!!$R1 3930
1 TraesCS3A01G324000 chr3B 562775335 562778633 3298 True 2021 3522 89.7635 95 3078 2 chr3B.!!$R2 2983
2 TraesCS3A01G324000 chr3D 430358756 430361035 2279 True 3472 3472 94.3740 824 3078 1 chr3D.!!$R1 2254
3 TraesCS3A01G324000 chr3D 430369253 430370573 1320 True 586 745 96.3115 104 826 2 chr3D.!!$R2 722
4 TraesCS3A01G324000 chr7B 965203 966070 867 False 1419 1419 96.4290 3077 3931 1 chr7B.!!$F1 854
5 TraesCS3A01G324000 chr5A 691680839 691681702 863 False 1410 1410 96.3010 3078 3931 1 chr5A.!!$F2 853
6 TraesCS3A01G324000 chr1A 1600692 1601558 866 False 1404 1404 96.0780 3075 3931 1 chr1A.!!$F2 856
7 TraesCS3A01G324000 chr1A 1534375 1535241 866 False 1399 1399 95.9630 3075 3931 1 chr1A.!!$F1 856
8 TraesCS3A01G324000 chrUn 194116301 194117163 862 True 1402 1402 96.1760 3078 3931 1 chrUn.!!$R1 853
9 TraesCS3A01G324000 chr6A 575520446 575521320 874 True 1402 1402 95.7710 3066 3931 1 chr6A.!!$R1 865
10 TraesCS3A01G324000 chr7A 77072326 77073204 878 True 1393 1393 95.4550 3062 3931 1 chr7A.!!$R1 869
11 TraesCS3A01G324000 chr4B 575730037 575730910 873 False 1393 1393 95.6520 3069 3931 1 chr4B.!!$F1 862
12 TraesCS3A01G324000 chr5B 127772116 127772985 869 False 1391 1391 95.6470 3068 3931 1 chr5B.!!$F1 863

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
230 231 0.108138 CACTCGGGCGAAAGAGGAAT 60.108 55.0 6.45 0.0 38.72 3.01 F
582 585 0.109132 CCATGCGAAACCAAGAAGGC 60.109 55.0 0.00 0.0 43.14 4.35 F
1538 2295 0.592637 CTGCAAGGCATGTTCGACAA 59.407 50.0 0.00 0.0 38.13 3.18 F
2343 3122 0.456221 ACTTATCGCTGGTGTCCTCG 59.544 55.0 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1171 1916 0.105593 TCGGATGAAGGCTGATGAGC 59.894 55.000 0.00 0.00 45.40 4.26 R
2254 3033 0.661020 CCGATAATTGGAACGGTGGC 59.339 55.000 0.00 0.00 40.42 5.01 R
2432 3211 0.827507 AAGGCAGGCGTGGTGATTTT 60.828 50.000 8.72 0.00 0.00 1.82 R
3496 4301 1.150536 GGCCAACTTGACCTGGTCA 59.849 57.895 25.12 25.12 41.09 4.02 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
33 34 7.356540 ACGATCTTGATAGTGAAGATTCTACG 58.643 38.462 0.00 0.00 39.72 3.51
34 35 7.226918 ACGATCTTGATAGTGAAGATTCTACGA 59.773 37.037 0.00 0.00 39.72 3.43
35 36 8.070769 CGATCTTGATAGTGAAGATTCTACGAA 58.929 37.037 0.00 0.00 39.72 3.85
36 37 9.906660 GATCTTGATAGTGAAGATTCTACGAAT 57.093 33.333 0.00 0.00 39.72 3.34
38 39 9.521503 TCTTGATAGTGAAGATTCTACGAATTG 57.478 33.333 0.00 0.00 0.00 2.32
39 40 7.700322 TGATAGTGAAGATTCTACGAATTGC 57.300 36.000 0.00 0.00 0.00 3.56
41 42 4.744570 AGTGAAGATTCTACGAATTGCGA 58.255 39.130 0.00 0.00 44.57 5.10
42 43 5.352284 AGTGAAGATTCTACGAATTGCGAT 58.648 37.500 0.00 0.00 44.57 4.58
43 44 5.460419 AGTGAAGATTCTACGAATTGCGATC 59.540 40.000 0.00 0.00 44.57 3.69
44 45 4.745125 TGAAGATTCTACGAATTGCGATCC 59.255 41.667 0.00 0.00 44.57 3.36
45 46 4.592485 AGATTCTACGAATTGCGATCCT 57.408 40.909 0.00 0.00 44.57 3.24
46 47 5.707242 AGATTCTACGAATTGCGATCCTA 57.293 39.130 0.00 0.00 44.57 2.94
47 48 5.462405 AGATTCTACGAATTGCGATCCTAC 58.538 41.667 0.00 0.00 44.57 3.18
48 49 3.637998 TCTACGAATTGCGATCCTACC 57.362 47.619 0.00 0.00 44.57 3.18
49 50 2.953648 TCTACGAATTGCGATCCTACCA 59.046 45.455 0.00 0.00 44.57 3.25
50 51 2.910688 ACGAATTGCGATCCTACCAT 57.089 45.000 0.00 0.00 44.57 3.55
51 52 2.755650 ACGAATTGCGATCCTACCATC 58.244 47.619 0.00 0.00 44.57 3.51
53 54 2.069273 GAATTGCGATCCTACCATCGG 58.931 52.381 5.10 0.00 44.89 4.18
54 55 1.338107 ATTGCGATCCTACCATCGGA 58.662 50.000 5.10 0.00 44.89 4.55
55 56 0.673985 TTGCGATCCTACCATCGGAG 59.326 55.000 5.10 0.00 45.77 4.63
56 57 1.080434 GCGATCCTACCATCGGAGC 60.080 63.158 5.10 0.00 44.89 4.70
57 58 1.528292 GCGATCCTACCATCGGAGCT 61.528 60.000 5.10 0.00 44.89 4.09
58 59 0.523966 CGATCCTACCATCGGAGCTC 59.476 60.000 4.71 4.71 41.71 4.09
59 60 0.892063 GATCCTACCATCGGAGCTCC 59.108 60.000 23.79 23.79 34.23 4.70
69 70 4.976996 GGAGCTCCGATCCGATTC 57.023 61.111 19.06 0.00 0.00 2.52
70 71 2.041976 GGAGCTCCGATCCGATTCA 58.958 57.895 19.06 0.00 0.00 2.57
71 72 0.389391 GGAGCTCCGATCCGATTCAA 59.611 55.000 19.06 0.00 0.00 2.69
72 73 1.202533 GGAGCTCCGATCCGATTCAAA 60.203 52.381 19.06 0.00 0.00 2.69
73 74 2.550978 GAGCTCCGATCCGATTCAAAA 58.449 47.619 0.87 0.00 0.00 2.44
74 75 3.134458 GAGCTCCGATCCGATTCAAAAT 58.866 45.455 0.87 0.00 0.00 1.82
75 76 3.134458 AGCTCCGATCCGATTCAAAATC 58.866 45.455 0.00 0.00 0.00 2.17
76 77 2.096713 GCTCCGATCCGATTCAAAATCG 60.097 50.000 13.63 13.63 40.41 3.34
77 78 1.864711 TCCGATCCGATTCAAAATCGC 59.135 47.619 14.83 3.19 39.63 4.58
78 79 1.397190 CCGATCCGATTCAAAATCGCG 60.397 52.381 14.83 0.00 39.63 5.87
79 80 1.521006 CGATCCGATTCAAAATCGCGA 59.479 47.619 13.09 13.09 39.95 5.87
80 81 2.155732 CGATCCGATTCAAAATCGCGAT 59.844 45.455 17.62 17.62 39.95 4.58
81 82 3.362986 CGATCCGATTCAAAATCGCGATT 60.363 43.478 27.94 27.94 39.95 3.34
82 83 3.585748 TCCGATTCAAAATCGCGATTC 57.414 42.857 32.56 18.89 39.95 2.52
83 84 3.194861 TCCGATTCAAAATCGCGATTCT 58.805 40.909 32.56 18.88 39.95 2.40
84 85 3.001228 TCCGATTCAAAATCGCGATTCTG 59.999 43.478 32.56 28.93 39.95 3.02
85 86 3.001228 CCGATTCAAAATCGCGATTCTGA 59.999 43.478 28.96 28.96 39.95 3.27
86 87 4.199331 CGATTCAAAATCGCGATTCTGAG 58.801 43.478 30.18 19.22 30.39 3.35
87 88 4.026558 CGATTCAAAATCGCGATTCTGAGA 60.027 41.667 30.18 22.83 30.39 3.27
88 89 5.500771 CGATTCAAAATCGCGATTCTGAGAA 60.501 40.000 30.18 27.70 30.39 2.87
89 90 4.584029 TCAAAATCGCGATTCTGAGAAC 57.416 40.909 28.96 0.00 0.00 3.01
90 91 3.370978 TCAAAATCGCGATTCTGAGAACC 59.629 43.478 28.96 0.00 0.00 3.62
91 92 2.969628 AATCGCGATTCTGAGAACCT 57.030 45.000 27.94 2.37 0.00 3.50
92 93 2.969628 ATCGCGATTCTGAGAACCTT 57.030 45.000 17.62 0.00 0.00 3.50
93 94 1.996292 TCGCGATTCTGAGAACCTTG 58.004 50.000 3.71 0.00 0.00 3.61
163 164 2.094597 TCCAGCCAAAATCGAAAGCATG 60.095 45.455 0.00 0.00 0.00 4.06
184 185 4.874977 GCTGGCTCCGGCGACTAC 62.875 72.222 9.30 0.00 38.65 2.73
206 207 4.660938 GGCAGCAACGGGAAGGGT 62.661 66.667 0.00 0.00 0.00 4.34
212 213 3.503839 AACGGGAAGGGTTGGCCA 61.504 61.111 0.00 0.00 36.17 5.36
228 229 2.646175 CCACTCGGGCGAAAGAGGA 61.646 63.158 6.45 0.00 38.72 3.71
230 231 0.108138 CACTCGGGCGAAAGAGGAAT 60.108 55.000 6.45 0.00 38.72 3.01
231 232 0.613777 ACTCGGGCGAAAGAGGAATT 59.386 50.000 6.45 0.00 38.72 2.17
237 238 1.468914 GGCGAAAGAGGAATTGGTGAC 59.531 52.381 0.00 0.00 0.00 3.67
252 254 2.625790 TGGTGACATTTTTACTGGTGCC 59.374 45.455 0.00 0.00 33.40 5.01
283 285 6.126565 GGTTGAGTATATTTAGGAGGGTTGGT 60.127 42.308 0.00 0.00 0.00 3.67
287 289 2.215942 ATTTAGGAGGGTTGGTGCAC 57.784 50.000 8.80 8.80 0.00 4.57
385 387 7.961326 ATTTTGCTCCTCTAACCAATTACAT 57.039 32.000 0.00 0.00 0.00 2.29
390 393 5.471456 GCTCCTCTAACCAATTACATGGATG 59.529 44.000 0.00 0.00 43.54 3.51
401 404 6.607198 CCAATTACATGGATGGGTTAGAGTTT 59.393 38.462 0.00 0.00 43.54 2.66
516 519 1.463214 TTGGAAGACCTGGGGAGCA 60.463 57.895 0.00 0.00 37.04 4.26
582 585 0.109132 CCATGCGAAACCAAGAAGGC 60.109 55.000 0.00 0.00 43.14 4.35
808 1541 4.019231 AGGAAAAGTTAGACCCTGATGACC 60.019 45.833 0.00 0.00 0.00 4.02
865 1600 1.051812 CTCCCTCACACAAGTCCACT 58.948 55.000 0.00 0.00 0.00 4.00
866 1601 2.248248 CTCCCTCACACAAGTCCACTA 58.752 52.381 0.00 0.00 0.00 2.74
1171 1916 1.678627 ACAGGAGCAGCAGTACTATCG 59.321 52.381 0.00 0.00 0.00 2.92
1204 1949 4.207281 CCGATGCCGCTTCCTCGA 62.207 66.667 0.92 0.00 33.07 4.04
1248 1993 1.000060 ACGCACGCCTTCTTGTAAGTA 60.000 47.619 0.00 0.00 0.00 2.24
1285 2038 0.685097 TTTCTTCTAGCTGCCCGTGT 59.315 50.000 0.00 0.00 0.00 4.49
1305 2058 1.342076 TGGATGACTAAGGTCCTCGCT 60.342 52.381 0.00 0.00 41.47 4.93
1538 2295 0.592637 CTGCAAGGCATGTTCGACAA 59.407 50.000 0.00 0.00 38.13 3.18
1540 2297 0.725784 GCAAGGCATGTTCGACAACG 60.726 55.000 0.00 0.00 41.26 4.10
1850 2607 1.211949 GGCCATACAGCTAGGGTTTCA 59.788 52.381 0.00 0.00 0.00 2.69
1885 2642 1.771255 ACCTCAGTTTCTCCTGCAGTT 59.229 47.619 13.81 0.00 32.32 3.16
2065 2830 3.311322 TCACTTTTTGTTGCTTCGATCGT 59.689 39.130 15.94 0.00 0.00 3.73
2254 3033 4.946478 ATCAACTCCCTATCTTTCCTCG 57.054 45.455 0.00 0.00 0.00 4.63
2343 3122 0.456221 ACTTATCGCTGGTGTCCTCG 59.544 55.000 0.00 0.00 0.00 4.63
2344 3123 0.872021 CTTATCGCTGGTGTCCTCGC 60.872 60.000 0.00 0.00 0.00 5.03
2345 3124 1.600511 TTATCGCTGGTGTCCTCGCA 61.601 55.000 0.00 0.00 0.00 5.10
2346 3125 1.391933 TATCGCTGGTGTCCTCGCAT 61.392 55.000 0.00 0.00 0.00 4.73
2429 3208 2.117941 GACCAAGTTGCGGTGAGTGC 62.118 60.000 0.00 0.00 36.69 4.40
2432 3211 3.414136 AAGTTGCGGTGAGTGCCCA 62.414 57.895 0.00 0.00 0.00 5.36
2441 3220 1.327303 GTGAGTGCCCAAAATCACCA 58.673 50.000 0.00 0.00 36.83 4.17
2442 3221 1.000274 GTGAGTGCCCAAAATCACCAC 60.000 52.381 0.00 0.00 36.83 4.16
2443 3222 0.240945 GAGTGCCCAAAATCACCACG 59.759 55.000 0.00 0.00 33.90 4.94
2445 3224 2.261361 GCCCAAAATCACCACGCC 59.739 61.111 0.00 0.00 0.00 5.68
2447 3226 1.586028 CCCAAAATCACCACGCCTG 59.414 57.895 0.00 0.00 0.00 4.85
2472 3251 1.001378 GCTGCGTCCACATTTCTTGTT 60.001 47.619 0.00 0.00 36.00 2.83
2475 3254 2.884012 TGCGTCCACATTTCTTGTTCAT 59.116 40.909 0.00 0.00 36.00 2.57
2503 3282 5.140177 CGGAACATCGCTTATAAATTGCTC 58.860 41.667 0.00 0.00 0.00 4.26
2516 3295 4.574599 AAATTGCTCAACACTGAACTCC 57.425 40.909 0.00 0.00 0.00 3.85
2534 3313 1.289231 TCCCTGCAGTCTCTGACCTAT 59.711 52.381 13.81 0.00 32.44 2.57
2643 3425 1.610038 CTGTTGCTTGGCTGTTGATGA 59.390 47.619 0.00 0.00 0.00 2.92
2681 3464 0.249073 CCGAGAATGCGAAGGACGAT 60.249 55.000 0.00 0.00 45.77 3.73
2917 3705 2.297033 TGAGGCTAAAGCAAAGCAAAGG 59.703 45.455 4.07 0.00 44.36 3.11
2919 3707 1.063031 GCTAAAGCAAAGCAAAGGCG 58.937 50.000 0.00 0.00 42.74 5.52
3031 3821 9.803507 AATAGATAATGATCCAAGCAATGAAGA 57.196 29.630 0.00 0.00 31.81 2.87
3362 4162 0.545309 CCTCTCCTCCAAGTCCACCA 60.545 60.000 0.00 0.00 0.00 4.17
3660 4465 2.311463 TCACAAGATCGAGATCCTCCC 58.689 52.381 9.27 0.00 38.58 4.30
3692 4497 1.675310 CAGGCCAATTCGTCCAGCA 60.675 57.895 5.01 0.00 0.00 4.41
3766 4571 1.852157 ATCAGGAACCCACCGTGCAT 61.852 55.000 0.00 0.00 34.73 3.96
3798 4603 1.471119 CAGATTGTGCAGCCTCCAAT 58.529 50.000 0.00 0.00 0.00 3.16
3898 4703 2.895865 CGCCGCTCTCCTCGTCTA 60.896 66.667 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.906660 ATTCGTAGAATCTTCACTATCAAGATC 57.093 33.333 0.00 0.00 45.90 2.75
12 13 9.521503 CAATTCGTAGAATCTTCACTATCAAGA 57.478 33.333 0.00 0.00 45.90 3.02
13 14 8.272176 GCAATTCGTAGAATCTTCACTATCAAG 58.728 37.037 0.00 0.00 45.90 3.02
14 15 7.043391 CGCAATTCGTAGAATCTTCACTATCAA 60.043 37.037 0.00 0.00 45.90 2.57
15 16 6.417930 CGCAATTCGTAGAATCTTCACTATCA 59.582 38.462 0.00 0.00 45.90 2.15
16 17 6.637254 TCGCAATTCGTAGAATCTTCACTATC 59.363 38.462 0.00 0.00 45.90 2.08
17 18 6.504398 TCGCAATTCGTAGAATCTTCACTAT 58.496 36.000 0.00 0.00 45.90 2.12
18 19 5.886992 TCGCAATTCGTAGAATCTTCACTA 58.113 37.500 0.00 0.00 45.90 2.74
19 20 4.744570 TCGCAATTCGTAGAATCTTCACT 58.255 39.130 0.00 0.00 45.90 3.41
20 21 5.332656 GGATCGCAATTCGTAGAATCTTCAC 60.333 44.000 0.00 0.00 45.90 3.18
21 22 4.745125 GGATCGCAATTCGTAGAATCTTCA 59.255 41.667 0.00 0.00 45.90 3.02
22 23 4.985409 AGGATCGCAATTCGTAGAATCTTC 59.015 41.667 0.00 0.00 45.90 2.87
23 24 4.950050 AGGATCGCAATTCGTAGAATCTT 58.050 39.130 0.00 0.00 45.90 2.40
24 25 4.592485 AGGATCGCAATTCGTAGAATCT 57.408 40.909 0.00 0.00 45.90 2.40
25 26 4.621886 GGTAGGATCGCAATTCGTAGAATC 59.378 45.833 0.00 0.00 45.90 2.52
26 27 4.038763 TGGTAGGATCGCAATTCGTAGAAT 59.961 41.667 0.00 0.00 45.90 2.40
27 28 3.382227 TGGTAGGATCGCAATTCGTAGAA 59.618 43.478 0.00 0.00 45.90 2.10
28 29 2.953648 TGGTAGGATCGCAATTCGTAGA 59.046 45.455 0.00 0.00 39.67 2.59
29 30 3.364889 TGGTAGGATCGCAATTCGTAG 57.635 47.619 0.00 0.00 39.67 3.51
30 31 3.610821 CGATGGTAGGATCGCAATTCGTA 60.611 47.826 0.00 0.00 38.90 3.43
31 32 2.755650 GATGGTAGGATCGCAATTCGT 58.244 47.619 0.00 0.00 39.67 3.85
32 33 1.721389 CGATGGTAGGATCGCAATTCG 59.279 52.381 0.00 0.00 38.90 3.34
33 34 2.069273 CCGATGGTAGGATCGCAATTC 58.931 52.381 0.00 0.00 43.22 2.17
34 35 1.691976 TCCGATGGTAGGATCGCAATT 59.308 47.619 0.00 0.00 43.22 2.32
35 36 1.273606 CTCCGATGGTAGGATCGCAAT 59.726 52.381 0.00 0.00 43.22 3.56
36 37 0.673985 CTCCGATGGTAGGATCGCAA 59.326 55.000 0.00 0.00 43.22 4.85
37 38 1.806461 GCTCCGATGGTAGGATCGCA 61.806 60.000 0.00 0.00 43.22 5.10
38 39 1.080434 GCTCCGATGGTAGGATCGC 60.080 63.158 0.00 0.00 43.22 4.58
39 40 0.523966 GAGCTCCGATGGTAGGATCG 59.476 60.000 0.87 0.00 44.00 3.69
40 41 0.892063 GGAGCTCCGATGGTAGGATC 59.108 60.000 19.06 0.00 37.13 3.36
41 42 3.059287 GGAGCTCCGATGGTAGGAT 57.941 57.895 19.06 0.00 37.13 3.24
42 43 4.601042 GGAGCTCCGATGGTAGGA 57.399 61.111 19.06 0.00 36.20 2.94
52 53 0.389391 TTGAATCGGATCGGAGCTCC 59.611 55.000 23.79 23.79 0.00 4.70
53 54 2.225068 TTTGAATCGGATCGGAGCTC 57.775 50.000 4.71 4.71 0.00 4.09
54 55 2.691409 TTTTGAATCGGATCGGAGCT 57.309 45.000 9.03 0.00 0.00 4.09
55 56 2.096713 CGATTTTGAATCGGATCGGAGC 60.097 50.000 13.62 4.40 38.11 4.70
56 57 2.096713 GCGATTTTGAATCGGATCGGAG 60.097 50.000 20.49 0.00 41.08 4.63
57 58 1.864711 GCGATTTTGAATCGGATCGGA 59.135 47.619 20.49 5.34 41.08 4.55
58 59 1.397190 CGCGATTTTGAATCGGATCGG 60.397 52.381 20.49 0.00 41.08 4.18
59 60 1.521006 TCGCGATTTTGAATCGGATCG 59.479 47.619 20.49 16.05 42.99 3.69
60 61 3.795561 ATCGCGATTTTGAATCGGATC 57.204 42.857 17.62 7.01 41.42 3.36
61 62 3.809832 AGAATCGCGATTTTGAATCGGAT 59.190 39.130 32.89 17.45 41.42 4.18
62 63 3.001228 CAGAATCGCGATTTTGAATCGGA 59.999 43.478 35.97 16.34 41.42 4.55
63 64 3.001228 TCAGAATCGCGATTTTGAATCGG 59.999 43.478 37.87 24.44 38.47 4.18
64 65 4.026558 TCTCAGAATCGCGATTTTGAATCG 60.027 41.667 38.17 30.50 40.11 3.34
65 66 5.395325 TCTCAGAATCGCGATTTTGAATC 57.605 39.130 38.17 25.40 40.11 2.52
66 67 5.447818 GGTTCTCAGAATCGCGATTTTGAAT 60.448 40.000 38.17 19.76 40.11 2.57
67 68 4.142902 GGTTCTCAGAATCGCGATTTTGAA 60.143 41.667 38.17 30.08 40.11 2.69
68 69 3.370978 GGTTCTCAGAATCGCGATTTTGA 59.629 43.478 37.32 37.32 38.91 2.69
69 70 3.372206 AGGTTCTCAGAATCGCGATTTTG 59.628 43.478 34.39 34.39 35.10 2.44
70 71 3.600388 AGGTTCTCAGAATCGCGATTTT 58.400 40.909 32.89 25.70 0.00 1.82
71 72 3.252974 AGGTTCTCAGAATCGCGATTT 57.747 42.857 32.89 20.24 0.00 2.17
72 73 2.932614 CAAGGTTCTCAGAATCGCGATT 59.067 45.455 32.97 32.97 0.00 3.34
73 74 2.544685 CAAGGTTCTCAGAATCGCGAT 58.455 47.619 17.62 17.62 0.00 4.58
74 75 1.404181 CCAAGGTTCTCAGAATCGCGA 60.404 52.381 13.09 13.09 0.00 5.87
75 76 1.002366 CCAAGGTTCTCAGAATCGCG 58.998 55.000 0.00 0.00 0.00 5.87
76 77 0.729690 GCCAAGGTTCTCAGAATCGC 59.270 55.000 0.00 0.00 0.00 4.58
77 78 1.373570 GGCCAAGGTTCTCAGAATCG 58.626 55.000 0.00 0.00 0.00 3.34
78 79 1.373570 CGGCCAAGGTTCTCAGAATC 58.626 55.000 2.24 0.00 0.00 2.52
79 80 0.035056 CCGGCCAAGGTTCTCAGAAT 60.035 55.000 2.24 0.00 0.00 2.40
80 81 1.374947 CCGGCCAAGGTTCTCAGAA 59.625 57.895 2.24 0.00 0.00 3.02
81 82 3.068881 CCGGCCAAGGTTCTCAGA 58.931 61.111 2.24 0.00 0.00 3.27
82 83 2.747855 GCCGGCCAAGGTTCTCAG 60.748 66.667 18.11 0.00 0.00 3.35
83 84 4.697756 CGCCGGCCAAGGTTCTCA 62.698 66.667 23.46 0.00 0.00 3.27
188 189 4.659172 CCCTTCCCGTTGCTGCCA 62.659 66.667 0.00 0.00 0.00 4.92
212 213 0.613777 AATTCCTCTTTCGCCCGAGT 59.386 50.000 0.00 0.00 0.00 4.18
228 229 5.296748 GCACCAGTAAAAATGTCACCAATT 58.703 37.500 0.00 0.00 0.00 2.32
230 231 3.068873 GGCACCAGTAAAAATGTCACCAA 59.931 43.478 0.00 0.00 0.00 3.67
231 232 2.625790 GGCACCAGTAAAAATGTCACCA 59.374 45.455 0.00 0.00 0.00 4.17
237 238 0.455972 CGGCGGCACCAGTAAAAATG 60.456 55.000 10.53 0.00 39.03 2.32
252 254 4.022589 TCCTAAATATACTCAACCTCGGCG 60.023 45.833 0.00 0.00 0.00 6.46
283 285 4.211330 TCCGGCCCAAAAGGTGCA 62.211 61.111 0.00 0.00 38.26 4.57
287 289 2.044946 CTCCTCCGGCCCAAAAGG 60.045 66.667 0.00 0.00 39.47 3.11
385 387 5.425539 CCTTAGAGAAACTCTAACCCATCCA 59.574 44.000 14.63 0.00 44.85 3.41
390 393 6.840181 AGTATCCCTTAGAGAAACTCTAACCC 59.160 42.308 14.63 3.34 44.85 4.11
401 404 4.863548 TCCGACAAAGTATCCCTTAGAGA 58.136 43.478 0.00 0.00 31.48 3.10
516 519 0.178903 TGGACTTGCCTCCACCTACT 60.179 55.000 0.00 0.00 35.23 2.57
582 585 4.215399 TGCTACTTCTGTTGGAATTTTCGG 59.785 41.667 0.00 0.00 33.01 4.30
736 1466 5.946298 TGCATGTTGAGAAGAATTTAGCTG 58.054 37.500 0.00 0.00 0.00 4.24
808 1541 2.678336 GGACAAAGAGGGTCGCTTAATG 59.322 50.000 0.00 0.00 36.12 1.90
1171 1916 0.105593 TCGGATGAAGGCTGATGAGC 59.894 55.000 0.00 0.00 45.40 4.26
1204 1949 1.820519 GTCCATGTGTGCATCACCAAT 59.179 47.619 14.23 2.95 45.61 3.16
1248 1993 3.526841 AGAAAGATGGAAGATGGAAGGCT 59.473 43.478 0.00 0.00 0.00 4.58
1305 2058 1.404181 CCGCTCCTGAAACTCGATCAA 60.404 52.381 0.00 0.00 0.00 2.57
1317 2070 3.452786 TCGCTTCTCCCGCTCCTG 61.453 66.667 0.00 0.00 0.00 3.86
1553 2310 1.298788 CCCAACACCGAAACGTTGC 60.299 57.895 0.00 0.00 40.93 4.17
1713 2470 1.080995 GCAAGAGAAGCTGCGACGAT 61.081 55.000 0.00 0.00 0.00 3.73
1806 2563 9.911138 GCCTCTGGTAGTAAACTACTAATATTC 57.089 37.037 17.40 2.86 46.06 1.75
1850 2607 7.995488 AGAAACTGAGGTTATGCATAGCTTAAT 59.005 33.333 18.52 4.60 34.90 1.40
1912 2669 3.452786 CGGGCTCGCTTCTCCTCA 61.453 66.667 0.00 0.00 0.00 3.86
2065 2830 2.679349 GCAAAAGGAAAACACCAGCCAA 60.679 45.455 0.00 0.00 0.00 4.52
2187 2966 3.181448 ACCTTTCCAAAAGGCGAGACTAA 60.181 43.478 16.50 0.00 41.10 2.24
2254 3033 0.661020 CCGATAATTGGAACGGTGGC 59.339 55.000 0.00 0.00 40.42 5.01
2343 3122 2.544267 GGTATCGGTCTAAAGTGCATGC 59.456 50.000 11.82 11.82 0.00 4.06
2344 3123 2.794910 CGGTATCGGTCTAAAGTGCATG 59.205 50.000 0.00 0.00 0.00 4.06
2345 3124 2.802057 GCGGTATCGGTCTAAAGTGCAT 60.802 50.000 0.00 0.00 36.79 3.96
2346 3125 1.470285 GCGGTATCGGTCTAAAGTGCA 60.470 52.381 0.00 0.00 36.79 4.57
2429 3208 1.586028 CAGGCGTGGTGATTTTGGG 59.414 57.895 0.00 0.00 0.00 4.12
2432 3211 0.827507 AAGGCAGGCGTGGTGATTTT 60.828 50.000 8.72 0.00 0.00 1.82
2445 3224 3.730761 GTGGACGCAGCAAGGCAG 61.731 66.667 0.00 0.00 0.00 4.85
2447 3226 2.146073 AAATGTGGACGCAGCAAGGC 62.146 55.000 0.00 0.00 0.00 4.35
2460 3239 6.435430 TCCGGAATATGAACAAGAAATGTG 57.565 37.500 0.00 0.00 42.99 3.21
2472 3251 3.469008 AAGCGATGTTCCGGAATATGA 57.531 42.857 28.70 10.48 0.00 2.15
2475 3254 7.572353 GCAATTTATAAGCGATGTTCCGGAATA 60.572 37.037 22.04 19.19 0.00 1.75
2503 3282 1.233019 CTGCAGGGAGTTCAGTGTTG 58.767 55.000 5.57 0.00 0.00 3.33
2516 3295 1.686052 GGATAGGTCAGAGACTGCAGG 59.314 57.143 19.93 0.00 32.47 4.85
2534 3313 4.312443 GGTTCACATTCTTCAAGTACGGA 58.688 43.478 0.00 0.00 0.00 4.69
2617 3398 2.034124 ACAGCCAAGCAACAGAAACAT 58.966 42.857 0.00 0.00 0.00 2.71
2619 3400 2.159254 TCAACAGCCAAGCAACAGAAAC 60.159 45.455 0.00 0.00 0.00 2.78
2622 3403 1.610038 CATCAACAGCCAAGCAACAGA 59.390 47.619 0.00 0.00 0.00 3.41
2623 3404 1.610038 TCATCAACAGCCAAGCAACAG 59.390 47.619 0.00 0.00 0.00 3.16
2626 3408 1.689984 TGTCATCAACAGCCAAGCAA 58.310 45.000 0.00 0.00 32.81 3.91
2643 3425 2.525368 GGAACCCTACCAAGCAAATGT 58.475 47.619 0.00 0.00 0.00 2.71
2681 3464 3.589654 CTTCTTCGGCTCGCCACCA 62.590 63.158 8.87 0.00 35.37 4.17
2919 3707 7.653647 ACTATCTTAGTACTCTAGCAACATGC 58.346 38.462 0.00 0.00 39.64 4.06
3015 3803 7.816031 TCTTTTGATTTCTTCATTGCTTGGATC 59.184 33.333 0.00 0.00 33.34 3.36
3031 3821 7.688343 TGGCCTTTCCAAATATCTTTTGATTT 58.312 30.769 3.32 0.00 43.21 2.17
3362 4162 2.235898 GCAAGAAGGAGGAGATGACTGT 59.764 50.000 0.00 0.00 0.00 3.55
3496 4301 1.150536 GGCCAACTTGACCTGGTCA 59.849 57.895 25.12 25.12 41.09 4.02
3660 4465 4.559063 CCTGCTCCATCGCCCAGG 62.559 72.222 0.00 0.00 38.93 4.45
3692 4497 3.322466 CCTCCGCCTGGTCCACTT 61.322 66.667 0.00 0.00 36.30 3.16
3898 4703 3.085119 ATAGCTACCGCCGCCGTTT 62.085 57.895 0.00 0.00 36.60 3.60


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

AutoCloner maintained by Alex Coulton.