Multiple sequence alignment - TraesCS5D01G418700

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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 TraesCS5D01G418700 chr5D 100.000 4397 0 0 1 4397 480365070 480360674 0.000000e+00 8120.0
1 TraesCS5D01G418700 chr5A 92.541 3821 169 39 1 3766 598865210 598861451 0.000000e+00 5371.0
2 TraesCS5D01G418700 chr5A 87.873 569 55 10 3823 4389 598860502 598859946 0.000000e+00 656.0
3 TraesCS5D01G418700 chr5B 90.016 3696 221 55 193 3819 588513939 588510323 0.000000e+00 4645.0
4 TraesCS5D01G418700 chr5B 84.122 592 55 14 3823 4389 588510043 588509466 1.800000e-148 536.0
5 TraesCS5D01G418700 chr6A 83.631 336 30 13 422 744 29402081 29401758 4.300000e-75 292.0
6 TraesCS5D01G418700 chr7B 86.567 268 20 11 481 744 116070940 116070685 9.310000e-72 281.0
7 TraesCS5D01G418700 chr4D 82.687 335 33 13 422 743 435252601 435252279 1.560000e-69 274.0
8 TraesCS5D01G418700 chr4D 82.524 206 20 8 481 682 361189402 361189209 2.720000e-37 167.0
9 TraesCS5D01G418700 chr6B 85.821 268 22 11 481 744 720150977 720151232 2.020000e-68 270.0
10 TraesCS5D01G418700 chr3B 85.448 268 23 10 481 744 711740306 711740561 9.380000e-67 265.0
11 TraesCS5D01G418700 chr7A 83.582 268 28 8 481 744 440950648 440950393 2.040000e-58 237.0
12 TraesCS5D01G418700 chr3D 97.059 34 1 0 2692 2725 515675666 515675633 1.710000e-04 58.4
13 TraesCS5D01G418700 chr3A 97.059 34 1 0 2692 2725 649938588 649938555 1.710000e-04 58.4


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 TraesCS5D01G418700 chr5D 480360674 480365070 4396 True 8120.0 8120 100.000 1 4397 1 chr5D.!!$R1 4396
1 TraesCS5D01G418700 chr5A 598859946 598865210 5264 True 3013.5 5371 90.207 1 4389 2 chr5A.!!$R1 4388
2 TraesCS5D01G418700 chr5B 588509466 588513939 4473 True 2590.5 4645 87.069 193 4389 2 chr5B.!!$R1 4196

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
593 621 0.036010 CAAATCAGTCAGCTCCCCGT 60.036 55.000 0.00 0.00 0.0 5.28 F
594 622 0.250513 AAATCAGTCAGCTCCCCGTC 59.749 55.000 0.00 0.00 0.0 4.79 F
787 837 0.978146 CACCGTCATCTCCTCCCCTT 60.978 60.000 0.00 0.00 0.0 3.95 F
791 841 1.057275 GTCATCTCCTCCCCTTCCCC 61.057 65.000 0.00 0.00 0.0 4.81 F
2358 2426 1.079127 CCACTGTAAGGCCGTCAGG 60.079 63.158 21.95 13.84 39.3 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 1992 1.283793 CGTGCACCTGCTTTCCAAG 59.716 57.895 12.15 0.0 42.66 3.61 R
2353 2421 1.375268 GCTCCTGCAGTGACCTGAC 60.375 63.158 13.81 0.0 41.50 3.51 R
2661 2729 1.925415 GCACGATGCCATGCTTGTCA 61.925 55.000 0.00 0.0 37.42 3.58 R
2727 2795 4.087892 GCTTCGGAGAGCAGGCCA 62.088 66.667 5.01 0.0 38.43 5.36 R
3479 3547 0.034089 ATAGACCTGGCCCTTGTTGC 60.034 55.000 0.00 0.0 0.00 4.17 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
150 152 7.147983 ACGAGAAAGGATCATATATGGTAGCTC 60.148 40.741 12.78 7.62 0.00 4.09
151 153 7.148000 CGAGAAAGGATCATATATGGTAGCTCA 60.148 40.741 12.78 0.00 0.00 4.26
153 155 8.703743 AGAAAGGATCATATATGGTAGCTCATC 58.296 37.037 12.78 6.37 0.00 2.92
183 185 5.700832 TGATAATAATCATCTTGTCACGGGC 59.299 40.000 0.00 0.00 37.20 6.13
249 262 5.470777 CGGGTTCTACATTTCCACTACAAAA 59.529 40.000 0.00 0.00 0.00 2.44
284 297 2.487445 GGCTTCTAATACTGGAAGGGGC 60.487 54.545 0.00 0.00 39.81 5.80
287 300 3.414759 TCTAATACTGGAAGGGGCTGA 57.585 47.619 0.00 0.00 39.30 4.26
289 302 3.648067 TCTAATACTGGAAGGGGCTGATG 59.352 47.826 0.00 0.00 39.30 3.07
294 307 2.696125 GAAGGGGCTGATGGGGGA 60.696 66.667 0.00 0.00 0.00 4.81
296 309 2.573893 GAAGGGGCTGATGGGGGAAC 62.574 65.000 0.00 0.00 0.00 3.62
298 311 4.506255 GGGCTGATGGGGGAACGG 62.506 72.222 0.00 0.00 0.00 4.44
341 354 9.455847 GAGTAGCAATGAACATTGGAAATTATC 57.544 33.333 23.05 8.71 46.14 1.75
354 367 9.030301 CATTGGAAATTATCGGAAATTAACACC 57.970 33.333 0.00 0.00 0.00 4.16
355 368 7.704578 TGGAAATTATCGGAAATTAACACCA 57.295 32.000 0.00 0.00 0.00 4.17
364 377 6.165577 TCGGAAATTAACACCAAGTACTACC 58.834 40.000 0.00 0.00 0.00 3.18
385 401 1.764054 CTCCTAGTCCCAGCCCCTG 60.764 68.421 0.00 0.00 0.00 4.45
474 498 2.046023 TGGATGTGGCCGAGCTTG 60.046 61.111 0.00 0.00 0.00 4.01
571 599 2.813474 GCACCGTATCTGCACGCA 60.813 61.111 0.00 0.00 40.59 5.24
586 614 1.237285 ACGCACCCAAATCAGTCAGC 61.237 55.000 0.00 0.00 0.00 4.26
592 620 0.745845 CCAAATCAGTCAGCTCCCCG 60.746 60.000 0.00 0.00 0.00 5.73
593 621 0.036010 CAAATCAGTCAGCTCCCCGT 60.036 55.000 0.00 0.00 0.00 5.28
594 622 0.250513 AAATCAGTCAGCTCCCCGTC 59.749 55.000 0.00 0.00 0.00 4.79
595 623 1.949847 AATCAGTCAGCTCCCCGTCG 61.950 60.000 0.00 0.00 0.00 5.12
781 831 1.050988 CATCCCCACCGTCATCTCCT 61.051 60.000 0.00 0.00 0.00 3.69
785 835 2.435693 CCACCGTCATCTCCTCCCC 61.436 68.421 0.00 0.00 0.00 4.81
786 836 1.381872 CACCGTCATCTCCTCCCCT 60.382 63.158 0.00 0.00 0.00 4.79
787 837 0.978146 CACCGTCATCTCCTCCCCTT 60.978 60.000 0.00 0.00 0.00 3.95
791 841 1.057275 GTCATCTCCTCCCCTTCCCC 61.057 65.000 0.00 0.00 0.00 4.81
796 847 3.711782 CCTCCCCTTCCCCCTCCT 61.712 72.222 0.00 0.00 0.00 3.69
858 909 1.166531 GGCCGAGAGAGAGAGAGAGC 61.167 65.000 0.00 0.00 0.00 4.09
1547 1615 3.060866 GAGGGTGCACTCCTTCGT 58.939 61.111 22.78 6.64 34.21 3.85
1648 1716 3.110178 CGAGGGCCGTGTTCGAAC 61.110 66.667 21.42 21.42 39.71 3.95
1649 1717 2.029964 GAGGGCCGTGTTCGAACA 59.970 61.111 26.53 26.53 39.71 3.18
1924 1992 1.675641 AACCTTCGCATGGTGAGCC 60.676 57.895 0.00 0.00 37.93 4.70
1926 1994 1.377725 CCTTCGCATGGTGAGCCTT 60.378 57.895 0.00 0.00 35.27 4.35
1941 2009 1.662044 CCTTGGAAAGCAGGTGCAC 59.338 57.895 8.80 8.80 44.44 4.57
2161 2229 6.094193 AGATCTTCGATATCATGAGCAACA 57.906 37.500 0.09 0.00 0.00 3.33
2353 2421 3.369381 CAGATCCACTGTAAGGCCG 57.631 57.895 0.00 0.00 41.30 6.13
2358 2426 1.079127 CCACTGTAAGGCCGTCAGG 60.079 63.158 21.95 13.84 39.30 3.86
2661 2729 3.244353 GGATGTACTACCAGCAGATGCAT 60.244 47.826 0.00 0.00 45.16 3.96
2709 2777 2.739704 CCACTACGCGTGCATGGTG 61.740 63.158 24.59 19.91 42.42 4.17
2754 2822 3.731295 CTCCGAAGCTCAGGAGTTC 57.269 57.895 22.52 0.00 46.68 3.01
2871 2939 2.007360 CAGAGAAGCTGCTGTCGATT 57.993 50.000 0.00 0.00 37.90 3.34
2877 2945 1.078848 GCTGCTGTCGATTGACCCT 60.079 57.895 10.69 0.00 44.86 4.34
2898 2966 0.951040 GCAACAGCGGTGCTTACTCT 60.951 55.000 15.82 0.00 36.40 3.24
2901 2969 2.103042 CAGCGGTGCTTACTCTGCC 61.103 63.158 0.00 0.00 41.60 4.85
2973 3041 3.372554 GAAGCGGAGGAAGGACGGG 62.373 68.421 0.00 0.00 0.00 5.28
3045 3113 1.330655 ACGTCTTCGGGGCAGATGAT 61.331 55.000 0.00 0.00 41.85 2.45
3046 3114 0.877649 CGTCTTCGGGGCAGATGATG 60.878 60.000 0.00 0.00 29.82 3.07
3089 3157 4.910585 GTACGGGATGGCGGCCAG 62.911 72.222 27.62 15.76 36.75 4.85
3110 3178 0.460987 GTCTGGGCGGACATCAAGAG 60.461 60.000 4.71 0.00 36.35 2.85
3114 3182 2.514824 GCGGACATCAAGAGGGCC 60.515 66.667 0.00 0.00 36.81 5.80
3117 3185 2.190578 GACATCAAGAGGGCCGGG 59.809 66.667 2.18 0.00 0.00 5.73
3150 3218 2.573869 CAGTCGGTCCTGCACGAT 59.426 61.111 0.21 0.00 41.53 3.73
3309 3377 3.377485 CAGCCATCAAGTTCATCTCCAAG 59.623 47.826 0.00 0.00 0.00 3.61
3312 3380 4.338879 CCATCAAGTTCATCTCCAAGGTT 58.661 43.478 0.00 0.00 0.00 3.50
3372 3440 1.826720 CACCATTTCAGGGATGGGTTG 59.173 52.381 7.91 0.00 46.69 3.77
3375 3443 1.205417 CATTTCAGGGATGGGTTGTGC 59.795 52.381 0.00 0.00 0.00 4.57
3378 3446 1.746615 CAGGGATGGGTTGTGCTCG 60.747 63.158 0.00 0.00 0.00 5.03
3423 3491 4.893608 CCTTTTGGTAATTTGGTTCCCAG 58.106 43.478 0.00 0.00 32.23 4.45
3436 3504 1.641192 GTTCCCAGGGAAGGAGGAATT 59.359 52.381 22.59 0.00 42.88 2.17
3437 3505 2.043115 GTTCCCAGGGAAGGAGGAATTT 59.957 50.000 22.59 0.00 42.88 1.82
3440 3508 4.126823 TCCCAGGGAAGGAGGAATTTATT 58.873 43.478 5.36 0.00 0.00 1.40
3441 3509 4.548250 TCCCAGGGAAGGAGGAATTTATTT 59.452 41.667 5.36 0.00 0.00 1.40
3442 3510 5.017323 TCCCAGGGAAGGAGGAATTTATTTT 59.983 40.000 5.36 0.00 0.00 1.82
3443 3511 5.726308 CCCAGGGAAGGAGGAATTTATTTTT 59.274 40.000 0.00 0.00 0.00 1.94
3444 3512 6.352137 CCCAGGGAAGGAGGAATTTATTTTTG 60.352 42.308 0.00 0.00 0.00 2.44
3461 3529 5.786401 TTTTTGTTTGTTGGTTCATTCCG 57.214 34.783 0.00 0.00 0.00 4.30
3479 3547 1.300233 GGCAGATCTAACCGCTCCG 60.300 63.158 0.00 0.00 0.00 4.63
3480 3548 1.951631 GCAGATCTAACCGCTCCGC 60.952 63.158 0.00 0.00 0.00 5.54
3483 3551 0.179108 AGATCTAACCGCTCCGCAAC 60.179 55.000 0.00 0.00 0.00 4.17
3500 3568 1.281867 CAACAAGGGCCAGGTCTATGA 59.718 52.381 6.18 0.00 0.00 2.15
3502 3570 1.492176 ACAAGGGCCAGGTCTATGATG 59.508 52.381 6.18 0.00 0.00 3.07
3514 3582 6.171213 CAGGTCTATGATGCATACATGTCAT 58.829 40.000 16.93 11.22 36.35 3.06
3523 3594 2.679336 GCATACATGTCATCACACTGCA 59.321 45.455 0.00 0.00 34.48 4.41
3540 3611 3.713248 ACTGCAGTATTCCAGATGGATCA 59.287 43.478 20.16 0.00 44.98 2.92
3571 3653 6.706295 CCAAATGGGTTCCAGCTAAATTTTA 58.294 36.000 0.00 0.00 36.75 1.52
3578 3660 6.425721 GGGTTCCAGCTAAATTTTACCAAAAC 59.574 38.462 0.00 0.00 32.37 2.43
3579 3661 7.214381 GGTTCCAGCTAAATTTTACCAAAACT 58.786 34.615 0.00 0.00 32.37 2.66
3580 3662 7.713507 GGTTCCAGCTAAATTTTACCAAAACTT 59.286 33.333 0.00 0.00 32.37 2.66
3581 3663 8.761497 GTTCCAGCTAAATTTTACCAAAACTTC 58.239 33.333 0.00 0.00 32.37 3.01
3592 3677 3.555966 ACCAAAACTTCTGGGAACTCAG 58.444 45.455 0.00 0.00 38.36 3.35
3609 3694 5.003096 ACTCAGGTGGGATTTGAAATCTT 57.997 39.130 16.58 0.00 0.00 2.40
3624 3709 9.985730 ATTTGAAATCTTTGCTTGATGACTTTA 57.014 25.926 0.00 0.00 0.00 1.85
3677 3773 1.976404 TGCCTTGATCCCAAAATGCAA 59.024 42.857 0.00 0.00 32.25 4.08
3723 3819 3.760580 AGACCTGTTTGTCTCCTCAAG 57.239 47.619 0.00 0.00 41.75 3.02
3774 4486 5.009410 GGTTCTCATGAATAGGCTGAATTGG 59.991 44.000 0.00 0.00 34.40 3.16
3777 4489 4.870636 TCATGAATAGGCTGAATTGGGTT 58.129 39.130 0.00 0.00 0.00 4.11
3785 4497 1.619654 CTGAATTGGGTTGCTGGTGA 58.380 50.000 0.00 0.00 0.00 4.02
3799 4511 0.036164 TGGTGACGTGATTTCCCCTG 59.964 55.000 0.00 0.00 0.00 4.45
3802 4514 1.002087 GTGACGTGATTTCCCCTGTCT 59.998 52.381 0.00 0.00 0.00 3.41
3819 4531 4.623932 TGTCTGGACAGCTTCTGTTAAT 57.376 40.909 0.66 0.00 45.44 1.40
3820 4532 5.738619 TGTCTGGACAGCTTCTGTTAATA 57.261 39.130 0.66 0.00 45.44 0.98
3821 4533 6.109156 TGTCTGGACAGCTTCTGTTAATAA 57.891 37.500 0.66 0.00 45.44 1.40
3828 4817 7.500892 TGGACAGCTTCTGTTAATAAGAAACAA 59.499 33.333 0.66 0.00 45.44 2.83
3854 4843 2.096496 GTGAAGAATCAATGCCTGTCCG 59.904 50.000 0.00 0.00 37.30 4.79
3859 4848 0.038166 ATCAATGCCTGTCCGGTGTT 59.962 50.000 0.00 0.00 34.25 3.32
3861 4850 1.072489 TCAATGCCTGTCCGGTGTTAA 59.928 47.619 0.00 0.00 34.25 2.01
3863 4852 2.491693 CAATGCCTGTCCGGTGTTAAAT 59.508 45.455 0.00 0.00 34.25 1.40
3881 4870 3.584733 AATCTAAGCCTGGTGATTCCC 57.415 47.619 0.00 0.00 34.77 3.97
3905 4894 2.833121 GGGCTGGGGTAATTGCCG 60.833 66.667 6.48 0.00 45.75 5.69
3921 4910 3.963383 TGCCGACAAGAAAGTTTCTTC 57.037 42.857 24.77 15.52 46.62 2.87
3924 4913 5.120399 TGCCGACAAGAAAGTTTCTTCTTA 58.880 37.500 24.77 8.47 46.62 2.10
3957 4946 2.406616 CCGTGTGGGTAATGGCAGC 61.407 63.158 0.00 0.00 0.00 5.25
3964 4953 1.595093 GGGTAATGGCAGCCACACAC 61.595 60.000 19.10 15.61 35.80 3.82
3965 4954 1.501741 GTAATGGCAGCCACACACG 59.498 57.895 19.10 0.00 35.80 4.49
3966 4955 1.673993 TAATGGCAGCCACACACGG 60.674 57.895 19.10 0.00 35.80 4.94
3967 4956 2.404566 TAATGGCAGCCACACACGGT 62.405 55.000 19.10 0.00 35.80 4.83
3989 4978 3.772572 TGATACGGTCTTGGGAAGATTGA 59.227 43.478 0.00 0.00 40.18 2.57
3999 4988 3.634504 TGGGAAGATTGATGGATTGGTG 58.365 45.455 0.00 0.00 0.00 4.17
4007 4996 2.421725 TGATGGATTGGTGATAGGCCT 58.578 47.619 11.78 11.78 0.00 5.19
4009 4998 3.181440 TGATGGATTGGTGATAGGCCTTC 60.181 47.826 12.58 9.40 0.00 3.46
4013 5002 3.391296 GGATTGGTGATAGGCCTTCAGTA 59.609 47.826 12.58 3.97 0.00 2.74
4032 5021 3.643792 AGTACAATCCTATCCTCACCTGC 59.356 47.826 0.00 0.00 0.00 4.85
4168 5164 4.072131 GAGTATTCAGGAACCTTGTGCAA 58.928 43.478 0.00 0.00 0.00 4.08
4169 5165 4.074970 AGTATTCAGGAACCTTGTGCAAG 58.925 43.478 5.03 5.03 38.14 4.01
4173 5169 1.002468 CAGGAACCTTGTGCAAGAACG 60.002 52.381 12.99 0.15 40.79 3.95
4174 5170 0.310854 GGAACCTTGTGCAAGAACGG 59.689 55.000 12.99 0.53 40.79 4.44
4176 5172 1.264288 GAACCTTGTGCAAGAACGGAG 59.736 52.381 12.99 0.00 40.79 4.63
4180 5176 1.334869 CTTGTGCAAGAACGGAGCTTT 59.665 47.619 6.08 0.00 40.79 3.51
4181 5177 2.248280 TGTGCAAGAACGGAGCTTTA 57.752 45.000 0.00 0.00 0.00 1.85
4182 5178 2.143122 TGTGCAAGAACGGAGCTTTAG 58.857 47.619 0.00 0.00 0.00 1.85
4185 5181 1.739067 CAAGAACGGAGCTTTAGGGG 58.261 55.000 0.00 0.00 0.00 4.79
4186 5182 0.035343 AAGAACGGAGCTTTAGGGGC 60.035 55.000 0.00 0.00 0.00 5.80
4187 5183 1.814169 GAACGGAGCTTTAGGGGCG 60.814 63.158 0.00 0.00 34.52 6.13
4188 5184 2.234913 GAACGGAGCTTTAGGGGCGA 62.235 60.000 0.00 0.00 34.52 5.54
4199 5195 2.375014 TAGGGGCGAGTGATGATACA 57.625 50.000 0.00 0.00 0.00 2.29
4237 5233 3.445096 ACTGCTAATGGGATGTTTTCTGC 59.555 43.478 0.00 0.00 0.00 4.26
4260 5256 4.496341 CCAAATGCATGTACGGAGCTTTAG 60.496 45.833 0.00 0.00 0.00 1.85
4305 5301 5.587388 AGTCAAATGCCGATGAAAATCAT 57.413 34.783 0.00 0.00 40.34 2.45
4311 5307 6.551385 AATGCCGATGAAAATCATAGTCTC 57.449 37.500 0.00 0.00 37.20 3.36
4351 5367 2.229784 GCTAAGGACAATTTGCTGCACT 59.770 45.455 0.00 0.00 0.00 4.40
4371 5387 2.111878 GGATGGCGTGGAGATGGG 59.888 66.667 0.00 0.00 0.00 4.00
4373 5389 1.224592 GATGGCGTGGAGATGGGTT 59.775 57.895 0.00 0.00 0.00 4.11
4393 5409 4.400961 GCCAGTTCTGCGGCTCCT 62.401 66.667 0.00 0.00 45.29 3.69
4394 5410 2.435586 CCAGTTCTGCGGCTCCTG 60.436 66.667 0.00 1.96 0.00 3.86
4395 5411 2.345244 CAGTTCTGCGGCTCCTGT 59.655 61.111 0.00 0.00 0.00 4.00
4396 5412 1.591703 CAGTTCTGCGGCTCCTGTA 59.408 57.895 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.143535 GCGCTCACTGCTTTTATCAAAAAC 60.144 41.667 0.00 0.00 40.11 2.43
249 262 3.446442 AGAAGCCAGAATCATTGTGGT 57.554 42.857 14.84 0.00 45.35 4.16
284 297 2.272146 CACCCGTTCCCCCATCAG 59.728 66.667 0.00 0.00 0.00 2.90
287 300 4.047125 CTGCACCCGTTCCCCCAT 62.047 66.667 0.00 0.00 0.00 4.00
341 354 5.933463 TGGTAGTACTTGGTGTTAATTTCCG 59.067 40.000 0.00 0.00 0.00 4.30
354 367 3.952967 GGACTAGGAGGTGGTAGTACTTG 59.047 52.174 0.00 0.00 28.68 3.16
355 368 3.053019 GGGACTAGGAGGTGGTAGTACTT 60.053 52.174 0.00 0.00 31.57 2.24
359 372 1.288335 CTGGGACTAGGAGGTGGTAGT 59.712 57.143 0.00 0.00 31.97 2.73
364 377 2.066999 GGGCTGGGACTAGGAGGTG 61.067 68.421 0.00 0.00 0.00 4.00
421 445 3.911661 AGAATGTGCTGCTCAAGTTTC 57.088 42.857 8.59 8.19 0.00 2.78
571 599 0.329596 GGGAGCTGACTGATTTGGGT 59.670 55.000 0.00 0.00 0.00 4.51
592 620 1.359459 GATTGGCTTCACCGACCGAC 61.359 60.000 0.00 0.00 43.94 4.79
593 621 1.079405 GATTGGCTTCACCGACCGA 60.079 57.895 0.00 0.00 43.94 4.69
594 622 2.106683 GGATTGGCTTCACCGACCG 61.107 63.158 0.00 0.00 43.94 4.79
595 623 0.608035 TTGGATTGGCTTCACCGACC 60.608 55.000 0.00 0.00 43.94 4.79
781 831 4.089757 CGAGGAGGGGGAAGGGGA 62.090 72.222 0.00 0.00 0.00 4.81
848 899 0.675208 TCTTGTCGCGCTCTCTCTCT 60.675 55.000 5.56 0.00 0.00 3.10
858 909 1.070577 CAGTTTTGTCCTCTTGTCGCG 60.071 52.381 0.00 0.00 0.00 5.87
975 1027 2.436824 GAAAGTCAGCGGGCTCCC 60.437 66.667 0.00 0.00 0.00 4.30
976 1028 2.436824 GGAAAGTCAGCGGGCTCC 60.437 66.667 0.00 0.00 0.00 4.70
977 1029 2.436824 GGGAAAGTCAGCGGGCTC 60.437 66.667 0.00 0.00 0.00 4.70
978 1030 4.394712 CGGGAAAGTCAGCGGGCT 62.395 66.667 0.00 0.00 0.00 5.19
986 1039 2.785258 GCATGTCGCGGGAAAGTC 59.215 61.111 6.13 0.00 0.00 3.01
1547 1615 4.069232 CCAGGCCGAGCTTGACGA 62.069 66.667 1.22 0.00 37.87 4.20
1578 1646 1.292223 GAGCACCGAGTTAGCCACA 59.708 57.895 0.00 0.00 0.00 4.17
1584 1652 2.831685 ACATGTTGAGCACCGAGTTA 57.168 45.000 0.00 0.00 0.00 2.24
1701 1769 2.764128 TCCATCCTCCCCAGACGC 60.764 66.667 0.00 0.00 0.00 5.19
1804 1872 1.453015 ACAGTGCCTTGGCGTCAAA 60.453 52.632 3.10 0.00 31.77 2.69
1845 1913 2.027385 GGCACCATGGAAGAAGAATCC 58.973 52.381 21.47 2.26 37.48 3.01
1924 1992 1.283793 CGTGCACCTGCTTTCCAAG 59.716 57.895 12.15 0.00 42.66 3.61
1926 1994 3.286751 GCGTGCACCTGCTTTCCA 61.287 61.111 12.15 0.00 42.66 3.53
1941 2009 2.061773 CCGCTCCTTAAGATGTATGCG 58.938 52.381 3.36 9.74 41.50 4.73
2161 2229 1.378646 TCCAGGCGACGACATCTCT 60.379 57.895 2.19 0.00 0.00 3.10
2353 2421 1.375268 GCTCCTGCAGTGACCTGAC 60.375 63.158 13.81 0.00 41.50 3.51
2533 2601 3.325716 AGCATTTCTTCAAACAGGCCAAT 59.674 39.130 5.01 0.00 0.00 3.16
2661 2729 1.925415 GCACGATGCCATGCTTGTCA 61.925 55.000 0.00 0.00 37.42 3.58
2727 2795 4.087892 GCTTCGGAGAGCAGGCCA 62.088 66.667 5.01 0.00 38.43 5.36
2853 2921 1.547820 TCAATCGACAGCAGCTTCTCT 59.452 47.619 0.00 0.00 0.00 3.10
2877 2945 2.112087 TAAGCACCGCTGTTGCCA 59.888 55.556 0.00 0.00 39.62 4.92
2889 2957 1.599047 GCAGAGGGCAGAGTAAGCA 59.401 57.895 0.00 0.00 43.97 3.91
2901 2969 1.805945 GGCGTAGACGTTGCAGAGG 60.806 63.158 3.73 0.00 42.22 3.69
2946 3014 0.836400 TCCTCCGCTTCCAGGTCTTT 60.836 55.000 0.00 0.00 0.00 2.52
2950 3018 2.294078 CCTTCCTCCGCTTCCAGGT 61.294 63.158 0.00 0.00 0.00 4.00
2973 3041 2.579738 GTCTCCTTCCTCACGGCC 59.420 66.667 0.00 0.00 0.00 6.13
2975 3043 2.885861 CCGTCTCCTTCCTCACGG 59.114 66.667 0.00 0.00 45.38 4.94
2976 3044 2.711922 CCCCGTCTCCTTCCTCACG 61.712 68.421 0.00 0.00 0.00 4.35
2985 3053 2.266055 CAGCTGAACCCCGTCTCC 59.734 66.667 8.42 0.00 0.00 3.71
3039 3107 2.599597 GGGTGCAGGGCATCATCT 59.400 61.111 3.66 0.00 42.13 2.90
3072 3140 4.910585 CTGGCCGCCATCCCGTAC 62.911 72.222 13.86 0.00 30.82 3.67
3089 3157 2.876368 CTTGATGTCCGCCCAGACCC 62.876 65.000 0.00 0.00 35.83 4.46
3091 3159 0.460987 CTCTTGATGTCCGCCCAGAC 60.461 60.000 0.00 0.00 37.28 3.51
3093 3161 1.153289 CCTCTTGATGTCCGCCCAG 60.153 63.158 0.00 0.00 0.00 4.45
3097 3165 2.514824 GGCCCTCTTGATGTCCGC 60.515 66.667 0.00 0.00 0.00 5.54
3098 3166 2.202932 CGGCCCTCTTGATGTCCG 60.203 66.667 0.00 0.00 0.00 4.79
3102 3170 1.452108 GAACCCGGCCCTCTTGATG 60.452 63.158 0.00 0.00 0.00 3.07
3117 3185 3.901797 CTGGGGGTCTGGCACGAAC 62.902 68.421 0.00 0.00 0.00 3.95
3131 3199 4.742201 CGTGCAGGACCGACTGGG 62.742 72.222 0.00 0.00 40.75 4.45
3150 3218 0.171231 CCTTGAGCTCGTCATCGACA 59.829 55.000 9.64 0.00 41.35 4.35
3204 3272 2.831742 AGGAGGCCGAACGCGATA 60.832 61.111 15.93 0.00 40.82 2.92
3243 3311 0.036388 GGTTCTTCATGACCCGCAGA 60.036 55.000 0.00 0.00 0.00 4.26
3285 3353 3.519107 TGGAGATGAACTTGATGGCTGTA 59.481 43.478 0.00 0.00 0.00 2.74
3291 3359 4.380233 GCAACCTTGGAGATGAACTTGATG 60.380 45.833 0.00 0.00 0.00 3.07
3309 3377 1.153349 GATCTCCCTGTCCGCAACC 60.153 63.158 0.00 0.00 0.00 3.77
3312 3380 1.402896 GGATGATCTCCCTGTCCGCA 61.403 60.000 0.00 0.00 38.19 5.69
3351 3419 1.381867 ACCCATCCCTGAAATGGTGA 58.618 50.000 1.79 0.00 41.84 4.02
3375 3443 6.662414 TTCTACCAATAATCTTTGCACGAG 57.338 37.500 0.00 0.00 0.00 4.18
3378 3446 7.812309 GGTTTTCTACCAATAATCTTTGCAC 57.188 36.000 0.00 0.00 46.92 4.57
3416 3484 1.299939 ATTCCTCCTTCCCTGGGAAC 58.700 55.000 24.22 0.00 40.10 3.62
3423 3491 7.936847 ACAAACAAAAATAAATTCCTCCTTCCC 59.063 33.333 0.00 0.00 0.00 3.97
3436 3504 7.011482 CCGGAATGAACCAACAAACAAAAATAA 59.989 33.333 0.00 0.00 0.00 1.40
3437 3505 6.480320 CCGGAATGAACCAACAAACAAAAATA 59.520 34.615 0.00 0.00 0.00 1.40
3440 3508 4.184629 CCGGAATGAACCAACAAACAAAA 58.815 39.130 0.00 0.00 0.00 2.44
3441 3509 3.786635 CCGGAATGAACCAACAAACAAA 58.213 40.909 0.00 0.00 0.00 2.83
3442 3510 2.482142 GCCGGAATGAACCAACAAACAA 60.482 45.455 5.05 0.00 0.00 2.83
3443 3511 1.067821 GCCGGAATGAACCAACAAACA 59.932 47.619 5.05 0.00 0.00 2.83
3444 3512 1.067821 TGCCGGAATGAACCAACAAAC 59.932 47.619 5.05 0.00 0.00 2.93
3461 3529 1.300233 CGGAGCGGTTAGATCTGCC 60.300 63.158 5.18 6.78 40.22 4.85
3479 3547 0.034089 ATAGACCTGGCCCTTGTTGC 60.034 55.000 0.00 0.00 0.00 4.17
3480 3548 1.281867 TCATAGACCTGGCCCTTGTTG 59.718 52.381 0.00 0.00 0.00 3.33
3483 3551 1.816961 GCATCATAGACCTGGCCCTTG 60.817 57.143 0.00 0.00 0.00 3.61
3489 3557 4.903054 ACATGTATGCATCATAGACCTGG 58.097 43.478 0.19 0.00 31.99 4.45
3500 3568 3.314357 GCAGTGTGATGACATGTATGCAT 59.686 43.478 3.79 3.79 33.66 3.96
3502 3570 2.679336 TGCAGTGTGATGACATGTATGC 59.321 45.455 0.00 7.47 33.63 3.14
3514 3582 3.369787 CCATCTGGAATACTGCAGTGTGA 60.370 47.826 29.57 15.85 41.55 3.58
3560 3641 7.289084 TCCCAGAAGTTTTGGTAAAATTTAGCT 59.711 33.333 14.82 0.00 32.23 3.32
3564 3646 7.857456 AGTTCCCAGAAGTTTTGGTAAAATTT 58.143 30.769 11.28 0.00 32.23 1.82
3571 3653 3.555966 CTGAGTTCCCAGAAGTTTTGGT 58.444 45.455 11.28 0.00 36.29 3.67
3578 3660 0.326264 CCCACCTGAGTTCCCAGAAG 59.674 60.000 0.00 0.00 36.29 2.85
3579 3661 0.104672 TCCCACCTGAGTTCCCAGAA 60.105 55.000 0.00 0.00 36.29 3.02
3580 3662 0.119155 ATCCCACCTGAGTTCCCAGA 59.881 55.000 0.00 0.00 36.29 3.86
3581 3663 0.995024 AATCCCACCTGAGTTCCCAG 59.005 55.000 0.00 0.00 0.00 4.45
3592 3677 4.541973 AGCAAAGATTTCAAATCCCACC 57.458 40.909 6.50 0.00 0.00 4.61
3609 3694 5.064707 GTCCGCTATTAAAGTCATCAAGCAA 59.935 40.000 0.00 0.00 0.00 3.91
3624 3709 8.908903 CCTAGAGATATCTATTTGTCCGCTATT 58.091 37.037 4.89 0.00 0.00 1.73
3704 3800 2.104963 ACCTTGAGGAGACAAACAGGTC 59.895 50.000 3.59 0.00 38.94 3.85
3708 3804 3.475566 CTCACCTTGAGGAGACAAACA 57.524 47.619 3.59 0.00 40.71 2.83
3744 3840 6.070251 TCAGCCTATTCATGAGAACCTTTGTA 60.070 38.462 0.00 0.00 36.39 2.41
3745 3841 4.946157 CAGCCTATTCATGAGAACCTTTGT 59.054 41.667 0.00 0.00 36.39 2.83
3746 3842 5.188434 TCAGCCTATTCATGAGAACCTTTG 58.812 41.667 0.00 0.00 36.39 2.77
3747 3843 5.441718 TCAGCCTATTCATGAGAACCTTT 57.558 39.130 0.00 0.00 36.39 3.11
3748 3844 5.441718 TTCAGCCTATTCATGAGAACCTT 57.558 39.130 0.00 0.00 36.39 3.50
3774 4486 0.951558 AAATCACGTCACCAGCAACC 59.048 50.000 0.00 0.00 0.00 3.77
3777 4489 0.605319 GGGAAATCACGTCACCAGCA 60.605 55.000 0.00 0.00 0.00 4.41
3785 4497 0.324943 CCAGACAGGGGAAATCACGT 59.675 55.000 0.00 0.00 0.00 4.49
3799 4511 6.398918 TCTTATTAACAGAAGCTGTCCAGAC 58.601 40.000 0.00 0.00 44.62 3.51
3802 4514 6.995686 TGTTTCTTATTAACAGAAGCTGTCCA 59.004 34.615 11.87 0.00 44.62 4.02
3821 4533 9.362539 GCATTGATTCTTCACATATTTGTTTCT 57.637 29.630 0.00 0.00 32.34 2.52
3828 4817 6.040166 GGACAGGCATTGATTCTTCACATATT 59.960 38.462 0.00 0.00 0.00 1.28
3854 4843 4.585879 TCACCAGGCTTAGATTTAACACC 58.414 43.478 0.00 0.00 0.00 4.16
3859 4848 4.476846 TGGGAATCACCAGGCTTAGATTTA 59.523 41.667 7.12 0.00 41.20 1.40
3861 4850 2.852449 TGGGAATCACCAGGCTTAGATT 59.148 45.455 5.75 5.75 41.20 2.40
3863 4852 1.965414 TGGGAATCACCAGGCTTAGA 58.035 50.000 0.00 0.00 41.20 2.10
3881 4870 0.625849 ATTACCCCAGCCCAGAACTG 59.374 55.000 0.00 0.00 34.82 3.16
3896 4885 5.758924 AGAAACTTTCTTGTCGGCAATTAC 58.241 37.500 1.35 0.00 36.36 1.89
3921 4910 6.690957 CCACACGGTGTTTGCATAAATATAAG 59.309 38.462 11.82 0.00 0.00 1.73
3924 4913 4.142271 CCCACACGGTGTTTGCATAAATAT 60.142 41.667 11.82 0.00 0.00 1.28
3957 4946 0.734942 GACCGTATCACCGTGTGTGG 60.735 60.000 0.00 0.00 45.48 4.17
3964 4953 0.533491 TTCCCAAGACCGTATCACCG 59.467 55.000 0.00 0.00 0.00 4.94
3965 4954 1.829222 TCTTCCCAAGACCGTATCACC 59.171 52.381 0.00 0.00 31.20 4.02
3966 4955 3.821421 ATCTTCCCAAGACCGTATCAC 57.179 47.619 0.00 0.00 41.01 3.06
3967 4956 3.772572 TCAATCTTCCCAAGACCGTATCA 59.227 43.478 0.00 0.00 41.01 2.15
3968 4957 4.402056 TCAATCTTCCCAAGACCGTATC 57.598 45.455 0.00 0.00 41.01 2.24
3969 4958 4.444876 CCATCAATCTTCCCAAGACCGTAT 60.445 45.833 0.00 0.00 41.01 3.06
3970 4959 3.118408 CCATCAATCTTCCCAAGACCGTA 60.118 47.826 0.00 0.00 41.01 4.02
3971 4960 2.356125 CCATCAATCTTCCCAAGACCGT 60.356 50.000 0.00 0.00 41.01 4.83
3972 4961 2.092968 TCCATCAATCTTCCCAAGACCG 60.093 50.000 0.00 0.00 41.01 4.79
3976 4965 4.098960 CACCAATCCATCAATCTTCCCAAG 59.901 45.833 0.00 0.00 0.00 3.61
3989 4978 2.785269 TGAAGGCCTATCACCAATCCAT 59.215 45.455 5.16 0.00 0.00 3.41
3999 4988 4.965200 AGGATTGTACTGAAGGCCTATC 57.035 45.455 5.16 6.85 0.00 2.08
4007 4996 5.363868 CAGGTGAGGATAGGATTGTACTGAA 59.636 44.000 0.00 0.00 0.00 3.02
4009 4998 4.502259 GCAGGTGAGGATAGGATTGTACTG 60.502 50.000 0.00 0.00 0.00 2.74
4013 5002 2.481441 TGCAGGTGAGGATAGGATTGT 58.519 47.619 0.00 0.00 0.00 2.71
4032 5021 8.931385 ACATTTTTAGTTAGGCAAATGCTATG 57.069 30.769 5.25 0.00 39.32 2.23
4168 5164 1.602771 GCCCCTAAAGCTCCGTTCT 59.397 57.895 0.00 0.00 0.00 3.01
4169 5165 1.814169 CGCCCCTAAAGCTCCGTTC 60.814 63.158 0.00 0.00 0.00 3.95
4173 5169 1.153349 CACTCGCCCCTAAAGCTCC 60.153 63.158 0.00 0.00 0.00 4.70
4174 5170 0.466124 ATCACTCGCCCCTAAAGCTC 59.534 55.000 0.00 0.00 0.00 4.09
4176 5172 0.178068 TCATCACTCGCCCCTAAAGC 59.822 55.000 0.00 0.00 0.00 3.51
4180 5176 2.239400 CTGTATCATCACTCGCCCCTA 58.761 52.381 0.00 0.00 0.00 3.53
4181 5177 1.043816 CTGTATCATCACTCGCCCCT 58.956 55.000 0.00 0.00 0.00 4.79
4182 5178 0.753262 ACTGTATCATCACTCGCCCC 59.247 55.000 0.00 0.00 0.00 5.80
4185 5181 2.032302 ACTCGACTGTATCATCACTCGC 59.968 50.000 0.00 0.00 0.00 5.03
4186 5182 3.547014 CCACTCGACTGTATCATCACTCG 60.547 52.174 0.00 0.00 0.00 4.18
4187 5183 3.378742 ACCACTCGACTGTATCATCACTC 59.621 47.826 0.00 0.00 0.00 3.51
4188 5184 3.357203 ACCACTCGACTGTATCATCACT 58.643 45.455 0.00 0.00 0.00 3.41
4237 5233 1.382522 AGCTCCGTACATGCATTTGG 58.617 50.000 0.00 0.00 0.00 3.28
4251 5247 2.824489 GTGCGCCCCTAAAGCTCC 60.824 66.667 4.18 0.00 0.00 4.70
4305 5301 3.634448 GCTGCTATTCCACAGAGAGACTA 59.366 47.826 0.00 0.00 35.90 2.59
4311 5307 1.602851 GCATGCTGCTATTCCACAGAG 59.397 52.381 11.37 0.00 40.96 3.35
4351 5367 1.689243 CCATCTCCACGCCATCCTCA 61.689 60.000 0.00 0.00 0.00 3.86
4371 5387 3.257933 CCGCAGAACTGGCAGAAC 58.742 61.111 23.66 14.03 0.00 3.01


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

AutoCloner maintained by Alex Coulton.