Multiple sequence alignment - TraesCS3D01G210600

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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 TraesCS3D01G210600 chr3D 100.000 4783 0 0 1 4783 279789897 279794679 0.000000e+00 8833.0
1 TraesCS3D01G210600 chr3B 93.602 2610 122 23 2201 4782 370730286 370727694 0.000000e+00 3853.0
2 TraesCS3D01G210600 chr3B 94.237 1926 70 16 1 1898 370732864 370730952 0.000000e+00 2904.0
3 TraesCS3D01G210600 chr3B 88.235 306 15 11 1898 2202 370730732 370730447 3.540000e-91 346.0
4 TraesCS3D01G210600 chr3B 97.436 39 1 0 1923 1961 50913432 50913394 3.090000e-07 67.6
5 TraesCS3D01G210600 chr3A 91.860 1634 86 26 2004 3607 359571942 359570326 0.000000e+00 2237.0
6 TraesCS3D01G210600 chr3A 94.425 1453 42 9 420 1852 359574260 359572827 0.000000e+00 2198.0
7 TraesCS3D01G210600 chr3A 91.304 1150 87 9 3633 4781 359570328 359569191 0.000000e+00 1557.0
8 TraesCS3D01G210600 chr3A 82.262 389 27 16 1 372 359578740 359578377 1.010000e-76 298.0
9 TraesCS3D01G210600 chr3A 93.706 143 6 1 1843 1982 359572220 359572078 1.350000e-50 211.0
10 TraesCS3D01G210600 chr2A 100.000 51 0 0 4152 4202 753789921 753789871 1.420000e-15 95.3
11 TraesCS3D01G210600 chr5A 91.837 49 3 1 1916 1963 477433300 477433252 3.090000e-07 67.6
12 TraesCS3D01G210600 chr6B 100.000 28 0 0 1934 1961 207108845 207108818 9.000000e-03 52.8


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 TraesCS3D01G210600 chr3D 279789897 279794679 4782 False 8833.000000 8833 100.000000 1 4783 1 chr3D.!!$F1 4782
1 TraesCS3D01G210600 chr3B 370727694 370732864 5170 True 2367.666667 3853 92.024667 1 4782 3 chr3B.!!$R2 4781
2 TraesCS3D01G210600 chr3A 359569191 359574260 5069 True 1550.750000 2237 92.823750 420 4781 4 chr3A.!!$R2 4361

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
29 30 0.318762 GTGCTCCAACGACTCCTTCT 59.681 55.000 0.00 0.0 0.00 2.85 F
524 540 0.466963 ACCGAAACCTGACCGTTTCT 59.533 50.000 11.25 0.0 46.18 2.52 F
808 825 1.003696 CCACCAACTCCTTCCTTCCTC 59.996 57.143 0.00 0.0 0.00 3.71 F
809 826 1.981495 CACCAACTCCTTCCTTCCTCT 59.019 52.381 0.00 0.0 0.00 3.69 F
810 827 3.173965 CACCAACTCCTTCCTTCCTCTA 58.826 50.000 0.00 0.0 0.00 2.43 F
1209 1244 3.201930 TGTACGTGTAGGTGGAGGGTATA 59.798 47.826 0.00 0.0 0.00 1.47 F
2818 4005 1.580059 ATAGGAAAGCCACCGGAAGA 58.420 50.000 9.46 0.0 36.29 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1144 1179 0.512518 CAGACGCTTCGATTTGCACA 59.487 50.000 0.00 0.0 0.00 4.57 R
1699 1740 2.125512 GTAGAGCTGGCCGGTGTG 60.126 66.667 14.55 0.0 0.00 3.82 R
2039 3030 3.135530 AGCAAACAGAGTGGATCTATCCC 59.864 47.826 6.54 0.0 46.59 3.85 R
2571 3737 4.224147 TCATTTCATTTGTCCTCCTCGGTA 59.776 41.667 0.00 0.0 0.00 4.02 R
2593 3759 8.666573 CATCCTAGTGATCTTTATCATTGCATC 58.333 37.037 0.00 0.0 43.87 3.91 R
2864 4051 1.053424 TCTTTGGCACCTAAGACGGT 58.947 50.000 9.15 0.0 34.07 4.83 R
4010 5202 0.035439 TTGGTTCCGATCTTCCAGGC 60.035 55.000 0.00 0.0 0.00 4.85 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
17 18 4.196778 TGGGCCAAACGTGCTCCA 62.197 61.111 2.13 0.00 0.00 3.86
27 28 1.006102 CGTGCTCCAACGACTCCTT 60.006 57.895 0.00 0.00 46.49 3.36
28 29 1.009389 CGTGCTCCAACGACTCCTTC 61.009 60.000 0.00 0.00 46.49 3.46
29 30 0.318762 GTGCTCCAACGACTCCTTCT 59.681 55.000 0.00 0.00 0.00 2.85
70 71 1.372997 CTCCGACAAGGACACACCG 60.373 63.158 0.00 0.00 45.98 4.94
79 80 0.467290 AGGACACACCGCCAAATGTT 60.467 50.000 0.00 0.00 44.74 2.71
84 85 1.729131 CACCGCCAAATGTTGTCGC 60.729 57.895 0.00 0.00 0.00 5.19
105 106 1.561769 TACATGGAGGTGGGGCACAG 61.562 60.000 0.00 0.00 35.86 3.66
207 208 7.667043 TTTGTAGTATGAATTTTCGCTGTCT 57.333 32.000 0.00 0.00 0.00 3.41
211 212 1.603456 TGAATTTTCGCTGTCTGCCA 58.397 45.000 0.00 0.00 38.78 4.92
212 213 2.161855 TGAATTTTCGCTGTCTGCCAT 58.838 42.857 0.00 0.00 38.78 4.40
214 215 3.005684 TGAATTTTCGCTGTCTGCCATTT 59.994 39.130 0.00 0.00 38.78 2.32
215 216 2.420628 TTTTCGCTGTCTGCCATTTG 57.579 45.000 0.00 0.00 38.78 2.32
216 217 1.317613 TTTCGCTGTCTGCCATTTGT 58.682 45.000 0.00 0.00 38.78 2.83
217 218 0.874390 TTCGCTGTCTGCCATTTGTC 59.126 50.000 0.00 0.00 38.78 3.18
218 219 0.955428 TCGCTGTCTGCCATTTGTCC 60.955 55.000 0.00 0.00 38.78 4.02
219 220 1.503542 GCTGTCTGCCATTTGTCCG 59.496 57.895 0.00 0.00 35.15 4.79
244 258 1.542030 CGAGCTAAGCTATGATCCGGT 59.458 52.381 0.00 0.00 39.88 5.28
286 301 3.647590 AGGGTTGCATGGATTTGAAACTT 59.352 39.130 0.00 0.00 35.75 2.66
293 308 7.649533 TGCATGGATTTGAAACTTCAGATAT 57.350 32.000 0.00 0.00 38.61 1.63
296 311 9.674824 GCATGGATTTGAAACTTCAGATATAAG 57.325 33.333 0.00 0.00 38.61 1.73
301 316 7.843490 TTTGAAACTTCAGATATAAGGGACG 57.157 36.000 0.00 0.00 38.61 4.79
302 317 5.357257 TGAAACTTCAGATATAAGGGACGC 58.643 41.667 0.00 0.00 32.50 5.19
304 319 2.296471 ACTTCAGATATAAGGGACGCGG 59.704 50.000 12.47 0.00 0.00 6.46
305 320 1.254026 TCAGATATAAGGGACGCGGG 58.746 55.000 12.47 0.00 0.00 6.13
323 338 2.099098 CGGGTGTGGGAGCAAAAATATC 59.901 50.000 0.00 0.00 0.00 1.63
327 342 4.646492 GGTGTGGGAGCAAAAATATCAGAT 59.354 41.667 0.00 0.00 0.00 2.90
337 352 6.017605 AGCAAAAATATCAGATGTGTCCGATC 60.018 38.462 0.00 0.00 0.00 3.69
347 362 3.640000 GTCCGATCAATGCCCGCG 61.640 66.667 0.00 0.00 0.00 6.46
348 363 3.844090 TCCGATCAATGCCCGCGA 61.844 61.111 8.23 0.00 0.00 5.87
350 365 2.324477 CGATCAATGCCCGCGAAC 59.676 61.111 8.23 0.00 0.00 3.95
351 366 2.460275 CGATCAATGCCCGCGAACA 61.460 57.895 8.23 5.38 0.00 3.18
352 367 1.062525 GATCAATGCCCGCGAACAC 59.937 57.895 8.23 0.00 0.00 3.32
380 396 3.676605 TCCGCGAGCGTTTGAGGA 61.677 61.111 8.23 7.90 34.62 3.71
395 411 2.507484 TGAGGAGCAGATTTGTTGTGG 58.493 47.619 0.00 0.00 0.00 4.17
411 427 3.266510 TGTGGGTGATTGTAGATGCTC 57.733 47.619 0.00 0.00 0.00 4.26
412 428 2.840038 TGTGGGTGATTGTAGATGCTCT 59.160 45.455 0.00 0.00 0.00 4.09
413 429 3.264193 TGTGGGTGATTGTAGATGCTCTT 59.736 43.478 0.00 0.00 0.00 2.85
414 430 4.469586 TGTGGGTGATTGTAGATGCTCTTA 59.530 41.667 0.00 0.00 0.00 2.10
429 445 1.476891 CTCTTACAACTAGGAGGCGCA 59.523 52.381 10.83 0.00 0.00 6.09
471 487 1.278985 TGGAGGAGTCAATGACGCATT 59.721 47.619 18.17 6.30 37.67 3.56
516 532 2.029964 GGTCGCACCGAAACCTGA 59.970 61.111 0.00 0.00 37.72 3.86
524 540 0.466963 ACCGAAACCTGACCGTTTCT 59.533 50.000 11.25 0.00 46.18 2.52
661 678 2.254737 ATCTGTCTGCCTGCTGCCTC 62.255 60.000 0.00 0.00 40.16 4.70
662 679 4.383861 TGTCTGCCTGCTGCCTCG 62.384 66.667 0.00 0.00 40.16 4.63
808 825 1.003696 CCACCAACTCCTTCCTTCCTC 59.996 57.143 0.00 0.00 0.00 3.71
809 826 1.981495 CACCAACTCCTTCCTTCCTCT 59.019 52.381 0.00 0.00 0.00 3.69
810 827 3.173965 CACCAACTCCTTCCTTCCTCTA 58.826 50.000 0.00 0.00 0.00 2.43
1144 1179 4.985538 TGTTAATTCTTGACCCTGCTTCT 58.014 39.130 0.00 0.00 0.00 2.85
1145 1180 4.761739 TGTTAATTCTTGACCCTGCTTCTG 59.238 41.667 0.00 0.00 0.00 3.02
1172 1207 6.022484 GCAAATCGAAGCGTCTGTAAATTAAC 60.022 38.462 0.00 0.00 0.00 2.01
1209 1244 3.201930 TGTACGTGTAGGTGGAGGGTATA 59.798 47.826 0.00 0.00 0.00 1.47
1506 1547 4.271816 CCGTCCTCCTCGGCATCG 62.272 72.222 0.00 0.00 41.48 3.84
1896 2773 8.448615 ACAACATTAATTACTTCCTTTCGCTAC 58.551 33.333 0.00 0.00 0.00 3.58
2023 3014 4.504461 GTCTCCAGTGTACAAATATGCTCG 59.496 45.833 0.00 0.00 0.00 5.03
2417 3579 5.818678 TGGTCCTGTAGTATTTTGTGTCT 57.181 39.130 0.00 0.00 0.00 3.41
2422 3584 7.156673 GTCCTGTAGTATTTTGTGTCTAACCA 58.843 38.462 0.00 0.00 0.00 3.67
2589 3755 6.494666 AAATATACCGAGGAGGACAAATGA 57.505 37.500 0.00 0.00 45.00 2.57
2593 3759 3.347216 ACCGAGGAGGACAAATGAAATG 58.653 45.455 0.00 0.00 45.00 2.32
2817 4004 2.092914 AGAATAGGAAAGCCACCGGAAG 60.093 50.000 9.46 0.00 36.29 3.46
2818 4005 1.580059 ATAGGAAAGCCACCGGAAGA 58.420 50.000 9.46 0.00 36.29 2.87
2858 4045 4.130118 CAGTGGCCCACAGATAGAATAAC 58.870 47.826 17.80 0.00 36.74 1.89
2864 4051 5.428253 GCCCACAGATAGAATAACTGACAA 58.572 41.667 0.00 0.00 43.36 3.18
2869 4056 6.253727 CACAGATAGAATAACTGACAACCGTC 59.746 42.308 0.00 0.00 43.36 4.79
3091 4283 9.060347 CAGCAAAATCATGTACATAACCTAGAT 57.940 33.333 8.32 3.22 0.00 1.98
3182 4374 9.097946 AGTAGTATTAACTAACTGACCAAACCT 57.902 33.333 0.00 0.00 39.90 3.50
3198 4390 0.761187 ACCTCATGCATGGTATCGCT 59.239 50.000 25.97 0.00 34.36 4.93
3225 4417 0.178068 ACAAGACAACGGTGCTGACT 59.822 50.000 0.00 0.00 0.00 3.41
3235 4427 3.691342 TGCTGACTAAGGCGGCGT 61.691 61.111 9.37 1.96 40.49 5.68
3297 4489 3.117888 AGGAGAAGAACAACAAGCTGGAA 60.118 43.478 0.00 0.00 0.00 3.53
3319 4511 1.436336 CACATCCCGACCTACGACC 59.564 63.158 0.00 0.00 45.77 4.79
3321 4513 2.117156 CATCCCGACCTACGACCGT 61.117 63.158 0.00 0.00 45.77 4.83
3507 4699 2.178521 GTCATGTCCGTCGACGCT 59.821 61.111 31.73 13.03 42.37 5.07
3629 4821 7.412063 TCTTTAATTCATTCATGATGACTGCG 58.588 34.615 7.80 0.00 44.28 5.18
3635 4827 4.696877 TCATTCATGATGACTGCGTTTCTT 59.303 37.500 7.80 0.00 39.83 2.52
3690 4882 4.219070 TGGTATGTACGTATATGCAGGACC 59.781 45.833 18.99 15.37 0.00 4.46
3702 4894 1.372997 CAGGACCACGACTGGAACG 60.373 63.158 0.00 0.00 40.55 3.95
3726 4918 1.303236 TTGTTCCACGAGGCCATGG 60.303 57.895 7.63 7.63 37.32 3.66
3764 4956 0.249741 CAACCGTGTTTCGTCCTCCT 60.250 55.000 0.00 0.00 37.94 3.69
3805 4997 6.565974 AGTATGCAGGAAGAGGAAGGATATA 58.434 40.000 0.00 0.00 0.00 0.86
3806 4998 7.195474 AGTATGCAGGAAGAGGAAGGATATAT 58.805 38.462 0.00 0.00 0.00 0.86
3814 5006 6.954684 GGAAGAGGAAGGATATATGTGTCCTA 59.045 42.308 8.20 0.00 44.36 2.94
3819 5011 7.491681 AGGAAGGATATATGTGTCCTAATCCT 58.508 38.462 17.61 17.61 44.36 3.24
3832 5024 4.040047 TCCTAATCCTGAGGAGCAATTCA 58.960 43.478 7.50 0.00 38.22 2.57
3923 5115 2.290641 TGTTTGCAATAGTCGGATGGGT 60.291 45.455 0.00 0.00 0.00 4.51
3959 5151 3.316029 CACTCTGCACCAACAAGATCAAA 59.684 43.478 0.00 0.00 0.00 2.69
3982 5174 3.385577 ACGAGAAAGAAGTCTTCAGTGC 58.614 45.455 14.97 1.13 34.61 4.40
3986 5178 3.319405 AGAAAGAAGTCTTCAGTGCGAGA 59.681 43.478 14.97 0.00 34.61 4.04
4010 5202 6.851222 AGCTAGAAATGTTTGTATCGGATG 57.149 37.500 0.00 0.00 0.00 3.51
4097 5290 3.648545 GCCAAGGGGTAGAAGATATGTCT 59.351 47.826 0.00 0.00 36.17 3.41
4202 5395 4.434713 AATGCAGACAAATTACCCGTTC 57.565 40.909 0.00 0.00 0.00 3.95
4249 5442 4.558226 TTGTATCACCTTCAGCACTGAT 57.442 40.909 0.31 0.00 39.64 2.90
4266 5459 1.005332 TGATGAAATCCCTTCGGGCAA 59.995 47.619 0.00 0.00 44.73 4.52
4271 5464 1.789576 AATCCCTTCGGGCAACACCT 61.790 55.000 0.00 0.00 43.94 4.00
4274 5467 1.376037 CCTTCGGGCAACACCTCTC 60.376 63.158 0.00 0.00 39.10 3.20
4284 5477 1.974236 CAACACCTCTCTCTCCACCTT 59.026 52.381 0.00 0.00 0.00 3.50
4288 5481 2.903135 CACCTCTCTCTCCACCTTCTTT 59.097 50.000 0.00 0.00 0.00 2.52
4306 5499 6.183360 CCTTCTTTCACGATAAACATCAGACC 60.183 42.308 0.00 0.00 0.00 3.85
4417 5610 2.861462 CAAACTTGCCAACGAAAGGA 57.139 45.000 0.00 0.00 0.00 3.36
4432 5625 2.294449 AAGGAAAAGGTTGGGAGCTC 57.706 50.000 4.71 4.71 32.03 4.09
4454 5647 1.148498 GCCACCTTAATCCCGAGGG 59.852 63.158 0.65 0.65 37.36 4.30
4561 5754 4.140924 TGACTCCTCAGCTGGGAATATAGA 60.141 45.833 17.43 0.87 31.92 1.98
4605 5800 0.477597 ACTTGACCAATGGAGGGGGA 60.478 55.000 6.16 0.00 0.00 4.81
4708 5903 3.392285 CACATCAGATACCCCTCATGGAA 59.608 47.826 0.00 0.00 35.39 3.53
4750 5945 7.277760 ACCTTTTTAGCAAACTTGATCACAAAC 59.722 33.333 0.00 0.00 35.49 2.93
4754 5949 4.925068 AGCAAACTTGATCACAAACTGAC 58.075 39.130 0.00 0.00 35.49 3.51
4782 5977 9.893305 CCTGTTTTGAAAAGAATTACGTATCTT 57.107 29.630 5.75 5.75 37.49 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.318762 AGAAGGAGTCGTTGGAGCAC 59.681 55.000 2.13 0.00 0.00 4.40
17 18 1.270358 GCCTGTCAAGAAGGAGTCGTT 60.270 52.381 0.00 0.00 36.91 3.85
27 28 2.922503 TGGAGCCGCCTGTCAAGA 60.923 61.111 0.00 0.00 37.63 3.02
28 29 2.743928 GTGGAGCCGCCTGTCAAG 60.744 66.667 0.00 0.00 37.63 3.02
29 30 4.329545 GGTGGAGCCGCCTGTCAA 62.330 66.667 11.82 0.00 42.89 3.18
54 55 3.041940 GCGGTGTGTCCTTGTCGG 61.042 66.667 0.00 0.00 0.00 4.79
70 71 0.236187 TGTACGCGACAACATTTGGC 59.764 50.000 15.93 0.00 34.15 4.52
79 80 1.214325 CACCTCCATGTACGCGACA 59.786 57.895 15.93 13.77 43.97 4.35
84 85 2.189521 GCCCCACCTCCATGTACG 59.810 66.667 0.00 0.00 0.00 3.67
133 134 0.748005 ATCAACATTTCCTCGCCGGG 60.748 55.000 2.18 0.00 0.00 5.73
211 212 1.940883 TAGCTCGTCGCCGGACAAAT 61.941 55.000 5.05 0.00 43.61 2.32
212 213 2.144833 TTAGCTCGTCGCCGGACAAA 62.145 55.000 5.05 0.00 43.61 2.83
214 215 3.047718 CTTAGCTCGTCGCCGGACA 62.048 63.158 5.05 0.00 43.61 4.02
215 216 2.278013 CTTAGCTCGTCGCCGGAC 60.278 66.667 5.05 0.00 40.39 4.79
216 217 4.189188 GCTTAGCTCGTCGCCGGA 62.189 66.667 5.05 0.00 40.39 5.14
217 218 2.131294 ATAGCTTAGCTCGTCGCCGG 62.131 60.000 11.09 0.00 40.44 6.13
218 219 0.999228 CATAGCTTAGCTCGTCGCCG 60.999 60.000 11.09 0.00 40.44 6.46
219 220 0.311165 TCATAGCTTAGCTCGTCGCC 59.689 55.000 11.09 0.00 40.44 5.54
221 222 2.726373 CGGATCATAGCTTAGCTCGTCG 60.726 54.545 11.09 4.11 40.44 5.12
222 223 2.414824 CCGGATCATAGCTTAGCTCGTC 60.415 54.545 11.09 4.84 40.44 4.20
223 224 1.542030 CCGGATCATAGCTTAGCTCGT 59.458 52.381 11.09 0.00 40.44 4.18
233 247 9.193133 CACTACATAAAGTAAACCGGATCATAG 57.807 37.037 9.46 0.00 30.92 2.23
244 258 6.300703 ACCCTGCAACACTACATAAAGTAAA 58.699 36.000 0.00 0.00 30.92 2.01
275 290 8.552034 CGTCCCTTATATCTGAAGTTTCAAATC 58.448 37.037 0.00 0.00 36.64 2.17
286 301 1.254026 CCCGCGTCCCTTATATCTGA 58.746 55.000 4.92 0.00 0.00 3.27
293 308 3.697747 CCACACCCGCGTCCCTTA 61.698 66.667 4.92 0.00 0.00 2.69
301 316 1.815817 ATTTTTGCTCCCACACCCGC 61.816 55.000 0.00 0.00 0.00 6.13
302 317 1.540267 TATTTTTGCTCCCACACCCG 58.460 50.000 0.00 0.00 0.00 5.28
304 319 4.016444 TCTGATATTTTTGCTCCCACACC 58.984 43.478 0.00 0.00 0.00 4.16
305 320 5.126061 ACATCTGATATTTTTGCTCCCACAC 59.874 40.000 0.00 0.00 0.00 3.82
323 338 1.600957 GGCATTGATCGGACACATCTG 59.399 52.381 0.00 0.00 0.00 2.90
327 342 1.449423 CGGGCATTGATCGGACACA 60.449 57.895 0.00 0.00 0.00 3.72
347 362 1.810030 GGACATCCCGAGCGTGTTC 60.810 63.158 0.00 0.00 0.00 3.18
348 363 2.264794 GGACATCCCGAGCGTGTT 59.735 61.111 0.00 0.00 0.00 3.32
359 374 2.014093 CTCAAACGCTCGCGGACATC 62.014 60.000 16.18 0.00 44.69 3.06
360 375 2.048597 TCAAACGCTCGCGGACAT 60.049 55.556 16.18 0.00 44.69 3.06
380 396 2.363306 TCACCCACAACAAATCTGCT 57.637 45.000 0.00 0.00 0.00 4.24
411 427 1.067142 TGTGCGCCTCCTAGTTGTAAG 60.067 52.381 4.18 0.00 0.00 2.34
412 428 0.970640 TGTGCGCCTCCTAGTTGTAA 59.029 50.000 4.18 0.00 0.00 2.41
413 429 0.245539 GTGTGCGCCTCCTAGTTGTA 59.754 55.000 4.18 0.00 0.00 2.41
414 430 1.004918 GTGTGCGCCTCCTAGTTGT 60.005 57.895 4.18 0.00 0.00 3.32
429 445 0.035317 TGCCATTGAGCTTCTCGTGT 59.965 50.000 0.00 0.00 32.35 4.49
471 487 0.178921 TGGGGCTAAAACCAATGCCA 60.179 50.000 5.21 0.00 46.53 4.92
516 532 0.470766 TGGTTACTGCCAGAAACGGT 59.529 50.000 0.00 0.00 33.97 4.83
524 540 2.967507 TTTGCCGCTGGTTACTGCCA 62.968 55.000 0.00 0.00 38.21 4.92
661 678 2.159462 GGGAAGAAGCTCAAATTCTGCG 60.159 50.000 0.00 0.00 37.10 5.18
662 679 2.821969 TGGGAAGAAGCTCAAATTCTGC 59.178 45.455 0.00 0.00 37.10 4.26
705 722 2.319890 AAAGTCGTGGGTTGGACGCT 62.320 55.000 0.00 0.00 38.20 5.07
708 725 0.942252 GTCAAAGTCGTGGGTTGGAC 59.058 55.000 0.00 0.00 0.00 4.02
866 891 2.625737 CTATATATGCAAGGCAGCGCT 58.374 47.619 2.64 2.64 43.65 5.92
1144 1179 0.512518 CAGACGCTTCGATTTGCACA 59.487 50.000 0.00 0.00 0.00 4.57
1145 1180 0.512952 ACAGACGCTTCGATTTGCAC 59.487 50.000 0.00 1.00 0.00 4.57
1172 1207 1.332375 CGTACACCAAAACCACCAGTG 59.668 52.381 0.00 0.00 34.61 3.66
1506 1547 4.115199 AAGGGCTGCGGATGGGAC 62.115 66.667 0.00 0.00 0.00 4.46
1658 1699 4.463879 CCTCCTGCTGCTGTCCCG 62.464 72.222 0.00 0.00 0.00 5.14
1699 1740 2.125512 GTAGAGCTGGCCGGTGTG 60.126 66.667 14.55 0.00 0.00 3.82
2039 3030 3.135530 AGCAAACAGAGTGGATCTATCCC 59.864 47.826 6.54 0.00 46.59 3.85
2050 3047 7.322664 TCTTTGAAAATTTCAGCAAACAGAGT 58.677 30.769 8.51 0.00 41.38 3.24
2557 3723 7.226128 GTCCTCCTCGGTATATTTTTGGTTAAG 59.774 40.741 0.00 0.00 0.00 1.85
2571 3737 4.224147 TCATTTCATTTGTCCTCCTCGGTA 59.776 41.667 0.00 0.00 0.00 4.02
2593 3759 8.666573 CATCCTAGTGATCTTTATCATTGCATC 58.333 37.037 0.00 0.00 43.87 3.91
2864 4051 1.053424 TCTTTGGCACCTAAGACGGT 58.947 50.000 9.15 0.00 34.07 4.83
2869 4056 5.931441 GTGCTATATCTTTGGCACCTAAG 57.069 43.478 4.70 4.70 46.17 2.18
2891 4078 1.999735 TGTCTTTTGCCGCTATTCTCG 59.000 47.619 0.00 0.00 0.00 4.04
3055 4247 6.105397 ACATGATTTTGCTGAAAGATGGTT 57.895 33.333 0.00 0.00 34.07 3.67
3056 4248 5.733620 ACATGATTTTGCTGAAAGATGGT 57.266 34.783 0.00 0.00 34.07 3.55
3057 4249 6.623486 TGTACATGATTTTGCTGAAAGATGG 58.377 36.000 0.00 0.00 34.07 3.51
3058 4250 9.791820 TTATGTACATGATTTTGCTGAAAGATG 57.208 29.630 18.81 0.00 34.07 2.90
3059 4251 9.793252 GTTATGTACATGATTTTGCTGAAAGAT 57.207 29.630 18.81 0.00 34.07 2.40
3064 4256 8.264347 TCTAGGTTATGTACATGATTTTGCTGA 58.736 33.333 18.81 3.44 0.00 4.26
3182 4374 1.688197 TCTGAGCGATACCATGCATGA 59.312 47.619 28.31 9.57 0.00 3.07
3198 4390 1.760613 ACCGTTGTCTTGTCCTTCTGA 59.239 47.619 0.00 0.00 0.00 3.27
3225 4417 0.969917 TTAGGTACCACGCCGCCTTA 60.970 55.000 15.94 0.00 32.90 2.69
3235 4427 1.822990 CTCCAGCGTCTTTAGGTACCA 59.177 52.381 15.94 0.00 0.00 3.25
3297 4489 0.108329 CGTAGGTCGGGATGTGCTTT 60.108 55.000 0.00 0.00 35.71 3.51
3360 4552 1.559682 GCCTTGGTGATCTGGACCTTA 59.440 52.381 2.68 0.00 34.26 2.69
3450 4642 3.005539 AGGCACTCCAGGATGCGT 61.006 61.111 14.25 12.75 43.02 5.24
3507 4699 1.982395 CTGCGGGGAGTAGGTGTCA 60.982 63.158 0.00 0.00 0.00 3.58
3635 4827 4.004314 TGAAGTTGTTTTTGTCCGAGACA 58.996 39.130 3.02 3.02 41.09 3.41
3649 4841 4.706842 ACCACCAGTAAGATGAAGTTGT 57.293 40.909 0.00 0.00 0.00 3.32
3690 4882 2.432628 GGCCTCGTTCCAGTCGTG 60.433 66.667 0.00 0.00 0.00 4.35
3702 4894 1.376037 CCTCGTGGAACAAGGCCTC 60.376 63.158 5.23 0.00 44.16 4.70
3726 4918 1.495951 CGTCGTTAACAGCCTTGGC 59.504 57.895 6.39 2.97 0.00 4.52
3751 4943 0.596577 CACGAGAGGAGGACGAAACA 59.403 55.000 0.00 0.00 0.00 2.83
3754 4946 1.303398 AGCACGAGAGGAGGACGAA 60.303 57.895 0.00 0.00 0.00 3.85
3805 4997 2.703007 GCTCCTCAGGATTAGGACACAT 59.297 50.000 0.00 0.00 38.24 3.21
3806 4998 2.111384 GCTCCTCAGGATTAGGACACA 58.889 52.381 0.00 0.00 38.24 3.72
3814 5006 4.396522 GCTATGAATTGCTCCTCAGGATT 58.603 43.478 0.00 0.00 0.00 3.01
3819 5011 3.870538 ATGGCTATGAATTGCTCCTCA 57.129 42.857 0.00 0.00 0.00 3.86
3832 5024 3.318275 CGGCTATATGACCGTATGGCTAT 59.682 47.826 14.39 0.00 44.46 2.97
3854 5046 5.175388 ACCATCTAACCTAACCTTTGGAC 57.825 43.478 0.00 0.00 0.00 4.02
3923 5115 0.252421 AGAGTGACTCATCAGGGGCA 60.252 55.000 15.86 0.00 34.75 5.36
3959 5151 4.794655 GCACTGAAGACTTCTTTCTCGTCT 60.795 45.833 16.02 0.00 39.53 4.18
3978 5170 3.601443 ACATTTCTAGCTTCTCGCACT 57.399 42.857 0.00 0.00 42.61 4.40
3982 5174 6.291849 CCGATACAAACATTTCTAGCTTCTCG 60.292 42.308 0.00 0.00 0.00 4.04
3986 5178 6.238484 GCATCCGATACAAACATTTCTAGCTT 60.238 38.462 0.00 0.00 0.00 3.74
4010 5202 0.035439 TTGGTTCCGATCTTCCAGGC 60.035 55.000 0.00 0.00 0.00 4.85
4097 5290 4.556697 TCTAAGGTATGGGAATGAGCTCA 58.443 43.478 20.79 20.79 0.00 4.26
4202 5395 2.233605 TATCCAGGTTCACGCCACCG 62.234 60.000 0.00 0.00 39.56 4.94
4266 5459 1.431243 AGAAGGTGGAGAGAGAGGTGT 59.569 52.381 0.00 0.00 0.00 4.16
4271 5464 2.558795 CGTGAAAGAAGGTGGAGAGAGA 59.441 50.000 0.00 0.00 0.00 3.10
4274 5467 3.601443 ATCGTGAAAGAAGGTGGAGAG 57.399 47.619 0.00 0.00 0.00 3.20
4284 5477 4.862574 CGGTCTGATGTTTATCGTGAAAGA 59.137 41.667 0.00 0.00 36.04 2.52
4288 5481 3.861276 ACGGTCTGATGTTTATCGTGA 57.139 42.857 0.00 0.00 36.04 4.35
4306 5499 4.873746 ATGGTGGTTCATCTATCCTACG 57.126 45.455 0.00 0.00 0.00 3.51
4314 5507 1.548719 TCGACGAATGGTGGTTCATCT 59.451 47.619 0.00 0.00 0.00 2.90
4408 5601 2.956333 CTCCCAACCTTTTCCTTTCGTT 59.044 45.455 0.00 0.00 0.00 3.85
4417 5610 0.537371 CGGTGAGCTCCCAACCTTTT 60.537 55.000 17.10 0.00 0.00 2.27
4432 5625 1.817941 CGGGATTAAGGTGGCGGTG 60.818 63.158 0.00 0.00 0.00 4.94
4454 5647 2.160205 GAGTTAGGTTGACAAAGGCCC 58.840 52.381 0.00 0.00 0.00 5.80
4546 5739 3.062763 CGCAAGTCTATATTCCCAGCTG 58.937 50.000 6.78 6.78 0.00 4.24
4582 5775 2.162681 CCCTCCATTGGTCAAGTTGAC 58.837 52.381 25.00 25.00 46.23 3.18
4605 5800 3.418684 GGTACCACAACAACAGGAGAT 57.581 47.619 7.15 0.00 0.00 2.75
4654 5849 2.741211 GTCAGCGTTTCGGTCCCC 60.741 66.667 0.00 0.00 34.62 4.81
4666 5861 1.745653 GCAACCTTATCCCTTGTCAGC 59.254 52.381 0.00 0.00 0.00 4.26
4708 5903 9.967346 GCTAAAAAGGTCAGAAGAGTAATTTTT 57.033 29.630 0.00 0.00 34.21 1.94
4718 5913 6.795399 TCAAGTTTGCTAAAAAGGTCAGAAG 58.205 36.000 0.00 0.00 0.00 2.85
4732 5927 4.202050 GGTCAGTTTGTGATCAAGTTTGCT 60.202 41.667 0.00 0.00 36.15 3.91
4750 5945 5.535753 ATTCTTTTCAAAACAGGGGTCAG 57.464 39.130 0.00 0.00 0.00 3.51
4754 5949 5.838529 ACGTAATTCTTTTCAAAACAGGGG 58.161 37.500 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.