Multiple sequence alignment - TraesCS3D01G109300

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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 TraesCS3D01G109300 chr3D 100.000 3387 0 0 1 3387 63005946 63009332 0.000000e+00 6255.0
1 TraesCS3D01G109300 chr3A 91.358 3101 129 56 358 3387 71793368 71796400 0.000000e+00 4113.0
2 TraesCS3D01G109300 chr3A 81.571 331 49 11 1349 1670 749282526 749282853 2.590000e-66 263.0
3 TraesCS3D01G109300 chr3B 92.049 2792 96 47 656 3387 101799029 101801754 0.000000e+00 3810.0
4 TraesCS3D01G109300 chr3B 90.813 283 20 3 231 512 101798602 101798879 1.150000e-99 374.0
5 TraesCS3D01G109300 chr3B 80.588 340 54 11 1340 1670 822832876 822833212 5.610000e-63 252.0
6 TraesCS3D01G109300 chr3B 96.000 100 4 0 545 644 101798881 101798980 2.700000e-36 163.0
7 TraesCS3D01G109300 chr3B 97.674 43 0 1 1685 1727 5598548 5598507 4.690000e-09 73.1
8 TraesCS3D01G109300 chr3B 97.674 43 0 1 1685 1727 456978563 456978604 4.690000e-09 73.1
9 TraesCS3D01G109300 chr1D 81.818 319 47 10 1355 1666 52576370 52576056 1.210000e-64 257.0
10 TraesCS3D01G109300 chr1D 79.085 306 51 7 1355 1649 435535372 435535069 7.410000e-47 198.0
11 TraesCS3D01G109300 chr1B 81.818 319 47 10 1355 1666 83640076 83639762 1.210000e-64 257.0
12 TraesCS3D01G109300 chr1B 95.349 43 1 1 1685 1727 57811509 57811468 2.180000e-07 67.6
13 TraesCS3D01G109300 chr1A 81.761 318 49 8 1355 1666 52237545 52237231 1.210000e-64 257.0
14 TraesCS3D01G109300 chr5B 86.538 156 14 6 1554 1706 243429413 243429262 7.520000e-37 165.0
15 TraesCS3D01G109300 chrUn 97.674 43 0 1 1685 1727 464945906 464945947 4.690000e-09 73.1
16 TraesCS3D01G109300 chr7A 97.674 43 0 1 1685 1727 623459797 623459756 4.690000e-09 73.1
17 TraesCS3D01G109300 chr7A 97.674 43 0 1 1685 1727 717180960 717180919 4.690000e-09 73.1


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 TraesCS3D01G109300 chr3D 63005946 63009332 3386 False 6255 6255 100.000 1 3387 1 chr3D.!!$F1 3386
1 TraesCS3D01G109300 chr3A 71793368 71796400 3032 False 4113 4113 91.358 358 3387 1 chr3A.!!$F1 3029
2 TraesCS3D01G109300 chr3B 101798602 101801754 3152 False 1449 3810 92.954 231 3387 3 chr3B.!!$F3 3156

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
70 71 0.465460 TTCTTCCCTTGTTGCTGCGT 60.465 50.000 0.0 0.0 0.00 5.24 F
79 80 0.515127 TGTTGCTGCGTTATTCGTGG 59.485 50.000 0.0 0.0 42.13 4.94 F
80 81 0.793861 GTTGCTGCGTTATTCGTGGA 59.206 50.000 0.0 0.0 42.13 4.02 F
616 621 1.004394 CCTACCCCAGGTTTCCAGAAC 59.996 57.143 0.0 0.0 39.91 3.01 F
2291 2384 0.803768 CGACCTGATCAACTGAGGCG 60.804 60.000 0.0 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1112 1181 1.145598 TATGCTGGCTGCTCTGCTC 59.854 57.895 17.45 0.0 43.37 4.26 R
1981 2074 3.087906 GTGGGGTAGCCGGACCAT 61.088 66.667 5.05 0.0 41.73 3.55 R
2068 2161 4.823276 CTGGAAGCGCTAGTCTGG 57.177 61.111 12.05 0.0 0.00 3.86 R
2332 2425 0.721718 CTCCGCCGTGAAATCTTGTC 59.278 55.000 0.00 0.0 0.00 3.18 R
3332 3500 0.988678 GGCTGTACCAATCCCCTCCT 60.989 60.000 0.00 0.0 38.86 3.69 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
23 24 6.319229 GTGTCACATCTTACGTTCACTATG 57.681 41.667 0.00 0.00 0.00 2.23
24 25 5.862323 GTGTCACATCTTACGTTCACTATGT 59.138 40.000 0.00 0.00 0.00 2.29
25 26 6.365247 GTGTCACATCTTACGTTCACTATGTT 59.635 38.462 0.00 0.00 0.00 2.71
26 27 6.926826 TGTCACATCTTACGTTCACTATGTTT 59.073 34.615 0.00 0.00 0.00 2.83
27 28 7.095816 TGTCACATCTTACGTTCACTATGTTTG 60.096 37.037 0.00 0.00 0.00 2.93
28 29 6.926826 TCACATCTTACGTTCACTATGTTTGT 59.073 34.615 0.00 0.00 0.00 2.83
29 30 7.009440 CACATCTTACGTTCACTATGTTTGTG 58.991 38.462 0.00 0.00 36.82 3.33
30 31 6.926826 ACATCTTACGTTCACTATGTTTGTGA 59.073 34.615 0.00 0.00 41.94 3.58
31 32 7.602644 ACATCTTACGTTCACTATGTTTGTGAT 59.397 33.333 0.00 0.00 42.95 3.06
32 33 7.576750 TCTTACGTTCACTATGTTTGTGATC 57.423 36.000 0.00 0.00 42.95 2.92
33 34 7.375834 TCTTACGTTCACTATGTTTGTGATCT 58.624 34.615 0.00 0.00 42.95 2.75
34 35 7.870954 TCTTACGTTCACTATGTTTGTGATCTT 59.129 33.333 0.00 0.00 42.95 2.40
35 36 6.861065 ACGTTCACTATGTTTGTGATCTTT 57.139 33.333 0.00 0.00 42.95 2.52
36 37 7.259290 ACGTTCACTATGTTTGTGATCTTTT 57.741 32.000 0.00 0.00 42.95 2.27
37 38 7.703328 ACGTTCACTATGTTTGTGATCTTTTT 58.297 30.769 0.00 0.00 42.95 1.94
57 58 4.400529 TTTTTGTCCCAGCTTTTCTTCC 57.599 40.909 0.00 0.00 0.00 3.46
58 59 1.995376 TTGTCCCAGCTTTTCTTCCC 58.005 50.000 0.00 0.00 0.00 3.97
59 60 1.149101 TGTCCCAGCTTTTCTTCCCT 58.851 50.000 0.00 0.00 0.00 4.20
60 61 1.499007 TGTCCCAGCTTTTCTTCCCTT 59.501 47.619 0.00 0.00 0.00 3.95
61 62 1.889170 GTCCCAGCTTTTCTTCCCTTG 59.111 52.381 0.00 0.00 0.00 3.61
62 63 1.499007 TCCCAGCTTTTCTTCCCTTGT 59.501 47.619 0.00 0.00 0.00 3.16
63 64 2.091333 TCCCAGCTTTTCTTCCCTTGTT 60.091 45.455 0.00 0.00 0.00 2.83
64 65 2.036346 CCCAGCTTTTCTTCCCTTGTTG 59.964 50.000 0.00 0.00 0.00 3.33
65 66 2.546584 CCAGCTTTTCTTCCCTTGTTGC 60.547 50.000 0.00 0.00 0.00 4.17
66 67 2.363359 CAGCTTTTCTTCCCTTGTTGCT 59.637 45.455 0.00 0.00 0.00 3.91
67 68 2.363359 AGCTTTTCTTCCCTTGTTGCTG 59.637 45.455 0.00 0.00 0.00 4.41
68 69 2.747436 CTTTTCTTCCCTTGTTGCTGC 58.253 47.619 0.00 0.00 0.00 5.25
69 70 0.667993 TTTCTTCCCTTGTTGCTGCG 59.332 50.000 0.00 0.00 0.00 5.18
70 71 0.465460 TTCTTCCCTTGTTGCTGCGT 60.465 50.000 0.00 0.00 0.00 5.24
71 72 0.465460 TCTTCCCTTGTTGCTGCGTT 60.465 50.000 0.00 0.00 0.00 4.84
72 73 1.202710 TCTTCCCTTGTTGCTGCGTTA 60.203 47.619 0.00 0.00 0.00 3.18
73 74 1.812571 CTTCCCTTGTTGCTGCGTTAT 59.187 47.619 0.00 0.00 0.00 1.89
74 75 1.904287 TCCCTTGTTGCTGCGTTATT 58.096 45.000 0.00 0.00 0.00 1.40
75 76 1.810151 TCCCTTGTTGCTGCGTTATTC 59.190 47.619 0.00 0.00 0.00 1.75
76 77 1.465689 CCCTTGTTGCTGCGTTATTCG 60.466 52.381 0.00 0.00 43.12 3.34
77 78 1.196808 CCTTGTTGCTGCGTTATTCGT 59.803 47.619 0.00 0.00 42.13 3.85
78 79 2.233355 CTTGTTGCTGCGTTATTCGTG 58.767 47.619 0.00 0.00 42.13 4.35
79 80 0.515127 TGTTGCTGCGTTATTCGTGG 59.485 50.000 0.00 0.00 42.13 4.94
80 81 0.793861 GTTGCTGCGTTATTCGTGGA 59.206 50.000 0.00 0.00 42.13 4.02
81 82 1.195900 GTTGCTGCGTTATTCGTGGAA 59.804 47.619 0.00 0.00 42.13 3.53
82 83 1.075542 TGCTGCGTTATTCGTGGAAG 58.924 50.000 0.00 0.00 42.13 3.46
83 84 1.076332 GCTGCGTTATTCGTGGAAGT 58.924 50.000 0.00 0.00 42.13 3.01
84 85 1.463444 GCTGCGTTATTCGTGGAAGTT 59.537 47.619 0.00 0.00 42.13 2.66
85 86 2.095919 GCTGCGTTATTCGTGGAAGTTT 60.096 45.455 0.00 0.00 42.13 2.66
86 87 3.123959 GCTGCGTTATTCGTGGAAGTTTA 59.876 43.478 0.00 0.00 42.13 2.01
87 88 4.724036 GCTGCGTTATTCGTGGAAGTTTAG 60.724 45.833 0.00 0.00 42.13 1.85
88 89 4.558178 TGCGTTATTCGTGGAAGTTTAGA 58.442 39.130 0.00 0.00 42.13 2.10
89 90 5.172934 TGCGTTATTCGTGGAAGTTTAGAT 58.827 37.500 0.00 0.00 42.13 1.98
90 91 5.062934 TGCGTTATTCGTGGAAGTTTAGATG 59.937 40.000 0.00 0.00 42.13 2.90
91 92 5.063060 GCGTTATTCGTGGAAGTTTAGATGT 59.937 40.000 0.00 0.00 42.13 3.06
92 93 6.466812 CGTTATTCGTGGAAGTTTAGATGTG 58.533 40.000 0.00 0.00 34.52 3.21
93 94 6.309494 CGTTATTCGTGGAAGTTTAGATGTGA 59.691 38.462 0.00 0.00 34.52 3.58
94 95 7.453838 GTTATTCGTGGAAGTTTAGATGTGAC 58.546 38.462 0.00 0.00 0.00 3.67
95 96 4.594123 TCGTGGAAGTTTAGATGTGACA 57.406 40.909 0.00 0.00 0.00 3.58
96 97 5.147330 TCGTGGAAGTTTAGATGTGACAT 57.853 39.130 0.00 0.00 0.00 3.06
97 98 5.168569 TCGTGGAAGTTTAGATGTGACATC 58.831 41.667 17.46 17.46 0.00 3.06
98 99 4.330074 CGTGGAAGTTTAGATGTGACATCC 59.670 45.833 21.05 6.31 33.11 3.51
99 100 5.491982 GTGGAAGTTTAGATGTGACATCCT 58.508 41.667 21.05 8.88 33.54 3.24
100 101 5.940470 GTGGAAGTTTAGATGTGACATCCTT 59.060 40.000 21.05 16.28 33.54 3.36
101 102 6.431234 GTGGAAGTTTAGATGTGACATCCTTT 59.569 38.462 21.05 6.50 33.54 3.11
102 103 7.606456 GTGGAAGTTTAGATGTGACATCCTTTA 59.394 37.037 21.05 5.51 33.54 1.85
103 104 8.160765 TGGAAGTTTAGATGTGACATCCTTTAA 58.839 33.333 21.05 11.07 33.54 1.52
104 105 9.010029 GGAAGTTTAGATGTGACATCCTTTAAA 57.990 33.333 21.05 15.77 30.62 1.52
108 109 9.959749 GTTTAGATGTGACATCCTTTAAAAACA 57.040 29.630 21.05 0.00 0.00 2.83
242 243 9.588096 AGGGAGTACTTTTTACTCATGAAAAAT 57.412 29.630 12.33 0.00 44.18 1.82
245 246 9.543018 GAGTACTTTTTACTCATGAAAAATCCG 57.457 33.333 6.22 2.51 42.49 4.18
248 249 4.712122 TTTACTCATGAAAAATCCGGGC 57.288 40.909 0.00 0.00 0.00 6.13
249 250 2.514458 ACTCATGAAAAATCCGGGCT 57.486 45.000 0.00 0.00 0.00 5.19
253 254 4.956075 ACTCATGAAAAATCCGGGCTAATT 59.044 37.500 0.00 0.00 0.00 1.40
257 258 5.828299 TGAAAAATCCGGGCTAATTACAG 57.172 39.130 0.00 0.00 0.00 2.74
258 259 5.258051 TGAAAAATCCGGGCTAATTACAGT 58.742 37.500 0.00 0.00 0.00 3.55
262 263 1.760613 TCCGGGCTAATTACAGTCAGG 59.239 52.381 0.00 0.00 36.89 3.86
291 293 3.625853 TCATGGATTATGCCCGTTTTCA 58.374 40.909 0.00 0.00 36.70 2.69
296 298 4.221703 TGGATTATGCCCGTTTTCAACAAT 59.778 37.500 0.00 0.00 0.00 2.71
300 302 4.864704 ATGCCCGTTTTCAACAATTACT 57.135 36.364 0.00 0.00 0.00 2.24
301 303 5.968528 ATGCCCGTTTTCAACAATTACTA 57.031 34.783 0.00 0.00 0.00 1.82
305 307 7.531716 TGCCCGTTTTCAACAATTACTATTAG 58.468 34.615 0.00 0.00 0.00 1.73
354 356 2.876581 ACAAATTCCTCCCCACACTTC 58.123 47.619 0.00 0.00 0.00 3.01
391 393 9.751542 AGCTCACAGAAATACACATATAAGTAC 57.248 33.333 0.00 0.00 0.00 2.73
616 621 1.004394 CCTACCCCAGGTTTCCAGAAC 59.996 57.143 0.00 0.00 39.91 3.01
643 673 5.125739 ACACGAACGAATATCTTCTCTTCCT 59.874 40.000 0.14 0.00 0.00 3.36
646 677 6.095720 ACGAACGAATATCTTCTCTTCCTTCT 59.904 38.462 0.14 0.00 0.00 2.85
884 937 3.532155 ATCCCCTCTCGCTGACGC 61.532 66.667 0.00 0.00 39.84 5.19
1038 1092 2.033424 GCTTGGTGTTCTTCTCCACAAC 59.967 50.000 0.00 0.00 39.10 3.32
1112 1181 1.035923 TCTTCCCATAGAGCAGAGCG 58.964 55.000 0.00 0.00 0.00 5.03
1124 1193 4.146075 AGAGCGAGCAGAGCAGCC 62.146 66.667 0.00 0.06 35.70 4.85
2008 2101 3.622263 TACCCCACCTCCCCTGCT 61.622 66.667 0.00 0.00 0.00 4.24
2080 2173 3.775654 GGCACCCAGACTAGCGCT 61.776 66.667 17.26 17.26 0.00 5.92
2291 2384 0.803768 CGACCTGATCAACTGAGGCG 60.804 60.000 0.00 0.00 0.00 5.52
2327 2420 3.243068 GCAAGTTCATTTTGTGACGAGGT 60.243 43.478 0.00 0.00 36.32 3.85
2366 2459 1.221021 GGAGGTGGCGGTAAGAAGG 59.779 63.158 0.00 0.00 0.00 3.46
2455 2551 6.576662 TTCCTGTACATAGCTGCTATCTAC 57.423 41.667 21.19 21.19 0.00 2.59
2505 2601 0.179062 CGGAAGGGAGGCAAGATGAG 60.179 60.000 0.00 0.00 0.00 2.90
2506 2602 1.207791 GGAAGGGAGGCAAGATGAGA 58.792 55.000 0.00 0.00 0.00 3.27
2507 2603 1.773653 GGAAGGGAGGCAAGATGAGAT 59.226 52.381 0.00 0.00 0.00 2.75
2565 2666 5.491078 TGAGGAAGTGTAGGAATTTACCCAT 59.509 40.000 0.00 0.00 0.00 4.00
2607 2711 3.457749 AGGGAAGAGATGGATTGGAACTC 59.542 47.826 0.00 0.00 0.00 3.01
2614 2718 1.358152 TGGATTGGAACTCGGAAGGT 58.642 50.000 0.00 0.00 0.00 3.50
2756 2882 1.153309 TCCTCGGCAGTGCATCATG 60.153 57.895 18.61 0.90 0.00 3.07
2770 2896 2.477825 CATCATGTGGACTAGCCGAAG 58.522 52.381 0.00 0.00 40.66 3.79
2771 2897 1.847328 TCATGTGGACTAGCCGAAGA 58.153 50.000 0.00 0.00 40.66 2.87
2772 2898 1.476891 TCATGTGGACTAGCCGAAGAC 59.523 52.381 0.00 0.00 40.66 3.01
2773 2899 1.478510 CATGTGGACTAGCCGAAGACT 59.521 52.381 0.00 0.00 40.66 3.24
2878 3014 4.580580 AGCATATTTTGTACCTTAGCTGCC 59.419 41.667 0.00 0.00 0.00 4.85
2879 3015 4.580580 GCATATTTTGTACCTTAGCTGCCT 59.419 41.667 0.00 0.00 0.00 4.75
2880 3016 5.763204 GCATATTTTGTACCTTAGCTGCCTA 59.237 40.000 0.00 0.00 0.00 3.93
2881 3017 6.073003 GCATATTTTGTACCTTAGCTGCCTAG 60.073 42.308 0.00 0.00 0.00 3.02
2910 3055 0.991920 ATCCCTGTTCGTCCAATGGT 59.008 50.000 0.00 0.00 0.00 3.55
3076 3226 8.660295 TCTATCTACCTGTTCTTTCCAGTAAA 57.340 34.615 0.00 0.00 0.00 2.01
3107 3259 7.932491 TGTGAATGAAATGAAATGGTTGATTGT 59.068 29.630 0.00 0.00 0.00 2.71
3111 3263 8.712285 ATGAAATGAAATGGTTGATTGTGATC 57.288 30.769 0.00 0.00 0.00 2.92
3113 3265 5.902613 ATGAAATGGTTGATTGTGATCGT 57.097 34.783 0.00 0.00 34.91 3.73
3114 3266 5.703978 TGAAATGGTTGATTGTGATCGTT 57.296 34.783 0.00 0.00 34.91 3.85
3115 3267 5.459768 TGAAATGGTTGATTGTGATCGTTG 58.540 37.500 0.00 0.00 34.91 4.10
3215 3379 0.676782 GTGGAACTCGGATGGTTGGG 60.677 60.000 0.00 0.00 0.00 4.12
3271 3435 4.779966 AGAGAGACCGGCGAGCGA 62.780 66.667 9.30 0.00 0.00 4.93
3272 3436 4.539881 GAGAGACCGGCGAGCGAC 62.540 72.222 9.30 0.00 0.00 5.19
3313 3481 0.109913 ACCTGGTCGTTTTCCCCTTC 59.890 55.000 0.00 0.00 0.00 3.46
3314 3482 0.608308 CCTGGTCGTTTTCCCCTTCC 60.608 60.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.862323 ACATAGTGAACGTAAGATGTGACAC 59.138 40.000 0.00 0.00 43.62 3.67
1 2 6.020971 ACATAGTGAACGTAAGATGTGACA 57.979 37.500 0.00 0.00 43.62 3.58
2 3 6.946229 AACATAGTGAACGTAAGATGTGAC 57.054 37.500 0.00 0.00 43.62 3.67
3 4 6.926826 ACAAACATAGTGAACGTAAGATGTGA 59.073 34.615 0.00 0.00 43.62 3.58
4 5 7.009440 CACAAACATAGTGAACGTAAGATGTG 58.991 38.462 0.00 0.00 39.30 3.21
5 6 6.926826 TCACAAACATAGTGAACGTAAGATGT 59.073 34.615 0.00 0.00 42.57 3.06
6 7 7.346208 TCACAAACATAGTGAACGTAAGATG 57.654 36.000 0.00 0.00 42.57 2.90
36 37 3.133901 GGGAAGAAAAGCTGGGACAAAAA 59.866 43.478 0.00 0.00 38.70 1.94
37 38 2.698274 GGGAAGAAAAGCTGGGACAAAA 59.302 45.455 0.00 0.00 38.70 2.44
38 39 2.091333 AGGGAAGAAAAGCTGGGACAAA 60.091 45.455 0.00 0.00 38.70 2.83
39 40 1.499007 AGGGAAGAAAAGCTGGGACAA 59.501 47.619 0.00 0.00 38.70 3.18
40 41 1.149101 AGGGAAGAAAAGCTGGGACA 58.851 50.000 0.00 0.00 0.00 4.02
41 42 1.889170 CAAGGGAAGAAAAGCTGGGAC 59.111 52.381 0.00 0.00 0.00 4.46
42 43 1.499007 ACAAGGGAAGAAAAGCTGGGA 59.501 47.619 0.00 0.00 0.00 4.37
43 44 2.001076 ACAAGGGAAGAAAAGCTGGG 57.999 50.000 0.00 0.00 0.00 4.45
44 45 2.546584 GCAACAAGGGAAGAAAAGCTGG 60.547 50.000 0.00 0.00 0.00 4.85
45 46 2.363359 AGCAACAAGGGAAGAAAAGCTG 59.637 45.455 0.00 0.00 0.00 4.24
46 47 2.363359 CAGCAACAAGGGAAGAAAAGCT 59.637 45.455 0.00 0.00 0.00 3.74
47 48 2.747436 CAGCAACAAGGGAAGAAAAGC 58.253 47.619 0.00 0.00 0.00 3.51
48 49 2.747436 GCAGCAACAAGGGAAGAAAAG 58.253 47.619 0.00 0.00 0.00 2.27
49 50 1.066908 CGCAGCAACAAGGGAAGAAAA 59.933 47.619 0.00 0.00 0.00 2.29
50 51 0.667993 CGCAGCAACAAGGGAAGAAA 59.332 50.000 0.00 0.00 0.00 2.52
51 52 0.465460 ACGCAGCAACAAGGGAAGAA 60.465 50.000 0.00 0.00 0.00 2.52
52 53 0.465460 AACGCAGCAACAAGGGAAGA 60.465 50.000 0.00 0.00 0.00 2.87
53 54 1.234821 TAACGCAGCAACAAGGGAAG 58.765 50.000 0.00 0.00 0.00 3.46
54 55 1.904287 ATAACGCAGCAACAAGGGAA 58.096 45.000 0.00 0.00 0.00 3.97
55 56 1.810151 GAATAACGCAGCAACAAGGGA 59.190 47.619 0.00 0.00 0.00 4.20
56 57 1.465689 CGAATAACGCAGCAACAAGGG 60.466 52.381 0.00 0.00 34.51 3.95
57 58 1.196808 ACGAATAACGCAGCAACAAGG 59.803 47.619 0.00 0.00 46.94 3.61
58 59 2.233355 CACGAATAACGCAGCAACAAG 58.767 47.619 0.00 0.00 46.94 3.16
59 60 1.069568 CCACGAATAACGCAGCAACAA 60.070 47.619 0.00 0.00 46.94 2.83
60 61 0.515127 CCACGAATAACGCAGCAACA 59.485 50.000 0.00 0.00 46.94 3.33
61 62 0.793861 TCCACGAATAACGCAGCAAC 59.206 50.000 0.00 0.00 46.94 4.17
62 63 1.463056 CTTCCACGAATAACGCAGCAA 59.537 47.619 0.00 0.00 46.94 3.91
63 64 1.075542 CTTCCACGAATAACGCAGCA 58.924 50.000 0.00 0.00 46.94 4.41
64 65 1.076332 ACTTCCACGAATAACGCAGC 58.924 50.000 0.00 0.00 46.94 5.25
65 66 3.806316 AAACTTCCACGAATAACGCAG 57.194 42.857 0.00 0.00 46.94 5.18
66 67 4.558178 TCTAAACTTCCACGAATAACGCA 58.442 39.130 0.00 0.00 46.94 5.24
67 68 5.063060 ACATCTAAACTTCCACGAATAACGC 59.937 40.000 0.00 0.00 46.94 4.84
69 70 7.117236 TGTCACATCTAAACTTCCACGAATAAC 59.883 37.037 0.00 0.00 0.00 1.89
70 71 7.156000 TGTCACATCTAAACTTCCACGAATAA 58.844 34.615 0.00 0.00 0.00 1.40
71 72 6.693466 TGTCACATCTAAACTTCCACGAATA 58.307 36.000 0.00 0.00 0.00 1.75
72 73 5.547465 TGTCACATCTAAACTTCCACGAAT 58.453 37.500 0.00 0.00 0.00 3.34
73 74 4.951254 TGTCACATCTAAACTTCCACGAA 58.049 39.130 0.00 0.00 0.00 3.85
74 75 4.594123 TGTCACATCTAAACTTCCACGA 57.406 40.909 0.00 0.00 0.00 4.35
75 76 4.330074 GGATGTCACATCTAAACTTCCACG 59.670 45.833 17.46 0.00 37.26 4.94
76 77 5.491982 AGGATGTCACATCTAAACTTCCAC 58.508 41.667 17.46 0.00 38.85 4.02
77 78 5.762179 AGGATGTCACATCTAAACTTCCA 57.238 39.130 17.46 0.00 38.85 3.53
78 79 8.561738 TTAAAGGATGTCACATCTAAACTTCC 57.438 34.615 17.46 0.00 37.45 3.46
82 83 9.959749 TGTTTTTAAAGGATGTCACATCTAAAC 57.040 29.630 17.46 15.71 0.00 2.01
207 208 9.551734 GAGTAAAAAGTACTCCCTCTGTAAAAA 57.448 33.333 0.00 0.00 38.33 1.94
208 209 8.707449 TGAGTAAAAAGTACTCCCTCTGTAAAA 58.293 33.333 10.24 0.00 42.32 1.52
209 210 8.253867 TGAGTAAAAAGTACTCCCTCTGTAAA 57.746 34.615 10.24 0.00 42.32 2.01
210 211 7.844493 TGAGTAAAAAGTACTCCCTCTGTAA 57.156 36.000 10.24 0.00 42.32 2.41
211 212 7.672660 TCATGAGTAAAAAGTACTCCCTCTGTA 59.327 37.037 10.24 0.00 42.32 2.74
212 213 6.497259 TCATGAGTAAAAAGTACTCCCTCTGT 59.503 38.462 10.24 0.00 42.32 3.41
213 214 6.936279 TCATGAGTAAAAAGTACTCCCTCTG 58.064 40.000 10.24 4.47 42.32 3.35
214 215 7.554959 TTCATGAGTAAAAAGTACTCCCTCT 57.445 36.000 10.24 0.00 42.32 3.69
215 216 8.617290 TTTTCATGAGTAAAAAGTACTCCCTC 57.383 34.615 10.24 0.00 42.32 4.30
216 217 8.990163 TTTTTCATGAGTAAAAAGTACTCCCT 57.010 30.769 10.24 0.00 42.32 4.20
217 218 9.841880 GATTTTTCATGAGTAAAAAGTACTCCC 57.158 33.333 8.89 0.00 42.32 4.30
218 219 9.841880 GGATTTTTCATGAGTAAAAAGTACTCC 57.158 33.333 8.89 7.55 42.32 3.85
219 220 9.543018 CGGATTTTTCATGAGTAAAAAGTACTC 57.457 33.333 8.89 6.57 43.06 2.59
220 221 8.512138 CCGGATTTTTCATGAGTAAAAAGTACT 58.488 33.333 8.89 0.00 38.72 2.73
221 222 7.753580 CCCGGATTTTTCATGAGTAAAAAGTAC 59.246 37.037 0.73 0.00 38.72 2.73
222 223 7.576098 GCCCGGATTTTTCATGAGTAAAAAGTA 60.576 37.037 0.73 0.00 38.72 2.24
223 224 6.687604 CCCGGATTTTTCATGAGTAAAAAGT 58.312 36.000 0.73 0.00 38.72 2.66
224 225 5.576774 GCCCGGATTTTTCATGAGTAAAAAG 59.423 40.000 0.73 4.96 38.72 2.27
225 226 5.245075 AGCCCGGATTTTTCATGAGTAAAAA 59.755 36.000 0.73 7.60 39.41 1.94
226 227 4.770010 AGCCCGGATTTTTCATGAGTAAAA 59.230 37.500 0.73 7.56 0.00 1.52
227 228 4.340617 AGCCCGGATTTTTCATGAGTAAA 58.659 39.130 0.73 1.57 0.00 2.01
228 229 3.963129 AGCCCGGATTTTTCATGAGTAA 58.037 40.909 0.73 0.00 0.00 2.24
229 230 3.644966 AGCCCGGATTTTTCATGAGTA 57.355 42.857 0.73 0.00 0.00 2.59
242 243 1.760613 CCTGACTGTAATTAGCCCGGA 59.239 52.381 0.73 0.00 0.00 5.14
245 246 4.081087 TGTTCTCCTGACTGTAATTAGCCC 60.081 45.833 0.00 0.00 0.00 5.19
248 249 6.925211 TGAGTGTTCTCCTGACTGTAATTAG 58.075 40.000 0.00 0.00 39.75 1.73
249 250 6.911250 TGAGTGTTCTCCTGACTGTAATTA 57.089 37.500 0.00 0.00 39.75 1.40
253 254 3.511540 CCATGAGTGTTCTCCTGACTGTA 59.488 47.826 0.00 0.00 38.15 2.74
257 258 3.902881 ATCCATGAGTGTTCTCCTGAC 57.097 47.619 0.00 0.00 38.15 3.51
258 259 5.685861 GCATAATCCATGAGTGTTCTCCTGA 60.686 44.000 0.00 0.00 38.15 3.86
262 263 3.817647 GGGCATAATCCATGAGTGTTCTC 59.182 47.826 0.00 0.00 36.69 2.87
296 298 9.950680 CGTCCGTAAATTTCCTACTAATAGTAA 57.049 33.333 1.48 0.00 29.00 2.24
300 302 8.465999 TCAACGTCCGTAAATTTCCTACTAATA 58.534 33.333 0.00 0.00 0.00 0.98
301 303 7.276438 GTCAACGTCCGTAAATTTCCTACTAAT 59.724 37.037 0.00 0.00 0.00 1.73
305 307 4.685628 TGTCAACGTCCGTAAATTTCCTAC 59.314 41.667 0.00 0.00 0.00 3.18
310 312 2.224784 GGCTGTCAACGTCCGTAAATTT 59.775 45.455 0.00 0.00 0.00 1.82
354 356 1.483827 TCTGTGAGCTGCTGGGATTAG 59.516 52.381 7.01 0.00 0.00 1.73
391 393 3.512680 CCACTTAGCGTAAGAGGAACTG 58.487 50.000 12.49 1.95 45.74 3.16
453 457 2.780643 CCTCGCATGTGCTTGTCG 59.219 61.111 0.00 0.00 39.32 4.35
468 472 0.762842 TATGTGTATCGCCCTGGCCT 60.763 55.000 3.32 0.00 37.98 5.19
469 473 0.602905 GTATGTGTATCGCCCTGGCC 60.603 60.000 1.86 0.00 37.98 5.36
470 474 0.944311 CGTATGTGTATCGCCCTGGC 60.944 60.000 0.00 0.00 37.85 4.85
471 475 0.944311 GCGTATGTGTATCGCCCTGG 60.944 60.000 0.00 0.00 43.41 4.45
472 476 1.275471 CGCGTATGTGTATCGCCCTG 61.275 60.000 0.00 0.00 45.85 4.45
479 483 1.069090 CCCAGGCGCGTATGTGTAT 59.931 57.895 8.43 0.00 0.00 2.29
616 621 6.062434 AGAGAAGATATTCGTTCGTGTAGG 57.938 41.667 0.00 0.00 0.00 3.18
643 673 1.228644 TCCGTCGGGTGGAAGAGAA 60.229 57.895 12.29 0.00 30.98 2.87
646 677 2.993264 GGTCCGTCGGGTGGAAGA 60.993 66.667 12.29 0.00 37.23 2.87
795 848 3.618780 GAGGCAGGGTGTCAGGCAG 62.619 68.421 0.00 0.00 0.00 4.85
891 944 1.343069 GGTCCCCACTATAGGCTCAG 58.657 60.000 4.43 0.00 0.00 3.35
943 997 0.816421 AACTAACTGGCGCCGTTTGT 60.816 50.000 31.18 30.19 33.06 2.83
953 1007 1.887320 CGGTCGTACGAACTAACTGG 58.113 55.000 29.02 10.28 35.47 4.00
1112 1181 1.145598 TATGCTGGCTGCTCTGCTC 59.854 57.895 17.45 0.00 43.37 4.26
1124 1193 3.408634 TCATCATCATGGCTGTATGCTG 58.591 45.455 0.00 0.00 42.39 4.41
1129 1198 3.671716 GCTCATCATCATCATGGCTGTA 58.328 45.455 0.00 0.00 0.00 2.74
1298 1382 3.878519 CTCGTCCTCGTCCTCCGC 61.879 72.222 0.00 0.00 38.33 5.54
1299 1383 3.203412 CCTCGTCCTCGTCCTCCG 61.203 72.222 0.00 0.00 38.33 4.63
1300 1384 3.519930 GCCTCGTCCTCGTCCTCC 61.520 72.222 0.00 0.00 38.33 4.30
1837 1921 4.514577 AATGGCGGCGACTCGGAG 62.515 66.667 16.45 2.83 0.00 4.63
1981 2074 3.087906 GTGGGGTAGCCGGACCAT 61.088 66.667 5.05 0.00 41.73 3.55
2068 2161 4.823276 CTGGAAGCGCTAGTCTGG 57.177 61.111 12.05 0.00 0.00 3.86
2080 2173 0.899717 GGTTGGCCATGAAGCTGGAA 60.900 55.000 6.09 0.00 38.69 3.53
2140 2233 1.079438 GGACTCCACCCTCTGGACT 59.921 63.158 0.00 0.00 44.99 3.85
2291 2384 3.314388 CTTGCAAGAACGGCGGCTC 62.314 63.158 22.31 7.57 0.00 4.70
2327 2420 1.428448 CCGTGAAATCTTGTCGAGCA 58.572 50.000 0.00 0.00 0.00 4.26
2332 2425 0.721718 CTCCGCCGTGAAATCTTGTC 59.278 55.000 0.00 0.00 0.00 3.18
2400 2493 6.479990 GCAACTGGAAATAGCAAAAGAAACTT 59.520 34.615 0.00 0.00 0.00 2.66
2455 2551 3.557898 CCGGGAATATTCACATGGGAGAG 60.558 52.174 17.68 0.00 0.00 3.20
2505 2601 3.803186 ATCCACCCATCCATCTTCATC 57.197 47.619 0.00 0.00 0.00 2.92
2506 2602 4.220724 CAAATCCACCCATCCATCTTCAT 58.779 43.478 0.00 0.00 0.00 2.57
2507 2603 3.011595 ACAAATCCACCCATCCATCTTCA 59.988 43.478 0.00 0.00 0.00 3.02
2607 2711 2.281484 CACCACCACCACCTTCCG 60.281 66.667 0.00 0.00 0.00 4.30
2614 2718 3.552384 GACGGACCACCACCACCA 61.552 66.667 0.00 0.00 35.59 4.17
2657 2761 2.490961 TCTTCACCATCCATCCATCCA 58.509 47.619 0.00 0.00 0.00 3.41
2658 2762 3.073503 TCATCTTCACCATCCATCCATCC 59.926 47.826 0.00 0.00 0.00 3.51
2659 2763 4.325119 CTCATCTTCACCATCCATCCATC 58.675 47.826 0.00 0.00 0.00 3.51
2660 2764 3.074094 CCTCATCTTCACCATCCATCCAT 59.926 47.826 0.00 0.00 0.00 3.41
2756 2882 1.135344 GTCAGTCTTCGGCTAGTCCAC 60.135 57.143 4.43 0.00 34.01 4.02
2770 2896 1.411493 GCGGTCGAAATCGGTCAGTC 61.411 60.000 2.63 0.00 40.29 3.51
2771 2897 1.445582 GCGGTCGAAATCGGTCAGT 60.446 57.895 2.63 0.00 40.29 3.41
2772 2898 2.165301 GGCGGTCGAAATCGGTCAG 61.165 63.158 2.63 0.00 40.29 3.51
2773 2899 2.125832 GGCGGTCGAAATCGGTCA 60.126 61.111 2.63 0.00 40.29 4.02
2878 3014 3.567478 ACAGGGATTAAAGGCTGCTAG 57.433 47.619 0.00 0.00 0.00 3.42
2879 3015 3.681594 CGAACAGGGATTAAAGGCTGCTA 60.682 47.826 0.00 0.00 0.00 3.49
2880 3016 2.728007 GAACAGGGATTAAAGGCTGCT 58.272 47.619 0.00 0.00 0.00 4.24
2881 3017 1.401905 CGAACAGGGATTAAAGGCTGC 59.598 52.381 0.00 0.00 0.00 5.25
2882 3018 2.678336 GACGAACAGGGATTAAAGGCTG 59.322 50.000 0.00 0.00 0.00 4.85
2883 3019 2.355818 GGACGAACAGGGATTAAAGGCT 60.356 50.000 0.00 0.00 0.00 4.58
2884 3020 2.014857 GGACGAACAGGGATTAAAGGC 58.985 52.381 0.00 0.00 0.00 4.35
2885 3021 3.343941 TGGACGAACAGGGATTAAAGG 57.656 47.619 0.00 0.00 0.00 3.11
2886 3022 4.096382 CCATTGGACGAACAGGGATTAAAG 59.904 45.833 0.00 0.00 0.00 1.85
2889 3025 2.574369 ACCATTGGACGAACAGGGATTA 59.426 45.455 10.37 0.00 0.00 1.75
2910 3055 2.039746 ACATTGGGGAGTTCGTTCATCA 59.960 45.455 0.00 0.00 0.00 3.07
3076 3226 9.426837 CAACCATTTCATTTCATTCACACTTAT 57.573 29.630 0.00 0.00 0.00 1.73
3171 3334 4.373116 ATTGTCGACCACGCCGCT 62.373 61.111 14.12 0.00 39.58 5.52
3177 3340 1.302511 AGCCACCATTGTCGACCAC 60.303 57.895 14.12 0.00 0.00 4.16
3215 3379 1.302033 CATCGCCCCCATACTGCTC 60.302 63.158 0.00 0.00 0.00 4.26
3332 3500 0.988678 GGCTGTACCAATCCCCTCCT 60.989 60.000 0.00 0.00 38.86 3.69


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

AutoCloner maintained by Alex Coulton.