Multiple sequence alignment - TraesCS7D01G422900

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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 TraesCS7D01G422900 chr7D 100.000 2720 0 0 1 2720 543556544 543559263 0.000000e+00 5024.0
1 TraesCS7D01G422900 chr7D 83.051 118 14 4 1 115 298914048 298914162 4.790000e-18 102.0
2 TraesCS7D01G422900 chr7B 94.699 1528 42 17 150 1661 586655534 586657038 0.000000e+00 2337.0
3 TraesCS7D01G422900 chr7B 96.505 1030 20 8 1694 2720 586657328 586658344 0.000000e+00 1688.0
4 TraesCS7D01G422900 chr7B 82.609 115 19 1 1 115 255006563 255006676 1.720000e-17 100.0
5 TraesCS7D01G422900 chr7B 100.000 31 0 0 130 160 586635185 586635215 1.050000e-04 58.4
6 TraesCS7D01G422900 chr4D 100.000 123 0 0 1 123 52242479 52242601 7.580000e-56 228.0
7 TraesCS7D01G422900 chr4A 98.387 124 2 0 1 124 30318424 30318301 4.560000e-53 219.0
8 TraesCS7D01G422900 chr3A 98.387 124 2 0 1 124 517778409 517778532 4.560000e-53 219.0
9 TraesCS7D01G422900 chr6B 96.774 124 4 0 1 124 257329028 257328905 9.870000e-50 207.0
10 TraesCS7D01G422900 chr6B 91.964 112 8 1 1 112 481047110 481047220 3.630000e-34 156.0
11 TraesCS7D01G422900 chr6D 90.323 124 11 1 1 124 339687690 339687568 7.790000e-36 161.0
12 TraesCS7D01G422900 chr6A 88.710 124 12 1 1 124 479885040 479884919 1.690000e-32 150.0


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 TraesCS7D01G422900 chr7D 543556544 543559263 2719 False 5024.0 5024 100.000 1 2720 1 chr7D.!!$F2 2719
1 TraesCS7D01G422900 chr7B 586655534 586658344 2810 False 2012.5 2337 95.602 150 2720 2 chr7B.!!$F3 2570

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
534 540 0.323360 CAGAAAATCCCCTTCCCGCA 60.323 55.0 0.0 0.0 0.00 5.69 F
723 729 0.392998 CCAAATCCCCAGGAGTGACG 60.393 60.0 0.0 0.0 34.05 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1952 0.039527 GCACCACGGCTTAAAGGTTG 60.040 55.0 0.0 0.00 30.44 3.77 R
2320 2594 0.763035 AACAAACTAGGACGGCACCT 59.237 50.0 0.0 5.59 43.32 4.00 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
20 21 3.788227 AACCCTCTGCACACATAAGAA 57.212 42.857 0.00 0.00 0.00 2.52
21 22 3.788227 ACCCTCTGCACACATAAGAAA 57.212 42.857 0.00 0.00 0.00 2.52
22 23 4.307032 ACCCTCTGCACACATAAGAAAT 57.693 40.909 0.00 0.00 0.00 2.17
23 24 5.435686 ACCCTCTGCACACATAAGAAATA 57.564 39.130 0.00 0.00 0.00 1.40
24 25 5.815581 ACCCTCTGCACACATAAGAAATAA 58.184 37.500 0.00 0.00 0.00 1.40
25 26 6.245408 ACCCTCTGCACACATAAGAAATAAA 58.755 36.000 0.00 0.00 0.00 1.40
26 27 6.891908 ACCCTCTGCACACATAAGAAATAAAT 59.108 34.615 0.00 0.00 0.00 1.40
27 28 8.052748 ACCCTCTGCACACATAAGAAATAAATA 58.947 33.333 0.00 0.00 0.00 1.40
28 29 8.902806 CCCTCTGCACACATAAGAAATAAATAA 58.097 33.333 0.00 0.00 0.00 1.40
29 30 9.941664 CCTCTGCACACATAAGAAATAAATAAG 57.058 33.333 0.00 0.00 0.00 1.73
30 31 9.941664 CTCTGCACACATAAGAAATAAATAAGG 57.058 33.333 0.00 0.00 0.00 2.69
31 32 9.461312 TCTGCACACATAAGAAATAAATAAGGT 57.539 29.630 0.00 0.00 0.00 3.50
32 33 9.507280 CTGCACACATAAGAAATAAATAAGGTG 57.493 33.333 0.00 0.00 0.00 4.00
33 34 9.237187 TGCACACATAAGAAATAAATAAGGTGA 57.763 29.630 0.00 0.00 0.00 4.02
42 43 9.642343 AAGAAATAAATAAGGTGATAAGGGGTC 57.358 33.333 0.00 0.00 0.00 4.46
43 44 8.225416 AGAAATAAATAAGGTGATAAGGGGTCC 58.775 37.037 0.00 0.00 0.00 4.46
44 45 4.808767 AAATAAGGTGATAAGGGGTCCC 57.191 45.455 0.00 0.00 0.00 4.46
45 46 2.201523 TAAGGTGATAAGGGGTCCCC 57.798 55.000 20.85 20.85 45.90 4.81
54 55 3.400054 GGGGTCCCCTTGTCGGAG 61.400 72.222 21.13 0.00 41.34 4.63
55 56 4.097361 GGGTCCCCTTGTCGGAGC 62.097 72.222 0.00 0.00 45.36 4.70
56 57 4.097361 GGTCCCCTTGTCGGAGCC 62.097 72.222 0.00 0.00 41.19 4.70
57 58 4.097361 GTCCCCTTGTCGGAGCCC 62.097 72.222 0.00 0.00 33.16 5.19
61 62 3.330720 CCTTGTCGGAGCCCCCTT 61.331 66.667 0.00 0.00 33.16 3.95
62 63 2.045926 CTTGTCGGAGCCCCCTTG 60.046 66.667 0.00 0.00 0.00 3.61
63 64 2.852075 TTGTCGGAGCCCCCTTGT 60.852 61.111 0.00 0.00 0.00 3.16
64 65 1.536907 TTGTCGGAGCCCCCTTGTA 60.537 57.895 0.00 0.00 0.00 2.41
65 66 1.550130 TTGTCGGAGCCCCCTTGTAG 61.550 60.000 0.00 0.00 0.00 2.74
66 67 2.365105 TCGGAGCCCCCTTGTAGG 60.365 66.667 0.00 0.00 34.30 3.18
80 81 4.781934 CCTTGTAGGGGTAAATTCCTCTG 58.218 47.826 0.00 0.00 38.92 3.35
81 82 4.227527 CCTTGTAGGGGTAAATTCCTCTGT 59.772 45.833 0.00 0.00 38.92 3.41
82 83 5.281037 CCTTGTAGGGGTAAATTCCTCTGTT 60.281 44.000 0.00 0.00 38.92 3.16
83 84 5.853572 TGTAGGGGTAAATTCCTCTGTTT 57.146 39.130 0.00 0.00 38.92 2.83
84 85 5.812286 TGTAGGGGTAAATTCCTCTGTTTC 58.188 41.667 0.00 0.00 38.92 2.78
85 86 5.550403 TGTAGGGGTAAATTCCTCTGTTTCT 59.450 40.000 0.00 0.00 38.92 2.52
86 87 5.600669 AGGGGTAAATTCCTCTGTTTCTT 57.399 39.130 0.00 0.00 36.86 2.52
87 88 5.325239 AGGGGTAAATTCCTCTGTTTCTTG 58.675 41.667 0.00 0.00 36.86 3.02
88 89 5.074515 AGGGGTAAATTCCTCTGTTTCTTGA 59.925 40.000 0.00 0.00 36.86 3.02
89 90 5.952347 GGGGTAAATTCCTCTGTTTCTTGAT 59.048 40.000 0.00 0.00 0.00 2.57
90 91 6.095580 GGGGTAAATTCCTCTGTTTCTTGATC 59.904 42.308 0.00 0.00 0.00 2.92
91 92 6.659242 GGGTAAATTCCTCTGTTTCTTGATCA 59.341 38.462 0.00 0.00 0.00 2.92
92 93 7.340487 GGGTAAATTCCTCTGTTTCTTGATCAT 59.660 37.037 0.00 0.00 0.00 2.45
93 94 8.743714 GGTAAATTCCTCTGTTTCTTGATCATT 58.256 33.333 0.00 0.00 0.00 2.57
98 99 8.964476 TTCCTCTGTTTCTTGATCATTATACC 57.036 34.615 0.00 0.00 0.00 2.73
99 100 8.324191 TCCTCTGTTTCTTGATCATTATACCT 57.676 34.615 0.00 0.00 0.00 3.08
100 101 8.424918 TCCTCTGTTTCTTGATCATTATACCTC 58.575 37.037 0.00 0.00 0.00 3.85
101 102 8.206867 CCTCTGTTTCTTGATCATTATACCTCA 58.793 37.037 0.00 0.00 0.00 3.86
102 103 8.948631 TCTGTTTCTTGATCATTATACCTCAC 57.051 34.615 0.00 0.00 0.00 3.51
103 104 8.762645 TCTGTTTCTTGATCATTATACCTCACT 58.237 33.333 0.00 0.00 0.00 3.41
104 105 9.388506 CTGTTTCTTGATCATTATACCTCACTT 57.611 33.333 0.00 0.00 0.00 3.16
105 106 9.739276 TGTTTCTTGATCATTATACCTCACTTT 57.261 29.630 0.00 0.00 0.00 2.66
106 107 9.994432 GTTTCTTGATCATTATACCTCACTTTG 57.006 33.333 0.00 0.00 0.00 2.77
107 108 9.739276 TTTCTTGATCATTATACCTCACTTTGT 57.261 29.630 0.00 0.00 0.00 2.83
115 116 9.391006 TCATTATACCTCACTTTGTATTTCACC 57.609 33.333 0.00 0.00 0.00 4.02
116 117 7.837202 TTATACCTCACTTTGTATTTCACCG 57.163 36.000 0.00 0.00 0.00 4.94
117 118 4.345859 ACCTCACTTTGTATTTCACCGA 57.654 40.909 0.00 0.00 0.00 4.69
118 119 4.315803 ACCTCACTTTGTATTTCACCGAG 58.684 43.478 0.00 0.00 0.00 4.63
119 120 3.684788 CCTCACTTTGTATTTCACCGAGG 59.315 47.826 0.00 0.00 0.00 4.63
120 121 4.562757 CCTCACTTTGTATTTCACCGAGGA 60.563 45.833 0.00 0.00 39.94 3.71
121 122 4.963373 TCACTTTGTATTTCACCGAGGAA 58.037 39.130 0.00 0.00 0.00 3.36
122 123 5.369833 TCACTTTGTATTTCACCGAGGAAA 58.630 37.500 0.00 4.34 40.72 3.13
123 124 5.237779 TCACTTTGTATTTCACCGAGGAAAC 59.762 40.000 0.00 0.00 39.40 2.78
125 126 5.238650 ACTTTGTATTTCACCGAGGAAACTG 59.761 40.000 0.00 0.00 44.43 3.16
126 127 4.610605 TGTATTTCACCGAGGAAACTGA 57.389 40.909 0.00 0.00 44.43 3.41
127 128 4.312443 TGTATTTCACCGAGGAAACTGAC 58.688 43.478 0.00 4.40 44.43 3.51
128 129 2.992124 TTTCACCGAGGAAACTGACA 57.008 45.000 0.00 0.00 44.43 3.58
129 130 3.485463 TTTCACCGAGGAAACTGACAT 57.515 42.857 0.00 0.00 44.43 3.06
130 131 4.610605 TTTCACCGAGGAAACTGACATA 57.389 40.909 0.00 0.00 44.43 2.29
131 132 3.587797 TCACCGAGGAAACTGACATAC 57.412 47.619 0.00 0.00 44.43 2.39
132 133 3.162666 TCACCGAGGAAACTGACATACT 58.837 45.455 0.00 0.00 44.43 2.12
133 134 4.338012 TCACCGAGGAAACTGACATACTA 58.662 43.478 0.00 0.00 44.43 1.82
134 135 4.954202 TCACCGAGGAAACTGACATACTAT 59.046 41.667 0.00 0.00 44.43 2.12
135 136 5.421056 TCACCGAGGAAACTGACATACTATT 59.579 40.000 0.00 0.00 44.43 1.73
136 137 6.070995 TCACCGAGGAAACTGACATACTATTT 60.071 38.462 0.00 0.00 44.43 1.40
137 138 7.123098 TCACCGAGGAAACTGACATACTATTTA 59.877 37.037 0.00 0.00 44.43 1.40
138 139 7.762615 CACCGAGGAAACTGACATACTATTTAA 59.237 37.037 0.00 0.00 44.43 1.52
139 140 8.483758 ACCGAGGAAACTGACATACTATTTAAT 58.516 33.333 0.00 0.00 44.43 1.40
140 141 9.326413 CCGAGGAAACTGACATACTATTTAATT 57.674 33.333 0.00 0.00 44.43 1.40
324 328 7.733402 ACGCAATTGACTAAAACTAAACCTA 57.267 32.000 10.34 0.00 0.00 3.08
326 330 7.019418 CGCAATTGACTAAAACTAAACCTACC 58.981 38.462 10.34 0.00 0.00 3.18
328 332 7.524065 CAATTGACTAAAACTAAACCTACCCG 58.476 38.462 0.00 0.00 0.00 5.28
329 333 4.568956 TGACTAAAACTAAACCTACCCGC 58.431 43.478 0.00 0.00 0.00 6.13
330 334 3.935203 GACTAAAACTAAACCTACCCGCC 59.065 47.826 0.00 0.00 0.00 6.13
351 355 2.359850 GGCACATCACCTCGCCAA 60.360 61.111 0.00 0.00 44.25 4.52
500 506 2.703798 CGTCCCGCTTCTACCCGAA 61.704 63.158 0.00 0.00 0.00 4.30
504 510 1.299926 CCGCTTCTACCCGAATCCG 60.300 63.158 0.00 0.00 0.00 4.18
505 511 1.949631 CGCTTCTACCCGAATCCGC 60.950 63.158 0.00 0.00 0.00 5.54
509 515 4.295119 CTACCCGAATCCGCCCGG 62.295 72.222 0.00 0.00 44.94 5.73
534 540 0.323360 CAGAAAATCCCCTTCCCGCA 60.323 55.000 0.00 0.00 0.00 5.69
662 668 2.048409 AGCAGCTGCAGTCGACAG 60.048 61.111 38.24 11.47 45.16 3.51
669 675 2.863658 CTGCAGTCGACAGCTTTAAC 57.136 50.000 29.51 4.49 0.00 2.01
670 676 1.461127 CTGCAGTCGACAGCTTTAACC 59.539 52.381 29.51 3.80 0.00 2.85
671 677 1.202592 TGCAGTCGACAGCTTTAACCA 60.203 47.619 29.51 8.47 0.00 3.67
672 678 2.076863 GCAGTCGACAGCTTTAACCAT 58.923 47.619 23.94 0.00 0.00 3.55
673 679 2.094417 GCAGTCGACAGCTTTAACCATC 59.906 50.000 23.94 0.00 0.00 3.51
674 680 2.673368 CAGTCGACAGCTTTAACCATCC 59.327 50.000 19.50 0.00 0.00 3.51
675 681 2.301870 AGTCGACAGCTTTAACCATCCA 59.698 45.455 19.50 0.00 0.00 3.41
681 687 0.455815 GCTTTAACCATCCAAGGCCG 59.544 55.000 0.00 0.00 0.00 6.13
709 715 6.298361 CAAGTTTTTCTCCCAAATCCCAAAT 58.702 36.000 0.00 0.00 0.00 2.32
723 729 0.392998 CCAAATCCCCAGGAGTGACG 60.393 60.000 0.00 0.00 34.05 4.35
743 749 2.406616 CGCGCTAGGTTTTGCCCAT 61.407 57.895 5.56 0.00 38.26 4.00
887 904 3.990318 GCCAGTATGCCAAGTAATTCC 57.010 47.619 0.00 0.00 31.97 3.01
906 923 5.682943 TTCCTTTTTCTGTATCCAACACG 57.317 39.130 0.00 0.00 33.45 4.49
915 932 7.851387 TTCTGTATCCAACACGCAATTAATA 57.149 32.000 0.00 0.00 33.45 0.98
916 933 7.851387 TCTGTATCCAACACGCAATTAATAA 57.149 32.000 0.00 0.00 33.45 1.40
917 934 8.445275 TCTGTATCCAACACGCAATTAATAAT 57.555 30.769 0.00 0.00 33.45 1.28
929 946 9.110617 CACGCAATTAATAATCTCTATGCTTTG 57.889 33.333 5.44 0.49 0.00 2.77
972 989 3.135712 TGCCTTAGCCTGATCCGATTTTA 59.864 43.478 0.00 0.00 38.69 1.52
973 990 4.202461 TGCCTTAGCCTGATCCGATTTTAT 60.202 41.667 0.00 0.00 38.69 1.40
998 1015 3.131223 TGCAGATCTTAGCCAGACAGTAC 59.869 47.826 0.00 0.00 32.83 2.73
1003 1020 3.617284 TCTTAGCCAGACAGTACGATGA 58.383 45.455 0.00 0.00 0.00 2.92
1059 1076 7.381766 ACGTTTCCTTGTTACAACTTAGTTT 57.618 32.000 0.00 0.00 0.00 2.66
1169 1186 3.436704 TCCATCGATTGTGAAAGTCTTGC 59.563 43.478 0.00 0.00 0.00 4.01
1253 1270 7.551585 TGTTTGTTCCATGTTGTTAATTGAGT 58.448 30.769 0.00 0.00 0.00 3.41
1269 1286 6.414408 AATTGAGTGCAAAGAGAAGATACG 57.586 37.500 0.00 0.00 37.59 3.06
1276 1293 3.109619 CAAAGAGAAGATACGAGTCCGC 58.890 50.000 0.00 0.00 39.95 5.54
1332 1349 8.638873 TCATACTGAAAAAGTCTCTAACAGTGA 58.361 33.333 0.00 0.00 40.56 3.41
1333 1350 9.429359 CATACTGAAAAAGTCTCTAACAGTGAT 57.571 33.333 0.00 0.00 40.56 3.06
1406 1423 4.672587 TTTGGAGTCTTGGAGGATATCG 57.327 45.455 0.00 0.00 0.00 2.92
1549 1566 4.120589 GGACCGATTAGATCCTCACAAAC 58.879 47.826 0.00 0.00 26.30 2.93
1621 1638 5.365314 GGGAACATTATTCCAGGCCAAAATA 59.635 40.000 5.01 2.78 40.32 1.40
1683 1951 9.378551 TCGATACATTTATACATTATTCCAGGC 57.621 33.333 0.00 0.00 0.00 4.85
1684 1952 8.612619 CGATACATTTATACATTATTCCAGGCC 58.387 37.037 0.00 0.00 0.00 5.19
1687 1955 7.951591 ACATTTATACATTATTCCAGGCCAAC 58.048 34.615 5.01 0.00 0.00 3.77
1688 1956 6.969993 TTTATACATTATTCCAGGCCAACC 57.030 37.500 5.01 0.00 0.00 3.77
1756 2030 6.527423 TGTCTTCCTACTTTCACGGTAAATT 58.473 36.000 0.00 0.00 0.00 1.82
1986 2260 7.886629 AGTCATTGTAGCATTATCCATGTTT 57.113 32.000 0.00 0.00 34.98 2.83
2061 2335 1.450312 GCCGTGCTAACCATGCTCT 60.450 57.895 0.00 0.00 0.00 4.09
2134 2408 7.678947 AAGTGAATACTTGTCATTCCTTGAG 57.321 36.000 0.00 0.00 45.17 3.02
2172 2446 1.722034 TGTTCTTCTCCAGCTGAGGT 58.278 50.000 17.39 0.00 41.76 3.85
2177 2451 2.301296 TCTTCTCCAGCTGAGGTCAAAG 59.699 50.000 17.39 9.67 41.76 2.77
2320 2594 5.244402 TCGGTTATCTTTGAGTGACTGGTTA 59.756 40.000 0.00 0.00 0.00 2.85
2322 2596 5.875359 GGTTATCTTTGAGTGACTGGTTAGG 59.125 44.000 0.00 0.00 0.00 2.69
2323 2597 6.465084 GTTATCTTTGAGTGACTGGTTAGGT 58.535 40.000 0.00 0.00 0.00 3.08
2324 2598 4.336889 TCTTTGAGTGACTGGTTAGGTG 57.663 45.455 0.00 0.00 0.00 4.00
2365 2639 7.418337 ACTTGTGTTGAACCTTATTTCCTTT 57.582 32.000 0.00 0.00 0.00 3.11
2395 2669 4.927267 AGGTCATGTCCTGGTTTATCAA 57.073 40.909 10.95 0.00 36.35 2.57
2437 2711 5.671493 ACCTTATGACCTCCGTTGATTTAG 58.329 41.667 0.00 0.00 0.00 1.85
2528 2802 7.676683 TCCTAATTATTTACTCTCTGCTGGT 57.323 36.000 0.00 0.00 0.00 4.00
2529 2803 8.090788 TCCTAATTATTTACTCTCTGCTGGTT 57.909 34.615 0.00 0.00 0.00 3.67
2530 2804 7.987458 TCCTAATTATTTACTCTCTGCTGGTTG 59.013 37.037 0.00 0.00 0.00 3.77
2531 2805 7.770897 CCTAATTATTTACTCTCTGCTGGTTGT 59.229 37.037 0.00 0.00 0.00 3.32
2532 2806 9.167311 CTAATTATTTACTCTCTGCTGGTTGTT 57.833 33.333 0.00 0.00 0.00 2.83
2533 2807 6.801539 TTATTTACTCTCTGCTGGTTGTTG 57.198 37.500 0.00 0.00 0.00 3.33
2534 2808 4.415881 TTTACTCTCTGCTGGTTGTTGA 57.584 40.909 0.00 0.00 0.00 3.18
2535 2809 4.415881 TTACTCTCTGCTGGTTGTTGAA 57.584 40.909 0.00 0.00 0.00 2.69
2536 2810 2.565841 ACTCTCTGCTGGTTGTTGAAC 58.434 47.619 0.00 0.00 0.00 3.18
2552 2826 7.254852 GTTGTTGAACTGTTGAACCTTGATAA 58.745 34.615 17.95 4.21 0.00 1.75
2571 2845 1.639722 ATTGGTTGGTTTAGGTGCCC 58.360 50.000 0.00 0.00 0.00 5.36
2593 2867 5.131067 CCTCCTAGTTTATTAACCCCTTGC 58.869 45.833 0.00 0.00 34.71 4.01
2669 2946 2.435059 GAGTGAGGCAAGCGGGAC 60.435 66.667 0.00 0.00 0.00 4.46
2712 2989 4.717629 GCAAAAGGAACGCCCGCC 62.718 66.667 0.00 0.00 40.87 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.788227 TTCTTATGTGTGCAGAGGGTT 57.212 42.857 0.00 0.00 0.00 4.11
1 2 3.788227 TTTCTTATGTGTGCAGAGGGT 57.212 42.857 0.00 0.00 0.00 4.34
2 3 6.757897 TTTATTTCTTATGTGTGCAGAGGG 57.242 37.500 0.00 0.00 0.00 4.30
3 4 9.941664 CTTATTTATTTCTTATGTGTGCAGAGG 57.058 33.333 0.00 0.00 0.00 3.69
4 5 9.941664 CCTTATTTATTTCTTATGTGTGCAGAG 57.058 33.333 0.00 0.00 0.00 3.35
5 6 9.461312 ACCTTATTTATTTCTTATGTGTGCAGA 57.539 29.630 0.00 0.00 0.00 4.26
6 7 9.507280 CACCTTATTTATTTCTTATGTGTGCAG 57.493 33.333 0.00 0.00 0.00 4.41
7 8 9.237187 TCACCTTATTTATTTCTTATGTGTGCA 57.763 29.630 0.00 0.00 0.00 4.57
16 17 9.642343 GACCCCTTATCACCTTATTTATTTCTT 57.358 33.333 0.00 0.00 0.00 2.52
17 18 8.225416 GGACCCCTTATCACCTTATTTATTTCT 58.775 37.037 0.00 0.00 0.00 2.52
18 19 7.450634 GGGACCCCTTATCACCTTATTTATTTC 59.549 40.741 0.00 0.00 0.00 2.17
19 20 7.302948 GGGACCCCTTATCACCTTATTTATTT 58.697 38.462 0.00 0.00 0.00 1.40
20 21 6.860034 GGGACCCCTTATCACCTTATTTATT 58.140 40.000 0.00 0.00 0.00 1.40
21 22 6.464530 GGGACCCCTTATCACCTTATTTAT 57.535 41.667 0.00 0.00 0.00 1.40
22 23 5.917545 GGGACCCCTTATCACCTTATTTA 57.082 43.478 0.00 0.00 0.00 1.40
23 24 4.808767 GGGACCCCTTATCACCTTATTT 57.191 45.455 0.00 0.00 0.00 1.40
44 45 3.330720 AAGGGGGCTCCGACAAGG 61.331 66.667 0.00 0.00 41.52 3.61
45 46 1.550130 TACAAGGGGGCTCCGACAAG 61.550 60.000 0.00 0.00 41.52 3.16
46 47 1.536907 TACAAGGGGGCTCCGACAA 60.537 57.895 0.00 0.00 41.52 3.18
47 48 1.987855 CTACAAGGGGGCTCCGACA 60.988 63.158 0.00 0.00 41.52 4.35
48 49 2.732619 CCTACAAGGGGGCTCCGAC 61.733 68.421 0.00 0.00 41.52 4.79
49 50 2.365105 CCTACAAGGGGGCTCCGA 60.365 66.667 0.00 0.00 41.52 4.55
58 59 4.227527 ACAGAGGAATTTACCCCTACAAGG 59.772 45.833 0.00 0.00 31.84 3.61
59 60 5.437191 ACAGAGGAATTTACCCCTACAAG 57.563 43.478 0.00 0.00 31.84 3.16
60 61 5.853572 AACAGAGGAATTTACCCCTACAA 57.146 39.130 0.00 0.00 31.84 2.41
61 62 5.550403 AGAAACAGAGGAATTTACCCCTACA 59.450 40.000 0.00 0.00 31.84 2.74
62 63 6.063496 AGAAACAGAGGAATTTACCCCTAC 57.937 41.667 0.00 0.00 31.84 3.18
63 64 6.273730 TCAAGAAACAGAGGAATTTACCCCTA 59.726 38.462 0.00 0.00 31.84 3.53
64 65 5.074515 TCAAGAAACAGAGGAATTTACCCCT 59.925 40.000 0.00 0.00 35.02 4.79
65 66 5.321927 TCAAGAAACAGAGGAATTTACCCC 58.678 41.667 0.00 0.00 0.00 4.95
66 67 6.659242 TGATCAAGAAACAGAGGAATTTACCC 59.341 38.462 0.00 0.00 0.00 3.69
67 68 7.687941 TGATCAAGAAACAGAGGAATTTACC 57.312 36.000 0.00 0.00 0.00 2.85
72 73 9.566432 GGTATAATGATCAAGAAACAGAGGAAT 57.434 33.333 0.00 0.00 0.00 3.01
73 74 8.772250 AGGTATAATGATCAAGAAACAGAGGAA 58.228 33.333 0.00 0.00 0.00 3.36
74 75 8.324191 AGGTATAATGATCAAGAAACAGAGGA 57.676 34.615 0.00 0.00 0.00 3.71
75 76 8.206867 TGAGGTATAATGATCAAGAAACAGAGG 58.793 37.037 0.00 0.00 0.00 3.69
76 77 9.039870 GTGAGGTATAATGATCAAGAAACAGAG 57.960 37.037 0.00 0.00 0.00 3.35
77 78 8.762645 AGTGAGGTATAATGATCAAGAAACAGA 58.237 33.333 0.00 0.00 0.00 3.41
78 79 8.954950 AGTGAGGTATAATGATCAAGAAACAG 57.045 34.615 0.00 0.00 0.00 3.16
79 80 9.739276 AAAGTGAGGTATAATGATCAAGAAACA 57.261 29.630 0.00 0.00 0.00 2.83
80 81 9.994432 CAAAGTGAGGTATAATGATCAAGAAAC 57.006 33.333 0.00 0.00 0.00 2.78
81 82 9.739276 ACAAAGTGAGGTATAATGATCAAGAAA 57.261 29.630 0.00 0.00 0.00 2.52
89 90 9.391006 GGTGAAATACAAAGTGAGGTATAATGA 57.609 33.333 0.00 0.00 30.37 2.57
90 91 8.335356 CGGTGAAATACAAAGTGAGGTATAATG 58.665 37.037 0.00 0.00 30.37 1.90
91 92 8.262227 TCGGTGAAATACAAAGTGAGGTATAAT 58.738 33.333 0.00 0.00 30.37 1.28
92 93 7.613585 TCGGTGAAATACAAAGTGAGGTATAA 58.386 34.615 0.00 0.00 30.37 0.98
93 94 7.172868 TCGGTGAAATACAAAGTGAGGTATA 57.827 36.000 0.00 0.00 30.37 1.47
94 95 6.045072 TCGGTGAAATACAAAGTGAGGTAT 57.955 37.500 0.00 0.00 0.00 2.73
95 96 5.471556 TCGGTGAAATACAAAGTGAGGTA 57.528 39.130 0.00 0.00 0.00 3.08
96 97 4.315803 CTCGGTGAAATACAAAGTGAGGT 58.684 43.478 0.00 0.00 0.00 3.85
97 98 3.684788 CCTCGGTGAAATACAAAGTGAGG 59.315 47.826 0.00 0.00 35.05 3.86
98 99 4.566004 TCCTCGGTGAAATACAAAGTGAG 58.434 43.478 0.00 0.00 0.00 3.51
99 100 4.610605 TCCTCGGTGAAATACAAAGTGA 57.389 40.909 0.00 0.00 0.00 3.41
100 101 5.238650 AGTTTCCTCGGTGAAATACAAAGTG 59.761 40.000 4.07 0.00 36.68 3.16
101 102 5.238650 CAGTTTCCTCGGTGAAATACAAAGT 59.761 40.000 4.07 0.00 36.68 2.66
102 103 5.468746 TCAGTTTCCTCGGTGAAATACAAAG 59.531 40.000 4.07 0.00 36.68 2.77
103 104 5.237779 GTCAGTTTCCTCGGTGAAATACAAA 59.762 40.000 4.07 0.00 36.68 2.83
104 105 4.753107 GTCAGTTTCCTCGGTGAAATACAA 59.247 41.667 4.07 0.00 36.68 2.41
105 106 4.202274 TGTCAGTTTCCTCGGTGAAATACA 60.202 41.667 4.07 6.48 36.68 2.29
106 107 4.312443 TGTCAGTTTCCTCGGTGAAATAC 58.688 43.478 4.07 4.60 36.68 1.89
107 108 4.610605 TGTCAGTTTCCTCGGTGAAATA 57.389 40.909 4.07 0.00 36.68 1.40
108 109 3.485463 TGTCAGTTTCCTCGGTGAAAT 57.515 42.857 4.07 0.00 36.68 2.17
109 110 2.992124 TGTCAGTTTCCTCGGTGAAA 57.008 45.000 0.00 0.00 32.02 2.69
110 111 3.576982 AGTATGTCAGTTTCCTCGGTGAA 59.423 43.478 0.00 0.00 0.00 3.18
111 112 3.162666 AGTATGTCAGTTTCCTCGGTGA 58.837 45.455 0.00 0.00 0.00 4.02
112 113 3.594603 AGTATGTCAGTTTCCTCGGTG 57.405 47.619 0.00 0.00 0.00 4.94
113 114 5.934402 AATAGTATGTCAGTTTCCTCGGT 57.066 39.130 0.00 0.00 0.00 4.69
114 115 8.888579 ATTAAATAGTATGTCAGTTTCCTCGG 57.111 34.615 0.00 0.00 0.00 4.63
132 133 9.694137 CGTTTTCCCCACTTTTGTAATTAAATA 57.306 29.630 0.00 0.00 0.00 1.40
133 134 8.205512 ACGTTTTCCCCACTTTTGTAATTAAAT 58.794 29.630 0.00 0.00 0.00 1.40
134 135 7.491696 CACGTTTTCCCCACTTTTGTAATTAAA 59.508 33.333 0.00 0.00 0.00 1.52
135 136 6.979238 CACGTTTTCCCCACTTTTGTAATTAA 59.021 34.615 0.00 0.00 0.00 1.40
136 137 6.505272 CACGTTTTCCCCACTTTTGTAATTA 58.495 36.000 0.00 0.00 0.00 1.40
137 138 5.353111 CACGTTTTCCCCACTTTTGTAATT 58.647 37.500 0.00 0.00 0.00 1.40
138 139 4.738243 GCACGTTTTCCCCACTTTTGTAAT 60.738 41.667 0.00 0.00 0.00 1.89
139 140 3.429135 GCACGTTTTCCCCACTTTTGTAA 60.429 43.478 0.00 0.00 0.00 2.41
140 141 2.099427 GCACGTTTTCCCCACTTTTGTA 59.901 45.455 0.00 0.00 0.00 2.41
141 142 1.134936 GCACGTTTTCCCCACTTTTGT 60.135 47.619 0.00 0.00 0.00 2.83
142 143 1.566404 GCACGTTTTCCCCACTTTTG 58.434 50.000 0.00 0.00 0.00 2.44
143 144 0.101579 CGCACGTTTTCCCCACTTTT 59.898 50.000 0.00 0.00 0.00 2.27
144 145 1.730451 CCGCACGTTTTCCCCACTTT 61.730 55.000 0.00 0.00 0.00 2.66
145 146 2.190841 CCGCACGTTTTCCCCACTT 61.191 57.895 0.00 0.00 0.00 3.16
146 147 2.593436 CCGCACGTTTTCCCCACT 60.593 61.111 0.00 0.00 0.00 4.00
147 148 2.900167 GACCGCACGTTTTCCCCAC 61.900 63.158 0.00 0.00 0.00 4.61
148 149 2.592287 GACCGCACGTTTTCCCCA 60.592 61.111 0.00 0.00 0.00 4.96
243 247 6.406961 GGTTGGACTGGATTTCTGAAAGTTTT 60.407 38.462 8.95 0.00 33.76 2.43
252 256 2.348472 TGAGGGTTGGACTGGATTTCT 58.652 47.619 0.00 0.00 0.00 2.52
329 333 2.187946 GAGGTGATGTGCCTCCGG 59.812 66.667 0.00 0.00 45.05 5.14
504 510 1.667154 GATTTTCTGCTTCCCCGGGC 61.667 60.000 17.73 3.70 0.00 6.13
505 511 1.037579 GGATTTTCTGCTTCCCCGGG 61.038 60.000 15.80 15.80 0.00 5.73
527 533 3.467226 GTCGGGGAGATGCGGGAA 61.467 66.667 0.00 0.00 0.00 3.97
534 540 3.148279 GTCAGCCGTCGGGGAGAT 61.148 66.667 14.38 0.00 38.47 2.75
650 656 1.461127 GGTTAAAGCTGTCGACTGCAG 59.539 52.381 37.86 20.74 42.33 4.41
662 668 0.455815 CGGCCTTGGATGGTTAAAGC 59.544 55.000 0.00 0.00 0.00 3.51
663 669 0.455815 GCGGCCTTGGATGGTTAAAG 59.544 55.000 0.00 0.00 0.00 1.85
664 670 1.309499 CGCGGCCTTGGATGGTTAAA 61.309 55.000 0.00 0.00 0.00 1.52
665 671 1.747367 CGCGGCCTTGGATGGTTAA 60.747 57.895 0.00 0.00 0.00 2.01
666 672 2.124901 CGCGGCCTTGGATGGTTA 60.125 61.111 0.00 0.00 0.00 2.85
674 680 2.969677 AAAAACTTGCCGCGGCCTTG 62.970 55.000 44.42 33.73 41.09 3.61
675 681 2.693250 GAAAAACTTGCCGCGGCCTT 62.693 55.000 44.42 29.64 41.09 4.35
681 687 0.387565 TTGGGAGAAAAACTTGCCGC 59.612 50.000 0.00 0.00 0.00 6.53
689 695 4.288366 GGGATTTGGGATTTGGGAGAAAAA 59.712 41.667 0.00 0.00 0.00 1.94
723 729 4.476410 GGCAAAACCTAGCGCGCC 62.476 66.667 30.33 10.31 34.51 6.53
729 735 1.006832 CGTCGATGGGCAAAACCTAG 58.993 55.000 0.00 0.00 39.10 3.02
812 829 1.298667 CGGTGGGGAAGTTAGGGTG 59.701 63.158 0.00 0.00 0.00 4.61
933 950 9.454859 GGCTAAGGCATGATAAATATTAAGAGT 57.545 33.333 0.00 0.00 40.87 3.24
958 975 6.135290 TCTGCAAAATAAAATCGGATCAGG 57.865 37.500 0.00 0.00 0.00 3.86
972 989 4.592942 TGTCTGGCTAAGATCTGCAAAAT 58.407 39.130 7.30 0.00 37.23 1.82
973 990 4.005650 CTGTCTGGCTAAGATCTGCAAAA 58.994 43.478 7.30 0.00 37.23 2.44
998 1015 3.066342 AGCTTCAGCATTTCCATTCATCG 59.934 43.478 0.75 0.00 45.16 3.84
1003 1020 4.710375 AGAATCAGCTTCAGCATTTCCATT 59.290 37.500 0.75 0.00 45.16 3.16
1103 1120 8.568732 TTATCCAATGTTTCTTTGTCGAAAAC 57.431 30.769 3.27 3.27 34.93 2.43
1144 1161 3.055530 AGACTTTCACAATCGATGGAGCT 60.056 43.478 6.84 0.00 0.00 4.09
1169 1186 5.576447 AATCCCGTGCTAAATGGTTTTAG 57.424 39.130 1.94 1.94 44.75 1.85
1253 1270 3.427638 CGGACTCGTATCTTCTCTTTGCA 60.428 47.826 0.00 0.00 0.00 4.08
1269 1286 2.887783 TCTCCATCAGAATAGCGGACTC 59.112 50.000 0.00 0.00 0.00 3.36
1276 1293 6.343716 ACAGCAGTATCTCCATCAGAATAG 57.656 41.667 0.00 0.00 33.62 1.73
1332 1349 5.936686 ACGTGCGTACAGTATAGTCATAT 57.063 39.130 4.09 0.00 0.00 1.78
1333 1350 6.843069 TTACGTGCGTACAGTATAGTCATA 57.157 37.500 4.09 0.00 0.00 2.15
1348 1365 1.662026 GCCTTTCCAGTTTTACGTGCG 60.662 52.381 0.00 0.00 0.00 5.34
1406 1423 5.886960 AGACTCACAATCTTTTGGCATAC 57.113 39.130 0.00 0.00 37.15 2.39
1558 1575 9.003658 ACAGGTACAATCATCTAAACTGAAAAG 57.996 33.333 0.00 0.00 0.00 2.27
1621 1638 5.243981 CACAGGACAAGTGAATGAGAAGAT 58.756 41.667 0.00 0.00 39.30 2.40
1661 1678 9.073475 GTTGGCCTGGAATAATGTATAAATGTA 57.927 33.333 3.32 0.00 0.00 2.29
1663 1680 7.233348 AGGTTGGCCTGGAATAATGTATAAATG 59.767 37.037 3.32 0.00 45.05 2.32
1675 1943 2.179427 GCTTAAAGGTTGGCCTGGAAT 58.821 47.619 3.32 0.00 46.33 3.01
1676 1944 1.627864 GCTTAAAGGTTGGCCTGGAA 58.372 50.000 3.32 0.00 46.33 3.53
1677 1945 0.251608 GGCTTAAAGGTTGGCCTGGA 60.252 55.000 3.32 0.00 46.33 3.86
1678 1946 1.595093 CGGCTTAAAGGTTGGCCTGG 61.595 60.000 3.32 0.00 46.33 4.45
1679 1947 0.893727 ACGGCTTAAAGGTTGGCCTG 60.894 55.000 3.32 0.00 46.33 4.85
1681 1949 1.584495 CACGGCTTAAAGGTTGGCC 59.416 57.895 0.00 0.00 41.02 5.36
1682 1950 1.176619 ACCACGGCTTAAAGGTTGGC 61.177 55.000 0.00 0.00 0.00 4.52
1683 1951 0.596082 CACCACGGCTTAAAGGTTGG 59.404 55.000 0.00 0.00 30.44 3.77
1684 1952 0.039527 GCACCACGGCTTAAAGGTTG 60.040 55.000 0.00 0.00 30.44 3.77
1687 1955 1.586154 CCTGCACCACGGCTTAAAGG 61.586 60.000 0.00 0.00 34.04 3.11
1688 1956 1.586154 CCCTGCACCACGGCTTAAAG 61.586 60.000 0.00 0.00 34.04 1.85
1689 1957 1.602323 CCCTGCACCACGGCTTAAA 60.602 57.895 0.00 0.00 34.04 1.52
1690 1958 2.033448 CCCTGCACCACGGCTTAA 59.967 61.111 0.00 0.00 34.04 1.85
1691 1959 4.715523 GCCCTGCACCACGGCTTA 62.716 66.667 2.80 0.00 39.70 3.09
1756 2030 9.290988 TCTTACAACTATTGAAGTTTGCCATAA 57.709 29.630 0.00 0.00 46.61 1.90
1929 2203 7.321745 GCATCTGCAAAGGTAAGTTAGTTAT 57.678 36.000 0.00 0.00 41.59 1.89
2134 2408 3.968649 ACATCACAAACAACACATGAGC 58.031 40.909 0.00 0.00 0.00 4.26
2172 2446 2.443255 AGGAACCCAGCTTCTTCTTTGA 59.557 45.455 0.00 0.00 0.00 2.69
2177 2451 0.962855 GCCAGGAACCCAGCTTCTTC 60.963 60.000 0.00 0.00 0.00 2.87
2298 2572 5.875359 CCTAACCAGTCACTCAAAGATAACC 59.125 44.000 0.00 0.00 0.00 2.85
2320 2594 0.763035 AACAAACTAGGACGGCACCT 59.237 50.000 0.00 5.59 43.32 4.00
2322 2596 3.396560 AGTTAACAAACTAGGACGGCAC 58.603 45.455 8.61 0.00 0.00 5.01
2323 2597 3.756933 AGTTAACAAACTAGGACGGCA 57.243 42.857 8.61 0.00 0.00 5.69
2324 2598 3.811497 ACAAGTTAACAAACTAGGACGGC 59.189 43.478 8.61 0.00 31.72 5.68
2365 2639 4.042809 ACCAGGACATGACCTAAATCAACA 59.957 41.667 16.55 0.00 38.32 3.33
2437 2711 6.049790 GGAGTTGATAAACTAGGACATGACC 58.950 44.000 6.05 6.05 32.22 4.02
2518 2792 2.092968 ACAGTTCAACAACCAGCAGAGA 60.093 45.455 0.00 0.00 32.22 3.10
2528 2802 5.913137 ATCAAGGTTCAACAGTTCAACAA 57.087 34.783 2.18 0.00 0.00 2.83
2529 2803 7.581213 ATTATCAAGGTTCAACAGTTCAACA 57.419 32.000 2.18 0.00 0.00 3.33
2530 2804 7.382218 CCAATTATCAAGGTTCAACAGTTCAAC 59.618 37.037 0.00 0.00 0.00 3.18
2531 2805 7.069331 ACCAATTATCAAGGTTCAACAGTTCAA 59.931 33.333 0.00 0.00 29.58 2.69
2532 2806 6.549364 ACCAATTATCAAGGTTCAACAGTTCA 59.451 34.615 0.00 0.00 29.58 3.18
2533 2807 6.981722 ACCAATTATCAAGGTTCAACAGTTC 58.018 36.000 0.00 0.00 29.58 3.01
2534 2808 6.976934 ACCAATTATCAAGGTTCAACAGTT 57.023 33.333 0.00 0.00 29.58 3.16
2535 2809 6.239289 CCAACCAATTATCAAGGTTCAACAGT 60.239 38.462 0.00 0.00 43.43 3.55
2536 2810 6.158598 CCAACCAATTATCAAGGTTCAACAG 58.841 40.000 0.00 0.00 43.43 3.16
2571 2845 5.823045 CAGCAAGGGGTTAATAAACTAGGAG 59.177 44.000 0.00 0.00 35.81 3.69
2593 2867 9.474920 AATAAACAATTATGGTTCAACACACAG 57.525 29.630 0.00 0.00 37.68 3.66
2634 2911 6.656693 CCTCACTCCAGCCCTTTATAATATTG 59.343 42.308 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.