Multiple sequence alignment - TraesCS6A01G048000

Loading Multiple Alignment...

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 TraesCS6A01G048000 chr6A 100.000 2537 0 0 1 2537 24259928 24257392 0.000000e+00 4686.0
1 TraesCS6A01G048000 chr6A 83.122 474 65 10 1549 2017 542333643 542334106 3.900000e-113 418.0
2 TraesCS6A01G048000 chrUn 92.386 1668 97 14 882 2537 93785753 93784104 0.000000e+00 2350.0
3 TraesCS6A01G048000 chrUn 83.120 468 62 10 1549 2009 431068417 431067960 6.530000e-111 411.0
4 TraesCS6A01G048000 chr6B 90.992 877 57 12 1670 2537 42701680 42702543 0.000000e+00 1162.0
5 TraesCS6A01G048000 chr6B 90.149 538 36 8 1670 2198 42731062 42730533 0.000000e+00 684.0
6 TraesCS6A01G048000 chr6B 92.704 466 33 1 882 1347 42736749 42736285 0.000000e+00 671.0
7 TraesCS6A01G048000 chr6B 93.895 344 18 3 2194 2537 42713640 42713300 1.350000e-142 516.0
8 TraesCS6A01G048000 chr6B 89.412 85 9 0 1342 1426 42701386 42701470 9.600000e-20 108.0
9 TraesCS6A01G048000 chr6D 91.837 735 58 2 151 884 125327252 125327985 0.000000e+00 1024.0
10 TraesCS6A01G048000 chr6D 93.492 461 27 2 422 882 125326472 125326929 0.000000e+00 682.0
11 TraesCS6A01G048000 chr2A 89.097 642 59 9 246 882 71548683 71549318 0.000000e+00 787.0
12 TraesCS6A01G048000 chr2A 89.097 642 59 9 246 882 71562845 71563480 0.000000e+00 787.0
13 TraesCS6A01G048000 chr2A 89.241 632 58 7 246 872 71563904 71564530 0.000000e+00 782.0
14 TraesCS6A01G048000 chr2A 89.082 632 59 7 246 872 71549740 71550366 0.000000e+00 776.0
15 TraesCS6A01G048000 chr7A 91.950 559 39 4 259 814 307104897 307105452 0.000000e+00 778.0
16 TraesCS6A01G048000 chr7A 92.441 463 33 2 421 882 307104077 307104538 0.000000e+00 660.0
17 TraesCS6A01G048000 chr7A 89.362 188 19 1 112 298 307104718 307104905 4.220000e-58 235.0
18 TraesCS6A01G048000 chr7A 92.593 54 2 2 1456 1508 279186724 279186672 2.710000e-10 76.8
19 TraesCS6A01G048000 chr1D 93.603 469 24 3 422 886 409018103 409018569 0.000000e+00 695.0
20 TraesCS6A01G048000 chr3B 84.058 483 53 14 1549 2017 20020833 20020361 6.440000e-121 444.0
21 TraesCS6A01G048000 chr7B 83.298 467 63 9 1549 2009 732126943 732126486 1.400000e-112 416.0
22 TraesCS6A01G048000 chr7B 88.333 60 5 2 1456 1514 654561996 654562054 1.260000e-08 71.3
23 TraesCS6A01G048000 chr5A 83.019 477 61 14 1552 2018 664938636 664939102 5.050000e-112 414.0
24 TraesCS6A01G048000 chr5B 82.845 478 63 15 1549 2017 380232199 380232666 6.530000e-111 411.0
25 TraesCS6A01G048000 chr5B 85.915 142 15 3 1467 1608 684365929 684365793 2.030000e-31 147.0
26 TraesCS6A01G048000 chr5D 81.020 490 66 20 1472 1954 542624320 542623851 5.160000e-97 364.0
27 TraesCS6A01G048000 chr7D 91.915 235 18 1 197 430 272283303 272283069 6.770000e-86 327.0
28 TraesCS6A01G048000 chr7D 90.638 235 20 2 197 430 16160734 16160967 6.820000e-81 311.0
29 TraesCS6A01G048000 chr7D 89.787 235 22 2 197 430 16159435 16159668 1.480000e-77 300.0
30 TraesCS6A01G048000 chr4D 93.443 61 1 3 1456 1515 92854217 92854159 1.250000e-13 87.9
31 TraesCS6A01G048000 chr1B 81.818 110 14 5 1456 1564 426904088 426904192 1.250000e-13 87.9
32 TraesCS6A01G048000 chr2B 90.164 61 4 2 1456 1515 248688341 248688282 7.520000e-11 78.7


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 TraesCS6A01G048000 chr6A 24257392 24259928 2536 True 4686.000000 4686 100.0000 1 2537 1 chr6A.!!$R1 2536
1 TraesCS6A01G048000 chrUn 93784104 93785753 1649 True 2350.000000 2350 92.3860 882 2537 1 chrUn.!!$R1 1655
2 TraesCS6A01G048000 chr6B 42730533 42731062 529 True 684.000000 684 90.1490 1670 2198 1 chr6B.!!$R2 528
3 TraesCS6A01G048000 chr6B 42701386 42702543 1157 False 635.000000 1162 90.2020 1342 2537 2 chr6B.!!$F1 1195
4 TraesCS6A01G048000 chr6D 125326472 125327985 1513 False 853.000000 1024 92.6645 151 884 2 chr6D.!!$F1 733
5 TraesCS6A01G048000 chr2A 71562845 71564530 1685 False 784.500000 787 89.1690 246 882 2 chr2A.!!$F2 636
6 TraesCS6A01G048000 chr2A 71548683 71550366 1683 False 781.500000 787 89.0895 246 882 2 chr2A.!!$F1 636
7 TraesCS6A01G048000 chr7A 307104077 307105452 1375 False 557.666667 778 91.2510 112 882 3 chr7A.!!$F1 770
8 TraesCS6A01G048000 chr7D 16159435 16160967 1532 False 305.500000 311 90.2125 197 430 2 chr7D.!!$F1 233

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
36 37 0.450583 GTCACGACTCTGGCGACATA 59.549 55.0 0.0 0.0 41.51 2.29 F
1021 2664 0.036388 GGAGACCATGAAGCGTTCCA 60.036 55.0 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 2774 0.318120 CGGGGAATGTTGCTGCTTTT 59.682 50.000 0.0 0.0 0.0 2.27 R
2143 3845 1.003839 GTGACCCTGCACGATCCAA 60.004 57.895 0.0 0.0 0.0 3.53 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
27 28 2.955402 GTGCTCCGTCACGACTCT 59.045 61.111 0.00 0.00 0.00 3.24
28 29 1.442857 GTGCTCCGTCACGACTCTG 60.443 63.158 0.00 0.00 0.00 3.35
29 30 2.179517 GCTCCGTCACGACTCTGG 59.820 66.667 0.00 0.00 0.00 3.86
30 31 2.179517 CTCCGTCACGACTCTGGC 59.820 66.667 0.00 0.00 0.00 4.85
31 32 3.669036 CTCCGTCACGACTCTGGCG 62.669 68.421 0.00 0.00 39.03 5.69
32 33 3.733960 CCGTCACGACTCTGGCGA 61.734 66.667 0.00 0.00 41.96 5.54
33 34 2.502080 CGTCACGACTCTGGCGAC 60.502 66.667 0.00 0.00 41.96 5.19
34 35 2.643272 GTCACGACTCTGGCGACA 59.357 61.111 0.00 0.00 39.59 4.35
35 36 1.213013 GTCACGACTCTGGCGACAT 59.787 57.895 0.00 0.00 41.51 3.06
36 37 0.450583 GTCACGACTCTGGCGACATA 59.549 55.000 0.00 0.00 41.51 2.29
37 38 0.450583 TCACGACTCTGGCGACATAC 59.549 55.000 0.00 0.00 41.51 2.39
38 39 0.861866 CACGACTCTGGCGACATACG 60.862 60.000 0.00 0.00 41.51 3.06
47 48 2.954868 CGACATACGCCGAGCACC 60.955 66.667 0.00 0.00 34.51 5.01
48 49 2.494918 GACATACGCCGAGCACCT 59.505 61.111 0.00 0.00 0.00 4.00
49 50 1.153628 GACATACGCCGAGCACCTT 60.154 57.895 0.00 0.00 0.00 3.50
50 51 1.146358 GACATACGCCGAGCACCTTC 61.146 60.000 0.00 0.00 0.00 3.46
51 52 1.141881 CATACGCCGAGCACCTTCT 59.858 57.895 0.00 0.00 0.00 2.85
52 53 0.872021 CATACGCCGAGCACCTTCTC 60.872 60.000 0.00 0.00 0.00 2.87
53 54 2.017559 ATACGCCGAGCACCTTCTCC 62.018 60.000 0.00 0.00 0.00 3.71
56 57 4.821589 CCGAGCACCTTCTCCGCC 62.822 72.222 0.00 0.00 0.00 6.13
58 59 4.070552 GAGCACCTTCTCCGCCGT 62.071 66.667 0.00 0.00 0.00 5.68
59 60 3.591254 GAGCACCTTCTCCGCCGTT 62.591 63.158 0.00 0.00 0.00 4.44
60 61 3.423154 GCACCTTCTCCGCCGTTG 61.423 66.667 0.00 0.00 0.00 4.10
61 62 2.342279 CACCTTCTCCGCCGTTGA 59.658 61.111 0.00 0.00 0.00 3.18
62 63 2.027625 CACCTTCTCCGCCGTTGAC 61.028 63.158 0.00 0.00 0.00 3.18
63 64 2.342279 CCTTCTCCGCCGTTGACA 59.658 61.111 0.00 0.00 0.00 3.58
64 65 2.027625 CCTTCTCCGCCGTTGACAC 61.028 63.158 0.00 0.00 0.00 3.67
65 66 1.300620 CTTCTCCGCCGTTGACACA 60.301 57.895 0.00 0.00 0.00 3.72
66 67 1.557443 CTTCTCCGCCGTTGACACAC 61.557 60.000 0.00 0.00 0.00 3.82
67 68 3.403057 CTCCGCCGTTGACACACG 61.403 66.667 3.98 3.98 40.02 4.49
68 69 4.210093 TCCGCCGTTGACACACGT 62.210 61.111 8.60 0.00 38.57 4.49
69 70 3.698463 CCGCCGTTGACACACGTC 61.698 66.667 8.60 0.00 42.93 4.34
70 71 2.657296 CGCCGTTGACACACGTCT 60.657 61.111 8.60 0.00 43.06 4.18
71 72 2.927618 CGCCGTTGACACACGTCTG 61.928 63.158 8.60 0.00 43.06 3.51
72 73 2.594962 GCCGTTGACACACGTCTGG 61.595 63.158 0.00 0.00 43.06 3.86
73 74 2.594962 CCGTTGACACACGTCTGGC 61.595 63.158 0.00 0.00 43.06 4.85
74 75 2.927618 CGTTGACACACGTCTGGCG 61.928 63.158 0.00 0.00 43.06 5.69
83 84 4.052229 CGTCTGGCGTCCTTCCGT 62.052 66.667 0.00 0.00 35.54 4.69
84 85 2.432628 GTCTGGCGTCCTTCCGTG 60.433 66.667 0.00 0.00 0.00 4.94
85 86 4.373116 TCTGGCGTCCTTCCGTGC 62.373 66.667 0.00 0.00 0.00 5.34
130 131 4.803426 GCCCGACGAGCCTGACTG 62.803 72.222 0.00 0.00 0.00 3.51
131 132 4.803426 CCCGACGAGCCTGACTGC 62.803 72.222 0.00 0.00 0.00 4.40
132 133 4.056125 CCGACGAGCCTGACTGCA 62.056 66.667 0.00 0.00 0.00 4.41
133 134 2.505777 CGACGAGCCTGACTGCAG 60.506 66.667 13.48 13.48 41.93 4.41
134 135 2.813042 GACGAGCCTGACTGCAGC 60.813 66.667 15.27 7.45 40.91 5.25
135 136 3.580100 GACGAGCCTGACTGCAGCA 62.580 63.158 15.27 12.02 40.91 4.41
136 137 2.814341 CGAGCCTGACTGCAGCAG 60.814 66.667 21.54 21.54 40.91 4.24
138 139 2.032223 AGCCTGACTGCAGCAGTG 59.968 61.111 33.03 18.98 45.44 3.66
139 140 3.735029 GCCTGACTGCAGCAGTGC 61.735 66.667 33.03 24.53 45.44 4.40
190 191 4.773117 GACGAGTCCGACCGCACC 62.773 72.222 8.70 0.00 39.50 5.01
192 193 4.351938 CGAGTCCGACCGCACCAA 62.352 66.667 0.00 0.00 38.22 3.67
193 194 2.029964 GAGTCCGACCGCACCAAA 59.970 61.111 0.00 0.00 0.00 3.28
194 195 2.280592 AGTCCGACCGCACCAAAC 60.281 61.111 0.00 0.00 0.00 2.93
195 196 3.708734 GTCCGACCGCACCAAACG 61.709 66.667 0.00 0.00 0.00 3.60
206 207 2.280524 CCAAACGCCGTGGACTCA 60.281 61.111 0.00 0.00 38.54 3.41
235 236 1.452651 CAGCCGATGCCTCCATGTT 60.453 57.895 0.00 0.00 38.69 2.71
240 241 1.451927 GATGCCTCCATGTTCGCCA 60.452 57.895 0.00 0.00 0.00 5.69
241 242 0.820891 GATGCCTCCATGTTCGCCAT 60.821 55.000 0.00 0.00 0.00 4.40
449 2092 0.961857 AAACCCGGAAACCATACGCC 60.962 55.000 0.73 0.00 0.00 5.68
451 2094 2.269562 CCGGAAACCATACGCCCA 59.730 61.111 0.00 0.00 0.00 5.36
469 2112 3.886123 CCCAAAGATAACCCAACTCGAT 58.114 45.455 0.00 0.00 0.00 3.59
487 2130 2.926200 CGATCACGAACTCAGAGCAATT 59.074 45.455 0.00 0.00 42.66 2.32
543 2186 5.314923 TCTTGGCAATCTTTATTCACTGC 57.685 39.130 0.00 0.00 0.00 4.40
598 2241 1.209504 ACACACACACACTAGCACCTT 59.790 47.619 0.00 0.00 0.00 3.50
607 2250 2.289694 ACACTAGCACCTTTGGCTACAG 60.290 50.000 0.00 0.00 42.62 2.74
640 2283 1.218316 GGAGCCTACACACGGAAGG 59.782 63.158 0.00 0.00 0.00 3.46
806 2449 0.523072 CACATGCACACAACTAGCCC 59.477 55.000 0.00 0.00 0.00 5.19
840 2483 1.295101 CACACATGACCCGGCTGTA 59.705 57.895 0.00 0.00 0.00 2.74
854 2497 2.671396 CGGCTGTACATGTAGTTGAACC 59.329 50.000 5.62 1.91 0.00 3.62
875 2518 7.556275 TGAACCAACCCAAGATCAGAATTATAC 59.444 37.037 0.00 0.00 0.00 1.47
886 2529 8.539770 AGATCAGAATTATACTAACAATGGCG 57.460 34.615 0.00 0.00 0.00 5.69
887 2530 8.367911 AGATCAGAATTATACTAACAATGGCGA 58.632 33.333 0.00 0.00 0.00 5.54
888 2531 7.709269 TCAGAATTATACTAACAATGGCGAC 57.291 36.000 0.00 0.00 0.00 5.19
891 2534 1.578583 ATACTAACAATGGCGACGGC 58.421 50.000 15.43 15.43 38.90 5.68
904 2547 1.007336 CGACGGCGGTGGCTATATTC 61.007 60.000 13.24 0.00 39.81 1.75
909 2552 1.071699 GGCGGTGGCTATATTCCTTGA 59.928 52.381 0.00 0.00 39.81 3.02
913 2556 3.306088 CGGTGGCTATATTCCTTGATCGT 60.306 47.826 0.00 0.00 0.00 3.73
921 2564 1.052617 TTCCTTGATCGTGTGGGTGA 58.947 50.000 0.00 0.00 0.00 4.02
930 2573 1.528309 GTGTGGGTGACAAGGGGTG 60.528 63.158 0.00 0.00 35.91 4.61
937 2580 1.839747 TGACAAGGGGTGTAGCGGT 60.840 57.895 0.00 0.00 41.96 5.68
938 2581 1.375523 GACAAGGGGTGTAGCGGTG 60.376 63.158 0.00 0.00 41.96 4.94
948 2591 1.153429 GTAGCGGTGGGTTGCTAGG 60.153 63.158 0.00 0.00 43.83 3.02
959 2602 0.822164 GTTGCTAGGGCTCCTTCGTA 59.178 55.000 0.00 0.00 39.59 3.43
960 2603 0.822164 TTGCTAGGGCTCCTTCGTAC 59.178 55.000 0.00 0.00 39.59 3.67
961 2604 1.359475 GCTAGGGCTCCTTCGTACG 59.641 63.158 9.53 9.53 34.61 3.67
962 2605 1.382692 GCTAGGGCTCCTTCGTACGT 61.383 60.000 16.05 0.00 34.61 3.57
965 2608 2.508663 GGCTCCTTCGTACGTGGC 60.509 66.667 16.05 12.46 0.00 5.01
972 2615 4.728102 TCGTACGTGGCGGCAAGG 62.728 66.667 26.94 18.21 0.00 3.61
1015 2658 2.546795 CCTACGATGGAGACCATGAAGC 60.547 54.545 8.06 0.00 45.26 3.86
1021 2664 0.036388 GGAGACCATGAAGCGTTCCA 60.036 55.000 0.00 0.00 0.00 3.53
1022 2665 1.363744 GAGACCATGAAGCGTTCCAG 58.636 55.000 0.00 0.00 0.00 3.86
1088 2731 2.124507 CTTCAAGGAGGGGGCGACAA 62.125 60.000 0.00 0.00 0.00 3.18
1134 2777 2.250939 CGCGGTGCAGAGGACAAAA 61.251 57.895 0.00 0.00 0.00 2.44
1143 2786 1.677576 CAGAGGACAAAAGCAGCAACA 59.322 47.619 0.00 0.00 0.00 3.33
1170 2813 0.686441 TAGGTGCCGCAGTAGATGGT 60.686 55.000 0.00 0.00 0.00 3.55
1172 2815 2.125147 TGCCGCAGTAGATGGTGC 60.125 61.111 0.00 0.00 36.27 5.01
1184 2827 2.937379 GATGGTGCAGCGCAGAGGAT 62.937 60.000 11.47 0.00 40.08 3.24
1200 2843 1.134670 AGGATTGAAGTAGCAGCGTCC 60.135 52.381 0.00 0.00 0.00 4.79
1335 2978 3.353836 CAACCAACACGGGAGGCG 61.354 66.667 0.00 0.00 40.22 5.52
1469 3112 2.989639 CTCGGGAAGTGGATGCCA 59.010 61.111 0.00 0.00 0.00 4.92
1485 3128 0.882042 GCCAGGATATGCAGGTGTCG 60.882 60.000 7.49 0.00 0.00 4.35
1492 3135 0.102300 TATGCAGGTGTCGATCCACG 59.898 55.000 11.23 0.00 44.09 4.94
1519 3162 2.676121 CCGGTTCCCAGCATGCAA 60.676 61.111 21.98 1.65 31.97 4.08
1981 3674 3.432186 GCATATGAGACTTAGTGTGCCCA 60.432 47.826 6.97 0.00 0.00 5.36
1985 3678 0.912486 AGACTTAGTGTGCCCATCCC 59.088 55.000 0.00 0.00 0.00 3.85
1986 3679 0.912486 GACTTAGTGTGCCCATCCCT 59.088 55.000 0.00 0.00 0.00 4.20
2009 3703 2.366916 CCTATGTCGAAATCCTGGCTCT 59.633 50.000 0.00 0.00 0.00 4.09
2038 3732 0.839277 TGTAGCCATGTAGCATGCCT 59.161 50.000 15.66 4.75 34.23 4.75
2082 3784 1.338579 ACTGCAAGAGCCTCAACTAGC 60.339 52.381 0.00 0.00 41.13 3.42
2089 3791 1.197430 AGCCTCAACTAGCTGCAGGT 61.197 55.000 23.72 23.72 38.11 4.00
2126 3828 2.540101 GAGTCCGGCAAAATCTATCGTG 59.460 50.000 0.00 0.00 0.00 4.35
2132 3834 4.273480 CCGGCAAAATCTATCGTGAAAGAT 59.727 41.667 0.00 0.00 33.87 2.40
2154 3856 4.944619 AAGATAGATCTTGGATCGTGCA 57.055 40.909 0.00 0.00 44.91 4.57
2223 3925 0.250793 ACGACCGCCACATCCAATTA 59.749 50.000 0.00 0.00 0.00 1.40
2264 3966 0.251474 AGCTGCTTGATCTTGCCCAA 60.251 50.000 0.00 0.00 0.00 4.12
2273 3975 3.942829 TGATCTTGCCCAAGTTACTGAG 58.057 45.455 7.80 0.00 39.38 3.35
2277 3979 1.378646 GCCCAAGTTACTGAGGCCC 60.379 63.158 13.17 0.00 37.66 5.80
2398 4100 3.763897 ACAAGCAAGAACAAAGTGAACCT 59.236 39.130 0.00 0.00 0.00 3.50
2413 4115 5.974108 AGTGAACCTATGTAACGTGCTATT 58.026 37.500 0.00 0.00 0.00 1.73
2432 4134 7.489757 GTGCTATTTACTCTAGTGAAGTTGGAG 59.510 40.741 0.00 0.00 0.00 3.86
2529 4231 0.918258 TTCCATGCCCATGAGCTACA 59.082 50.000 9.73 0.00 41.20 2.74
2532 4234 1.027357 CATGCCCATGAGCTACAACC 58.973 55.000 0.00 0.00 41.20 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.442857 CAGAGTCGTGACGGAGCAC 60.443 63.158 4.70 0.00 36.20 4.40
11 12 2.626780 CCAGAGTCGTGACGGAGCA 61.627 63.158 4.70 0.00 36.20 4.26
12 13 2.179517 CCAGAGTCGTGACGGAGC 59.820 66.667 4.70 0.00 36.20 4.70
13 14 2.179517 GCCAGAGTCGTGACGGAG 59.820 66.667 4.70 0.00 36.20 4.63
14 15 3.733960 CGCCAGAGTCGTGACGGA 61.734 66.667 4.70 0.00 36.20 4.69
15 16 3.733960 TCGCCAGAGTCGTGACGG 61.734 66.667 4.70 0.00 36.20 4.79
16 17 2.502080 GTCGCCAGAGTCGTGACG 60.502 66.667 0.00 0.00 36.20 4.35
17 18 0.450583 TATGTCGCCAGAGTCGTGAC 59.549 55.000 5.15 5.15 40.41 3.67
18 19 0.450583 GTATGTCGCCAGAGTCGTGA 59.549 55.000 0.00 0.00 0.00 4.35
19 20 0.861866 CGTATGTCGCCAGAGTCGTG 60.862 60.000 0.00 0.00 0.00 4.35
20 21 1.428219 CGTATGTCGCCAGAGTCGT 59.572 57.895 0.00 0.00 0.00 4.34
21 22 4.286967 CGTATGTCGCCAGAGTCG 57.713 61.111 0.00 0.00 0.00 4.18
30 31 2.884087 AAGGTGCTCGGCGTATGTCG 62.884 60.000 6.85 1.58 46.81 4.35
31 32 1.146358 GAAGGTGCTCGGCGTATGTC 61.146 60.000 6.85 0.00 0.00 3.06
32 33 1.153628 GAAGGTGCTCGGCGTATGT 60.154 57.895 6.85 0.00 0.00 2.29
33 34 0.872021 GAGAAGGTGCTCGGCGTATG 60.872 60.000 6.85 0.00 0.00 2.39
34 35 1.437986 GAGAAGGTGCTCGGCGTAT 59.562 57.895 6.85 0.00 0.00 3.06
35 36 2.707849 GGAGAAGGTGCTCGGCGTA 61.708 63.158 6.85 0.00 35.74 4.42
36 37 4.070552 GGAGAAGGTGCTCGGCGT 62.071 66.667 6.85 0.00 35.74 5.68
39 40 4.821589 GGCGGAGAAGGTGCTCGG 62.822 72.222 0.00 0.00 38.02 4.63
41 42 3.591254 AACGGCGGAGAAGGTGCTC 62.591 63.158 13.24 0.00 0.00 4.26
42 43 3.626924 AACGGCGGAGAAGGTGCT 61.627 61.111 13.24 0.00 0.00 4.40
43 44 3.423154 CAACGGCGGAGAAGGTGC 61.423 66.667 13.24 0.00 0.00 5.01
44 45 2.027625 GTCAACGGCGGAGAAGGTG 61.028 63.158 13.24 0.00 0.00 4.00
45 46 2.342648 GTCAACGGCGGAGAAGGT 59.657 61.111 13.24 0.00 0.00 3.50
46 47 2.027625 GTGTCAACGGCGGAGAAGG 61.028 63.158 13.24 0.00 0.00 3.46
47 48 1.300620 TGTGTCAACGGCGGAGAAG 60.301 57.895 13.24 0.00 0.00 2.85
48 49 1.593209 GTGTGTCAACGGCGGAGAA 60.593 57.895 13.24 0.00 0.00 2.87
49 50 2.028484 GTGTGTCAACGGCGGAGA 59.972 61.111 13.24 5.52 0.00 3.71
50 51 3.403057 CGTGTGTCAACGGCGGAG 61.403 66.667 13.24 2.63 39.89 4.63
67 68 2.432628 CACGGAAGGACGCCAGAC 60.433 66.667 0.00 0.00 37.37 3.51
68 69 4.373116 GCACGGAAGGACGCCAGA 62.373 66.667 0.00 0.00 37.37 3.86
113 114 4.803426 CAGTCAGGCTCGTCGGGC 62.803 72.222 9.11 9.11 0.00 6.13
114 115 4.803426 GCAGTCAGGCTCGTCGGG 62.803 72.222 0.00 0.00 0.00 5.14
115 116 3.978723 CTGCAGTCAGGCTCGTCGG 62.979 68.421 5.25 0.00 36.68 4.79
116 117 2.505777 CTGCAGTCAGGCTCGTCG 60.506 66.667 5.25 0.00 36.68 5.12
117 118 2.813042 GCTGCAGTCAGGCTCGTC 60.813 66.667 16.64 0.00 40.65 4.20
118 119 3.586461 CTGCTGCAGTCAGGCTCGT 62.586 63.158 21.21 0.00 40.65 4.18
119 120 2.814341 CTGCTGCAGTCAGGCTCG 60.814 66.667 21.21 5.48 40.65 5.03
120 121 2.033755 CACTGCTGCAGTCAGGCTC 61.034 63.158 30.96 9.89 43.43 4.70
121 122 2.032223 CACTGCTGCAGTCAGGCT 59.968 61.111 30.96 7.37 43.43 4.58
122 123 3.735029 GCACTGCTGCAGTCAGGC 61.735 66.667 30.96 26.14 43.43 4.85
123 124 3.420606 CGCACTGCTGCAGTCAGG 61.421 66.667 30.96 21.04 43.43 3.86
124 125 2.664185 ACGCACTGCTGCAGTCAG 60.664 61.111 30.96 26.83 43.43 3.51
125 126 2.662857 GACGCACTGCTGCAGTCA 60.663 61.111 30.96 12.72 43.43 3.41
126 127 3.418068 GGACGCACTGCTGCAGTC 61.418 66.667 30.96 22.71 43.43 3.51
173 174 4.773117 GGTGCGGTCGGACTCGTC 62.773 72.222 14.05 11.17 36.67 4.20
175 176 3.851845 TTTGGTGCGGTCGGACTCG 62.852 63.158 14.05 10.83 36.67 4.18
176 177 2.029964 TTTGGTGCGGTCGGACTC 59.970 61.111 14.05 5.91 36.67 3.36
177 178 2.280592 GTTTGGTGCGGTCGGACT 60.281 61.111 14.05 0.00 36.67 3.85
178 179 3.708734 CGTTTGGTGCGGTCGGAC 61.709 66.667 6.47 6.47 35.66 4.79
186 187 4.322385 GTCCACGGCGTTTGGTGC 62.322 66.667 11.19 4.04 35.42 5.01
187 188 2.590575 AGTCCACGGCGTTTGGTG 60.591 61.111 11.19 0.00 35.42 4.17
188 189 2.280592 GAGTCCACGGCGTTTGGT 60.281 61.111 11.19 0.00 35.42 3.67
189 190 2.280524 TGAGTCCACGGCGTTTGG 60.281 61.111 11.19 10.51 35.18 3.28
190 191 2.604174 GGTGAGTCCACGGCGTTTG 61.604 63.158 11.19 4.61 44.09 2.93
191 192 2.280592 GGTGAGTCCACGGCGTTT 60.281 61.111 11.19 0.00 44.09 3.60
192 193 4.657824 CGGTGAGTCCACGGCGTT 62.658 66.667 11.19 0.00 44.09 4.84
218 219 1.153086 GAACATGGAGGCATCGGCT 60.153 57.895 0.00 0.00 42.48 5.52
254 255 4.980805 GGAGGTGGTGCGCGTGAA 62.981 66.667 8.43 0.00 0.00 3.18
449 2092 4.332819 GTGATCGAGTTGGGTTATCTTTGG 59.667 45.833 0.00 0.00 0.00 3.28
451 2094 4.081862 TCGTGATCGAGTTGGGTTATCTTT 60.082 41.667 0.00 0.00 41.35 2.52
469 2112 1.800586 GCAATTGCTCTGAGTTCGTGA 59.199 47.619 23.21 0.00 38.21 4.35
506 2149 1.343465 CCAAGATATAGGCCGGTTCGT 59.657 52.381 1.90 0.00 0.00 3.85
518 2161 7.521099 CGCAGTGAATAAAGATTGCCAAGATAT 60.521 37.037 0.00 0.00 0.00 1.63
530 2173 2.095969 CGCCAAACGCAGTGAATAAAGA 60.096 45.455 0.00 0.00 45.00 2.52
551 2194 1.080501 TGTGTGCGAGCTGTAGAGC 60.081 57.895 3.08 3.08 46.64 4.09
607 2250 4.408821 TCCATGGCACCTGGCGTC 62.409 66.667 6.96 0.00 46.16 5.19
640 2283 3.258971 AGACAAGAGGCAAGATGTAGC 57.741 47.619 0.00 0.00 0.00 3.58
785 2428 0.877071 GCTAGTTGTGTGCATGTGCT 59.123 50.000 6.55 0.00 42.66 4.40
806 2449 0.250124 TGTGGCCGGTTGAGTTAGTG 60.250 55.000 1.90 0.00 0.00 2.74
840 2483 3.586470 TGGGTTGGTTCAACTACATGT 57.414 42.857 2.69 2.69 43.14 3.21
854 2497 9.613428 TGTTAGTATAATTCTGATCTTGGGTTG 57.387 33.333 0.00 0.00 0.00 3.77
875 2518 2.701006 CGCCGTCGCCATTGTTAG 59.299 61.111 0.00 0.00 0.00 2.34
884 2527 3.569049 ATATAGCCACCGCCGTCGC 62.569 63.158 0.00 0.00 34.57 5.19
885 2528 1.006571 AATATAGCCACCGCCGTCG 60.007 57.895 0.00 0.00 34.57 5.12
886 2529 0.669625 GGAATATAGCCACCGCCGTC 60.670 60.000 0.00 0.00 34.57 4.79
887 2530 1.119574 AGGAATATAGCCACCGCCGT 61.120 55.000 0.00 0.00 34.57 5.68
888 2531 0.034896 AAGGAATATAGCCACCGCCG 59.965 55.000 0.00 0.00 34.57 6.46
891 2534 3.254060 CGATCAAGGAATATAGCCACCG 58.746 50.000 0.00 0.00 0.00 4.94
904 2547 0.034756 TGTCACCCACACGATCAAGG 59.965 55.000 0.00 0.00 0.00 3.61
909 2552 1.374947 CCCTTGTCACCCACACGAT 59.625 57.895 0.00 0.00 33.41 3.73
913 2556 0.694783 TACACCCCTTGTCACCCACA 60.695 55.000 0.00 0.00 39.91 4.17
921 2564 2.747686 CACCGCTACACCCCTTGT 59.252 61.111 0.00 0.00 42.84 3.16
930 2573 1.153429 CCTAGCAACCCACCGCTAC 60.153 63.158 0.00 0.00 39.70 3.58
937 2580 1.541368 AAGGAGCCCTAGCAACCCA 60.541 57.895 0.00 0.00 43.56 4.51
938 2581 1.224870 GAAGGAGCCCTAGCAACCC 59.775 63.158 0.00 0.00 43.56 4.11
948 2591 2.508663 GCCACGTACGAAGGAGCC 60.509 66.667 27.23 11.81 0.00 4.70
961 2604 4.813235 TATGCCCCTTGCCGCCAC 62.813 66.667 0.00 0.00 40.16 5.01
962 2605 4.504596 CTATGCCCCTTGCCGCCA 62.505 66.667 0.00 0.00 40.16 5.69
1003 2646 1.363744 CTGGAACGCTTCATGGTCTC 58.636 55.000 0.00 0.00 0.00 3.36
1030 2673 4.899239 CGATGGGCAGTCGGGCTC 62.899 72.222 3.22 0.00 42.84 4.70
1071 2714 2.528127 TTGTCGCCCCCTCCTTGA 60.528 61.111 0.00 0.00 0.00 3.02
1117 2760 1.576421 CTTTTGTCCTCTGCACCGC 59.424 57.895 0.00 0.00 0.00 5.68
1119 2762 0.595095 CTGCTTTTGTCCTCTGCACC 59.405 55.000 0.00 0.00 0.00 5.01
1121 2764 0.466007 TGCTGCTTTTGTCCTCTGCA 60.466 50.000 0.00 0.00 0.00 4.41
1131 2774 0.318120 CGGGGAATGTTGCTGCTTTT 59.682 50.000 0.00 0.00 0.00 2.27
1132 2775 0.827507 ACGGGGAATGTTGCTGCTTT 60.828 50.000 0.00 0.00 0.00 3.51
1134 2777 0.392998 CTACGGGGAATGTTGCTGCT 60.393 55.000 0.00 0.00 0.00 4.24
1143 2786 4.171103 GCGGCACCTACGGGGAAT 62.171 66.667 0.00 0.00 38.76 3.01
1170 2813 1.003476 TTCAATCCTCTGCGCTGCA 60.003 52.632 9.73 3.35 36.92 4.41
1172 2815 2.200067 CTACTTCAATCCTCTGCGCTG 58.800 52.381 9.73 8.88 0.00 5.18
1184 2827 1.080093 CCGGACGCTGCTACTTCAA 60.080 57.895 0.00 0.00 0.00 2.69
1294 2937 4.473520 CCGACTGCCCGAGCCATT 62.474 66.667 0.00 0.00 38.69 3.16
1317 2960 2.203294 GCCTCCCGTGTTGGTTGT 60.203 61.111 0.00 0.00 35.15 3.32
1335 2978 2.894387 GACCCTGCGCATCTCTGC 60.894 66.667 12.24 0.00 45.31 4.26
1376 3019 1.021390 ACGAAGCCTGGAAAGATGCG 61.021 55.000 0.00 0.00 0.00 4.73
1429 3072 1.787847 CCATCTTCGTCGCCAACAC 59.212 57.895 0.00 0.00 0.00 3.32
1452 3095 1.153289 CTGGCATCCACTTCCCGAG 60.153 63.158 0.00 0.00 0.00 4.63
1463 3106 1.202855 ACACCTGCATATCCTGGCATC 60.203 52.381 0.00 0.00 39.65 3.91
1469 3112 1.620819 GGATCGACACCTGCATATCCT 59.379 52.381 0.00 0.00 32.00 3.24
1485 3128 4.771684 GCAACATGTGCGTGGATC 57.228 55.556 0.00 0.00 45.10 3.36
1519 3162 1.134310 TCATCATCTGTGCATCCGCTT 60.134 47.619 0.00 0.00 39.64 4.68
1531 3174 2.749280 TGTGTTGTCGCTCATCATCT 57.251 45.000 0.00 0.00 0.00 2.90
1605 3248 5.687166 ACACGGGGAAAGATGATTAGTTA 57.313 39.130 0.00 0.00 0.00 2.24
1893 3586 1.887956 GCCATGGTGTGAACATGTCCT 60.888 52.381 14.67 0.00 43.15 3.85
1896 3589 1.820519 GATGCCATGGTGTGAACATGT 59.179 47.619 14.67 0.00 43.15 3.21
1897 3590 2.097036 AGATGCCATGGTGTGAACATG 58.903 47.619 14.67 0.00 44.03 3.21
1898 3591 2.372264 GAGATGCCATGGTGTGAACAT 58.628 47.619 14.67 6.80 0.00 2.71
1899 3592 1.614051 GGAGATGCCATGGTGTGAACA 60.614 52.381 14.67 1.28 36.34 3.18
1900 3593 1.098050 GGAGATGCCATGGTGTGAAC 58.902 55.000 14.67 0.00 36.34 3.18
1958 3651 2.797156 GGCACACTAAGTCTCATATGCG 59.203 50.000 0.00 0.00 32.59 4.73
1981 3674 2.907042 GGATTTCGACATAGGGAGGGAT 59.093 50.000 0.00 0.00 0.00 3.85
1985 3678 2.548920 GCCAGGATTTCGACATAGGGAG 60.549 54.545 0.00 0.00 0.00 4.30
1986 3679 1.416401 GCCAGGATTTCGACATAGGGA 59.584 52.381 0.00 0.00 0.00 4.20
2009 3703 1.345009 ACATGGCTACACCCAGGGATA 60.345 52.381 14.54 3.04 40.81 2.59
2038 3732 2.922740 AGAAACCGCCTTGTAGTTGA 57.077 45.000 0.00 0.00 0.00 3.18
2082 3784 2.749044 ATGCCGCTCAACCTGCAG 60.749 61.111 6.78 6.78 37.12 4.41
2126 3828 9.352784 CACGATCCAAGATCTATCTTATCTTTC 57.647 37.037 4.93 0.00 44.84 2.62
2132 3834 5.047731 CCTGCACGATCCAAGATCTATCTTA 60.048 44.000 4.93 0.00 44.84 2.10
2141 3843 1.191489 TGACCCTGCACGATCCAAGA 61.191 55.000 0.00 0.00 0.00 3.02
2143 3845 1.003839 GTGACCCTGCACGATCCAA 60.004 57.895 0.00 0.00 0.00 3.53
2223 3925 2.204306 CCCCTCCACCCTTCCCTT 60.204 66.667 0.00 0.00 0.00 3.95
2264 3966 2.409570 GAATAGGGGGCCTCAGTAACT 58.590 52.381 5.99 0.00 34.61 2.24
2273 3975 1.153756 CATGTGGGAATAGGGGGCC 59.846 63.158 0.00 0.00 0.00 5.80
2277 3979 6.155049 AGTTGAAAAATCATGTGGGAATAGGG 59.845 38.462 0.00 0.00 0.00 3.53
2380 4082 5.438761 ACATAGGTTCACTTTGTTCTTGC 57.561 39.130 0.00 0.00 38.03 4.01
2398 4100 9.112725 TCACTAGAGTAAATAGCACGTTACATA 57.887 33.333 0.00 0.19 33.49 2.29
2413 4115 4.417437 AGGCTCCAACTTCACTAGAGTAA 58.583 43.478 0.00 0.00 0.00 2.24
2452 4154 8.394877 CCACGACTTCACTTGCAATAATAATAA 58.605 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.