Multiple sequence alignment - TraesCS1D01G115600

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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 TraesCS1D01G115600 chr1D 100.000 3508 0 0 1 3508 111541339 111544846 0.000000e+00 6479
1 TraesCS1D01G115600 chr5B 96.929 2507 75 1 1002 3508 398162275 398164779 0.000000e+00 4202
2 TraesCS1D01G115600 chr3B 96.663 2517 81 2 992 3508 24551277 24548764 0.000000e+00 4180
3 TraesCS1D01G115600 chr3B 90.899 934 36 24 480 1411 335124900 335125786 0.000000e+00 1208
4 TraesCS1D01G115600 chr3B 86.936 421 25 5 103 521 335124579 335124971 2.480000e-121 446
5 TraesCS1D01G115600 chr3B 95.732 164 4 3 101 262 24552193 24552031 9.660000e-66 261
6 TraesCS1D01G115600 chr3B 91.892 185 8 6 102 280 250972516 250972699 5.810000e-63 252
7 TraesCS1D01G115600 chr3B 91.758 182 9 6 102 278 214794221 214794041 7.520000e-62 248
8 TraesCS1D01G115600 chr2A 96.075 2522 96 2 988 3508 762103241 762100722 0.000000e+00 4106
9 TraesCS1D01G115600 chr2A 91.986 836 44 12 480 1314 655782648 655781835 0.000000e+00 1151
10 TraesCS1D01G115600 chr2A 93.775 498 26 5 101 597 655782997 655782504 0.000000e+00 743
11 TraesCS1D01G115600 chr6A 95.649 2528 105 4 983 3508 64590404 64592928 0.000000e+00 4054
12 TraesCS1D01G115600 chr6A 78.630 861 108 47 166 991 68970633 68969814 5.230000e-138 501
13 TraesCS1D01G115600 chr2D 95.480 2522 108 3 988 3508 99341841 99339325 0.000000e+00 4021
14 TraesCS1D01G115600 chr7B 95.309 2537 107 7 973 3508 290095412 290092887 0.000000e+00 4015
15 TraesCS1D01G115600 chr5A 95.366 2525 114 2 985 3508 642648390 642650912 0.000000e+00 4012
16 TraesCS1D01G115600 chr2B 95.293 2528 114 4 983 3508 25160296 25157772 0.000000e+00 4004
17 TraesCS1D01G115600 chr1A 95.044 2522 121 3 988 3508 448883324 448880806 0.000000e+00 3962
18 TraesCS1D01G115600 chr1A 91.346 104 6 1 1 101 117906468 117906571 4.720000e-29 139
19 TraesCS1D01G115600 chr4A 90.817 893 45 26 102 963 618999750 618998864 0.000000e+00 1160
20 TraesCS1D01G115600 chr6B 86.364 352 30 4 163 496 438103628 438103979 5.530000e-98 368
21 TraesCS1D01G115600 chr5D 95.349 172 6 2 95 264 236421482 236421311 4.460000e-69 272
22 TraesCS1D01G115600 chr1B 87.500 112 3 2 1 101 170569448 170569559 6.150000e-23 119


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 TraesCS1D01G115600 chr1D 111541339 111544846 3507 False 6479.0 6479 100.0000 1 3508 1 chr1D.!!$F1 3507
1 TraesCS1D01G115600 chr5B 398162275 398164779 2504 False 4202.0 4202 96.9290 1002 3508 1 chr5B.!!$F1 2506
2 TraesCS1D01G115600 chr3B 24548764 24552193 3429 True 2220.5 4180 96.1975 101 3508 2 chr3B.!!$R2 3407
3 TraesCS1D01G115600 chr3B 335124579 335125786 1207 False 827.0 1208 88.9175 103 1411 2 chr3B.!!$F2 1308
4 TraesCS1D01G115600 chr2A 762100722 762103241 2519 True 4106.0 4106 96.0750 988 3508 1 chr2A.!!$R1 2520
5 TraesCS1D01G115600 chr2A 655781835 655782997 1162 True 947.0 1151 92.8805 101 1314 2 chr2A.!!$R2 1213
6 TraesCS1D01G115600 chr6A 64590404 64592928 2524 False 4054.0 4054 95.6490 983 3508 1 chr6A.!!$F1 2525
7 TraesCS1D01G115600 chr6A 68969814 68970633 819 True 501.0 501 78.6300 166 991 1 chr6A.!!$R1 825
8 TraesCS1D01G115600 chr2D 99339325 99341841 2516 True 4021.0 4021 95.4800 988 3508 1 chr2D.!!$R1 2520
9 TraesCS1D01G115600 chr7B 290092887 290095412 2525 True 4015.0 4015 95.3090 973 3508 1 chr7B.!!$R1 2535
10 TraesCS1D01G115600 chr5A 642648390 642650912 2522 False 4012.0 4012 95.3660 985 3508 1 chr5A.!!$F1 2523
11 TraesCS1D01G115600 chr2B 25157772 25160296 2524 True 4004.0 4004 95.2930 983 3508 1 chr2B.!!$R1 2525
12 TraesCS1D01G115600 chr1A 448880806 448883324 2518 True 3962.0 3962 95.0440 988 3508 1 chr1A.!!$R1 2520
13 TraesCS1D01G115600 chr4A 618998864 618999750 886 True 1160.0 1160 90.8170 102 963 1 chr4A.!!$R1 861

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
822 1119 0.107508 CTGGGTGGACTGCATCGATT 60.108 55.0 0.00 0.0 0.00 3.34 F
1013 1500 0.823356 AGCACCATGTCTTTGGCGTT 60.823 50.0 0.00 0.0 40.68 4.84 F
1664 2153 0.924090 GAGTTTCAGCGCGTCTATGG 59.076 55.0 8.43 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 2400 0.805322 GAGTACGAGGACGAGAGCGA 60.805 60.000 0.00 0.0 42.66 4.93 R
2175 2664 1.141657 CATGGGGATGTACCTGACTGG 59.858 57.143 0.00 0.0 42.93 4.00 R
3095 3586 1.667510 TGACGATGCTTGCGCTCAA 60.668 52.632 9.73 0.0 36.97 3.02 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
22 23 5.835113 ACCAGTACAATCATAAATGCACC 57.165 39.130 0.00 0.00 0.00 5.01
23 24 5.260424 ACCAGTACAATCATAAATGCACCA 58.740 37.500 0.00 0.00 0.00 4.17
24 25 5.357878 ACCAGTACAATCATAAATGCACCAG 59.642 40.000 0.00 0.00 0.00 4.00
25 26 5.589855 CCAGTACAATCATAAATGCACCAGA 59.410 40.000 0.00 0.00 0.00 3.86
26 27 6.238566 CCAGTACAATCATAAATGCACCAGAG 60.239 42.308 0.00 0.00 0.00 3.35
27 28 4.644103 ACAATCATAAATGCACCAGAGC 57.356 40.909 0.00 0.00 0.00 4.09
28 29 4.275810 ACAATCATAAATGCACCAGAGCT 58.724 39.130 0.00 0.00 34.99 4.09
29 30 4.337555 ACAATCATAAATGCACCAGAGCTC 59.662 41.667 5.27 5.27 34.99 4.09
30 31 3.920231 TCATAAATGCACCAGAGCTCT 57.080 42.857 11.45 11.45 34.99 4.09
31 32 3.538591 TCATAAATGCACCAGAGCTCTG 58.461 45.455 32.84 32.84 43.40 3.35
32 33 3.198417 TCATAAATGCACCAGAGCTCTGA 59.802 43.478 39.34 23.11 46.59 3.27
33 34 1.818642 AAATGCACCAGAGCTCTGAC 58.181 50.000 39.34 28.02 46.59 3.51
34 35 0.390866 AATGCACCAGAGCTCTGACG 60.391 55.000 39.34 29.59 46.59 4.35
35 36 1.253593 ATGCACCAGAGCTCTGACGA 61.254 55.000 39.34 22.24 46.59 4.20
36 37 1.290324 GCACCAGAGCTCTGACGAA 59.710 57.895 39.34 0.00 46.59 3.85
37 38 0.735632 GCACCAGAGCTCTGACGAAG 60.736 60.000 39.34 25.86 46.59 3.79
38 39 0.884514 CACCAGAGCTCTGACGAAGA 59.115 55.000 39.34 0.00 46.59 2.87
39 40 1.476085 CACCAGAGCTCTGACGAAGAT 59.524 52.381 39.34 15.81 46.59 2.40
40 41 1.476085 ACCAGAGCTCTGACGAAGATG 59.524 52.381 39.34 23.89 46.59 2.90
41 42 1.747924 CCAGAGCTCTGACGAAGATGA 59.252 52.381 39.34 0.00 46.59 2.92
42 43 2.165234 CCAGAGCTCTGACGAAGATGAA 59.835 50.000 39.34 0.00 46.59 2.57
43 44 3.178267 CAGAGCTCTGACGAAGATGAAC 58.822 50.000 35.69 0.00 46.59 3.18
44 45 3.088532 AGAGCTCTGACGAAGATGAACT 58.911 45.455 17.42 0.00 33.29 3.01
45 46 3.119531 AGAGCTCTGACGAAGATGAACTG 60.120 47.826 17.42 0.00 33.29 3.16
46 47 2.822561 AGCTCTGACGAAGATGAACTGA 59.177 45.455 0.00 0.00 33.29 3.41
47 48 3.119531 AGCTCTGACGAAGATGAACTGAG 60.120 47.826 0.00 0.00 33.29 3.35
48 49 3.119673 GCTCTGACGAAGATGAACTGAGA 60.120 47.826 0.00 0.00 33.29 3.27
49 50 4.661125 CTCTGACGAAGATGAACTGAGAG 58.339 47.826 0.00 0.00 33.29 3.20
50 51 4.075682 TCTGACGAAGATGAACTGAGAGT 58.924 43.478 0.00 0.00 0.00 3.24
51 52 5.246307 TCTGACGAAGATGAACTGAGAGTA 58.754 41.667 0.00 0.00 0.00 2.59
52 53 5.883115 TCTGACGAAGATGAACTGAGAGTAT 59.117 40.000 0.00 0.00 0.00 2.12
53 54 6.037720 TCTGACGAAGATGAACTGAGAGTATC 59.962 42.308 0.00 0.00 0.00 2.24
54 55 5.648092 TGACGAAGATGAACTGAGAGTATCA 59.352 40.000 0.00 0.00 37.82 2.15
55 56 6.151144 TGACGAAGATGAACTGAGAGTATCAA 59.849 38.462 0.00 0.00 37.52 2.57
56 57 6.925211 ACGAAGATGAACTGAGAGTATCAAA 58.075 36.000 0.00 0.00 37.52 2.69
57 58 7.032580 ACGAAGATGAACTGAGAGTATCAAAG 58.967 38.462 0.00 0.00 37.52 2.77
58 59 7.032580 CGAAGATGAACTGAGAGTATCAAAGT 58.967 38.462 0.00 0.00 37.52 2.66
59 60 7.219917 CGAAGATGAACTGAGAGTATCAAAGTC 59.780 40.741 0.00 0.00 37.52 3.01
60 61 6.872920 AGATGAACTGAGAGTATCAAAGTCC 58.127 40.000 0.00 0.00 37.52 3.85
61 62 6.438741 AGATGAACTGAGAGTATCAAAGTCCA 59.561 38.462 0.00 0.00 37.52 4.02
62 63 5.784177 TGAACTGAGAGTATCAAAGTCCAC 58.216 41.667 0.00 0.00 37.52 4.02
63 64 5.304357 TGAACTGAGAGTATCAAAGTCCACA 59.696 40.000 0.00 0.00 37.52 4.17
64 65 5.398603 ACTGAGAGTATCAAAGTCCACAG 57.601 43.478 0.00 0.00 37.52 3.66
65 66 5.080337 ACTGAGAGTATCAAAGTCCACAGA 58.920 41.667 0.00 0.00 37.52 3.41
66 67 5.540337 ACTGAGAGTATCAAAGTCCACAGAA 59.460 40.000 0.00 0.00 37.52 3.02
67 68 6.030548 TGAGAGTATCAAAGTCCACAGAAG 57.969 41.667 0.00 0.00 37.82 2.85
68 69 5.540337 TGAGAGTATCAAAGTCCACAGAAGT 59.460 40.000 0.00 0.00 37.82 3.01
69 70 6.719829 TGAGAGTATCAAAGTCCACAGAAGTA 59.280 38.462 0.00 0.00 37.82 2.24
70 71 7.094162 TGAGAGTATCAAAGTCCACAGAAGTAG 60.094 40.741 0.00 0.00 37.82 2.57
71 72 6.948886 AGAGTATCAAAGTCCACAGAAGTAGA 59.051 38.462 0.00 0.00 37.82 2.59
72 73 7.617723 AGAGTATCAAAGTCCACAGAAGTAGAT 59.382 37.037 0.00 0.00 37.82 1.98
73 74 8.140112 AGTATCAAAGTCCACAGAAGTAGATT 57.860 34.615 0.00 0.00 0.00 2.40
74 75 8.254508 AGTATCAAAGTCCACAGAAGTAGATTC 58.745 37.037 0.00 0.00 38.28 2.52
75 76 5.794894 TCAAAGTCCACAGAAGTAGATTCC 58.205 41.667 0.00 0.00 38.84 3.01
76 77 4.828072 AAGTCCACAGAAGTAGATTCCC 57.172 45.455 0.00 0.00 38.84 3.97
77 78 2.761208 AGTCCACAGAAGTAGATTCCCG 59.239 50.000 0.00 0.00 38.84 5.14
78 79 2.496470 GTCCACAGAAGTAGATTCCCGT 59.504 50.000 0.00 0.00 38.84 5.28
79 80 3.698040 GTCCACAGAAGTAGATTCCCGTA 59.302 47.826 0.00 0.00 38.84 4.02
80 81 4.341520 GTCCACAGAAGTAGATTCCCGTAT 59.658 45.833 0.00 0.00 38.84 3.06
81 82 4.583489 TCCACAGAAGTAGATTCCCGTATC 59.417 45.833 0.00 0.00 38.84 2.24
82 83 4.585162 CCACAGAAGTAGATTCCCGTATCT 59.415 45.833 0.00 0.00 38.84 1.98
83 84 5.278561 CCACAGAAGTAGATTCCCGTATCTC 60.279 48.000 0.00 0.00 38.84 2.75
84 85 5.533154 CACAGAAGTAGATTCCCGTATCTCT 59.467 44.000 0.00 0.00 38.84 3.10
85 86 5.533154 ACAGAAGTAGATTCCCGTATCTCTG 59.467 44.000 0.00 0.00 38.84 3.35
86 87 5.765677 CAGAAGTAGATTCCCGTATCTCTGA 59.234 44.000 0.00 0.00 38.84 3.27
87 88 5.766174 AGAAGTAGATTCCCGTATCTCTGAC 59.234 44.000 0.00 0.00 38.84 3.51
88 89 4.066490 AGTAGATTCCCGTATCTCTGACG 58.934 47.826 0.00 0.00 36.34 4.35
89 90 3.210232 AGATTCCCGTATCTCTGACGA 57.790 47.619 0.00 0.00 42.98 4.20
90 91 3.552875 AGATTCCCGTATCTCTGACGAA 58.447 45.455 0.00 0.00 42.98 3.85
91 92 3.952323 AGATTCCCGTATCTCTGACGAAA 59.048 43.478 0.00 0.00 42.98 3.46
92 93 3.498927 TTCCCGTATCTCTGACGAAAC 57.501 47.619 0.00 0.00 42.98 2.78
93 94 2.439409 TCCCGTATCTCTGACGAAACA 58.561 47.619 0.00 0.00 42.98 2.83
94 95 3.021695 TCCCGTATCTCTGACGAAACAT 58.978 45.455 0.00 0.00 42.98 2.71
95 96 4.201657 TCCCGTATCTCTGACGAAACATA 58.798 43.478 0.00 0.00 42.98 2.29
96 97 4.036027 TCCCGTATCTCTGACGAAACATAC 59.964 45.833 0.00 0.00 42.98 2.39
97 98 4.036498 CCCGTATCTCTGACGAAACATACT 59.964 45.833 0.00 0.00 42.98 2.12
98 99 5.450137 CCCGTATCTCTGACGAAACATACTT 60.450 44.000 0.00 0.00 42.98 2.24
99 100 5.681982 CCGTATCTCTGACGAAACATACTTC 59.318 44.000 0.00 0.00 42.98 3.01
161 162 4.472833 ACATTCTAGTCTCTTGGCATCCTT 59.527 41.667 0.00 0.00 0.00 3.36
369 382 2.160417 TCGATGTCAGATCGATCGATGG 59.840 50.000 33.86 24.02 44.42 3.51
571 693 4.293648 CCGTGTGCGTCCACCTCA 62.294 66.667 1.78 0.00 41.35 3.86
572 694 2.734723 CGTGTGCGTCCACCTCAG 60.735 66.667 1.78 0.00 41.35 3.35
573 695 2.357517 GTGTGCGTCCACCTCAGG 60.358 66.667 0.00 0.00 41.35 3.86
574 696 4.314440 TGTGCGTCCACCTCAGGC 62.314 66.667 0.00 0.00 41.35 4.85
578 700 4.742201 CGTCCACCTCAGGCCGTG 62.742 72.222 0.00 0.00 0.00 4.94
579 701 3.626924 GTCCACCTCAGGCCGTGT 61.627 66.667 0.00 0.00 0.00 4.49
580 702 3.625897 TCCACCTCAGGCCGTGTG 61.626 66.667 0.00 3.44 0.00 3.82
615 737 2.585247 GTACATCTGCGTCCGCCC 60.585 66.667 9.43 0.00 41.09 6.13
822 1119 0.107508 CTGGGTGGACTGCATCGATT 60.108 55.000 0.00 0.00 0.00 3.34
1013 1500 0.823356 AGCACCATGTCTTTGGCGTT 60.823 50.000 0.00 0.00 40.68 4.84
1036 1523 4.559502 GCTATGTTGCCATCCCGT 57.440 55.556 0.00 0.00 32.29 5.28
1483 1970 1.203441 TCAGCCCTCTGGTGATGCTT 61.203 55.000 0.00 0.00 46.14 3.91
1570 2057 4.884744 TCTACACTCAGAGTTCTGCTATCC 59.115 45.833 0.00 0.00 43.46 2.59
1664 2153 0.924090 GAGTTTCAGCGCGTCTATGG 59.076 55.000 8.43 0.00 0.00 2.74
1911 2400 2.637383 GGTCCGCTCTCGTGAAGGT 61.637 63.158 8.05 0.00 0.00 3.50
2175 2664 2.000447 GTTGAGCGACCATTGTCTACC 59.000 52.381 0.00 0.00 39.47 3.18
2353 2843 6.323739 TCTTGCCACTTCTTCCTTTTATGTTT 59.676 34.615 0.00 0.00 0.00 2.83
2400 2890 5.652014 CCTTACCATGAACCTATTTTCTGCA 59.348 40.000 0.00 0.00 0.00 4.41
2565 3055 0.670546 CTTCCGCTACCACCACACTG 60.671 60.000 0.00 0.00 0.00 3.66
2692 3182 0.473694 TCTTCTGGGGCCTGTCTCAA 60.474 55.000 0.84 0.00 0.00 3.02
3030 3521 2.794350 CTCCAAAATGTTGCGTGGTTTC 59.206 45.455 0.00 0.00 33.01 2.78
3095 3586 2.953821 CGCTCAAAATGGCGTGGT 59.046 55.556 0.00 0.00 45.34 4.16
3257 3748 4.957327 AGGTATTCCTCTAGAGCGTCTTTT 59.043 41.667 14.73 0.00 40.58 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.589855 TCTGGTGCATTTATGATTGTACTGG 59.410 40.000 0.00 0.00 0.00 4.00
2 3 6.682423 TCTGGTGCATTTATGATTGTACTG 57.318 37.500 0.00 0.00 0.00 2.74
4 5 5.297776 AGCTCTGGTGCATTTATGATTGTAC 59.702 40.000 0.00 0.00 34.99 2.90
5 6 5.439721 AGCTCTGGTGCATTTATGATTGTA 58.560 37.500 0.00 0.00 34.99 2.41
7 8 4.579340 AGAGCTCTGGTGCATTTATGATTG 59.421 41.667 17.42 0.00 34.99 2.67
8 9 4.579340 CAGAGCTCTGGTGCATTTATGATT 59.421 41.667 32.30 0.00 40.20 2.57
10 11 3.198417 TCAGAGCTCTGGTGCATTTATGA 59.802 43.478 36.92 15.53 43.91 2.15
11 12 3.311871 GTCAGAGCTCTGGTGCATTTATG 59.688 47.826 36.92 13.51 43.91 1.90
12 13 3.539604 GTCAGAGCTCTGGTGCATTTAT 58.460 45.455 36.92 0.58 43.91 1.40
13 14 2.675032 CGTCAGAGCTCTGGTGCATTTA 60.675 50.000 36.92 17.22 43.91 1.40
14 15 1.818642 GTCAGAGCTCTGGTGCATTT 58.181 50.000 36.92 1.94 43.91 2.32
15 16 0.390866 CGTCAGAGCTCTGGTGCATT 60.391 55.000 36.92 2.73 43.91 3.56
16 17 1.217511 CGTCAGAGCTCTGGTGCAT 59.782 57.895 36.92 3.54 43.91 3.96
17 18 1.463553 TTCGTCAGAGCTCTGGTGCA 61.464 55.000 36.92 20.72 43.91 4.57
18 19 0.735632 CTTCGTCAGAGCTCTGGTGC 60.736 60.000 36.92 26.31 43.91 5.01
19 20 0.884514 TCTTCGTCAGAGCTCTGGTG 59.115 55.000 36.92 29.17 43.91 4.17
20 21 1.476085 CATCTTCGTCAGAGCTCTGGT 59.524 52.381 36.92 10.08 43.91 4.00
21 22 1.747924 TCATCTTCGTCAGAGCTCTGG 59.252 52.381 36.92 24.70 43.91 3.86
22 23 3.119531 AGTTCATCTTCGTCAGAGCTCTG 60.120 47.826 33.73 33.73 45.08 3.35
23 24 3.088532 AGTTCATCTTCGTCAGAGCTCT 58.911 45.455 11.45 11.45 33.87 4.09
24 25 3.119673 TCAGTTCATCTTCGTCAGAGCTC 60.120 47.826 5.27 5.27 33.87 4.09
25 26 2.822561 TCAGTTCATCTTCGTCAGAGCT 59.177 45.455 0.00 0.00 33.87 4.09
26 27 3.119673 TCTCAGTTCATCTTCGTCAGAGC 60.120 47.826 0.00 0.00 33.87 4.09
27 28 4.155826 ACTCTCAGTTCATCTTCGTCAGAG 59.844 45.833 0.00 0.00 33.87 3.35
28 29 4.075682 ACTCTCAGTTCATCTTCGTCAGA 58.924 43.478 0.00 0.00 35.33 3.27
29 30 4.433186 ACTCTCAGTTCATCTTCGTCAG 57.567 45.455 0.00 0.00 0.00 3.51
30 31 5.648092 TGATACTCTCAGTTCATCTTCGTCA 59.352 40.000 0.00 0.00 0.00 4.35
31 32 6.125327 TGATACTCTCAGTTCATCTTCGTC 57.875 41.667 0.00 0.00 0.00 4.20
32 33 6.516739 TTGATACTCTCAGTTCATCTTCGT 57.483 37.500 0.00 0.00 34.68 3.85
33 34 7.032580 ACTTTGATACTCTCAGTTCATCTTCG 58.967 38.462 0.00 0.00 34.68 3.79
34 35 7.491048 GGACTTTGATACTCTCAGTTCATCTTC 59.509 40.741 0.00 0.00 34.68 2.87
35 36 7.038729 TGGACTTTGATACTCTCAGTTCATCTT 60.039 37.037 0.00 0.00 34.68 2.40
36 37 6.438741 TGGACTTTGATACTCTCAGTTCATCT 59.561 38.462 0.00 0.00 34.68 2.90
37 38 6.533367 GTGGACTTTGATACTCTCAGTTCATC 59.467 42.308 0.00 0.00 34.68 2.92
38 39 6.014242 TGTGGACTTTGATACTCTCAGTTCAT 60.014 38.462 0.00 0.00 34.68 2.57
39 40 5.304357 TGTGGACTTTGATACTCTCAGTTCA 59.696 40.000 0.00 0.00 34.68 3.18
40 41 5.784177 TGTGGACTTTGATACTCTCAGTTC 58.216 41.667 0.00 0.00 34.68 3.01
41 42 5.540337 TCTGTGGACTTTGATACTCTCAGTT 59.460 40.000 0.00 0.00 34.68 3.16
42 43 5.080337 TCTGTGGACTTTGATACTCTCAGT 58.920 41.667 0.00 0.00 34.68 3.41
43 44 5.651387 TCTGTGGACTTTGATACTCTCAG 57.349 43.478 0.00 0.00 34.68 3.35
44 45 5.540337 ACTTCTGTGGACTTTGATACTCTCA 59.460 40.000 0.00 0.00 0.00 3.27
45 46 6.031751 ACTTCTGTGGACTTTGATACTCTC 57.968 41.667 0.00 0.00 0.00 3.20
46 47 6.948886 TCTACTTCTGTGGACTTTGATACTCT 59.051 38.462 0.00 0.00 0.00 3.24
47 48 7.159322 TCTACTTCTGTGGACTTTGATACTC 57.841 40.000 0.00 0.00 0.00 2.59
48 49 7.726033 ATCTACTTCTGTGGACTTTGATACT 57.274 36.000 0.00 0.00 36.52 2.12
49 50 7.492994 GGAATCTACTTCTGTGGACTTTGATAC 59.507 40.741 0.00 0.00 36.52 2.24
50 51 7.364762 GGGAATCTACTTCTGTGGACTTTGATA 60.365 40.741 0.00 0.00 36.52 2.15
51 52 6.410540 GGAATCTACTTCTGTGGACTTTGAT 58.589 40.000 0.00 0.00 36.52 2.57
52 53 5.280011 GGGAATCTACTTCTGTGGACTTTGA 60.280 44.000 0.00 0.00 36.52 2.69
53 54 4.938226 GGGAATCTACTTCTGTGGACTTTG 59.062 45.833 0.00 0.00 36.52 2.77
54 55 4.322801 CGGGAATCTACTTCTGTGGACTTT 60.323 45.833 0.00 0.00 36.52 2.66
55 56 3.195825 CGGGAATCTACTTCTGTGGACTT 59.804 47.826 0.00 0.00 36.52 3.01
56 57 2.761208 CGGGAATCTACTTCTGTGGACT 59.239 50.000 0.00 0.00 36.52 3.85
57 58 2.496470 ACGGGAATCTACTTCTGTGGAC 59.504 50.000 0.00 0.00 36.52 4.02
58 59 2.816411 ACGGGAATCTACTTCTGTGGA 58.184 47.619 0.00 0.00 38.05 4.02
59 60 4.585162 AGATACGGGAATCTACTTCTGTGG 59.415 45.833 0.00 0.00 34.40 4.17
60 61 5.533154 AGAGATACGGGAATCTACTTCTGTG 59.467 44.000 0.00 0.00 36.33 3.66
61 62 5.533154 CAGAGATACGGGAATCTACTTCTGT 59.467 44.000 0.00 0.00 36.33 3.41
62 63 5.765677 TCAGAGATACGGGAATCTACTTCTG 59.234 44.000 0.00 0.00 36.33 3.02
63 64 5.766174 GTCAGAGATACGGGAATCTACTTCT 59.234 44.000 0.00 0.00 36.33 2.85
64 65 5.334260 CGTCAGAGATACGGGAATCTACTTC 60.334 48.000 0.00 0.00 36.33 3.01
65 66 4.515944 CGTCAGAGATACGGGAATCTACTT 59.484 45.833 0.00 0.00 36.33 2.24
66 67 4.066490 CGTCAGAGATACGGGAATCTACT 58.934 47.826 0.00 0.00 36.33 2.57
67 68 4.063689 TCGTCAGAGATACGGGAATCTAC 58.936 47.826 0.00 0.00 40.68 2.59
68 69 4.347360 TCGTCAGAGATACGGGAATCTA 57.653 45.455 0.00 0.00 40.68 1.98
69 70 3.210232 TCGTCAGAGATACGGGAATCT 57.790 47.619 0.00 0.00 40.68 2.40
70 71 3.984508 TTCGTCAGAGATACGGGAATC 57.015 47.619 0.00 0.00 40.68 2.52
71 72 3.446161 TGTTTCGTCAGAGATACGGGAAT 59.554 43.478 0.00 0.00 40.68 3.01
72 73 2.821378 TGTTTCGTCAGAGATACGGGAA 59.179 45.455 0.00 0.00 40.68 3.97
73 74 2.439409 TGTTTCGTCAGAGATACGGGA 58.561 47.619 0.00 0.00 40.68 5.14
74 75 2.933495 TGTTTCGTCAGAGATACGGG 57.067 50.000 0.00 0.00 40.68 5.28
75 76 5.171147 AGTATGTTTCGTCAGAGATACGG 57.829 43.478 0.00 0.00 40.68 4.02
76 77 6.487960 AGAAGTATGTTTCGTCAGAGATACG 58.512 40.000 0.00 0.00 41.64 3.06
77 78 7.755822 ACAAGAAGTATGTTTCGTCAGAGATAC 59.244 37.037 0.00 0.00 32.33 2.24
78 79 7.827701 ACAAGAAGTATGTTTCGTCAGAGATA 58.172 34.615 0.00 0.00 32.33 1.98
79 80 6.692486 ACAAGAAGTATGTTTCGTCAGAGAT 58.308 36.000 0.00 0.00 32.33 2.75
80 81 6.085555 ACAAGAAGTATGTTTCGTCAGAGA 57.914 37.500 0.00 0.00 32.33 3.10
81 82 6.771188 AACAAGAAGTATGTTTCGTCAGAG 57.229 37.500 0.00 0.00 37.74 3.35
82 83 7.654568 TCTAACAAGAAGTATGTTTCGTCAGA 58.345 34.615 0.00 0.00 41.11 3.27
83 84 7.595502 ACTCTAACAAGAAGTATGTTTCGTCAG 59.404 37.037 0.00 0.00 41.11 3.51
84 85 7.431249 ACTCTAACAAGAAGTATGTTTCGTCA 58.569 34.615 0.00 0.00 41.11 4.35
85 86 7.870588 ACTCTAACAAGAAGTATGTTTCGTC 57.129 36.000 0.00 0.00 41.11 4.20
86 87 9.924650 ATAACTCTAACAAGAAGTATGTTTCGT 57.075 29.630 0.00 0.00 41.11 3.85
161 162 2.825532 GAGGATGCCAAAAGGCTACAAA 59.174 45.455 8.11 0.00 35.66 2.83
297 305 4.775058 TCGAGAGAAGAAGACTGGAAAG 57.225 45.455 0.00 0.00 37.03 2.62
369 382 1.270550 AGTGGCAGTGTATTTGCTTGC 59.729 47.619 0.00 0.00 41.27 4.01
563 685 3.625897 CACACGGCCTGAGGTGGA 61.626 66.667 12.39 0.00 38.46 4.02
587 709 0.179100 CAGATGTACACGGCCTGAGG 60.179 60.000 0.00 0.00 0.00 3.86
588 710 0.807667 GCAGATGTACACGGCCTGAG 60.808 60.000 16.01 0.00 0.00 3.35
589 711 1.218047 GCAGATGTACACGGCCTGA 59.782 57.895 16.01 0.00 0.00 3.86
590 712 2.167219 CGCAGATGTACACGGCCTG 61.167 63.158 0.00 4.94 0.00 4.85
591 713 2.184322 CGCAGATGTACACGGCCT 59.816 61.111 0.00 0.00 0.00 5.19
592 714 2.125673 ACGCAGATGTACACGGCC 60.126 61.111 0.00 0.00 0.00 6.13
593 715 2.165301 GGACGCAGATGTACACGGC 61.165 63.158 0.00 0.00 0.00 5.68
594 716 1.872234 CGGACGCAGATGTACACGG 60.872 63.158 0.00 0.00 0.00 4.94
595 717 2.505498 GCGGACGCAGATGTACACG 61.505 63.158 12.31 0.00 41.49 4.49
596 718 2.165301 GGCGGACGCAGATGTACAC 61.165 63.158 18.95 0.00 44.11 2.90
597 719 2.183300 GGCGGACGCAGATGTACA 59.817 61.111 18.95 0.00 44.11 2.90
598 720 2.585247 GGGCGGACGCAGATGTAC 60.585 66.667 18.95 0.00 44.11 2.90
599 721 2.758327 AGGGCGGACGCAGATGTA 60.758 61.111 18.95 0.00 44.11 2.29
600 722 4.457496 CAGGGCGGACGCAGATGT 62.457 66.667 18.95 0.00 44.11 3.06
615 737 3.074999 GCCTGAGGAGACGGAGCAG 62.075 68.421 0.65 0.00 0.00 4.24
822 1119 1.887242 GCACACACGAAGCAGGTGA 60.887 57.895 8.52 0.00 38.73 4.02
1036 1523 0.254462 TCAAATATCACCGGGCAGCA 59.746 50.000 6.32 0.00 0.00 4.41
1162 1649 2.736826 GGGTAGGAGCCACAGGAGC 61.737 68.421 0.00 0.00 35.40 4.70
1483 1970 2.295349 GACGGACCACAGACAAGTAGAA 59.705 50.000 0.00 0.00 0.00 2.10
1664 2153 2.027625 CGGAGCCGTGACAAGAACC 61.028 63.158 0.00 0.00 34.35 3.62
1781 2270 0.963962 CTGAAGCAAACCAGCACCAT 59.036 50.000 0.00 0.00 36.85 3.55
1911 2400 0.805322 GAGTACGAGGACGAGAGCGA 60.805 60.000 0.00 0.00 42.66 4.93
2094 2583 2.370189 AGAACCTGAAGCAGCAAGTAGT 59.630 45.455 0.00 0.00 0.00 2.73
2175 2664 1.141657 CATGGGGATGTACCTGACTGG 59.858 57.143 0.00 0.00 42.93 4.00
2353 2843 3.603532 GAGGCACATGAGAAACATCTGA 58.396 45.455 0.00 0.00 37.07 3.27
2400 2890 5.013183 ACAACCAGAATTAGTAAGCTGACCT 59.987 40.000 14.08 0.00 0.00 3.85
2633 3123 2.450609 TAGTCGAGAACCACAAAGGC 57.549 50.000 0.00 0.00 43.14 4.35
2692 3182 3.776969 TGGCATTGTAAGGAGACATCTCT 59.223 43.478 8.74 0.00 42.48 3.10
2862 3353 4.991153 AGTGTAGCGAGAGAAATCATCA 57.009 40.909 0.00 0.00 0.00 3.07
3030 3521 2.125106 GTACCCTGCTCGGCAAGG 60.125 66.667 10.80 10.80 44.92 3.61
3084 3575 2.953821 CGCTCAACCACGCCATTT 59.046 55.556 0.00 0.00 0.00 2.32
3095 3586 1.667510 TGACGATGCTTGCGCTCAA 60.668 52.632 9.73 0.00 36.97 3.02
3257 3748 7.515586 AGCAGAATAATCAGGAGAATGATCAA 58.484 34.615 0.00 0.00 39.00 2.57
3370 3863 3.826524 TGTTCATCACTGTAGCCCAAAA 58.173 40.909 0.00 0.00 0.00 2.44
3371 3864 3.500448 TGTTCATCACTGTAGCCCAAA 57.500 42.857 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.