Multiple sequence alignment - TraesCS7D01G475600

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 TraesCS7D01G475600 chr7D 100.000 3629 0 0 1 3629 587729733 587726105 0.000000e+00 6702.0
1 TraesCS7D01G475600 chr7D 89.811 1747 140 20 960 2701 587554382 587556095 0.000000e+00 2206.0
2 TraesCS7D01G475600 chr7D 85.517 870 82 20 2 849 587552323 587553170 0.000000e+00 869.0
3 TraesCS7D01G475600 chr7D 100.000 29 0 0 929 957 587554410 587554438 2.000000e-03 54.7
4 TraesCS7D01G475600 chr7D 100.000 29 0 0 929 957 587728746 587728718 2.000000e-03 54.7
5 TraesCS7D01G475600 chr7A 90.940 2362 157 27 377 2701 679388206 679390547 0.000000e+00 3123.0
6 TraesCS7D01G475600 chr7A 90.855 2362 159 27 377 2701 679376738 679379079 0.000000e+00 3112.0
7 TraesCS7D01G475600 chr7A 93.284 1772 88 11 933 2701 679525167 679526910 0.000000e+00 2584.0
8 TraesCS7D01G475600 chr7A 92.282 1218 91 1 1484 2701 679362210 679363424 0.000000e+00 1725.0
9 TraesCS7D01G475600 chr7A 87.638 1270 130 11 1392 2646 679531645 679530388 0.000000e+00 1450.0
10 TraesCS7D01G475600 chr7A 90.097 515 47 4 2701 3214 679526941 679527452 0.000000e+00 665.0
11 TraesCS7D01G475600 chr7A 86.678 608 39 19 273 852 679523810 679524403 1.420000e-178 636.0
12 TraesCS7D01G475600 chr7A 92.982 342 20 4 3290 3629 679364338 679364677 2.520000e-136 496.0
13 TraesCS7D01G475600 chr7A 92.420 343 20 5 3290 3629 679379997 679380336 5.450000e-133 484.0
14 TraesCS7D01G475600 chr7A 85.979 378 41 5 2848 3223 679390873 679391240 9.440000e-106 394.0
15 TraesCS7D01G475600 chr7A 83.461 393 41 12 2844 3223 679363758 679364139 9.650000e-91 344.0
16 TraesCS7D01G475600 chr7A 83.249 394 42 12 2844 3223 679379414 679379797 1.250000e-89 340.0
17 TraesCS7D01G475600 chr7A 82.415 381 41 9 3249 3627 679528356 679528712 3.520000e-80 309.0
18 TraesCS7D01G475600 chr7A 100.000 82 0 0 2701 2782 679379118 679379199 6.280000e-33 152.0
19 TraesCS7D01G475600 chr7A 98.780 82 1 0 2701 2782 679363463 679363544 2.920000e-31 147.0
20 TraesCS7D01G475600 chr7A 95.946 74 3 0 3220 3293 679364174 679364247 1.770000e-23 121.0
21 TraesCS7D01G475600 chr7A 95.946 74 3 0 3220 3293 679379832 679379905 1.770000e-23 121.0
22 TraesCS7D01G475600 chr7A 91.026 78 7 0 377 454 679362091 679362168 4.960000e-19 106.0
23 TraesCS7D01G475600 chr7A 90.909 77 5 2 3220 3294 679391275 679391351 6.410000e-18 102.0
24 TraesCS7D01G475600 chr7A 95.745 47 2 0 2740 2786 679390612 679390658 3.890000e-10 76.8
25 TraesCS7D01G475600 chrUn 91.786 1960 118 24 490 2423 361996740 361994798 0.000000e+00 2687.0
26 TraesCS7D01G475600 chrUn 91.739 1961 119 24 490 2423 361873502 361871558 0.000000e+00 2684.0
27 TraesCS7D01G475600 chrUn 90.888 845 52 17 971 1798 393981393 393982229 0.000000e+00 1110.0
28 TraesCS7D01G475600 chrUn 85.000 240 16 9 768 987 234008815 234008576 3.650000e-55 226.0
29 TraesCS7D01G475600 chrUn 84.018 219 13 10 768 965 354101059 354100842 1.330000e-44 191.0
30 TraesCS7D01G475600 chrUn 84.018 219 13 10 768 965 423802662 423802445 1.330000e-44 191.0
31 TraesCS7D01G475600 chrUn 84.444 90 14 0 7 96 15531392 15531481 4.990000e-14 89.8
32 TraesCS7D01G475600 chrUn 87.719 57 2 4 686 739 354101105 354101051 1.090000e-05 62.1
33 TraesCS7D01G475600 chrUn 87.719 57 2 4 686 739 423802708 423802654 1.090000e-05 62.1
34 TraesCS7D01G475600 chr7B 91.404 1745 125 13 971 2701 658879957 658881690 0.000000e+00 2368.0
35 TraesCS7D01G475600 chr7B 84.455 431 58 8 2798 3223 658624051 658624477 2.020000e-112 416.0
36 TraesCS7D01G475600 chr7B 84.223 431 59 7 2798 3223 658749216 658749642 9.380000e-111 411.0
37 TraesCS7D01G475600 chr7B 85.000 240 16 9 768 987 658621993 658622232 3.650000e-55 226.0
38 TraesCS7D01G475600 chr7B 85.000 240 16 9 768 987 658879707 658879946 3.650000e-55 226.0
39 TraesCS7D01G475600 chr7B 98.837 86 1 0 2701 2786 658749147 658749232 1.740000e-33 154.0
40 TraesCS7D01G475600 chr7B 97.674 86 2 0 2701 2786 658623982 658624067 8.120000e-32 148.0
41 TraesCS7D01G475600 chr7B 97.619 84 2 0 2701 2784 658881730 658881813 1.050000e-30 145.0
42 TraesCS7D01G475600 chr7B 91.489 47 1 2 686 729 658732477 658732523 1.090000e-05 62.1
43 TraesCS7D01G475600 chr5B 80.952 252 41 7 3 254 657394697 657394941 3.700000e-45 193.0
44 TraesCS7D01G475600 chr2B 80.469 256 42 7 2 257 767498212 767497965 4.780000e-44 189.0
45 TraesCS7D01G475600 chr4A 80.162 247 40 7 2 246 731341187 731340948 3.720000e-40 176.0
46 TraesCS7D01G475600 chr3A 79.297 256 45 7 2 257 43016198 43016445 4.820000e-39 172.0
47 TraesCS7D01G475600 chr3A 79.297 256 45 7 2 257 43639446 43639693 4.820000e-39 172.0
48 TraesCS7D01G475600 chr2D 75.591 254 52 8 2 255 449563907 449563664 2.290000e-22 117.0
49 TraesCS7D01G475600 chr2A 75.904 249 48 11 9 255 78462122 78462360 2.290000e-22 117.0
50 TraesCS7D01G475600 chr3B 80.342 117 18 4 2 117 754521729 754521841 2.320000e-12 84.2


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 TraesCS7D01G475600 chr7D 587726105 587729733 3628 True 3378.350000 6702 100.000000 1 3629 2 chr7D.!!$R1 3628
1 TraesCS7D01G475600 chr7D 587552323 587556095 3772 False 1043.233333 2206 91.776000 2 2701 3 chr7D.!!$F1 2699
2 TraesCS7D01G475600 chr7A 679530388 679531645 1257 True 1450.000000 1450 87.638000 1392 2646 1 chr7A.!!$R1 1254
3 TraesCS7D01G475600 chr7A 679523810 679528712 4902 False 1048.500000 2584 88.118500 273 3627 4 chr7A.!!$F4 3354
4 TraesCS7D01G475600 chr7A 679388206 679391351 3145 False 923.950000 3123 90.893250 377 3294 4 chr7A.!!$F3 2917
5 TraesCS7D01G475600 chr7A 679376738 679380336 3598 False 841.800000 3112 92.494000 377 3629 5 chr7A.!!$F2 3252
6 TraesCS7D01G475600 chr7A 679362091 679364677 2586 False 489.833333 1725 92.412833 377 3629 6 chr7A.!!$F1 3252
7 TraesCS7D01G475600 chrUn 361994798 361996740 1942 True 2687.000000 2687 91.786000 490 2423 1 chrUn.!!$R3 1933
8 TraesCS7D01G475600 chrUn 361871558 361873502 1944 True 2684.000000 2684 91.739000 490 2423 1 chrUn.!!$R2 1933
9 TraesCS7D01G475600 chrUn 393981393 393982229 836 False 1110.000000 1110 90.888000 971 1798 1 chrUn.!!$F2 827
10 TraesCS7D01G475600 chr7B 658879707 658881813 2106 False 913.000000 2368 91.341000 768 2784 3 chr7B.!!$F4 2016
11 TraesCS7D01G475600 chr7B 658621993 658624477 2484 False 263.333333 416 89.043000 768 3223 3 chr7B.!!$F2 2455

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
75 79 0.254178 AGGCAGGTGACTAATGCTGG 59.746 55.0 7.62 0.0 40.21 4.85 F
166 170 0.318360 GGCTAGCGTTTTTGCCGTTT 60.318 50.0 9.00 0.0 35.79 3.60 F
2088 3976 0.037232 GCAAGGCCTTCTCGTACTGT 60.037 55.0 17.29 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 3856 0.832135 TGAGAAGGTTGCCCGACTCT 60.832 55.0 0.00 0.0 38.06 3.24 R
2228 4119 0.035056 GGTGGGTATGCTGAGTTGCT 60.035 55.0 0.00 0.0 0.00 3.91 R
2932 5054 0.996583 AAAAGGGCCGGGATAAGTCA 59.003 50.0 2.18 0.0 0.00 3.41 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
46 50 1.165907 TTCTTTGACGGCTGCTGTGG 61.166 55.000 20.51 6.50 0.00 4.17
71 75 2.322355 CCAGAGGCAGGTGACTAATG 57.678 55.000 0.00 0.00 40.21 1.90
72 76 1.661341 CAGAGGCAGGTGACTAATGC 58.339 55.000 0.00 0.50 40.21 3.56
75 79 0.254178 AGGCAGGTGACTAATGCTGG 59.746 55.000 7.62 0.00 40.21 4.85
82 86 3.146066 GGTGACTAATGCTGGTGTCAAA 58.854 45.455 0.00 0.00 40.47 2.69
87 91 4.460263 ACTAATGCTGGTGTCAAACTCAA 58.540 39.130 0.00 0.00 0.00 3.02
89 93 3.996150 ATGCTGGTGTCAAACTCAAAG 57.004 42.857 0.00 0.00 0.00 2.77
90 94 2.023673 TGCTGGTGTCAAACTCAAAGG 58.976 47.619 0.00 0.00 0.00 3.11
94 98 4.672409 CTGGTGTCAAACTCAAAGGTTTC 58.328 43.478 0.00 0.00 37.32 2.78
96 100 5.502079 TGGTGTCAAACTCAAAGGTTTCTA 58.498 37.500 0.00 0.00 37.32 2.10
97 101 5.355910 TGGTGTCAAACTCAAAGGTTTCTAC 59.644 40.000 0.00 0.00 37.32 2.59
98 102 5.499047 GTGTCAAACTCAAAGGTTTCTACG 58.501 41.667 0.00 0.00 37.32 3.51
111 115 5.295152 AGGTTTCTACGGTCTTGTTTGTAG 58.705 41.667 0.00 0.00 36.49 2.74
116 120 6.592798 TCTACGGTCTTGTTTGTAGTTTTG 57.407 37.500 0.00 0.00 36.53 2.44
117 121 4.023739 ACGGTCTTGTTTGTAGTTTTGC 57.976 40.909 0.00 0.00 0.00 3.68
127 131 3.988379 TGTAGTTTTGCTTCTTGGCTG 57.012 42.857 0.00 0.00 0.00 4.85
128 132 2.622942 TGTAGTTTTGCTTCTTGGCTGG 59.377 45.455 0.00 0.00 0.00 4.85
160 164 3.001576 GCGAAGGCTAGCGTTTTTG 57.998 52.632 22.52 16.13 35.83 2.44
162 166 0.454452 CGAAGGCTAGCGTTTTTGCC 60.454 55.000 22.52 9.47 45.21 4.52
164 168 2.951458 GGCTAGCGTTTTTGCCGT 59.049 55.556 9.00 0.00 35.79 5.68
165 169 1.284715 GGCTAGCGTTTTTGCCGTT 59.715 52.632 9.00 0.00 35.79 4.44
166 170 0.318360 GGCTAGCGTTTTTGCCGTTT 60.318 50.000 9.00 0.00 35.79 3.60
167 171 0.775861 GCTAGCGTTTTTGCCGTTTG 59.224 50.000 0.00 0.00 34.65 2.93
168 172 0.775861 CTAGCGTTTTTGCCGTTTGC 59.224 50.000 0.00 0.00 41.77 3.68
169 173 0.382515 TAGCGTTTTTGCCGTTTGCT 59.617 45.000 0.00 0.00 42.00 3.91
170 174 0.869880 AGCGTTTTTGCCGTTTGCTC 60.870 50.000 0.00 0.00 42.00 4.26
171 175 1.142778 GCGTTTTTGCCGTTTGCTCA 61.143 50.000 0.00 0.00 42.00 4.26
172 176 0.845768 CGTTTTTGCCGTTTGCTCAG 59.154 50.000 0.00 0.00 42.00 3.35
173 177 1.797348 CGTTTTTGCCGTTTGCTCAGT 60.797 47.619 0.00 0.00 42.00 3.41
174 178 2.267426 GTTTTTGCCGTTTGCTCAGTT 58.733 42.857 0.00 0.00 42.00 3.16
180 184 2.881513 TGCCGTTTGCTCAGTTTTATCA 59.118 40.909 0.00 0.00 42.00 2.15
182 186 3.670627 GCCGTTTGCTCAGTTTTATCAGG 60.671 47.826 0.00 0.00 36.87 3.86
185 189 4.666655 CGTTTGCTCAGTTTTATCAGGTCG 60.667 45.833 0.00 0.00 0.00 4.79
193 197 6.802608 TCAGTTTTATCAGGTCGGTATGTAG 58.197 40.000 0.00 0.00 0.00 2.74
196 200 7.010183 CAGTTTTATCAGGTCGGTATGTAGTTG 59.990 40.741 0.00 0.00 0.00 3.16
197 201 6.778834 TTTATCAGGTCGGTATGTAGTTGA 57.221 37.500 0.00 0.00 0.00 3.18
198 202 4.650754 ATCAGGTCGGTATGTAGTTGAC 57.349 45.455 0.00 0.00 0.00 3.18
199 203 3.693807 TCAGGTCGGTATGTAGTTGACT 58.306 45.455 0.00 0.00 0.00 3.41
200 204 4.084287 TCAGGTCGGTATGTAGTTGACTT 58.916 43.478 0.00 0.00 0.00 3.01
201 205 5.255687 TCAGGTCGGTATGTAGTTGACTTA 58.744 41.667 0.00 0.00 0.00 2.24
202 206 5.889853 TCAGGTCGGTATGTAGTTGACTTAT 59.110 40.000 0.00 0.00 0.00 1.73
204 208 5.301298 AGGTCGGTATGTAGTTGACTTATCC 59.699 44.000 0.00 0.00 0.00 2.59
215 220 9.877222 TGTAGTTGACTTATCCTATGATCCTTA 57.123 33.333 0.00 0.00 32.18 2.69
438 463 2.346739 GCCACACAGCTGAGCTCT 59.653 61.111 23.35 0.00 36.40 4.09
439 464 1.302351 GCCACACAGCTGAGCTCTT 60.302 57.895 23.35 0.00 36.40 2.85
517 552 1.154169 GGTACGATGTGACGCACGA 60.154 57.895 14.80 0.91 37.14 4.35
553 588 2.508439 CACGCCGCAATACCTCGT 60.508 61.111 0.00 0.00 0.00 4.18
597 632 4.580551 GCCGGGGTACGTCGGATG 62.581 72.222 23.75 0.00 45.81 3.51
653 696 3.068691 CTCGCGAGGGGAAGTCCA 61.069 66.667 28.40 0.00 37.91 4.02
766 813 2.037871 CCCACTTGAAAACCACCCG 58.962 57.895 0.00 0.00 0.00 5.28
912 1121 6.057533 TCCGTCGACTCAATAAATACTCCTA 58.942 40.000 14.70 0.00 0.00 2.94
925 1134 9.871238 AATAAATACTCCTAATATACGGTGCTG 57.129 33.333 0.00 0.00 0.00 4.41
927 1136 3.840991 ACTCCTAATATACGGTGCTGGA 58.159 45.455 0.00 0.00 0.00 3.86
928 1137 3.827302 ACTCCTAATATACGGTGCTGGAG 59.173 47.826 0.00 0.00 43.73 3.86
1136 2998 2.701107 CATCTCAGCCATGGCATCTAG 58.299 52.381 37.18 25.73 44.88 2.43
1137 2999 1.798626 TCTCAGCCATGGCATCTAGT 58.201 50.000 37.18 14.13 44.88 2.57
1138 3000 2.962859 TCTCAGCCATGGCATCTAGTA 58.037 47.619 37.18 13.62 44.88 1.82
1211 3073 2.879026 CTCACGGAGGATACGATCTTCA 59.121 50.000 0.00 0.00 46.39 3.02
1212 3074 2.879026 TCACGGAGGATACGATCTTCAG 59.121 50.000 0.00 0.00 46.39 3.02
1254 3116 1.023513 GCGCTCTCAAATCTGCCACT 61.024 55.000 0.00 0.00 0.00 4.00
1255 3117 1.740380 GCGCTCTCAAATCTGCCACTA 60.740 52.381 0.00 0.00 0.00 2.74
1357 3221 8.139989 GCACTATTTTGAGGATATTTTGAGCAT 58.860 33.333 0.00 0.00 0.00 3.79
1398 3271 2.675844 CTGTTCGGTTGTTTCAGTGACA 59.324 45.455 0.00 0.00 0.00 3.58
1788 3670 1.219664 CACCTATTCCGCGTTCCCA 59.780 57.895 4.92 0.00 0.00 4.37
1974 3856 3.555324 TTCGGGTGCAGCCAGTCA 61.555 61.111 32.71 11.91 39.65 3.41
2058 3946 3.141488 CTCGCTACCCAGACCGCT 61.141 66.667 0.00 0.00 0.00 5.52
2088 3976 0.037232 GCAAGGCCTTCTCGTACTGT 60.037 55.000 17.29 0.00 0.00 3.55
2101 3989 0.745845 GTACTGTCTCCCGCCGACTA 60.746 60.000 0.00 0.00 32.70 2.59
2228 4119 2.615465 CCATCAGGGTGGGAGGCAA 61.615 63.158 0.00 0.00 35.55 4.52
2232 4123 3.185203 AGGGTGGGAGGCAAGCAA 61.185 61.111 0.00 0.00 0.00 3.91
2583 4474 3.143675 CACGCTTGAGGTGCTGTAT 57.856 52.632 0.00 0.00 0.00 2.29
2846 4967 8.015658 CGGTAGTTTAAGAATGGAAAAAGTCTG 58.984 37.037 0.00 0.00 0.00 3.51
2887 5009 5.105432 GGTAGTTAGAGTCGGAAATGAACCT 60.105 44.000 0.00 0.00 0.00 3.50
2910 5032 5.880054 TGAACTCGAAATCCCTGAAATTC 57.120 39.130 0.00 0.00 0.00 2.17
2930 5052 4.322080 TCGCACCCTGTCTTATCTAATG 57.678 45.455 0.00 0.00 0.00 1.90
2932 5054 3.493350 CGCACCCTGTCTTATCTAATGCT 60.493 47.826 0.00 0.00 0.00 3.79
2982 5441 5.449107 ACGCCTATACTATTGAACGTCAT 57.551 39.130 0.00 0.00 0.00 3.06
3041 5500 1.205893 GTGAGGGTCGAGCAAGAGAAT 59.794 52.381 17.59 0.00 0.00 2.40
3077 6023 0.687354 AGGACACCTTCAGCGTGAAT 59.313 50.000 0.00 0.00 35.59 2.57
3120 6076 2.932614 CGCTCACTGGAAAAGATAGGTG 59.067 50.000 0.00 0.00 0.00 4.00
3230 6227 6.358974 AATTAACCAAAAGCATAGCCAACT 57.641 33.333 0.00 0.00 0.00 3.16
3325 6435 4.462508 TGATTTCCAAACACACAAAGCA 57.537 36.364 0.00 0.00 0.00 3.91
3351 6461 9.956720 ATGCATAGATAAAAGAAAAGAAATCGG 57.043 29.630 0.00 0.00 0.00 4.18
3360 6470 7.761038 AAAGAAAAGAAATCGGGATAGTTGT 57.239 32.000 0.00 0.00 0.00 3.32
3374 6484 5.975939 GGGATAGTTGTCGTATTGTAGACAC 59.024 44.000 0.00 0.00 45.71 3.67
3375 6485 6.405065 GGGATAGTTGTCGTATTGTAGACACA 60.405 42.308 0.00 0.00 45.71 3.72
3408 6519 1.410153 GCAATTTGACATGGCTAGGGG 59.590 52.381 0.00 0.00 0.00 4.79
3427 6538 7.147915 GCTAGGGGAAAAATGTCATGTCAATAA 60.148 37.037 0.00 0.00 0.00 1.40
3428 6539 7.738437 AGGGGAAAAATGTCATGTCAATAAT 57.262 32.000 0.00 0.00 0.00 1.28
3430 6541 8.260114 AGGGGAAAAATGTCATGTCAATAATTC 58.740 33.333 0.00 0.79 0.00 2.17
3504 6616 5.540400 AAAAATGACATGGGCCATGATAG 57.460 39.130 44.42 24.26 43.81 2.08
3606 6718 8.474025 TGCCATGGTCTAAAATAATTAAGTTGG 58.526 33.333 14.67 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.893808 ACCACAGCAGCCGTCAAAG 60.894 57.895 0.00 0.00 0.00 2.77
31 32 2.591429 CACCACAGCAGCCGTCAA 60.591 61.111 0.00 0.00 0.00 3.18
33 34 4.626081 ACCACCACAGCAGCCGTC 62.626 66.667 0.00 0.00 0.00 4.79
34 35 4.935495 CACCACCACAGCAGCCGT 62.935 66.667 0.00 0.00 0.00 5.68
41 45 2.033141 CCTCTGGCACCACCACAG 59.967 66.667 0.00 0.00 46.36 3.66
57 61 0.035056 ACCAGCATTAGTCACCTGCC 60.035 55.000 0.00 0.00 36.56 4.85
59 63 2.289631 TGACACCAGCATTAGTCACCTG 60.290 50.000 0.00 0.00 36.20 4.00
67 71 4.278170 CCTTTGAGTTTGACACCAGCATTA 59.722 41.667 0.00 0.00 0.00 1.90
68 72 3.068590 CCTTTGAGTTTGACACCAGCATT 59.931 43.478 0.00 0.00 0.00 3.56
69 73 2.624838 CCTTTGAGTTTGACACCAGCAT 59.375 45.455 0.00 0.00 0.00 3.79
71 75 2.024414 ACCTTTGAGTTTGACACCAGC 58.976 47.619 0.00 0.00 0.00 4.85
72 76 4.399303 AGAAACCTTTGAGTTTGACACCAG 59.601 41.667 0.00 0.00 40.01 4.00
75 79 5.499047 CGTAGAAACCTTTGAGTTTGACAC 58.501 41.667 0.00 0.00 40.01 3.67
82 86 4.141779 ACAAGACCGTAGAAACCTTTGAGT 60.142 41.667 0.00 0.00 0.00 3.41
87 91 4.520179 ACAAACAAGACCGTAGAAACCTT 58.480 39.130 0.00 0.00 0.00 3.50
89 93 5.052481 ACTACAAACAAGACCGTAGAAACC 58.948 41.667 0.00 0.00 35.86 3.27
90 94 6.594284 AACTACAAACAAGACCGTAGAAAC 57.406 37.500 0.00 0.00 35.86 2.78
94 98 5.007332 AGCAAAACTACAAACAAGACCGTAG 59.993 40.000 0.00 0.00 37.84 3.51
96 100 3.692593 AGCAAAACTACAAACAAGACCGT 59.307 39.130 0.00 0.00 0.00 4.83
97 101 4.287238 AGCAAAACTACAAACAAGACCG 57.713 40.909 0.00 0.00 0.00 4.79
98 102 5.891451 AGAAGCAAAACTACAAACAAGACC 58.109 37.500 0.00 0.00 0.00 3.85
111 115 2.602257 AACCAGCCAAGAAGCAAAAC 57.398 45.000 0.00 0.00 34.23 2.43
134 138 1.165270 GCTAGCCTTCGCCAAAAGAA 58.835 50.000 2.29 0.00 34.57 2.52
135 139 1.019278 CGCTAGCCTTCGCCAAAAGA 61.019 55.000 9.66 0.00 34.57 2.52
137 141 0.887387 AACGCTAGCCTTCGCCAAAA 60.887 50.000 9.66 0.00 34.57 2.44
138 142 0.887387 AAACGCTAGCCTTCGCCAAA 60.887 50.000 9.66 0.00 34.57 3.28
139 143 0.887387 AAAACGCTAGCCTTCGCCAA 60.887 50.000 9.66 0.00 34.57 4.52
140 144 0.887387 AAAAACGCTAGCCTTCGCCA 60.887 50.000 9.66 0.00 34.57 5.69
141 145 0.454452 CAAAAACGCTAGCCTTCGCC 60.454 55.000 9.66 0.00 34.57 5.54
142 146 1.065572 GCAAAAACGCTAGCCTTCGC 61.066 55.000 9.66 6.06 0.00 4.70
143 147 0.454452 GGCAAAAACGCTAGCCTTCG 60.454 55.000 9.66 0.00 43.70 3.79
144 148 0.454452 CGGCAAAAACGCTAGCCTTC 60.454 55.000 9.66 0.00 44.85 3.46
145 149 1.170290 ACGGCAAAAACGCTAGCCTT 61.170 50.000 9.66 0.31 44.85 4.35
147 151 0.318360 AAACGGCAAAAACGCTAGCC 60.318 50.000 9.66 0.00 43.61 3.93
148 152 0.775861 CAAACGGCAAAAACGCTAGC 59.224 50.000 4.06 4.06 34.00 3.42
151 155 3.699671 GCAAACGGCAAAAACGCT 58.300 50.000 0.00 0.00 43.97 5.07
160 164 3.492313 CTGATAAAACTGAGCAAACGGC 58.508 45.455 0.00 0.00 45.30 5.68
162 166 4.666655 CGACCTGATAAAACTGAGCAAACG 60.667 45.833 0.00 0.00 0.00 3.60
164 168 3.751175 CCGACCTGATAAAACTGAGCAAA 59.249 43.478 0.00 0.00 0.00 3.68
165 169 3.244422 ACCGACCTGATAAAACTGAGCAA 60.244 43.478 0.00 0.00 0.00 3.91
166 170 2.301870 ACCGACCTGATAAAACTGAGCA 59.698 45.455 0.00 0.00 0.00 4.26
167 171 2.973945 ACCGACCTGATAAAACTGAGC 58.026 47.619 0.00 0.00 0.00 4.26
168 172 5.661458 ACATACCGACCTGATAAAACTGAG 58.339 41.667 0.00 0.00 0.00 3.35
169 173 5.670792 ACATACCGACCTGATAAAACTGA 57.329 39.130 0.00 0.00 0.00 3.41
170 174 6.570692 ACTACATACCGACCTGATAAAACTG 58.429 40.000 0.00 0.00 0.00 3.16
171 175 6.786967 ACTACATACCGACCTGATAAAACT 57.213 37.500 0.00 0.00 0.00 2.66
172 176 7.009907 GTCAACTACATACCGACCTGATAAAAC 59.990 40.741 0.00 0.00 0.00 2.43
173 177 7.037438 GTCAACTACATACCGACCTGATAAAA 58.963 38.462 0.00 0.00 0.00 1.52
174 178 6.379133 AGTCAACTACATACCGACCTGATAAA 59.621 38.462 0.00 0.00 0.00 1.40
180 184 5.301298 GGATAAGTCAACTACATACCGACCT 59.699 44.000 0.00 0.00 0.00 3.85
182 186 6.388435 AGGATAAGTCAACTACATACCGAC 57.612 41.667 0.00 0.00 0.00 4.79
224 229 9.967451 TTTCAATGGTAATATGTGTCTCCTTTA 57.033 29.630 0.00 0.00 0.00 1.85
225 230 8.877864 TTTCAATGGTAATATGTGTCTCCTTT 57.122 30.769 0.00 0.00 0.00 3.11
226 231 8.877864 TTTTCAATGGTAATATGTGTCTCCTT 57.122 30.769 0.00 0.00 0.00 3.36
227 232 8.877864 TTTTTCAATGGTAATATGTGTCTCCT 57.122 30.769 0.00 0.00 0.00 3.69
319 331 3.695606 TGGACTGGAGGCAGCGAC 61.696 66.667 0.00 0.00 0.00 5.19
532 567 1.488261 GAGGTATTGCGGCGTGCTAC 61.488 60.000 9.37 7.50 46.63 3.58
553 588 0.524414 TTTGCTTCTCGGTCGATCGA 59.476 50.000 21.21 21.21 37.60 3.59
635 678 3.069318 GGACTTCCCCTCGCGAGT 61.069 66.667 32.41 15.66 0.00 4.18
637 680 3.068691 CTGGACTTCCCCTCGCGA 61.069 66.667 9.26 9.26 34.29 5.87
700 747 2.158959 CGCGCCTTTGTCCGAGTAG 61.159 63.158 0.00 0.00 0.00 2.57
730 777 2.633657 CAGATAATGCCGCCGTGC 59.366 61.111 0.00 0.00 0.00 5.34
752 799 2.570284 GGCCCGGGTGGTTTTCAAG 61.570 63.158 24.63 0.00 36.04 3.02
912 1121 2.394632 TGGACTCCAGCACCGTATATT 58.605 47.619 0.00 0.00 0.00 1.28
1072 2934 1.683943 GAGCCCTGCATGCTTTCATA 58.316 50.000 20.33 0.00 39.69 2.15
1073 2935 1.381928 CGAGCCCTGCATGCTTTCAT 61.382 55.000 20.33 1.85 39.69 2.57
1074 2936 2.042259 CGAGCCCTGCATGCTTTCA 61.042 57.895 20.33 0.00 39.69 2.69
1075 2937 2.796651 CGAGCCCTGCATGCTTTC 59.203 61.111 20.33 8.13 39.69 2.62
1211 3073 1.337260 CGTGCAGAACCTTGTAGCTCT 60.337 52.381 0.00 0.00 0.00 4.09
1212 3074 1.071605 CGTGCAGAACCTTGTAGCTC 58.928 55.000 0.00 0.00 0.00 4.09
1254 3116 0.913934 TGGGCTGGGAGCAGTTGATA 60.914 55.000 0.00 0.00 44.75 2.15
1255 3117 1.792757 TTGGGCTGGGAGCAGTTGAT 61.793 55.000 0.00 0.00 44.75 2.57
1357 3221 3.559655 CAGAGGAAACACGATGACAAACA 59.440 43.478 0.00 0.00 0.00 2.83
1608 3490 2.033194 GTACTCCAACGTGCCCAGC 61.033 63.158 0.00 0.00 0.00 4.85
1776 3658 2.745884 CTGCATGGGAACGCGGAA 60.746 61.111 12.47 0.00 36.59 4.30
1863 3745 3.244345 CGTCGCCGTATTTGACAATGTAT 59.756 43.478 0.00 0.00 32.91 2.29
1974 3856 0.832135 TGAGAAGGTTGCCCGACTCT 60.832 55.000 0.00 0.00 38.06 3.24
2228 4119 0.035056 GGTGGGTATGCTGAGTTGCT 60.035 55.000 0.00 0.00 0.00 3.91
2232 4123 1.330655 CCGAGGTGGGTATGCTGAGT 61.331 60.000 0.00 0.00 0.00 3.41
2430 4321 1.000938 GAGAACACCAGTACGACGGTT 60.001 52.381 0.00 0.00 31.41 4.44
2565 4456 0.723414 CATACAGCACCTCAAGCGTG 59.277 55.000 0.00 0.00 37.01 5.34
2569 4460 2.263077 GACGTCATACAGCACCTCAAG 58.737 52.381 11.55 0.00 0.00 3.02
2571 4462 0.170339 CGACGTCATACAGCACCTCA 59.830 55.000 17.16 0.00 0.00 3.86
2600 4491 1.299648 CCAGCCTTGAATCCCACGA 59.700 57.895 0.00 0.00 0.00 4.35
2607 4498 3.072486 GCATGCGCCAGCCTTGAAT 62.072 57.895 4.18 0.00 44.33 2.57
2649 4540 7.526192 CGAACTGGAGATCCCAATAGTATCAAT 60.526 40.741 4.71 0.00 46.07 2.57
2818 4756 5.632244 TTTTCCATTCTTAAACTACCGGC 57.368 39.130 0.00 0.00 0.00 6.13
2863 4985 5.105432 AGGTTCATTTCCGACTCTAACTACC 60.105 44.000 0.00 0.00 0.00 3.18
2869 4991 5.011738 AGTTCAAGGTTCATTTCCGACTCTA 59.988 40.000 0.00 0.00 0.00 2.43
2887 5009 5.106712 CGAATTTCAGGGATTTCGAGTTCAA 60.107 40.000 0.00 0.00 0.00 2.69
2910 5032 2.802816 GCATTAGATAAGACAGGGTGCG 59.197 50.000 0.00 0.00 0.00 5.34
2930 5052 1.984288 AAGGGCCGGGATAAGTCAGC 61.984 60.000 2.18 0.00 0.00 4.26
2932 5054 0.996583 AAAAGGGCCGGGATAAGTCA 59.003 50.000 2.18 0.00 0.00 3.41
2955 5084 6.204359 ACGTTCAATAGTATAGGCGTACAAG 58.796 40.000 0.00 0.00 0.00 3.16
2982 5441 1.559682 GCTGGGAGGTCCTGTCAAATA 59.440 52.381 0.00 0.00 36.89 1.40
3041 5500 6.045955 GGTGTCCTTTTAGCAAACAAATTCA 58.954 36.000 0.00 0.00 0.00 2.57
3077 6023 2.174639 ACAAGTTTGTCCATGTGGAGGA 59.825 45.455 1.07 0.00 46.49 3.71
3100 6046 3.935828 GACACCTATCTTTTCCAGTGAGC 59.064 47.826 0.00 0.00 0.00 4.26
3179 6137 8.512138 AGTCGGGTGAAGAAATATTAGTTTTTG 58.488 33.333 0.00 0.00 0.00 2.44
3299 6409 6.867816 GCTTTGTGTGTTTGGAAATCATGATA 59.132 34.615 9.04 0.00 0.00 2.15
3311 6421 4.548494 TCTATGCATGCTTTGTGTGTTTG 58.452 39.130 20.33 0.00 0.00 2.93
3325 6435 9.956720 CCGATTTCTTTTCTTTTATCTATGCAT 57.043 29.630 3.79 3.79 0.00 3.96
3351 6461 6.558009 TGTGTCTACAATACGACAACTATCC 58.442 40.000 0.00 0.00 41.35 2.59
3360 6470 3.926821 TGCACTGTGTCTACAATACGA 57.073 42.857 9.86 0.00 36.14 3.43
3476 6587 6.382282 TCATGGCCCATGTCATTTTTATTGTA 59.618 34.615 22.70 0.00 41.98 2.41
3477 6588 5.189342 TCATGGCCCATGTCATTTTTATTGT 59.811 36.000 22.70 0.00 41.98 2.71
3486 6598 4.458256 TTTCTATCATGGCCCATGTCAT 57.542 40.909 22.70 12.69 41.98 3.06
3519 6631 4.098914 ACATGGCAAGTTTTCCTGTCTA 57.901 40.909 0.00 0.00 0.00 2.59
3606 6718 4.766375 TGGTAGTCTTTTAGGTAGCATGC 58.234 43.478 10.51 10.51 0.00 4.06


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

AutoCloner maintained by Alex Coulton.