Multiple sequence alignment - TraesCS1B01G199000

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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 TraesCS1B01G199000 chr1B 100.000 4593 0 0 731 5323 357205665 357210257 0.000000e+00 8482.0
1 TraesCS1B01G199000 chr1B 100.000 367 0 0 1 367 357204935 357205301 0.000000e+00 678.0
2 TraesCS1B01G199000 chr1D 94.892 3896 114 29 784 4639 255837637 255833787 0.000000e+00 6013.0
3 TraesCS1B01G199000 chr1D 93.212 604 23 5 4737 5323 255833787 255833185 0.000000e+00 872.0
4 TraesCS1B01G199000 chr1D 91.209 364 19 7 11 366 255838070 255837712 2.880000e-132 483.0
5 TraesCS1B01G199000 chr1A 93.554 3987 131 48 746 4690 328257765 328253863 0.000000e+00 5823.0
6 TraesCS1B01G199000 chr1A 94.464 578 20 5 4752 5323 328253586 328253015 0.000000e+00 880.0
7 TraesCS1B01G199000 chr1A 88.312 231 14 6 145 366 328257989 328257763 1.140000e-66 265.0
8 TraesCS1B01G199000 chr1A 92.086 139 11 0 4 142 328258326 328258188 4.210000e-46 196.0
9 TraesCS1B01G199000 chr1A 100.000 44 0 0 4711 4754 328253788 328253745 1.230000e-11 82.4
10 TraesCS1B01G199000 chr2D 80.469 128 23 2 15 142 355291632 355291507 4.390000e-16 97.1


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 TraesCS1B01G199000 chr1B 357204935 357210257 5322 False 4580.00 8482 100.000000 1 5323 2 chr1B.!!$F1 5322
1 TraesCS1B01G199000 chr1D 255833185 255838070 4885 True 2456.00 6013 93.104333 11 5323 3 chr1D.!!$R1 5312
2 TraesCS1B01G199000 chr1A 328253015 328258326 5311 True 1449.28 5823 93.683200 4 5323 5 chr1A.!!$R1 5319

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
171 375 1.299541 CAACAGTCACACACCACTCC 58.700 55.0 0.00 0.0 0.0 3.85 F
1766 2025 0.035439 GAAGGTTGGCAGGGAATCGA 60.035 55.0 0.00 0.0 0.0 3.59 F
2639 2924 0.109458 CGACCGTGCACTGCTTAGTA 60.109 55.0 16.19 0.0 0.0 1.82 F
3607 3934 0.168128 GAATTGGCGAACGGAAGGTG 59.832 55.0 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 2397 1.250328 CTACCTCACGGTACACACCA 58.750 55.0 0.00 0.00 46.14 4.17 R
3525 3852 2.159707 CGGGAAAGTGACTGCAAATACG 60.160 50.0 0.00 0.00 0.00 3.06 R
4114 4448 0.452618 CAGTACATTTGCACGTGCCG 60.453 55.0 35.72 23.25 41.18 5.69 R
4472 4825 0.789383 GTTCGCAAACGCATCTTCGG 60.789 55.0 0.00 0.00 39.84 4.30 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
84 85 9.934190 CATGTTTCATACGATCAAATCACATTA 57.066 29.630 0.00 0.00 0.00 1.90
118 119 1.678970 GATTCCCCCAGCAAAGCGT 60.679 57.895 0.00 0.00 0.00 5.07
163 360 3.527533 TGTAGGAACACAACAGTCACAC 58.472 45.455 0.00 0.00 0.00 3.82
164 361 2.779755 AGGAACACAACAGTCACACA 57.220 45.000 0.00 0.00 0.00 3.72
166 363 1.400494 GGAACACAACAGTCACACACC 59.600 52.381 0.00 0.00 0.00 4.16
167 364 2.080693 GAACACAACAGTCACACACCA 58.919 47.619 0.00 0.00 0.00 4.17
171 375 1.299541 CAACAGTCACACACCACTCC 58.700 55.000 0.00 0.00 0.00 3.85
256 460 7.512887 CGAAAATAAATGACACAACACACACAC 60.513 37.037 0.00 0.00 0.00 3.82
257 461 5.826601 ATAAATGACACAACACACACACA 57.173 34.783 0.00 0.00 0.00 3.72
258 462 3.485947 AATGACACAACACACACACAC 57.514 42.857 0.00 0.00 0.00 3.82
259 463 1.884235 TGACACAACACACACACACA 58.116 45.000 0.00 0.00 0.00 3.72
264 468 1.742831 ACAACACACACACACACATCC 59.257 47.619 0.00 0.00 0.00 3.51
293 497 6.045955 ACAAACATCAACAATAAAACGGCTT 58.954 32.000 0.00 0.00 0.00 4.35
1263 1521 2.360350 CCACAGCAATCCACCGCT 60.360 61.111 0.00 0.00 39.66 5.52
1575 1834 0.949105 GGTGGACGTTCGCTGACATT 60.949 55.000 7.45 0.00 0.00 2.71
1581 1840 0.865111 CGTTCGCTGACATTGTTCCA 59.135 50.000 0.00 0.00 0.00 3.53
1674 1933 4.191662 TCTTTTTCTCGACTCGTTTTGC 57.808 40.909 0.00 0.00 0.00 3.68
1676 1935 3.585748 TTTTCTCGACTCGTTTTGCAG 57.414 42.857 0.00 0.00 0.00 4.41
1766 2025 0.035439 GAAGGTTGGCAGGGAATCGA 60.035 55.000 0.00 0.00 0.00 3.59
1835 2100 2.492088 GGGACACCCTCTATTTTGTTGC 59.508 50.000 0.00 0.00 41.34 4.17
1836 2101 3.421844 GGACACCCTCTATTTTGTTGCT 58.578 45.455 0.00 0.00 0.00 3.91
1837 2102 3.191371 GGACACCCTCTATTTTGTTGCTG 59.809 47.826 0.00 0.00 0.00 4.41
1839 2104 2.094545 CACCCTCTATTTTGTTGCTGGC 60.095 50.000 0.00 0.00 0.00 4.85
1842 2107 3.119352 CCCTCTATTTTGTTGCTGGCTTC 60.119 47.826 0.00 0.00 0.00 3.86
1843 2108 3.507233 CCTCTATTTTGTTGCTGGCTTCA 59.493 43.478 0.00 0.00 0.00 3.02
1897 2169 3.587797 AGAACCAGAGATACGCGAAAA 57.412 42.857 15.93 0.00 0.00 2.29
1908 2180 2.525750 ACGCGAAAATACTGTGCATG 57.474 45.000 15.93 0.00 0.00 4.06
2036 2308 3.248043 TGCACTGCACTACCAATCC 57.752 52.632 0.00 0.00 31.71 3.01
2037 2309 0.692476 TGCACTGCACTACCAATCCT 59.308 50.000 0.00 0.00 31.71 3.24
2120 2397 3.154710 GCTAGTAAAGGTTTTGTGCCCT 58.845 45.455 0.00 0.00 0.00 5.19
2540 2817 5.362430 TGTTCCCTTTGTTTTAGTTCTGCAT 59.638 36.000 0.00 0.00 0.00 3.96
2639 2924 0.109458 CGACCGTGCACTGCTTAGTA 60.109 55.000 16.19 0.00 0.00 1.82
2805 3099 6.062258 AGGTTGCAAAGGCTTACTAAGATA 57.938 37.500 0.00 0.00 41.91 1.98
2965 3259 6.487331 CACCCTTACAGTTACAACATGGTTTA 59.513 38.462 0.00 0.00 0.00 2.01
3002 3296 1.946984 ACTGGACTGGGACGGATTAA 58.053 50.000 0.00 0.00 38.67 1.40
3094 3388 7.386025 GCTTTTTCATTTATCAAGTTCCAAGCT 59.614 33.333 0.00 0.00 0.00 3.74
3104 3398 2.102578 AGTTCCAAGCTTTGCAAGTGT 58.897 42.857 0.00 0.00 0.00 3.55
3105 3399 2.497273 AGTTCCAAGCTTTGCAAGTGTT 59.503 40.909 0.00 0.00 0.00 3.32
3106 3400 3.055891 AGTTCCAAGCTTTGCAAGTGTTT 60.056 39.130 0.00 0.00 0.00 2.83
3107 3401 3.163630 TCCAAGCTTTGCAAGTGTTTC 57.836 42.857 0.00 0.00 0.00 2.78
3108 3402 2.495270 TCCAAGCTTTGCAAGTGTTTCA 59.505 40.909 0.00 0.00 0.00 2.69
3109 3403 3.056250 TCCAAGCTTTGCAAGTGTTTCAA 60.056 39.130 0.00 0.00 0.00 2.69
3110 3404 3.683822 CCAAGCTTTGCAAGTGTTTCAAA 59.316 39.130 0.00 0.00 0.00 2.69
3111 3405 4.435917 CCAAGCTTTGCAAGTGTTTCAAAC 60.436 41.667 0.00 0.00 0.00 2.93
3147 3467 4.163458 AGTTATATCGTCCTTTTGGGCTGA 59.837 41.667 0.00 0.00 43.43 4.26
3148 3468 2.396590 TATCGTCCTTTTGGGCTGAC 57.603 50.000 0.00 0.00 43.43 3.51
3149 3469 0.693049 ATCGTCCTTTTGGGCTGACT 59.307 50.000 0.00 0.00 43.43 3.41
3150 3470 1.344065 TCGTCCTTTTGGGCTGACTA 58.656 50.000 0.00 0.00 43.43 2.59
3151 3471 1.906574 TCGTCCTTTTGGGCTGACTAT 59.093 47.619 0.00 0.00 43.43 2.12
3152 3472 2.304761 TCGTCCTTTTGGGCTGACTATT 59.695 45.455 0.00 0.00 43.43 1.73
3153 3473 3.516300 TCGTCCTTTTGGGCTGACTATTA 59.484 43.478 0.00 0.00 43.43 0.98
3154 3474 3.871594 CGTCCTTTTGGGCTGACTATTAG 59.128 47.826 0.00 0.00 43.43 1.73
3155 3475 3.628032 GTCCTTTTGGGCTGACTATTAGC 59.372 47.826 0.00 0.00 42.03 3.09
3156 3476 3.265737 TCCTTTTGGGCTGACTATTAGCA 59.734 43.478 0.00 0.00 42.88 3.49
3157 3477 3.629398 CCTTTTGGGCTGACTATTAGCAG 59.371 47.826 0.00 9.45 42.88 4.24
3158 3478 4.265073 CTTTTGGGCTGACTATTAGCAGT 58.735 43.478 13.21 0.00 42.88 4.40
3159 3479 4.301072 TTTGGGCTGACTATTAGCAGTT 57.699 40.909 13.21 0.00 42.88 3.16
3160 3480 3.266510 TGGGCTGACTATTAGCAGTTG 57.733 47.619 13.21 0.00 42.88 3.16
3161 3481 2.837591 TGGGCTGACTATTAGCAGTTGA 59.162 45.455 13.21 0.82 42.88 3.18
3162 3482 3.198872 GGGCTGACTATTAGCAGTTGAC 58.801 50.000 13.21 5.57 42.88 3.18
3163 3483 3.118592 GGGCTGACTATTAGCAGTTGACT 60.119 47.826 13.21 0.00 42.88 3.41
3164 3484 4.116238 GGCTGACTATTAGCAGTTGACTC 58.884 47.826 13.21 1.28 42.88 3.36
3165 3485 4.382040 GGCTGACTATTAGCAGTTGACTCA 60.382 45.833 13.21 0.00 42.88 3.41
3166 3486 5.355596 GCTGACTATTAGCAGTTGACTCAT 58.644 41.667 13.21 0.00 40.81 2.90
3167 3487 5.814705 GCTGACTATTAGCAGTTGACTCATT 59.185 40.000 13.21 0.00 40.81 2.57
3168 3488 6.980978 GCTGACTATTAGCAGTTGACTCATTA 59.019 38.462 13.21 0.00 40.81 1.90
3169 3489 7.655328 GCTGACTATTAGCAGTTGACTCATTAT 59.345 37.037 13.21 0.00 40.81 1.28
3170 3490 9.539825 CTGACTATTAGCAGTTGACTCATTATT 57.460 33.333 6.86 0.00 0.00 1.40
3171 3491 9.890629 TGACTATTAGCAGTTGACTCATTATTT 57.109 29.630 0.00 0.00 0.00 1.40
3525 3852 7.334421 ACAATATAATTACATGCATCGGGTCTC 59.666 37.037 0.00 0.00 0.00 3.36
3548 3875 1.593196 TTTGCAGTCACTTTCCCGAG 58.407 50.000 0.00 0.00 0.00 4.63
3607 3934 0.168128 GAATTGGCGAACGGAAGGTG 59.832 55.000 0.00 0.00 0.00 4.00
3622 3949 0.535102 AGGTGCCACTTCAAACCTCG 60.535 55.000 0.00 0.00 38.73 4.63
3780 4114 5.163982 GGCTAACATGTAGAGTTTGTCGAAC 60.164 44.000 0.00 0.00 38.58 3.95
3826 4160 4.923281 ACTTTTCATGAGCCATTTAAACGC 59.077 37.500 0.00 0.00 0.00 4.84
4114 4448 2.101750 GCAGTAGGAAGGAGTAGGAAGC 59.898 54.545 0.00 0.00 0.00 3.86
4227 4561 6.531021 ACTAATTGTTGTTGTAGTGTAGGCT 58.469 36.000 0.00 0.00 0.00 4.58
4232 4566 4.141574 TGTTGTTGTAGTGTAGGCTTTCCT 60.142 41.667 0.00 0.00 46.57 3.36
4315 4649 5.411669 ACAATTTAGCCGATCTTCTCGTTTT 59.588 36.000 0.00 0.00 46.18 2.43
4316 4650 6.072673 ACAATTTAGCCGATCTTCTCGTTTTT 60.073 34.615 0.00 0.00 46.18 1.94
4367 4719 2.015587 CTCTCAGAGCCATCCAAAAGC 58.984 52.381 0.00 0.00 0.00 3.51
4472 4825 6.721321 TCAATGAACTTTCGTGTTTAGGTTC 58.279 36.000 0.00 0.00 35.20 3.62
4473 4826 5.684550 ATGAACTTTCGTGTTTAGGTTCC 57.315 39.130 0.00 0.00 34.15 3.62
4505 4858 1.901650 GCGAACGGTTGCCTCTTCAG 61.902 60.000 0.00 0.00 0.00 3.02
4529 4882 2.762472 CTCAATGCTGCGTACTTTTCG 58.238 47.619 0.00 0.00 0.00 3.46
4544 4900 4.444536 ACTTTTCGCACAACTTGGTACTA 58.555 39.130 0.00 0.00 0.00 1.82
4655 5011 8.885346 AGCTCTTAATATAAATGGGCTCTACTT 58.115 33.333 0.00 0.00 0.00 2.24
4656 5012 8.940952 GCTCTTAATATAAATGGGCTCTACTTG 58.059 37.037 0.00 0.00 0.00 3.16
4660 5016 7.693969 AATATAAATGGGCTCTACTTGCATC 57.306 36.000 0.00 0.00 0.00 3.91
4669 5025 3.869912 GCTCTACTTGCATCCTTGGTTGA 60.870 47.826 2.19 0.00 0.00 3.18
4678 5034 8.761689 ACTTGCATCCTTGGTTGATTATTATTT 58.238 29.630 2.19 0.00 0.00 1.40
4705 5107 0.685458 ATGTTCTGCAATGGAGGGCC 60.685 55.000 1.05 0.00 0.00 5.80
4770 5341 2.916702 TACATGCCACTGCTGGATAG 57.083 50.000 0.00 0.00 40.55 2.08
4810 5381 3.022607 GCATTCTTCTGCAAGCTGTTT 57.977 42.857 0.00 0.00 41.87 2.83
4898 5469 1.852157 AGGGGAATGCACAGGACCA 60.852 57.895 0.00 0.00 0.00 4.02
4932 5503 7.290248 TGACCCACCAAAACCTATTGAATAAAA 59.710 33.333 0.00 0.00 31.84 1.52
5080 5670 6.470877 CGAGTACTGCTTCTCTTATGAAACTC 59.529 42.308 0.00 0.00 31.08 3.01
5081 5671 7.475137 AGTACTGCTTCTCTTATGAAACTCT 57.525 36.000 0.00 0.00 0.00 3.24
5185 5775 7.560262 TCCCTAATGTCTTCTATTTCTTCTCGA 59.440 37.037 0.00 0.00 0.00 4.04
5203 5793 4.974275 TCTCGACAGTATAACGCATTAAGC 59.026 41.667 0.00 0.00 40.87 3.09
5228 5818 1.971962 GCTGCAACTGAAAACGATTCG 59.028 47.619 4.14 4.14 0.00 3.34
5229 5819 2.574322 CTGCAACTGAAAACGATTCGG 58.426 47.619 11.29 11.31 0.00 4.30
5230 5820 1.265635 TGCAACTGAAAACGATTCGGG 59.734 47.619 11.29 7.69 0.00 5.14
5300 5890 6.489675 CAGCTTAAGAAATGTATTGCGACAT 58.510 36.000 6.67 0.00 41.92 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.989155 AAAATACATACTCCCTCCGATACA 57.011 37.500 0.00 0.00 0.00 2.29
1 2 8.583296 ACTTAAAATACATACTCCCTCCGATAC 58.417 37.037 0.00 0.00 0.00 2.24
2 3 8.716674 ACTTAAAATACATACTCCCTCCGATA 57.283 34.615 0.00 0.00 0.00 2.92
84 85 6.614906 TGGGGGAATCAGTTGCAATATATTTT 59.385 34.615 0.59 0.00 0.00 1.82
107 108 0.447801 GATACCACACGCTTTGCTGG 59.552 55.000 0.00 0.00 34.36 4.85
198 402 2.436109 GGCTGGCTTGGTCCTTGA 59.564 61.111 0.00 0.00 0.00 3.02
231 435 7.274468 TGTGTGTGTGTTGTGTCATTTATTTTC 59.726 33.333 0.00 0.00 0.00 2.29
256 460 5.185668 TGATGTTTGTTGAAGGATGTGTG 57.814 39.130 0.00 0.00 0.00 3.82
257 461 5.126869 TGTTGATGTTTGTTGAAGGATGTGT 59.873 36.000 0.00 0.00 0.00 3.72
258 462 5.590145 TGTTGATGTTTGTTGAAGGATGTG 58.410 37.500 0.00 0.00 0.00 3.21
259 463 5.850557 TGTTGATGTTTGTTGAAGGATGT 57.149 34.783 0.00 0.00 0.00 3.06
264 468 8.055402 CCGTTTTATTGTTGATGTTTGTTGAAG 58.945 33.333 0.00 0.00 0.00 3.02
293 497 3.193263 TGCGTCGGTTGTGTACTTTTTA 58.807 40.909 0.00 0.00 0.00 1.52
327 532 3.385193 AAAACTTTGCTGCGCCTATTT 57.615 38.095 4.18 0.00 0.00 1.40
1089 1347 2.042025 GAGGAGGAGGAGGCAGCT 60.042 66.667 0.00 0.00 0.00 4.24
1158 1416 4.415332 GACGACGAAGAGCCGGCA 62.415 66.667 31.54 0.00 37.43 5.69
1253 1511 1.411041 GTACCTAGGAGCGGTGGATT 58.589 55.000 17.98 0.00 35.98 3.01
1263 1521 1.424302 CGAGGGAGATGGTACCTAGGA 59.576 57.143 17.98 0.00 34.02 2.94
1454 1713 7.950124 ACAAAAGAAAGGGGAGAAGATTGATTA 59.050 33.333 0.00 0.00 0.00 1.75
1575 1834 2.028476 CCCAATCACGTAGTCTGGAACA 60.028 50.000 6.69 0.00 41.61 3.18
1581 1840 2.906354 GATTGCCCAATCACGTAGTCT 58.094 47.619 14.39 0.00 44.89 3.24
1674 1933 5.106396 CCTTCTTGGCATTGTTCTTCTACTG 60.106 44.000 0.00 0.00 0.00 2.74
1676 1935 5.302357 CCTTCTTGGCATTGTTCTTCTAC 57.698 43.478 0.00 0.00 0.00 2.59
1752 2011 3.343617 CTTACTTTCGATTCCCTGCCAA 58.656 45.455 0.00 0.00 0.00 4.52
1834 2099 1.386533 ATACATGCAGTGAAGCCAGC 58.613 50.000 0.00 0.00 0.00 4.85
1835 2100 2.751259 ACAATACATGCAGTGAAGCCAG 59.249 45.455 0.00 0.00 0.00 4.85
1836 2101 2.794103 ACAATACATGCAGTGAAGCCA 58.206 42.857 0.00 0.00 0.00 4.75
1837 2102 3.855689 AACAATACATGCAGTGAAGCC 57.144 42.857 0.00 0.00 0.00 4.35
1875 2147 4.707030 TTTCGCGTATCTCTGGTTCTAA 57.293 40.909 5.77 0.00 0.00 2.10
1908 2180 4.989168 CCCCTAGCGAAATGTATCTGTTAC 59.011 45.833 0.00 0.00 0.00 2.50
1986 2258 4.919774 TGCTAGGGTGTTCAAATAAGGA 57.080 40.909 0.00 0.00 0.00 3.36
1988 2260 7.156876 TGAAATGCTAGGGTGTTCAAATAAG 57.843 36.000 0.00 0.00 0.00 1.73
2029 2301 7.931015 TGTCTAATAGATTGGTAGGATTGGT 57.069 36.000 0.00 0.00 0.00 3.67
2030 2302 8.210946 TGTTGTCTAATAGATTGGTAGGATTGG 58.789 37.037 0.00 0.00 0.00 3.16
2031 2303 9.613428 TTGTTGTCTAATAGATTGGTAGGATTG 57.387 33.333 0.00 0.00 0.00 2.67
2032 2304 9.838339 CTTGTTGTCTAATAGATTGGTAGGATT 57.162 33.333 0.00 0.00 0.00 3.01
2033 2305 8.993424 ACTTGTTGTCTAATAGATTGGTAGGAT 58.007 33.333 0.00 0.00 0.00 3.24
2034 2306 8.375493 ACTTGTTGTCTAATAGATTGGTAGGA 57.625 34.615 0.00 0.00 0.00 2.94
2035 2307 9.449719 AAACTTGTTGTCTAATAGATTGGTAGG 57.550 33.333 0.00 0.00 0.00 3.18
2037 2309 9.226606 CCAAACTTGTTGTCTAATAGATTGGTA 57.773 33.333 6.79 0.00 0.00 3.25
2120 2397 1.250328 CTACCTCACGGTACACACCA 58.750 55.000 0.00 0.00 46.14 4.17
2540 2817 7.203910 ACATTTATAAACAACCGAAGCAACAA 58.796 30.769 0.00 0.00 0.00 2.83
2574 2851 8.826765 AGGAACCTAAACAAGAAGATCTTATGA 58.173 33.333 21.48 4.77 33.78 2.15
2582 2867 5.445964 AGCAAAGGAACCTAAACAAGAAGA 58.554 37.500 0.00 0.00 0.00 2.87
2583 2868 5.532779 AGAGCAAAGGAACCTAAACAAGAAG 59.467 40.000 0.00 0.00 0.00 2.85
2584 2869 5.299279 CAGAGCAAAGGAACCTAAACAAGAA 59.701 40.000 0.00 0.00 0.00 2.52
2782 3076 4.367039 TCTTAGTAAGCCTTTGCAACCT 57.633 40.909 0.00 0.00 41.13 3.50
2805 3099 5.104259 AGAGAACAGTTTGGTCAAAGAGT 57.896 39.130 0.00 0.00 36.30 3.24
3094 3388 6.851222 TTGAAAGTTTGAAACACTTGCAAA 57.149 29.167 11.02 0.00 43.85 3.68
3110 3404 9.530633 GGACGATATAACTTCTGTATTGAAAGT 57.469 33.333 0.00 0.00 0.00 2.66
3111 3405 9.751542 AGGACGATATAACTTCTGTATTGAAAG 57.248 33.333 0.00 0.00 0.00 2.62
3147 3467 8.616076 GCAAATAATGAGTCAACTGCTAATAGT 58.384 33.333 0.00 0.00 0.00 2.12
3148 3468 8.834465 AGCAAATAATGAGTCAACTGCTAATAG 58.166 33.333 13.08 0.00 37.14 1.73
3149 3469 8.615211 CAGCAAATAATGAGTCAACTGCTAATA 58.385 33.333 13.88 0.00 36.79 0.98
3150 3470 7.121759 ACAGCAAATAATGAGTCAACTGCTAAT 59.878 33.333 13.88 6.50 36.79 1.73
3151 3471 6.430925 ACAGCAAATAATGAGTCAACTGCTAA 59.569 34.615 13.88 0.00 36.79 3.09
3152 3472 5.939883 ACAGCAAATAATGAGTCAACTGCTA 59.060 36.000 13.88 0.00 36.79 3.49
3153 3473 4.763793 ACAGCAAATAATGAGTCAACTGCT 59.236 37.500 0.00 4.56 39.38 4.24
3154 3474 5.051891 ACAGCAAATAATGAGTCAACTGC 57.948 39.130 0.00 2.20 0.00 4.40
3155 3475 7.584108 TGTTACAGCAAATAATGAGTCAACTG 58.416 34.615 0.00 0.00 0.00 3.16
3156 3476 7.744087 TGTTACAGCAAATAATGAGTCAACT 57.256 32.000 0.00 0.00 0.00 3.16
3157 3477 7.059488 CGTTGTTACAGCAAATAATGAGTCAAC 59.941 37.037 0.00 0.00 0.00 3.18
3158 3478 7.041712 TCGTTGTTACAGCAAATAATGAGTCAA 60.042 33.333 0.00 0.00 0.00 3.18
3159 3479 6.425417 TCGTTGTTACAGCAAATAATGAGTCA 59.575 34.615 0.00 0.00 0.00 3.41
3160 3480 6.827641 TCGTTGTTACAGCAAATAATGAGTC 58.172 36.000 0.00 0.00 0.00 3.36
3161 3481 6.795098 TCGTTGTTACAGCAAATAATGAGT 57.205 33.333 0.00 0.00 0.00 3.41
3162 3482 7.463544 TGATCGTTGTTACAGCAAATAATGAG 58.536 34.615 0.00 0.00 31.63 2.90
3163 3483 7.371126 TGATCGTTGTTACAGCAAATAATGA 57.629 32.000 0.00 0.00 32.34 2.57
3164 3484 8.619146 AATGATCGTTGTTACAGCAAATAATG 57.381 30.769 0.00 0.00 0.00 1.90
3168 3488 9.075519 CAAATAATGATCGTTGTTACAGCAAAT 57.924 29.630 10.54 0.00 0.00 2.32
3169 3489 7.540400 CCAAATAATGATCGTTGTTACAGCAAA 59.460 33.333 10.54 0.00 0.00 3.68
3170 3490 7.026562 CCAAATAATGATCGTTGTTACAGCAA 58.973 34.615 10.54 0.00 0.00 3.91
3171 3491 6.150307 ACCAAATAATGATCGTTGTTACAGCA 59.850 34.615 10.54 0.00 0.00 4.41
3172 3492 6.468956 CACCAAATAATGATCGTTGTTACAGC 59.531 38.462 10.54 0.00 0.00 4.40
3429 3750 6.796705 ACAGTAATAAAGCTGTACACAACC 57.203 37.500 0.00 0.00 43.30 3.77
3525 3852 2.159707 CGGGAAAGTGACTGCAAATACG 60.160 50.000 0.00 0.00 0.00 3.06
3607 3934 3.643159 AAATTCGAGGTTTGAAGTGGC 57.357 42.857 0.00 0.00 0.00 5.01
3780 4114 3.766151 TCATGAAGTCGCTTTACCTACG 58.234 45.455 0.00 0.00 0.00 3.51
4114 4448 0.452618 CAGTACATTTGCACGTGCCG 60.453 55.000 35.72 23.25 41.18 5.69
4227 4561 4.161377 CACCCCTTGTTGAGAAAAAGGAAA 59.839 41.667 6.83 0.00 42.65 3.13
4232 4566 3.390175 TCCACCCCTTGTTGAGAAAAA 57.610 42.857 0.00 0.00 0.00 1.94
4315 4649 4.927425 GGCAGAAACGTATACTGACAGAAA 59.073 41.667 10.08 0.00 39.23 2.52
4316 4650 4.219944 AGGCAGAAACGTATACTGACAGAA 59.780 41.667 19.41 0.00 41.55 3.02
4317 4651 3.762288 AGGCAGAAACGTATACTGACAGA 59.238 43.478 19.41 0.00 41.55 3.41
4318 4652 4.111375 AGGCAGAAACGTATACTGACAG 57.889 45.455 19.41 0.00 41.55 3.51
4319 4653 4.242475 CAAGGCAGAAACGTATACTGACA 58.758 43.478 19.41 0.00 41.55 3.58
4320 4654 3.617263 CCAAGGCAGAAACGTATACTGAC 59.383 47.826 16.77 14.68 39.66 3.51
4321 4655 3.512329 TCCAAGGCAGAAACGTATACTGA 59.488 43.478 16.77 0.00 34.07 3.41
4322 4656 3.857052 TCCAAGGCAGAAACGTATACTG 58.143 45.455 0.56 10.72 35.14 2.74
4323 4657 3.767673 TCTCCAAGGCAGAAACGTATACT 59.232 43.478 0.56 0.00 0.00 2.12
4324 4658 4.119442 TCTCCAAGGCAGAAACGTATAC 57.881 45.455 0.00 0.00 0.00 1.47
4325 4659 4.222145 AGTTCTCCAAGGCAGAAACGTATA 59.778 41.667 0.00 0.00 31.60 1.47
4326 4660 3.008049 AGTTCTCCAAGGCAGAAACGTAT 59.992 43.478 0.00 0.00 31.60 3.06
4327 4661 2.367567 AGTTCTCCAAGGCAGAAACGTA 59.632 45.455 0.00 0.00 31.60 3.57
4328 4662 1.141053 AGTTCTCCAAGGCAGAAACGT 59.859 47.619 0.00 0.00 31.60 3.99
4329 4663 1.801178 GAGTTCTCCAAGGCAGAAACG 59.199 52.381 0.00 0.00 31.60 3.60
4330 4664 3.070748 GAGAGTTCTCCAAGGCAGAAAC 58.929 50.000 0.00 0.00 37.02 2.78
4367 4719 6.677781 ATACAGATTACATTTTCCGGTGTG 57.322 37.500 0.00 0.00 0.00 3.82
4443 4796 1.798223 CACGAAAGTTCATTGAGCCGA 59.202 47.619 0.00 0.00 46.40 5.54
4450 4803 5.277634 CGGAACCTAAACACGAAAGTTCATT 60.278 40.000 0.00 0.00 46.40 2.57
4453 4806 3.803778 TCGGAACCTAAACACGAAAGTTC 59.196 43.478 0.00 0.00 46.40 3.01
4472 4825 0.789383 GTTCGCAAACGCATCTTCGG 60.789 55.000 0.00 0.00 39.84 4.30
4473 4826 2.613971 GTTCGCAAACGCATCTTCG 58.386 52.632 0.00 0.00 39.84 3.79
4489 4842 1.608283 GCTACTGAAGAGGCAACCGTT 60.608 52.381 0.00 0.00 37.17 4.44
4493 4846 2.751166 TGAGCTACTGAAGAGGCAAC 57.249 50.000 0.00 0.00 0.00 4.17
4529 4882 3.058914 CAGCAAGTAGTACCAAGTTGTGC 60.059 47.826 12.53 2.56 31.26 4.57
4533 4886 2.552373 GGGCAGCAAGTAGTACCAAGTT 60.552 50.000 0.00 0.00 0.00 2.66
4544 4900 3.897505 AGTTCTATTTTTGGGCAGCAAGT 59.102 39.130 0.00 0.00 0.00 3.16
4644 5000 1.065199 CAAGGATGCAAGTAGAGCCCA 60.065 52.381 0.00 0.00 0.00 5.36
4655 5011 8.756927 TGAAAATAATAATCAACCAAGGATGCA 58.243 29.630 0.00 0.00 0.00 3.96
4656 5012 9.768662 ATGAAAATAATAATCAACCAAGGATGC 57.231 29.630 0.00 0.00 0.00 3.91
4678 5034 5.336929 CCTCCATTGCAGAACATTGAATGAA 60.337 40.000 12.80 0.00 32.46 2.57
4705 5107 2.825836 GATCCCTGCCTGGTTGCG 60.826 66.667 0.00 0.00 0.00 4.85
4810 5381 2.148052 TAGGGTGCCCGTTGGTTCA 61.148 57.895 0.98 0.00 41.95 3.18
4898 5469 4.086457 GGTTTTGGTGGGTCATAGATTGT 58.914 43.478 0.00 0.00 0.00 2.71
5080 5670 1.660167 TGGCTTTCGCATCATCTGAG 58.340 50.000 0.00 0.00 38.10 3.35
5081 5671 2.011947 CTTGGCTTTCGCATCATCTGA 58.988 47.619 0.00 0.00 38.10 3.27
5124 5714 5.438761 AGAAACATAGCAAGGTGAAACAC 57.561 39.130 0.00 0.00 39.98 3.32
5125 5715 5.592282 TGAAGAAACATAGCAAGGTGAAACA 59.408 36.000 0.00 0.00 39.98 2.83
5203 5793 2.032054 TCGTTTTCAGTTGCAGCAAGAG 59.968 45.455 8.49 4.12 0.00 2.85
5228 5818 1.474330 ATTCACGATGCCTTTTCCCC 58.526 50.000 0.00 0.00 0.00 4.81
5229 5819 4.398044 TCTTTATTCACGATGCCTTTTCCC 59.602 41.667 0.00 0.00 0.00 3.97
5230 5820 5.560966 TCTTTATTCACGATGCCTTTTCC 57.439 39.130 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.