Multiple sequence alignment - TraesCS3D01G223900

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 TraesCS3D01G223900 chr3D 100.000 3069 0 0 2911 5979 305454745 305451677 0.000000e+00 5668.0
1 TraesCS3D01G223900 chr3D 100.000 2643 0 0 1 2643 305457655 305455013 0.000000e+00 4881.0
2 TraesCS3D01G223900 chr3B 94.626 2419 87 17 260 2643 416275138 416277548 0.000000e+00 3707.0
3 TraesCS3D01G223900 chr3B 96.144 1141 24 5 4109 5239 416279123 416280253 0.000000e+00 1845.0
4 TraesCS3D01G223900 chr3B 97.146 876 20 3 3239 4110 416278168 416279042 0.000000e+00 1474.0
5 TraesCS3D01G223900 chr3B 91.704 675 42 6 5309 5979 416280282 416280946 0.000000e+00 924.0
6 TraesCS3D01G223900 chr3B 96.538 260 9 0 1 260 416274643 416274902 1.190000e-116 431.0
7 TraesCS3D01G223900 chr3B 82.133 347 42 11 1668 2001 189709314 189709653 4.560000e-71 279.0
8 TraesCS3D01G223900 chr3B 96.000 150 6 0 2978 3127 416278039 416278188 1.660000e-60 244.0
9 TraesCS3D01G223900 chr3B 100.000 81 0 0 2911 2991 416277926 416278006 3.730000e-32 150.0
10 TraesCS3D01G223900 chr3A 96.558 2063 58 11 3184 5239 423489321 423487265 0.000000e+00 3404.0
11 TraesCS3D01G223900 chr3A 91.439 1320 59 9 285 1576 423491923 423490630 0.000000e+00 1762.0
12 TraesCS3D01G223900 chr3A 94.630 689 32 4 5293 5979 423487263 423486578 0.000000e+00 1062.0
13 TraesCS3D01G223900 chr3A 83.358 673 75 15 1764 2407 423490615 423489951 6.680000e-164 588.0
14 TraesCS3D01G223900 chr3A 97.692 260 6 0 1 260 423492444 423492185 1.180000e-121 448.0
15 TraesCS3D01G223900 chr3A 94.186 172 6 1 2476 2643 423489931 423489760 5.940000e-65 259.0
16 TraesCS3D01G223900 chr3A 95.139 144 7 0 3033 3176 423489628 423489485 1.680000e-55 228.0
17 TraesCS3D01G223900 chr3A 94.545 55 1 1 5237 5291 584446826 584446774 3.840000e-12 84.2
18 TraesCS3D01G223900 chr7A 79.564 367 49 13 1652 2001 37188116 37188473 7.740000e-59 239.0
19 TraesCS3D01G223900 chr2A 79.292 367 50 14 1652 2001 70447577 70447934 3.600000e-57 233.0
20 TraesCS3D01G223900 chr7D 94.545 55 3 0 5223 5277 169823470 169823416 1.070000e-12 86.1
21 TraesCS3D01G223900 chr4A 93.103 58 2 2 5237 5292 266960519 266960576 3.840000e-12 84.2
22 TraesCS3D01G223900 chr2D 94.444 54 3 0 5238 5291 474500934 474500881 3.840000e-12 84.2
23 TraesCS3D01G223900 chr2D 91.667 60 2 1 5238 5294 629605559 629605500 4.970000e-11 80.5
24 TraesCS3D01G223900 chr5D 91.667 60 2 1 5235 5291 549645438 549645497 4.970000e-11 80.5
25 TraesCS3D01G223900 chr5D 86.301 73 3 6 5208 5277 545227759 545227827 8.310000e-09 73.1
26 TraesCS3D01G223900 chr7B 90.164 61 3 3 5228 5288 72767257 72767314 6.430000e-10 76.8
27 TraesCS3D01G223900 chr4B 85.915 71 6 4 5209 5277 398249920 398249988 8.310000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G223900 chr3D 305451677 305457655 5978 True 5274.500000 5668 100.000000 1 5979 2 chr3D.!!$R1 5978
1 TraesCS3D01G223900 chr3B 416274643 416280946 6303 False 1253.571429 3707 96.022571 1 5979 7 chr3B.!!$F2 5978
2 TraesCS3D01G223900 chr3A 423486578 423492444 5866 True 1107.285714 3404 93.286000 1 5979 7 chr3A.!!$R2 5978

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
282 521 0.324943 TCGAGAGCTTGGGGGAAAAG 59.675 55.000 0.0 0.0 0.00 2.27 F
1236 1483 0.820871 GTGTTGGCAAAGGACACCAA 59.179 50.000 0.0 0.0 41.08 3.67 F
1341 1594 2.060383 TCCACAGCCTCCATCTCCG 61.060 63.158 0.0 0.0 0.00 4.63 F
3235 3940 1.006922 GCAGCAGGTTTGAAGTGGC 60.007 57.895 0.0 0.0 0.00 5.01 F
4187 4979 0.175760 GCAGCGGACAGTTCCAGATA 59.824 55.000 0.0 0.0 43.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 1879 0.741221 GGACTGATCAACACGGAGCC 60.741 60.000 0.0 0.0 0.0 4.70 R
3219 3924 0.825010 CCTGCCACTTCAAACCTGCT 60.825 55.000 0.0 0.0 0.0 4.24 R
3328 4033 6.865834 AAATTAGCACATCATTTAACCCCA 57.134 33.333 0.0 0.0 0.0 4.96 R
4195 4987 0.240145 GCCGCCTTTTTCCAGTGTAC 59.760 55.000 0.0 0.0 0.0 2.90 R
5525 6346 0.040067 GTTCCTTCTGCCAAAGTGCG 60.040 55.000 0.0 0.0 0.0 5.34 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
177 178 9.374960 CTATAGATTAAACGTACGGACAACTAC 57.625 37.037 21.06 4.09 0.00 2.73
196 197 3.861276 ACGTCTATCATTGAACACGGA 57.139 42.857 15.56 0.00 0.00 4.69
260 261 4.580580 CCATCTGGGTAAACTGGCTAAATC 59.419 45.833 0.00 0.00 0.00 2.17
262 263 3.589735 TCTGGGTAAACTGGCTAAATCCA 59.410 43.478 0.00 0.00 34.42 3.41
263 264 4.229582 TCTGGGTAAACTGGCTAAATCCAT 59.770 41.667 0.00 0.00 35.22 3.41
282 521 0.324943 TCGAGAGCTTGGGGGAAAAG 59.675 55.000 0.00 0.00 0.00 2.27
317 556 2.484651 CGAGTAGGTCCCACGATATGAG 59.515 54.545 0.00 0.00 0.00 2.90
320 559 4.742012 AGTAGGTCCCACGATATGAGAAT 58.258 43.478 0.00 0.00 0.00 2.40
361 600 3.561143 AGTTTGCACATCACCTTGGTAA 58.439 40.909 0.00 0.00 0.00 2.85
362 601 4.151883 AGTTTGCACATCACCTTGGTAAT 58.848 39.130 0.00 0.00 0.00 1.89
364 603 2.722094 TGCACATCACCTTGGTAATCC 58.278 47.619 0.00 0.00 0.00 3.01
472 713 6.228258 GGAAGCATATATAAAGGACAACGGA 58.772 40.000 0.00 0.00 0.00 4.69
559 800 6.072112 TGCTTCATTCCTGTTTCAGTAAAC 57.928 37.500 0.00 0.00 44.40 2.01
622 863 9.008965 GTGATTATAGCAGAGAGAGATTACTGA 57.991 37.037 0.00 0.00 32.90 3.41
838 1082 1.743252 CTTGAGAGGGAGGCGCAAC 60.743 63.158 10.83 1.38 0.00 4.17
874 1118 8.141268 CCTGAACCTGAAGCTTGTTATTTAAAA 58.859 33.333 2.10 0.00 0.00 1.52
879 1123 8.787852 ACCTGAAGCTTGTTATTTAAAAGAGAG 58.212 33.333 2.10 0.00 0.00 3.20
880 1124 8.787852 CCTGAAGCTTGTTATTTAAAAGAGAGT 58.212 33.333 2.10 0.00 0.00 3.24
895 1139 0.912006 AGAGTCCTCTGCCTTTCCCC 60.912 60.000 0.00 0.00 38.75 4.81
920 1164 3.072330 TCACAAGCAATCCACACCTCTTA 59.928 43.478 0.00 0.00 0.00 2.10
1236 1483 0.820871 GTGTTGGCAAAGGACACCAA 59.179 50.000 0.00 0.00 41.08 3.67
1341 1594 2.060383 TCCACAGCCTCCATCTCCG 61.060 63.158 0.00 0.00 0.00 4.63
1509 1778 3.559238 AATTGCTGTTCGCTAACTTGG 57.441 42.857 2.53 0.00 40.11 3.61
1594 1863 8.416329 ACATTTCCTTTTGTAATCCATATCAGC 58.584 33.333 0.00 0.00 0.00 4.26
1677 1946 7.553881 TGGGCTTTCTAAGATTAGAATTTCG 57.446 36.000 14.16 6.52 45.99 3.46
1699 1968 7.127012 TCGGTATTTGTATATTTGGAGTGGA 57.873 36.000 0.00 0.00 0.00 4.02
1731 2000 7.505585 AGGTAGTGTGAAGATTTGGATTTTTGA 59.494 33.333 0.00 0.00 0.00 2.69
1733 2002 7.111247 AGTGTGAAGATTTGGATTTTTGACA 57.889 32.000 0.00 0.00 0.00 3.58
1762 2031 6.564709 ATGATCCGATGTACATTTCATTGG 57.435 37.500 10.30 1.39 44.16 3.16
1869 2138 8.565896 TTCTGTAGTCAGTATTTGCATGATTT 57.434 30.769 0.00 0.00 41.91 2.17
1942 2211 3.070878 TCACATGTCCACACTTCAAGCTA 59.929 43.478 0.00 0.00 0.00 3.32
1957 2226 5.395682 TCAAGCTAGTACGGCTTTTCTTA 57.604 39.130 20.75 7.09 46.24 2.10
2075 2395 6.783892 ATTTTTGCACGCAAGAAACATATT 57.216 29.167 11.19 0.00 43.62 1.28
2081 2401 4.675146 GCACGCAAGAAACATATTGATGGT 60.675 41.667 0.00 0.00 43.62 3.55
2106 2426 9.522804 GTAAAAATTGTGATGAACCAACAGTAA 57.477 29.630 0.00 0.00 0.00 2.24
2260 2594 2.292569 CTCATGGAAATTGGGAGATGCG 59.707 50.000 0.00 0.00 0.00 4.73
2322 2656 4.023193 ACAGTGTATTTGGGCTTCTTTTCG 60.023 41.667 0.00 0.00 0.00 3.46
2443 2783 3.954904 GGGATCTGAGCTCTACAAGTGTA 59.045 47.826 16.19 0.00 0.00 2.90
2449 2789 5.639506 TCTGAGCTCTACAAGTGTATTTTGC 59.360 40.000 16.19 0.00 0.00 3.68
2472 2812 3.443681 CGCTGGGTTCATTTTATGGAACT 59.556 43.478 0.00 0.00 42.29 3.01
2494 2834 7.457024 ACTAGAGTCTAGTCTTTTGAGAACC 57.543 40.000 24.42 0.00 0.00 3.62
2579 2923 5.078411 AGCATCTACAGTTCTTGTACCAG 57.922 43.478 0.00 0.00 41.29 4.00
3163 3712 8.908678 GTTTAAGACCGTAAAACATTTCCAATC 58.091 33.333 0.00 0.00 34.12 2.67
3165 3714 5.321927 AGACCGTAAAACATTTCCAATCCT 58.678 37.500 0.00 0.00 0.00 3.24
3176 3725 8.821686 AACATTTCCAATCCTACATTGATACA 57.178 30.769 0.00 0.00 0.00 2.29
3177 3726 8.821686 ACATTTCCAATCCTACATTGATACAA 57.178 30.769 0.00 0.00 0.00 2.41
3179 3728 8.685427 CATTTCCAATCCTACATTGATACAACA 58.315 33.333 0.00 0.00 0.00 3.33
3181 3730 9.913310 TTTCCAATCCTACATTGATACAACATA 57.087 29.630 0.00 0.00 0.00 2.29
3182 3731 9.913310 TTCCAATCCTACATTGATACAACATAA 57.087 29.630 0.00 0.00 0.00 1.90
3219 3924 2.916702 ATGTCTAAGATCATGCCGCA 57.083 45.000 0.00 0.00 0.00 5.69
3235 3940 1.006922 GCAGCAGGTTTGAAGTGGC 60.007 57.895 0.00 0.00 0.00 5.01
3236 3941 1.737355 GCAGCAGGTTTGAAGTGGCA 61.737 55.000 0.00 0.00 0.00 4.92
3241 3946 2.879756 GCAGGTTTGAAGTGGCAGGATA 60.880 50.000 0.00 0.00 0.00 2.59
3252 3957 8.359875 TGAAGTGGCAGGATATTTGAAAATAA 57.640 30.769 0.00 0.00 34.79 1.40
3328 4033 7.201688 GGCAAAGGTGAAACACAAAAACATAAT 60.202 33.333 0.00 0.00 39.98 1.28
3706 4415 7.733402 TCAGTACTGTATACCAAAACAAACC 57.267 36.000 21.99 0.00 0.00 3.27
3709 4418 5.934935 ACTGTATACCAAAACAAACCTCG 57.065 39.130 0.00 0.00 0.00 4.63
3780 4489 1.346395 TCAAATGTCGTAGTGGCTGGT 59.654 47.619 0.00 0.00 0.00 4.00
3785 4494 2.172679 TGTCGTAGTGGCTGGTATCAA 58.827 47.619 0.00 0.00 0.00 2.57
3819 4528 2.740981 CTCACAGTGCCATCTCAAGTTC 59.259 50.000 0.00 0.00 0.00 3.01
3965 4674 4.448210 TGCGGTAATTCCTCTTTATGACC 58.552 43.478 0.00 0.00 0.00 4.02
3980 4689 8.154649 TCTTTATGACCAACTTCAAGAAGAAC 57.845 34.615 16.16 3.98 40.79 3.01
4062 4772 5.607119 GTGTCCACGTGAAACATATCTTT 57.393 39.130 19.30 0.00 35.74 2.52
4066 4776 6.706716 TGTCCACGTGAAACATATCTTTAACA 59.293 34.615 19.30 0.00 35.74 2.41
4083 4793 9.736023 ATCTTTAACAAGAATTTGAGAACACAC 57.264 29.630 0.00 0.00 42.53 3.82
4093 4803 8.402472 AGAATTTGAGAACACACGACAATTTAA 58.598 29.630 0.00 0.00 0.00 1.52
4095 4805 7.728580 TTTGAGAACACACGACAATTTAAAC 57.271 32.000 0.00 0.00 0.00 2.01
4186 4978 1.078848 GCAGCGGACAGTTCCAGAT 60.079 57.895 0.00 0.00 43.00 2.90
4187 4979 0.175760 GCAGCGGACAGTTCCAGATA 59.824 55.000 0.00 0.00 43.00 1.98
4188 4980 1.202580 GCAGCGGACAGTTCCAGATAT 60.203 52.381 0.00 0.00 43.00 1.63
4189 4981 2.035961 GCAGCGGACAGTTCCAGATATA 59.964 50.000 0.00 0.00 43.00 0.86
4190 4982 3.492656 GCAGCGGACAGTTCCAGATATAA 60.493 47.826 0.00 0.00 43.00 0.98
4191 4983 4.302455 CAGCGGACAGTTCCAGATATAAG 58.698 47.826 0.00 0.00 43.00 1.73
4192 4984 4.038042 CAGCGGACAGTTCCAGATATAAGA 59.962 45.833 0.00 0.00 43.00 2.10
4193 4985 4.279671 AGCGGACAGTTCCAGATATAAGAG 59.720 45.833 0.00 0.00 43.00 2.85
4194 4986 4.559704 GCGGACAGTTCCAGATATAAGAGG 60.560 50.000 0.00 0.00 43.00 3.69
4195 4987 4.021894 CGGACAGTTCCAGATATAAGAGGG 60.022 50.000 0.00 0.00 43.00 4.30
4208 5006 8.265055 CAGATATAAGAGGGTACACTGGAAAAA 58.735 37.037 0.00 0.00 0.00 1.94
4226 5024 2.050714 GGCGGCGAATCGTATCGA 60.051 61.111 12.98 0.00 45.48 3.59
4314 5112 2.224843 TGTCTTGTTCCATGCAGGTGAT 60.225 45.455 0.00 0.00 39.02 3.06
4684 5482 4.840772 CAGTTCTATTGCGACAAAAGAACG 59.159 41.667 7.62 0.00 46.72 3.95
4816 5614 0.178068 CAGGGATCACACTTACCGGG 59.822 60.000 6.32 0.00 0.00 5.73
4930 5728 2.103771 TCCCATAGCTTGTCTGCAGATC 59.896 50.000 21.47 13.93 34.99 2.75
5240 6049 9.681062 ATGCCAATACAAAGTATAAGTGTTACT 57.319 29.630 0.00 0.00 0.00 2.24
5241 6050 9.158233 TGCCAATACAAAGTATAAGTGTTACTC 57.842 33.333 0.00 0.00 0.00 2.59
5242 6051 8.610035 GCCAATACAAAGTATAAGTGTTACTCC 58.390 37.037 0.00 0.00 0.00 3.85
5243 6052 9.106070 CCAATACAAAGTATAAGTGTTACTCCC 57.894 37.037 0.00 0.00 0.00 4.30
5244 6053 9.886132 CAATACAAAGTATAAGTGTTACTCCCT 57.114 33.333 0.00 0.00 0.00 4.20
5246 6055 6.944096 ACAAAGTATAAGTGTTACTCCCTCC 58.056 40.000 0.00 0.00 0.00 4.30
5247 6056 5.848833 AAGTATAAGTGTTACTCCCTCCG 57.151 43.478 0.00 0.00 0.00 4.63
5248 6057 4.864726 AGTATAAGTGTTACTCCCTCCGT 58.135 43.478 0.00 0.00 0.00 4.69
5249 6058 4.886489 AGTATAAGTGTTACTCCCTCCGTC 59.114 45.833 0.00 0.00 0.00 4.79
5250 6059 1.264295 AAGTGTTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
5251 6060 0.614134 AGTGTTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
5252 6061 0.901580 GTGTTACTCCCTCCGTCCCA 60.902 60.000 0.00 0.00 0.00 4.37
5253 6062 0.042131 TGTTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00
5254 6063 1.288633 TGTTACTCCCTCCGTCCCATA 59.711 52.381 0.00 0.00 0.00 2.74
5255 6064 2.292389 TGTTACTCCCTCCGTCCCATAA 60.292 50.000 0.00 0.00 0.00 1.90
5256 6065 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
5257 6066 4.154942 GTTACTCCCTCCGTCCCATAATA 58.845 47.826 0.00 0.00 0.00 0.98
5258 6067 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
5259 6068 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
5260 6069 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5261 6070 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
5262 6071 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
5263 6072 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
5264 6073 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
5265 6074 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
5266 6075 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
5267 6076 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
5268 6077 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
5269 6078 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
5270 6079 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
5288 6097 4.301072 TTTTTACACTGGATGGAGGGAG 57.699 45.455 0.00 0.00 0.00 4.30
5289 6098 2.642171 TTACACTGGATGGAGGGAGT 57.358 50.000 0.00 0.00 0.00 3.85
5290 6099 3.769189 TTACACTGGATGGAGGGAGTA 57.231 47.619 0.00 0.00 0.00 2.59
5291 6100 2.166907 ACACTGGATGGAGGGAGTAG 57.833 55.000 0.00 0.00 0.00 2.57
5370 6191 2.554893 GCCAACATCGGTAAAGGTGAAA 59.445 45.455 0.00 0.00 0.00 2.69
5382 6203 6.973474 CGGTAAAGGTGAAACAAATGTTAACA 59.027 34.615 11.41 11.41 39.98 2.41
5459 6280 4.872691 AGATTCAGAAACGGATTGCTACAG 59.127 41.667 0.00 0.00 0.00 2.74
5532 6353 5.234752 AGGAAAAGTTTGTTTTCGCACTTT 58.765 33.333 4.59 0.00 40.43 2.66
5547 6368 1.000938 CACTTTGGCAGAAGGAACAGC 60.001 52.381 12.03 0.00 0.00 4.40
5687 6508 1.135803 GCAGCGCGAAAAGGAAATGTA 60.136 47.619 12.10 0.00 0.00 2.29
5807 6632 6.682863 CAGAATAAGTGAAAGCGAATTAACCG 59.317 38.462 0.00 0.00 0.00 4.44
5830 6655 6.096036 CGTTAGAACATGACAGAGAAGTGAT 58.904 40.000 0.00 0.00 0.00 3.06
5831 6656 6.034363 CGTTAGAACATGACAGAGAAGTGATG 59.966 42.308 0.00 0.00 38.77 3.07
5954 6779 8.543862 TCTAGCATTATAACTCGACGAGAATA 57.456 34.615 30.56 21.80 33.32 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 178 3.116300 CCTCCGTGTTCAATGATAGACG 58.884 50.000 7.66 7.66 0.00 4.18
253 254 2.805099 CCAAGCTCTCGATGGATTTAGC 59.195 50.000 0.00 0.00 36.27 3.09
260 261 1.626356 TTCCCCCAAGCTCTCGATGG 61.626 60.000 0.00 0.00 0.00 3.51
262 263 0.991920 TTTTCCCCCAAGCTCTCGAT 59.008 50.000 0.00 0.00 0.00 3.59
263 264 0.324943 CTTTTCCCCCAAGCTCTCGA 59.675 55.000 0.00 0.00 0.00 4.04
320 559 8.231837 GCAAACTCGTAGTTTTCATATTGGTTA 58.768 33.333 9.38 0.00 45.38 2.85
338 577 1.069022 CCAAGGTGATGTGCAAACTCG 60.069 52.381 0.00 0.00 0.00 4.18
559 800 0.443869 CGCATCTTCTTTGACACCGG 59.556 55.000 0.00 0.00 0.00 5.28
622 863 8.686334 GGTGAACCACATCTATTATGACATTTT 58.314 33.333 0.00 0.00 35.86 1.82
838 1082 2.362889 GGTTCAGGGTGGCCATGG 60.363 66.667 9.72 7.63 35.84 3.66
846 1090 0.846693 ACAAGCTTCAGGTTCAGGGT 59.153 50.000 0.00 0.00 32.86 4.34
879 1123 2.677848 GGGGGAAAGGCAGAGGAC 59.322 66.667 0.00 0.00 0.00 3.85
895 1139 0.883833 GTGTGGATTGCTTGTGAGGG 59.116 55.000 0.00 0.00 0.00 4.30
920 1164 9.621629 GGTAGTAGATAGATAGACAGCATACAT 57.378 37.037 0.00 0.00 0.00 2.29
944 1188 1.018910 GTGTTTGTACGTGCTTGGGT 58.981 50.000 4.97 0.00 0.00 4.51
1236 1483 2.046285 GCTTGGCTGGTATGGCGTT 61.046 57.895 0.00 0.00 35.06 4.84
1341 1594 0.957888 GTCTGCCCTTTCCACAGCTC 60.958 60.000 0.00 0.00 0.00 4.09
1509 1778 1.251251 GGGGAATGCATGATGCTACC 58.749 55.000 19.19 16.96 45.31 3.18
1610 1879 0.741221 GGACTGATCAACACGGAGCC 60.741 60.000 0.00 0.00 0.00 4.70
1677 1946 8.747538 AGTTCCACTCCAAATATACAAATACC 57.252 34.615 0.00 0.00 0.00 2.73
1699 1968 5.765182 CCAAATCTTCACACTACCTGAAGTT 59.235 40.000 7.78 0.00 43.51 2.66
1731 2000 6.596309 ATGTACATCGGATCATATGTCTGT 57.404 37.500 13.64 3.96 37.50 3.41
1733 2002 7.670364 TGAAATGTACATCGGATCATATGTCT 58.330 34.615 9.23 0.00 37.50 3.41
1762 2031 3.428180 CGATGACGATGGATCATAGGACC 60.428 52.174 0.00 0.00 42.66 4.46
1778 2047 2.688446 TCATGTGAGGGTAGTCGATGAC 59.312 50.000 0.00 0.00 0.00 3.06
1869 2138 7.309744 CCAATAAAATTTCCAGTAAGCACAGGA 60.310 37.037 0.00 0.00 38.49 3.86
1910 2179 6.061441 AGTGTGGACATGTGAATAACAGAAA 58.939 36.000 1.15 0.00 43.64 2.52
1918 2187 3.254166 GCTTGAAGTGTGGACATGTGAAT 59.746 43.478 1.15 0.00 0.00 2.57
1942 2211 7.832685 AGGGAAAAATATAAGAAAAGCCGTACT 59.167 33.333 0.00 0.00 0.00 2.73
1957 2226 8.034804 CGTGATTCCTCAAAAAGGGAAAAATAT 58.965 33.333 0.00 0.00 46.23 1.28
1984 2272 2.618709 CCCACTTTGTTCACCAAGAGAC 59.381 50.000 0.00 0.00 33.75 3.36
2046 2363 6.904011 TGTTTCTTGCGTGCAAAAATATTTTG 59.096 30.769 14.04 10.42 35.33 2.44
2047 2364 7.009568 TGTTTCTTGCGTGCAAAAATATTTT 57.990 28.000 7.64 7.64 35.33 1.82
2075 2395 7.295322 TGGTTCATCACAATTTTTACCATCA 57.705 32.000 0.00 0.00 30.00 3.07
2081 2401 9.522804 GTTACTGTTGGTTCATCACAATTTTTA 57.477 29.630 0.00 0.00 0.00 1.52
2163 2495 6.660521 TGCCTCTACATCAAACATTTTCATCT 59.339 34.615 0.00 0.00 0.00 2.90
2165 2497 6.839124 TGCCTCTACATCAAACATTTTCAT 57.161 33.333 0.00 0.00 0.00 2.57
2168 2500 7.944729 AGTATGCCTCTACATCAAACATTTT 57.055 32.000 0.00 0.00 0.00 1.82
2177 2509 6.291377 TGGATTTCAAGTATGCCTCTACATC 58.709 40.000 0.00 0.00 0.00 3.06
2322 2656 5.640783 CAGAAAATGAGGATTTCTTTTGGCC 59.359 40.000 0.00 0.00 42.85 5.36
2410 2750 3.509575 AGCTCAGATCCCTAAGCTAATCG 59.490 47.826 6.89 0.00 43.04 3.34
2421 2761 2.763448 ACACTTGTAGAGCTCAGATCCC 59.237 50.000 17.77 0.00 0.00 3.85
2443 2783 0.975887 AATGAACCCAGCGGCAAAAT 59.024 45.000 1.45 0.00 0.00 1.82
2449 2789 2.374184 TCCATAAAATGAACCCAGCGG 58.626 47.619 0.00 0.00 0.00 5.52
2472 2812 7.005296 AGTGGTTCTCAAAAGACTAGACTCTA 58.995 38.462 0.00 0.00 0.00 2.43
3047 3596 4.012374 TCAAGAGATCATTTTCCCTGCAC 58.988 43.478 0.00 0.00 0.00 4.57
3124 3673 6.859017 ACGGTCTTAAACATGAAAACACTTT 58.141 32.000 0.00 0.00 0.00 2.66
3194 3899 5.107298 GCGGCATGATCTTAGACATAGAAAC 60.107 44.000 0.00 0.00 0.00 2.78
3201 3906 1.807755 GCTGCGGCATGATCTTAGACA 60.808 52.381 14.08 0.00 38.54 3.41
3219 3924 0.825010 CCTGCCACTTCAAACCTGCT 60.825 55.000 0.00 0.00 0.00 4.24
3228 3933 9.651913 TTTTATTTTCAAATATCCTGCCACTTC 57.348 29.630 0.00 0.00 31.47 3.01
3328 4033 6.865834 AAATTAGCACATCATTTAACCCCA 57.134 33.333 0.00 0.00 0.00 4.96
3706 4415 1.533625 TGGAATCAAAACTGCCCGAG 58.466 50.000 0.00 0.00 0.00 4.63
3709 4418 4.096984 CAGAGTATGGAATCAAAACTGCCC 59.903 45.833 0.00 0.00 0.00 5.36
3780 4489 6.262944 ACTGTGAGCTGTTGACAATTTTGATA 59.737 34.615 0.00 0.00 0.00 2.15
3785 4494 3.489738 GCACTGTGAGCTGTTGACAATTT 60.490 43.478 12.86 0.00 0.00 1.82
3885 4594 1.262417 TCTGCAGGTGTATTCCGTCA 58.738 50.000 15.13 0.00 0.00 4.35
3965 4674 7.095691 TGCAAAACAAAGTTCTTCTTGAAGTTG 60.096 33.333 9.80 9.22 44.85 3.16
3980 4689 4.687018 TGCATGCTAGATTGCAAAACAAAG 59.313 37.500 20.33 4.42 45.30 2.77
4062 4772 6.314152 TGTCGTGTGTTCTCAAATTCTTGTTA 59.686 34.615 0.00 0.00 33.94 2.41
4066 4776 5.811399 TTGTCGTGTGTTCTCAAATTCTT 57.189 34.783 0.00 0.00 0.00 2.52
4083 4793 8.125728 AGTTTGTTGGAATGTTTAAATTGTCG 57.874 30.769 0.00 0.00 0.00 4.35
4093 4803 9.010029 CCTTACACTATAGTTTGTTGGAATGTT 57.990 33.333 1.56 0.00 0.00 2.71
4095 4805 7.120579 TGCCTTACACTATAGTTTGTTGGAATG 59.879 37.037 1.56 0.00 0.00 2.67
4112 4904 7.857885 GCTTTCAGTTAATCATATGCCTTACAC 59.142 37.037 0.00 1.57 0.00 2.90
4114 4906 7.930217 TGCTTTCAGTTAATCATATGCCTTAC 58.070 34.615 0.00 0.00 0.00 2.34
4128 4920 3.327757 ACAGAGGGACATGCTTTCAGTTA 59.672 43.478 0.00 0.00 0.00 2.24
4186 4978 6.577638 GCCTTTTTCCAGTGTACCCTCTTATA 60.578 42.308 0.00 0.00 0.00 0.98
4187 4979 5.806734 GCCTTTTTCCAGTGTACCCTCTTAT 60.807 44.000 0.00 0.00 0.00 1.73
4188 4980 4.506095 GCCTTTTTCCAGTGTACCCTCTTA 60.506 45.833 0.00 0.00 0.00 2.10
4189 4981 3.750922 GCCTTTTTCCAGTGTACCCTCTT 60.751 47.826 0.00 0.00 0.00 2.85
4190 4982 2.224793 GCCTTTTTCCAGTGTACCCTCT 60.225 50.000 0.00 0.00 0.00 3.69
4191 4983 2.160205 GCCTTTTTCCAGTGTACCCTC 58.840 52.381 0.00 0.00 0.00 4.30
4192 4984 1.544759 CGCCTTTTTCCAGTGTACCCT 60.545 52.381 0.00 0.00 0.00 4.34
4193 4985 0.879090 CGCCTTTTTCCAGTGTACCC 59.121 55.000 0.00 0.00 0.00 3.69
4194 4986 0.879090 CCGCCTTTTTCCAGTGTACC 59.121 55.000 0.00 0.00 0.00 3.34
4195 4987 0.240145 GCCGCCTTTTTCCAGTGTAC 59.760 55.000 0.00 0.00 0.00 2.90
4208 5006 2.050351 CGATACGATTCGCCGCCT 60.050 61.111 5.86 0.00 31.60 5.52
4226 5024 5.261209 TGTGTAACTGCAAAAGATGCTTT 57.739 34.783 1.83 0.00 45.91 3.51
4314 5112 6.504238 CCTGTCTGGATGGAGATGCAATCA 62.504 50.000 0.00 0.00 42.03 2.57
4684 5482 3.382855 TGCTGATGTTTGATTTGTGCAC 58.617 40.909 10.75 10.75 0.00 4.57
4816 5614 2.220313 TGCACGGGTTTAAGTTGTACC 58.780 47.619 0.00 0.76 0.00 3.34
4930 5728 0.821711 TGTTCCCAGCAGGTTTTCCG 60.822 55.000 0.00 0.00 46.35 4.30
5218 6026 9.886132 AGGGAGTAACACTTATACTTTGTATTG 57.114 33.333 0.00 0.00 33.85 1.90
5239 6048 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
5240 6049 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
5241 6050 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
5242 6051 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
5243 6052 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
5244 6053 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
5245 6054 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
5246 6055 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
5267 6076 3.655777 ACTCCCTCCATCCAGTGTAAAAA 59.344 43.478 0.00 0.00 0.00 1.94
5268 6077 3.256704 ACTCCCTCCATCCAGTGTAAAA 58.743 45.455 0.00 0.00 0.00 1.52
5269 6078 2.915869 ACTCCCTCCATCCAGTGTAAA 58.084 47.619 0.00 0.00 0.00 2.01
5270 6079 2.642171 ACTCCCTCCATCCAGTGTAA 57.358 50.000 0.00 0.00 0.00 2.41
5271 6080 2.856864 TCTACTCCCTCCATCCAGTGTA 59.143 50.000 0.00 0.00 0.00 2.90
5272 6081 1.646447 TCTACTCCCTCCATCCAGTGT 59.354 52.381 0.00 0.00 0.00 3.55
5273 6082 2.461300 TCTACTCCCTCCATCCAGTG 57.539 55.000 0.00 0.00 0.00 3.66
5274 6083 3.491766 TTTCTACTCCCTCCATCCAGT 57.508 47.619 0.00 0.00 0.00 4.00
5275 6084 6.500589 TTATTTTCTACTCCCTCCATCCAG 57.499 41.667 0.00 0.00 0.00 3.86
5276 6085 8.757307 ATATTATTTTCTACTCCCTCCATCCA 57.243 34.615 0.00 0.00 0.00 3.41
5281 6090 9.438228 GCTGTAATATTATTTTCTACTCCCTCC 57.562 37.037 0.00 0.00 0.00 4.30
5282 6091 9.998106 TGCTGTAATATTATTTTCTACTCCCTC 57.002 33.333 0.00 0.00 0.00 4.30
5283 6092 9.780186 GTGCTGTAATATTATTTTCTACTCCCT 57.220 33.333 0.00 0.00 0.00 4.20
5284 6093 9.780186 AGTGCTGTAATATTATTTTCTACTCCC 57.220 33.333 0.00 0.00 0.00 4.30
5312 6121 9.727859 TTAAATAGTAAGGTGTAGAATGTGCAA 57.272 29.630 0.00 0.00 0.00 4.08
5370 6191 6.463755 GGGATTCTTGGGTTGTTAACATTTGT 60.464 38.462 9.56 0.00 0.00 2.83
5382 6203 3.541242 TGTCATTGGGATTCTTGGGTT 57.459 42.857 0.00 0.00 0.00 4.11
5525 6346 0.040067 GTTCCTTCTGCCAAAGTGCG 60.040 55.000 0.00 0.00 0.00 5.34
5532 6353 1.774110 TTTTGCTGTTCCTTCTGCCA 58.226 45.000 0.00 0.00 0.00 4.92
5619 6440 5.654317 TGTGTATGTTGCAAATGCTTTTG 57.346 34.783 18.17 18.17 44.18 2.44
5776 6601 7.678194 TTCGCTTTCACTTATTCTGTTTTTG 57.322 32.000 0.00 0.00 0.00 2.44
5782 6607 6.682863 CGGTTAATTCGCTTTCACTTATTCTG 59.317 38.462 0.00 0.00 0.00 3.02
5788 6613 4.823790 AACGGTTAATTCGCTTTCACTT 57.176 36.364 0.00 0.00 0.00 3.16
5807 6632 7.093354 TCATCACTTCTCTGTCATGTTCTAAC 58.907 38.462 0.00 0.00 0.00 2.34
5830 6655 4.529377 ACGGAGGGAGTAGTTAACAAATCA 59.471 41.667 8.61 0.00 0.00 2.57
5831 6656 5.082251 ACGGAGGGAGTAGTTAACAAATC 57.918 43.478 8.61 2.11 0.00 2.17


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

AutoCloner maintained by Alex Coulton.