Multiple sequence alignment - TraesCS6D01G123200

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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 TraesCS6D01G123200 chr6D 100.000 3248 0 0 1 3248 88104762 88101515 0.000000e+00 5999.0
1 TraesCS6D01G123200 chr6A 91.072 2677 144 44 114 2737 106081677 106079043 0.000000e+00 3531.0
2 TraesCS6D01G123200 chr6A 83.106 367 14 13 2922 3248 106078961 106078603 1.140000e-74 291.0
3 TraesCS6D01G123200 chr6A 91.549 71 5 1 2768 2837 106079044 106078974 2.670000e-16 97.1
4 TraesCS6D01G123200 chr6A 96.078 51 2 0 2961 3011 616825964 616825914 2.080000e-12 84.2
5 TraesCS6D01G123200 chr6B 93.229 2437 102 28 765 3182 166623466 166621074 0.000000e+00 3528.0
6 TraesCS6D01G123200 chr6B 90.625 96 9 0 22 117 359864728 359864633 9.460000e-26 128.0
7 TraesCS6D01G123200 chr4B 82.353 238 29 11 3014 3248 410811027 410811254 9.190000e-46 195.0
8 TraesCS6D01G123200 chr4B 91.489 94 7 1 24 117 423051086 423050994 9.460000e-26 128.0
9 TraesCS6D01G123200 chr4B 89.691 97 9 1 20 115 20800603 20800507 4.400000e-24 122.0
10 TraesCS6D01G123200 chr2A 94.253 87 5 0 30 116 138434519 138434605 2.030000e-27 134.0
11 TraesCS6D01G123200 chr7D 93.103 87 6 0 31 117 498229922 498229836 9.460000e-26 128.0
12 TraesCS6D01G123200 chr7D 90.411 73 3 4 220 292 234804193 234804125 3.450000e-15 93.5
13 TraesCS6D01G123200 chr5B 93.103 87 6 0 31 117 264876302 264876388 9.460000e-26 128.0
14 TraesCS6D01G123200 chr5B 89.744 78 6 2 216 292 670831419 670831495 7.420000e-17 99.0
15 TraesCS6D01G123200 chr1D 89.691 97 8 2 25 119 318382885 318382789 4.400000e-24 122.0
16 TraesCS6D01G123200 chr1B 90.323 93 9 0 23 115 211324724 211324816 4.400000e-24 122.0
17 TraesCS6D01G123200 chr1B 87.654 81 5 4 213 292 82036189 82036113 4.460000e-14 89.8
18 TraesCS6D01G123200 chr1B 86.585 82 2 1 2961 3042 373693381 373693453 7.470000e-12 82.4
19 TraesCS6D01G123200 chr4D 86.364 110 13 2 8 115 469582381 469582272 5.690000e-23 119.0
20 TraesCS6D01G123200 chr7B 96.667 60 2 0 233 292 361147176 361147117 2.060000e-17 100.0
21 TraesCS6D01G123200 chr2B 95.238 63 3 0 230 292 129661938 129662000 2.060000e-17 100.0
22 TraesCS6D01G123200 chr2B 90.541 74 2 4 219 292 146957249 146957181 3.450000e-15 93.5
23 TraesCS6D01G123200 chr3B 88.889 81 7 2 218 296 228607036 228606956 7.420000e-17 99.0
24 TraesCS6D01G123200 chr2D 91.667 72 4 2 232 302 448409279 448409209 7.420000e-17 99.0
25 TraesCS6D01G123200 chr7A 90.141 71 7 0 222 292 238816393 238816463 3.450000e-15 93.5
26 TraesCS6D01G123200 chrUn 96.078 51 2 0 2961 3011 341586027 341585977 2.080000e-12 84.2
27 TraesCS6D01G123200 chrUn 86.585 82 2 1 2961 3042 453615321 453615393 7.470000e-12 82.4
28 TraesCS6D01G123200 chr4A 96.078 51 2 0 2961 3011 714759915 714759865 2.080000e-12 84.2
29 TraesCS6D01G123200 chr1A 96.078 51 2 0 2961 3011 574280301 574280251 2.080000e-12 84.2
30 TraesCS6D01G123200 chr1A 97.778 45 1 0 2967 3011 592564354 592564310 9.660000e-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 TraesCS6D01G123200 chr6D 88101515 88104762 3247 True 5999.000000 5999 100.000000 1 3248 1 chr6D.!!$R1 3247
1 TraesCS6D01G123200 chr6A 106078603 106081677 3074 True 1306.366667 3531 88.575667 114 3248 3 chr6A.!!$R2 3134
2 TraesCS6D01G123200 chr6B 166621074 166623466 2392 True 3528.000000 3528 93.229000 765 3182 1 chr6B.!!$R1 2417

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
795 835 0.108138 GACCCATCAACCGACTCCAG 60.108 60.000 0.0 0.0 0.0 3.86 F
796 836 1.450312 CCCATCAACCGACTCCAGC 60.450 63.158 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1699 0.602905 CCTGTGTGAAGACGAACCCC 60.603 60.0 0.0 0.0 0.00 4.95 R
2718 2792 0.617413 CAGGTCAGACTTGCCCTCAT 59.383 55.0 0.0 0.0 27.85 2.90 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
39 40 5.208121 TCATTCAAAAATGATACCCCCTCC 58.792 41.667 0.00 0.00 44.94 4.30
40 41 3.290948 TCAAAAATGATACCCCCTCCG 57.709 47.619 0.00 0.00 0.00 4.63
41 42 2.578940 TCAAAAATGATACCCCCTCCGT 59.421 45.455 0.00 0.00 0.00 4.69
42 43 3.781407 TCAAAAATGATACCCCCTCCGTA 59.219 43.478 0.00 0.00 0.00 4.02
43 44 4.227754 TCAAAAATGATACCCCCTCCGTAA 59.772 41.667 0.00 0.00 0.00 3.18
44 45 4.866327 AAAATGATACCCCCTCCGTAAA 57.134 40.909 0.00 0.00 0.00 2.01
45 46 4.432980 AAATGATACCCCCTCCGTAAAG 57.567 45.455 0.00 0.00 0.00 1.85
46 47 2.852714 TGATACCCCCTCCGTAAAGA 57.147 50.000 0.00 0.00 0.00 2.52
47 48 3.119009 TGATACCCCCTCCGTAAAGAA 57.881 47.619 0.00 0.00 0.00 2.52
48 49 3.452878 TGATACCCCCTCCGTAAAGAAA 58.547 45.455 0.00 0.00 0.00 2.52
49 50 4.042174 TGATACCCCCTCCGTAAAGAAAT 58.958 43.478 0.00 0.00 0.00 2.17
50 51 5.218179 TGATACCCCCTCCGTAAAGAAATA 58.782 41.667 0.00 0.00 0.00 1.40
51 52 5.847817 TGATACCCCCTCCGTAAAGAAATAT 59.152 40.000 0.00 0.00 0.00 1.28
52 53 7.018150 TGATACCCCCTCCGTAAAGAAATATA 58.982 38.462 0.00 0.00 0.00 0.86
53 54 7.513436 TGATACCCCCTCCGTAAAGAAATATAA 59.487 37.037 0.00 0.00 0.00 0.98
54 55 6.183810 ACCCCCTCCGTAAAGAAATATAAG 57.816 41.667 0.00 0.00 0.00 1.73
55 56 5.907079 ACCCCCTCCGTAAAGAAATATAAGA 59.093 40.000 0.00 0.00 0.00 2.10
56 57 6.042897 ACCCCCTCCGTAAAGAAATATAAGAG 59.957 42.308 0.00 0.00 0.00 2.85
57 58 5.932883 CCCCTCCGTAAAGAAATATAAGAGC 59.067 44.000 0.00 0.00 0.00 4.09
58 59 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
59 60 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
60 61 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
61 62 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
62 63 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
63 64 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
64 65 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
69 70 9.654663 AAGAAATATAAGAGCGTTTAGAACACT 57.345 29.630 0.00 0.00 0.00 3.55
76 77 7.870588 AAGAGCGTTTAGAACACTACTTTAG 57.129 36.000 0.00 0.00 0.00 1.85
77 78 6.979465 AGAGCGTTTAGAACACTACTTTAGT 58.021 36.000 0.00 0.00 40.28 2.24
91 92 7.948034 ACTACTTTAGTGATCTAAGCACTCT 57.052 36.000 0.48 0.00 44.85 3.24
92 93 8.356000 ACTACTTTAGTGATCTAAGCACTCTT 57.644 34.615 0.48 0.00 44.85 2.85
93 94 9.463902 ACTACTTTAGTGATCTAAGCACTCTTA 57.536 33.333 0.48 0.00 44.85 2.10
159 160 8.752005 ACATGGCAAGTACTATTTCAATACAT 57.248 30.769 0.00 0.00 0.00 2.29
160 161 8.623903 ACATGGCAAGTACTATTTCAATACATG 58.376 33.333 0.00 0.00 36.48 3.21
161 162 7.566760 TGGCAAGTACTATTTCAATACATGG 57.433 36.000 0.00 0.00 0.00 3.66
166 167 9.289303 CAAGTACTATTTCAATACATGGCAAAC 57.711 33.333 0.00 0.00 0.00 2.93
168 169 9.189156 AGTACTATTTCAATACATGGCAAACAT 57.811 29.630 0.00 0.00 41.57 2.71
169 170 9.801873 GTACTATTTCAATACATGGCAAACATT 57.198 29.630 0.00 0.00 37.84 2.71
246 247 8.866970 ATAGTACTAGTAAATGCTACTCCCTC 57.133 38.462 8.85 0.00 0.00 4.30
247 248 6.069994 AGTACTAGTAAATGCTACTCCCTCC 58.930 44.000 3.61 0.00 0.00 4.30
248 249 3.890147 ACTAGTAAATGCTACTCCCTCCG 59.110 47.826 0.00 0.00 0.00 4.63
249 250 2.748388 AGTAAATGCTACTCCCTCCGT 58.252 47.619 0.00 0.00 0.00 4.69
250 251 3.105283 AGTAAATGCTACTCCCTCCGTT 58.895 45.455 0.00 0.00 0.00 4.44
251 252 2.693267 AAATGCTACTCCCTCCGTTC 57.307 50.000 0.00 0.00 0.00 3.95
254 255 0.543410 TGCTACTCCCTCCGTTCCAA 60.543 55.000 0.00 0.00 0.00 3.53
255 256 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
257 258 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
258 259 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
259 260 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
260 261 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
262 263 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
264 265 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
265 266 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
267 268 6.346096 CCTCCGTTCCAAAATAGATGACTAA 58.654 40.000 0.00 0.00 32.04 2.24
269 270 7.201617 CCTCCGTTCCAAAATAGATGACTAAAC 60.202 40.741 0.00 0.00 32.04 2.01
270 271 7.391620 TCCGTTCCAAAATAGATGACTAAACT 58.608 34.615 0.00 0.00 32.04 2.66
271 272 7.881232 TCCGTTCCAAAATAGATGACTAAACTT 59.119 33.333 0.00 0.00 32.04 2.66
272 273 8.512138 CCGTTCCAAAATAGATGACTAAACTTT 58.488 33.333 0.00 0.00 32.04 2.66
404 406 2.346847 CACTAAGACATGTTGAGCGCTC 59.653 50.000 30.42 30.42 0.00 5.03
411 413 2.807895 GTTGAGCGCTCGCCGTTA 60.808 61.111 30.75 10.94 43.17 3.18
412 414 2.807895 TTGAGCGCTCGCCGTTAC 60.808 61.111 30.75 7.24 43.17 2.50
422 424 2.408704 GCTCGCCGTTACAGCAATATAG 59.591 50.000 0.00 0.00 33.06 1.31
425 427 2.729882 CGCCGTTACAGCAATATAGGTC 59.270 50.000 0.00 0.00 0.00 3.85
435 437 4.214119 CAGCAATATAGGTCGTTGGATTGG 59.786 45.833 0.00 0.00 0.00 3.16
444 446 1.543802 TCGTTGGATTGGCATGGTTTC 59.456 47.619 0.00 0.00 0.00 2.78
446 448 2.094078 CGTTGGATTGGCATGGTTTCAT 60.094 45.455 0.00 0.00 0.00 2.57
661 691 8.793592 ACCAGAGAAGAAATTAAACCACATAAC 58.206 33.333 0.00 0.00 0.00 1.89
684 714 6.637657 ACGACCCTACAATACTAAGGAAAAG 58.362 40.000 0.00 0.00 31.64 2.27
689 719 3.014623 ACAATACTAAGGAAAAGCCGCC 58.985 45.455 0.00 0.00 43.43 6.13
704 734 0.384106 CCGCCGCAAAAACAAAATGC 60.384 50.000 0.00 0.00 36.74 3.56
712 742 5.107875 CCGCAAAAACAAAATGCTAAGAGAC 60.108 40.000 0.00 0.00 37.92 3.36
731 761 5.186797 AGAGACCCACAGAAAACTCATCTAG 59.813 44.000 0.00 0.00 0.00 2.43
739 769 6.815641 CACAGAAAACTCATCTAGTACATGCT 59.184 38.462 0.00 0.00 37.50 3.79
740 770 6.815641 ACAGAAAACTCATCTAGTACATGCTG 59.184 38.462 0.00 0.00 37.50 4.41
743 773 7.547370 AGAAAACTCATCTAGTACATGCTGAAC 59.453 37.037 0.00 0.00 37.50 3.18
744 774 4.926244 ACTCATCTAGTACATGCTGAACG 58.074 43.478 0.00 0.00 36.36 3.95
745 775 4.399618 ACTCATCTAGTACATGCTGAACGT 59.600 41.667 0.00 0.00 36.36 3.99
746 776 5.105716 ACTCATCTAGTACATGCTGAACGTT 60.106 40.000 0.00 0.00 36.36 3.99
747 777 5.340803 TCATCTAGTACATGCTGAACGTTC 58.659 41.667 21.42 21.42 0.00 3.95
748 778 5.125578 TCATCTAGTACATGCTGAACGTTCT 59.874 40.000 27.32 10.02 0.00 3.01
749 779 5.386958 TCTAGTACATGCTGAACGTTCTT 57.613 39.130 27.32 8.55 0.00 2.52
755 795 0.746204 TGCTGAACGTTCTTGTGCCA 60.746 50.000 27.32 12.76 0.00 4.92
790 830 2.818274 GCCGACCCATCAACCGAC 60.818 66.667 0.00 0.00 0.00 4.79
791 831 2.978824 CCGACCCATCAACCGACT 59.021 61.111 0.00 0.00 0.00 4.18
792 832 1.153628 CCGACCCATCAACCGACTC 60.154 63.158 0.00 0.00 0.00 3.36
795 835 0.108138 GACCCATCAACCGACTCCAG 60.108 60.000 0.00 0.00 0.00 3.86
796 836 1.450312 CCCATCAACCGACTCCAGC 60.450 63.158 0.00 0.00 0.00 4.85
820 874 2.579684 ATCGGAGAAAGAGCCCGTGC 62.580 60.000 0.00 0.00 43.58 5.34
827 881 2.185310 AAAGAGCCCGTGCGGAATCT 62.185 55.000 12.71 11.30 44.33 2.40
829 883 4.162690 AGCCCGTGCGGAATCTCC 62.163 66.667 12.71 0.00 44.33 3.71
1092 1162 2.501128 GACCTGCAGCGCCTCATA 59.499 61.111 8.66 0.00 0.00 2.15
1650 1720 1.557443 GGTTCGTCTTCACACAGGCG 61.557 60.000 0.00 0.00 43.52 5.52
1971 2041 1.738099 CGACTTCTTCCTGGTGCCG 60.738 63.158 0.00 0.00 0.00 5.69
2031 2101 1.240256 TTCCGATTGAAAACCGTGGG 58.760 50.000 0.00 0.00 23.02 4.61
2160 2230 2.100631 GGATGTCAAGGCCGACGTG 61.101 63.158 9.92 1.70 38.84 4.49
2571 2644 6.440647 TCAGATGGTAACCACTGAGATAGTTT 59.559 38.462 0.00 0.00 37.04 2.66
2582 2655 5.691305 CACTGAGATAGTTTGCTGAGATAGC 59.309 44.000 0.00 0.00 45.03 2.97
2608 2682 1.342975 ACACAAATAGGGGGATTGGGC 60.343 52.381 0.00 0.00 30.58 5.36
2706 2780 9.679661 TTTCTAAAAATAGTCTATGTGCCATCA 57.320 29.630 0.00 0.00 0.00 3.07
2707 2781 9.679661 TTCTAAAAATAGTCTATGTGCCATCAA 57.320 29.630 0.00 0.00 0.00 2.57
2718 2792 1.079956 GCCATCAAACAATGCGCCA 60.080 52.632 4.18 0.00 0.00 5.69
2719 2793 0.460635 GCCATCAAACAATGCGCCAT 60.461 50.000 4.18 0.00 0.00 4.40
2778 2852 4.850386 ACCACTTATCCACTTTTAGGACCT 59.150 41.667 0.00 0.00 38.13 3.85
2807 2881 1.415672 ATGACCCAACCGACACACCT 61.416 55.000 0.00 0.00 0.00 4.00
2818 2892 2.618053 CGACACACCTGGAATACCTTC 58.382 52.381 0.00 0.00 37.04 3.46
2840 2922 5.224888 TCAGACGCATTTTACTCGTTTAGT 58.775 37.500 0.00 0.00 42.62 2.24
2841 2923 5.693104 TCAGACGCATTTTACTCGTTTAGTT 59.307 36.000 0.00 0.00 39.80 2.24
2894 2976 8.567285 TGATCTTTTCTACTCAAATTTCCTCC 57.433 34.615 0.00 0.00 0.00 4.30
2897 2979 6.426937 TCTTTTCTACTCAAATTTCCTCCACG 59.573 38.462 0.00 0.00 0.00 4.94
2952 3036 0.850100 TTGGTTTGCTCAAGGAGGGA 59.150 50.000 0.00 0.00 0.00 4.20
3052 3137 8.974060 AAAATCAGAGGACTACAACAAAAGTA 57.026 30.769 0.00 0.00 0.00 2.24
3066 3151 4.389374 ACAAAAGTAGTGTGGATGGAGTG 58.611 43.478 0.00 0.00 0.00 3.51
3067 3152 2.770164 AAGTAGTGTGGATGGAGTGC 57.230 50.000 0.00 0.00 0.00 4.40
3068 3153 0.532573 AGTAGTGTGGATGGAGTGCG 59.467 55.000 0.00 0.00 0.00 5.34
3094 3179 6.681777 CCTTAGACCATTTTGAGTCCTTTTG 58.318 40.000 0.00 0.00 33.29 2.44
3116 3218 3.840666 GGGGCTCTTATAGATGTGGATCA 59.159 47.826 0.00 0.00 0.00 2.92
3147 3249 8.694975 GAATTTTTCCAGAATCTCTTTTAGGC 57.305 34.615 0.00 0.00 0.00 3.93
3195 3319 4.446889 GGATCTATCTTTGGCCTCAATGGT 60.447 45.833 3.32 0.00 38.35 3.55
3204 3328 5.404466 TTGGCCTCAATGGTAATTCTTTG 57.596 39.130 3.32 0.00 38.35 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.451206 AGGGGGTATCATTTTTGAATGAATATT 57.549 29.630 5.98 0.00 41.90 1.28
12 13 9.093458 GAGGGGGTATCATTTTTGAATGAATAT 57.907 33.333 5.98 0.00 41.90 1.28
13 14 7.508977 GGAGGGGGTATCATTTTTGAATGAATA 59.491 37.037 5.98 0.00 41.90 1.75
14 15 6.327365 GGAGGGGGTATCATTTTTGAATGAAT 59.673 38.462 5.98 0.00 41.90 2.57
15 16 5.660864 GGAGGGGGTATCATTTTTGAATGAA 59.339 40.000 5.98 0.00 41.90 2.57
16 17 5.208121 GGAGGGGGTATCATTTTTGAATGA 58.792 41.667 4.50 4.50 42.68 2.57
17 18 4.037923 CGGAGGGGGTATCATTTTTGAATG 59.962 45.833 0.00 0.00 0.00 2.67
18 19 4.215109 CGGAGGGGGTATCATTTTTGAAT 58.785 43.478 0.00 0.00 0.00 2.57
19 20 3.010808 ACGGAGGGGGTATCATTTTTGAA 59.989 43.478 0.00 0.00 0.00 2.69
20 21 2.578940 ACGGAGGGGGTATCATTTTTGA 59.421 45.455 0.00 0.00 0.00 2.69
21 22 3.012934 ACGGAGGGGGTATCATTTTTG 57.987 47.619 0.00 0.00 0.00 2.44
22 23 4.866327 TTACGGAGGGGGTATCATTTTT 57.134 40.909 0.00 0.00 0.00 1.94
23 24 4.475747 TCTTTACGGAGGGGGTATCATTTT 59.524 41.667 0.00 0.00 0.00 1.82
24 25 4.042174 TCTTTACGGAGGGGGTATCATTT 58.958 43.478 0.00 0.00 0.00 2.32
25 26 3.660959 TCTTTACGGAGGGGGTATCATT 58.339 45.455 0.00 0.00 0.00 2.57
26 27 3.339713 TCTTTACGGAGGGGGTATCAT 57.660 47.619 0.00 0.00 0.00 2.45
27 28 2.852714 TCTTTACGGAGGGGGTATCA 57.147 50.000 0.00 0.00 0.00 2.15
28 29 4.701651 ATTTCTTTACGGAGGGGGTATC 57.298 45.455 0.00 0.00 0.00 2.24
29 30 7.736234 TCTTATATTTCTTTACGGAGGGGGTAT 59.264 37.037 0.00 0.00 0.00 2.73
30 31 7.075148 TCTTATATTTCTTTACGGAGGGGGTA 58.925 38.462 0.00 0.00 0.00 3.69
31 32 5.907079 TCTTATATTTCTTTACGGAGGGGGT 59.093 40.000 0.00 0.00 0.00 4.95
32 33 6.429521 TCTTATATTTCTTTACGGAGGGGG 57.570 41.667 0.00 0.00 0.00 5.40
33 34 5.932883 GCTCTTATATTTCTTTACGGAGGGG 59.067 44.000 0.00 0.00 0.00 4.79
34 35 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
35 36 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
36 37 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
37 38 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
38 39 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
66 67 8.247562 AAGAGTGCTTAGATCACTAAAGTAGTG 58.752 37.037 8.79 8.79 44.09 2.74
67 68 7.948034 AGAGTGCTTAGATCACTAAAGTAGT 57.052 36.000 0.00 0.00 44.09 2.73
132 133 9.845740 TGTATTGAAATAGTACTTGCCATGTAT 57.154 29.630 0.00 0.00 0.00 2.29
133 134 9.845740 ATGTATTGAAATAGTACTTGCCATGTA 57.154 29.630 0.00 0.00 0.00 2.29
134 135 8.623903 CATGTATTGAAATAGTACTTGCCATGT 58.376 33.333 0.00 0.00 0.00 3.21
224 225 5.048852 CGGAGGGAGTAGCATTTACTAGTAC 60.049 48.000 0.91 0.00 0.00 2.73
229 230 2.748388 ACGGAGGGAGTAGCATTTACT 58.252 47.619 0.00 0.00 0.00 2.24
238 239 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
239 240 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
240 241 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
241 242 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
242 243 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
243 244 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
244 245 7.549488 AGTTTAGTCATCTATTTTGGAACGGAG 59.451 37.037 0.00 0.00 0.00 4.63
245 246 7.391620 AGTTTAGTCATCTATTTTGGAACGGA 58.608 34.615 0.00 0.00 0.00 4.69
246 247 7.611213 AGTTTAGTCATCTATTTTGGAACGG 57.389 36.000 0.00 0.00 0.00 4.44
347 348 7.210718 TCATACCAAATATCGACGACTACAT 57.789 36.000 0.00 0.00 0.00 2.29
381 383 2.092838 GCGCTCAACATGTCTTAGTGTC 59.907 50.000 0.00 0.00 0.00 3.67
383 385 2.341257 AGCGCTCAACATGTCTTAGTG 58.659 47.619 2.64 5.08 0.00 2.74
384 386 2.611518 GAGCGCTCAACATGTCTTAGT 58.388 47.619 31.91 0.00 0.00 2.24
389 391 2.397252 GCGAGCGCTCAACATGTC 59.603 61.111 34.69 8.60 38.26 3.06
404 406 2.729882 GACCTATATTGCTGTAACGGCG 59.270 50.000 4.80 4.80 38.82 6.46
411 413 4.689612 ATCCAACGACCTATATTGCTGT 57.310 40.909 0.00 0.00 0.00 4.40
412 414 4.214119 CCAATCCAACGACCTATATTGCTG 59.786 45.833 0.00 0.00 0.00 4.41
422 424 0.965363 ACCATGCCAATCCAACGACC 60.965 55.000 0.00 0.00 0.00 4.79
425 427 1.271934 TGAAACCATGCCAATCCAACG 59.728 47.619 0.00 0.00 0.00 4.10
435 437 1.031571 TCTCGGCCATGAAACCATGC 61.032 55.000 2.24 0.00 39.96 4.06
620 650 1.063266 TCTGGTTTTTCAGCCCTGGTT 60.063 47.619 0.00 0.00 34.91 3.67
621 651 0.555769 TCTGGTTTTTCAGCCCTGGT 59.444 50.000 0.00 0.00 34.91 4.00
622 652 1.202927 TCTCTGGTTTTTCAGCCCTGG 60.203 52.381 0.00 0.00 34.91 4.45
623 653 2.276732 TCTCTGGTTTTTCAGCCCTG 57.723 50.000 0.00 0.00 34.91 4.45
624 654 2.443255 TCTTCTCTGGTTTTTCAGCCCT 59.557 45.455 0.00 0.00 34.91 5.19
625 655 2.863809 TCTTCTCTGGTTTTTCAGCCC 58.136 47.619 0.00 0.00 34.91 5.19
635 665 8.793592 GTTATGTGGTTTAATTTCTTCTCTGGT 58.206 33.333 0.00 0.00 0.00 4.00
661 691 5.522824 GCTTTTCCTTAGTATTGTAGGGTCG 59.477 44.000 0.00 0.00 0.00 4.79
684 714 0.384106 CATTTTGTTTTTGCGGCGGC 60.384 50.000 9.78 9.68 40.52 6.53
689 719 5.107875 GGTCTCTTAGCATTTTGTTTTTGCG 60.108 40.000 0.00 0.00 41.22 4.85
704 734 5.215252 TGAGTTTTCTGTGGGTCTCTTAG 57.785 43.478 0.00 0.00 0.00 2.18
712 742 6.037786 TGTACTAGATGAGTTTTCTGTGGG 57.962 41.667 0.00 0.00 39.81 4.61
731 761 3.799035 CACAAGAACGTTCAGCATGTAC 58.201 45.455 28.78 0.18 37.40 2.90
739 769 1.444119 GGCTGGCACAAGAACGTTCA 61.444 55.000 28.78 7.22 38.70 3.18
740 770 1.282875 GGCTGGCACAAGAACGTTC 59.717 57.895 20.71 20.71 38.70 3.95
743 773 2.639286 GTGGCTGGCACAAGAACG 59.361 61.111 27.01 0.00 38.70 3.95
744 774 2.639286 CGTGGCTGGCACAAGAAC 59.361 61.111 29.98 6.20 38.70 3.01
745 775 3.286751 GCGTGGCTGGCACAAGAA 61.287 61.111 29.98 0.00 38.70 2.52
746 776 3.848301 ATGCGTGGCTGGCACAAGA 62.848 57.895 29.98 15.49 44.23 3.02
747 777 3.367743 ATGCGTGGCTGGCACAAG 61.368 61.111 29.98 17.76 44.23 3.16
748 778 3.672447 CATGCGTGGCTGGCACAA 61.672 61.111 29.98 19.53 44.23 3.33
749 779 4.953010 ACATGCGTGGCTGGCACA 62.953 61.111 29.98 15.07 44.23 4.57
755 795 2.563798 CCCAACAACATGCGTGGCT 61.564 57.895 11.36 0.00 0.00 4.75
791 831 1.208052 CTTTCTCCGATTCTGGCTGGA 59.792 52.381 0.00 0.00 0.00 3.86
792 832 1.208052 TCTTTCTCCGATTCTGGCTGG 59.792 52.381 0.00 0.00 0.00 4.85
795 835 1.294857 GCTCTTTCTCCGATTCTGGC 58.705 55.000 0.00 0.00 0.00 4.85
796 836 1.474143 GGGCTCTTTCTCCGATTCTGG 60.474 57.143 0.00 0.00 0.00 3.86
820 874 2.202932 CGGCCACAGGAGATTCCG 60.203 66.667 2.24 0.00 42.75 4.30
829 883 4.431131 AAGATGGGCCGGCCACAG 62.431 66.667 44.46 0.00 37.98 3.66
973 1042 1.028868 GCTGCGGATGCTTTCCTCTT 61.029 55.000 0.00 0.00 42.99 2.85
975 1044 2.476320 GGCTGCGGATGCTTTCCTC 61.476 63.158 0.00 0.00 42.99 3.71
977 1046 3.880846 CGGCTGCGGATGCTTTCC 61.881 66.667 0.00 0.00 43.34 3.13
978 1047 4.543084 GCGGCTGCGGATGCTTTC 62.543 66.667 11.68 0.00 43.34 2.62
1629 1699 0.602905 CCTGTGTGAAGACGAACCCC 60.603 60.000 0.00 0.00 0.00 4.95
1650 1720 3.787001 CTGGCCTTCCTCCCGACC 61.787 72.222 3.32 0.00 0.00 4.79
1896 1966 1.094073 CCTCCTTGCGCATCTTGGAG 61.094 60.000 27.57 27.57 42.72 3.86
2031 2101 2.174319 GTTCGCCGGCAGAGGAATC 61.174 63.158 28.98 11.90 0.00 2.52
2484 2554 6.239261 CCCAACATATAGGCAATGCAAATGTA 60.239 38.462 7.79 0.00 0.00 2.29
2501 2571 4.186077 TGTTTGTCCCTTTCCCAACATA 57.814 40.909 0.00 0.00 0.00 2.29
2582 2655 2.883026 TCCCCCTATTTGTGTTGGTTG 58.117 47.619 0.00 0.00 0.00 3.77
2608 2682 7.037438 CCATACAAGAAATTGATCAACCCTTG 58.963 38.462 27.29 27.29 36.54 3.61
2706 2780 1.892338 CCCTCATGGCGCATTGTTT 59.108 52.632 10.83 0.00 0.00 2.83
2707 2781 3.607163 CCCTCATGGCGCATTGTT 58.393 55.556 10.83 0.00 0.00 2.83
2718 2792 0.617413 CAGGTCAGACTTGCCCTCAT 59.383 55.000 0.00 0.00 27.85 2.90
2719 2793 1.483595 CCAGGTCAGACTTGCCCTCA 61.484 60.000 7.17 0.00 27.85 3.86
2731 2805 1.132977 TCACAAGTCCTACCCAGGTCA 60.133 52.381 0.00 0.00 43.18 4.02
2749 2823 6.884295 CCTAAAAGTGGATAAGTGGTTCATCA 59.116 38.462 0.00 0.00 0.00 3.07
2778 2852 4.581824 GTCGGTTGGGTCATACTAGTATCA 59.418 45.833 12.62 5.27 0.00 2.15
2807 2881 3.627395 AATGCGTCTGAAGGTATTCCA 57.373 42.857 0.00 0.00 34.28 3.53
2818 2892 5.511088 ACTAAACGAGTAAAATGCGTCTG 57.489 39.130 0.00 0.00 36.27 3.51
2849 2931 7.684529 AGATCAGTTCAACATCCTAACTTTCT 58.315 34.615 0.00 0.00 31.21 2.52
2850 2932 7.913674 AGATCAGTTCAACATCCTAACTTTC 57.086 36.000 0.00 0.00 31.21 2.62
2858 2940 7.604164 TGAGTAGAAAAGATCAGTTCAACATCC 59.396 37.037 10.10 0.00 0.00 3.51
2860 2942 8.908786 TTGAGTAGAAAAGATCAGTTCAACAT 57.091 30.769 10.10 0.00 0.00 2.71
2894 2976 4.625742 CCACTTGTTCTACTTGGATACGTG 59.374 45.833 0.00 0.00 42.51 4.49
2897 2979 5.411669 CCAACCACTTGTTCTACTTGGATAC 59.588 44.000 0.00 0.00 34.00 2.24
3052 3137 2.665000 CCGCACTCCATCCACACT 59.335 61.111 0.00 0.00 0.00 3.55
3066 3151 1.401905 CTCAAAATGGTCTAAGGCCGC 59.598 52.381 0.00 0.00 0.00 6.53
3067 3152 2.678336 GACTCAAAATGGTCTAAGGCCG 59.322 50.000 0.00 0.00 0.00 6.13
3068 3153 3.017442 GGACTCAAAATGGTCTAAGGCC 58.983 50.000 0.00 0.00 33.46 5.19
3094 3179 3.840666 TGATCCACATCTATAAGAGCCCC 59.159 47.826 0.00 0.00 0.00 5.80
3147 3249 3.259374 ACATCACACCTTCACTCTACCTG 59.741 47.826 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.