Multiple sequence alignment - TraesCS1D01G268800

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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 TraesCS1D01G268800 chr1D 100.000 4587 0 0 1 4587 364388183 364383597 0.000000e+00 8471
1 TraesCS1D01G268800 chr1A 94.321 3592 129 30 1046 4587 463403089 463399523 0.000000e+00 5433
2 TraesCS1D01G268800 chr1A 85.990 985 67 37 1 954 463404361 463403417 0.000000e+00 989
3 TraesCS1D01G268800 chr1A 90.123 81 8 0 4114 4194 463399948 463399868 6.280000e-19 106
4 TraesCS1D01G268800 chr1B 96.502 2773 92 5 1129 3900 487682191 487679423 0.000000e+00 4578
5 TraesCS1D01G268800 chr1B 90.170 529 35 12 442 970 487683009 487682498 0.000000e+00 673
6 TraesCS1D01G268800 chr1B 87.619 525 33 6 4016 4508 487679068 487678544 8.550000e-162 580
7 TraesCS1D01G268800 chr1B 92.629 407 20 3 1 406 487683403 487683006 1.110000e-160 577
8 TraesCS1D01G268800 chr6B 94.823 1951 96 5 1147 3094 500525863 500523915 0.000000e+00 3038
9 TraesCS1D01G268800 chr5A 93.795 1950 97 4 1147 3094 396680471 396682398 0.000000e+00 2909
10 TraesCS1D01G268800 chr3B 87.379 103 13 0 1742 1844 627615397 627615295 8.060000e-23 119


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 TraesCS1D01G268800 chr1D 364383597 364388183 4586 True 8471 8471 100.000000 1 4587 1 chr1D.!!$R1 4586
1 TraesCS1D01G268800 chr1A 463399523 463404361 4838 True 2176 5433 90.144667 1 4587 3 chr1A.!!$R1 4586
2 TraesCS1D01G268800 chr1B 487678544 487683403 4859 True 1602 4578 91.730000 1 4508 4 chr1B.!!$R1 4507
3 TraesCS1D01G268800 chr6B 500523915 500525863 1948 True 3038 3038 94.823000 1147 3094 1 chr6B.!!$R1 1947
4 TraesCS1D01G268800 chr5A 396680471 396682398 1927 False 2909 2909 93.795000 1147 3094 1 chr5A.!!$F1 1947

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
970 1024 0.172578 TCGACGGAATGCCACACTAG 59.827 55.0 0.0 0.0 0.0 2.57 F
2452 2744 0.181587 TCACGGTGGTGGTGTTTGAT 59.818 50.0 8.5 0.0 44.5 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2824 3116 0.037326 GCCGGAGACTGAACATGTGA 60.037 55.0 5.05 0.0 0.0 3.58 R
4158 4699 0.250166 GGCGTAACTGACACCAGGTT 60.250 55.0 0.00 0.0 44.6 3.50 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
79 85 3.367292 GGCGTGAATCCATCAACAAACAT 60.367 43.478 0.00 0.00 40.50 2.71
171 177 1.407437 CCCGTATCTCAGGCTTTGCTT 60.407 52.381 0.00 0.00 0.00 3.91
173 179 1.063174 CGTATCTCAGGCTTTGCTTGC 59.937 52.381 0.00 0.00 35.58 4.01
174 180 2.363683 GTATCTCAGGCTTTGCTTGCT 58.636 47.619 0.00 0.00 35.58 3.91
183 189 2.791396 CTTTGCTTGCTGCGACGCAT 62.791 55.000 24.71 0.00 46.63 4.73
199 205 1.953138 CATGAGATCGTCTGCGGCC 60.953 63.158 0.00 0.00 38.89 6.13
206 212 2.721971 ATCGTCTGCGGCCATCATCC 62.722 60.000 2.24 0.00 38.89 3.51
234 240 3.059393 GCTTCAAATTCAAAAGCACCTGC 60.059 43.478 12.14 0.00 43.77 4.85
252 259 3.622163 CCTGCTGATCTGAATCTGTCAAC 59.378 47.826 3.42 0.00 35.22 3.18
253 260 4.251268 CTGCTGATCTGAATCTGTCAACA 58.749 43.478 3.42 0.00 35.22 3.33
254 261 4.251268 TGCTGATCTGAATCTGTCAACAG 58.749 43.478 3.42 3.69 45.08 3.16
255 262 3.622163 GCTGATCTGAATCTGTCAACAGG 59.378 47.826 10.13 0.00 43.91 4.00
256 263 3.603532 TGATCTGAATCTGTCAACAGGC 58.396 45.455 10.13 1.88 43.91 4.85
257 264 3.262660 TGATCTGAATCTGTCAACAGGCT 59.737 43.478 10.13 0.00 43.91 4.58
267 275 1.740025 GTCAACAGGCTACTCCAATGC 59.260 52.381 0.00 0.00 37.29 3.56
324 332 0.461339 CGTCCTTGGGGTTCGTATGG 60.461 60.000 0.00 0.00 0.00 2.74
408 416 4.864334 GGGGCCCATGTGAGCGAG 62.864 72.222 26.86 0.00 0.00 5.03
422 430 4.363990 CGAGCGGCTGTGTGGAGT 62.364 66.667 7.50 0.00 0.00 3.85
423 431 2.031163 GAGCGGCTGTGTGGAGTT 59.969 61.111 7.50 0.00 0.00 3.01
424 432 2.029844 GAGCGGCTGTGTGGAGTTC 61.030 63.158 7.50 0.00 0.00 3.01
425 433 3.414700 GCGGCTGTGTGGAGTTCG 61.415 66.667 0.00 0.00 0.00 3.95
426 434 2.738521 CGGCTGTGTGGAGTTCGG 60.739 66.667 0.00 0.00 0.00 4.30
427 435 3.050275 GGCTGTGTGGAGTTCGGC 61.050 66.667 0.00 0.00 0.00 5.54
428 436 2.031163 GCTGTGTGGAGTTCGGCT 59.969 61.111 0.00 0.00 0.00 5.52
429 437 2.320587 GCTGTGTGGAGTTCGGCTG 61.321 63.158 0.00 0.00 0.00 4.85
430 438 1.069765 CTGTGTGGAGTTCGGCTGT 59.930 57.895 0.00 0.00 0.00 4.40
431 439 1.224069 CTGTGTGGAGTTCGGCTGTG 61.224 60.000 0.00 0.00 0.00 3.66
432 440 1.227556 GTGTGGAGTTCGGCTGTGT 60.228 57.895 0.00 0.00 0.00 3.72
433 441 1.227527 TGTGGAGTTCGGCTGTGTG 60.228 57.895 0.00 0.00 0.00 3.82
434 442 1.069090 GTGGAGTTCGGCTGTGTGA 59.931 57.895 0.00 0.00 0.00 3.58
435 443 0.946221 GTGGAGTTCGGCTGTGTGAG 60.946 60.000 0.00 0.00 0.00 3.51
442 450 2.659063 CGGCTGTGTGAGATGGGGA 61.659 63.158 0.00 0.00 0.00 4.81
604 648 1.524621 GTCCAGCACATCCATCCCG 60.525 63.158 0.00 0.00 0.00 5.14
667 711 4.077184 CGCCTCCCACTACGCCAA 62.077 66.667 0.00 0.00 0.00 4.52
671 715 3.296709 CTCCCACTACGCCAACGCT 62.297 63.158 0.00 0.00 45.53 5.07
770 817 1.982958 AGGGTCTTTTATCGTGTGGGT 59.017 47.619 0.00 0.00 0.00 4.51
794 841 1.270147 GGGCCGTCACGCTTTATCTAT 60.270 52.381 0.00 0.00 0.00 1.98
880 927 1.811645 GAGGCGCTACAGATCCCTCC 61.812 65.000 7.64 0.00 36.85 4.30
886 933 0.747255 CTACAGATCCCTCCACCGTG 59.253 60.000 0.00 0.00 0.00 4.94
891 945 4.974438 TCCCTCCACCGTGCCCTT 62.974 66.667 0.00 0.00 0.00 3.95
892 946 4.722700 CCCTCCACCGTGCCCTTG 62.723 72.222 0.00 0.00 0.00 3.61
893 947 3.953775 CCTCCACCGTGCCCTTGT 61.954 66.667 0.00 0.00 0.00 3.16
894 948 2.669569 CTCCACCGTGCCCTTGTG 60.670 66.667 0.00 0.00 0.00 3.33
970 1024 0.172578 TCGACGGAATGCCACACTAG 59.827 55.000 0.00 0.00 0.00 2.57
971 1025 1.421410 CGACGGAATGCCACACTAGC 61.421 60.000 0.00 0.00 0.00 3.42
972 1026 1.078426 ACGGAATGCCACACTAGCC 60.078 57.895 0.00 0.00 0.00 3.93
973 1027 1.819632 CGGAATGCCACACTAGCCC 60.820 63.158 0.00 0.00 0.00 5.19
974 1028 1.453928 GGAATGCCACACTAGCCCC 60.454 63.158 0.00 0.00 0.00 5.80
975 1029 1.453928 GAATGCCACACTAGCCCCC 60.454 63.158 0.00 0.00 0.00 5.40
976 1030 2.210144 GAATGCCACACTAGCCCCCA 62.210 60.000 0.00 0.00 0.00 4.96
977 1031 2.499303 AATGCCACACTAGCCCCCAC 62.499 60.000 0.00 0.00 0.00 4.61
978 1032 3.330720 GCCACACTAGCCCCCACT 61.331 66.667 0.00 0.00 0.00 4.00
979 1033 2.990479 CCACACTAGCCCCCACTC 59.010 66.667 0.00 0.00 0.00 3.51
980 1034 2.670148 CCACACTAGCCCCCACTCC 61.670 68.421 0.00 0.00 0.00 3.85
981 1035 1.918293 CACACTAGCCCCCACTCCA 60.918 63.158 0.00 0.00 0.00 3.86
982 1036 1.918800 ACACTAGCCCCCACTCCAC 60.919 63.158 0.00 0.00 0.00 4.02
983 1037 1.613630 CACTAGCCCCCACTCCACT 60.614 63.158 0.00 0.00 0.00 4.00
984 1038 1.306226 ACTAGCCCCCACTCCACTC 60.306 63.158 0.00 0.00 0.00 3.51
985 1039 2.040606 TAGCCCCCACTCCACTCC 59.959 66.667 0.00 0.00 0.00 3.85
986 1040 3.635869 TAGCCCCCACTCCACTCCC 62.636 68.421 0.00 0.00 0.00 4.30
988 1042 4.675303 CCCCCACTCCACTCCCCA 62.675 72.222 0.00 0.00 0.00 4.96
989 1043 3.330720 CCCCACTCCACTCCCCAC 61.331 72.222 0.00 0.00 0.00 4.61
990 1044 2.203998 CCCACTCCACTCCCCACT 60.204 66.667 0.00 0.00 0.00 4.00
991 1045 2.294078 CCCACTCCACTCCCCACTC 61.294 68.421 0.00 0.00 0.00 3.51
992 1046 2.294078 CCACTCCACTCCCCACTCC 61.294 68.421 0.00 0.00 0.00 3.85
993 1047 2.122954 ACTCCACTCCCCACTCCC 59.877 66.667 0.00 0.00 0.00 4.30
994 1048 2.689034 CTCCACTCCCCACTCCCC 60.689 72.222 0.00 0.00 0.00 4.81
995 1049 3.537506 TCCACTCCCCACTCCCCA 61.538 66.667 0.00 0.00 0.00 4.96
996 1050 3.330720 CCACTCCCCACTCCCCAC 61.331 72.222 0.00 0.00 0.00 4.61
997 1051 3.706373 CACTCCCCACTCCCCACG 61.706 72.222 0.00 0.00 0.00 4.94
1423 1713 1.153745 CCAGGTCTTCGCCTTCTCG 60.154 63.158 0.00 0.00 36.58 4.04
1768 2058 4.409218 GTGTACCTCCGCGTCGCA 62.409 66.667 18.75 0.00 0.00 5.10
1933 2225 4.287781 TTTGTCGCGTCGGAGCCA 62.288 61.111 5.77 0.00 0.00 4.75
2020 2312 1.335145 GCATTATGCTGCCCCTCAAT 58.665 50.000 10.27 0.00 40.96 2.57
2030 2322 1.753848 CCCCTCAATGCCGCAATGA 60.754 57.895 10.66 10.66 0.00 2.57
2086 2378 4.308458 TGGTACAGCCTTGCGCGT 62.308 61.111 8.43 0.00 44.76 6.01
2197 2489 2.788030 GAGTCGACTTACTACAGCAGC 58.212 52.381 21.08 0.00 0.00 5.25
2263 2555 1.133809 TCCTTGAGGTGGGGGTTCTG 61.134 60.000 0.00 0.00 36.34 3.02
2269 2561 3.580319 GTGGGGGTTCTGGGTGCT 61.580 66.667 0.00 0.00 0.00 4.40
2383 2675 1.358877 TCATGAACACGCTGAATCCG 58.641 50.000 0.00 0.00 0.00 4.18
2386 2678 0.882484 TGAACACGCTGAATCCGCAA 60.882 50.000 0.00 0.00 0.00 4.85
2452 2744 0.181587 TCACGGTGGTGGTGTTTGAT 59.818 50.000 8.50 0.00 44.50 2.57
2479 2771 1.407979 CAGATTGGGAGCAAGAATGGC 59.592 52.381 0.00 0.00 32.57 4.40
2698 2990 2.534298 CCGAAGATGCACTACTCACAG 58.466 52.381 0.00 0.00 0.00 3.66
2800 3092 4.087892 CTGCGGAGGGAGGTGGTG 62.088 72.222 0.00 0.00 0.00 4.17
2824 3116 3.071206 ACGCTCGATGTGGGCTCT 61.071 61.111 0.00 0.00 0.00 4.09
3031 3323 8.497745 ACCATCTTCCTCTACATGTTTATGATT 58.502 33.333 2.30 0.00 37.73 2.57
3103 3395 0.539051 AGCTATCGCAGGCTGAGTTT 59.461 50.000 20.86 9.99 37.41 2.66
3280 3572 2.040278 CTGAGCTGGAGGGACCCT 59.960 66.667 14.79 14.79 38.00 4.34
3493 3785 3.491619 GCCAGAGCATTCGACAGAAGATA 60.492 47.826 0.00 0.00 40.09 1.98
3505 3797 5.104109 TCGACAGAAGATAAAAATGGGGGAT 60.104 40.000 0.00 0.00 0.00 3.85
3507 3799 5.211201 ACAGAAGATAAAAATGGGGGATGG 58.789 41.667 0.00 0.00 0.00 3.51
3601 3893 8.814038 AATGAGTTGATTAATTTAGAGGCAGT 57.186 30.769 0.00 0.00 0.00 4.40
3602 3894 8.814038 ATGAGTTGATTAATTTAGAGGCAGTT 57.186 30.769 0.00 0.00 0.00 3.16
3638 3933 9.316730 TGTAATAAGGTGTCGGTTTATATGTTC 57.683 33.333 0.00 0.00 0.00 3.18
3656 3951 1.182667 TCGTCTGCTTAGCTAGGCAA 58.817 50.000 27.93 17.29 37.85 4.52
3850 4145 5.192927 TGCCCCTAATCTTGTTCTTGTATG 58.807 41.667 0.00 0.00 0.00 2.39
3891 4190 7.806180 TCCTTCCCTTTTCTCCAGAAATATAG 58.194 38.462 2.59 0.00 42.83 1.31
3923 4282 1.758440 TTGTTCTGAGGCGCTCACCT 61.758 55.000 7.64 0.00 45.04 4.00
3925 4284 1.004560 TTCTGAGGCGCTCACCTTG 60.005 57.895 7.64 0.00 41.32 3.61
3929 4288 0.884704 TGAGGCGCTCACCTTGTTTC 60.885 55.000 7.64 0.00 41.32 2.78
3930 4289 0.884704 GAGGCGCTCACCTTGTTTCA 60.885 55.000 7.64 0.00 41.32 2.69
3931 4290 0.886490 AGGCGCTCACCTTGTTTCAG 60.886 55.000 7.64 0.00 36.28 3.02
3932 4291 0.884704 GGCGCTCACCTTGTTTCAGA 60.885 55.000 7.64 0.00 0.00 3.27
3933 4292 0.514691 GCGCTCACCTTGTTTCAGAG 59.485 55.000 0.00 0.00 0.00 3.35
3935 4294 1.541233 CGCTCACCTTGTTTCAGAGGT 60.541 52.381 0.00 0.00 46.99 3.85
3936 4295 2.147150 GCTCACCTTGTTTCAGAGGTC 58.853 52.381 0.00 0.00 44.28 3.85
3937 4296 2.485479 GCTCACCTTGTTTCAGAGGTCA 60.485 50.000 0.00 0.00 44.28 4.02
3938 4297 3.134458 CTCACCTTGTTTCAGAGGTCAC 58.866 50.000 0.00 0.00 44.28 3.67
3939 4298 2.503765 TCACCTTGTTTCAGAGGTCACA 59.496 45.455 0.00 0.00 44.28 3.58
3940 4299 2.614057 CACCTTGTTTCAGAGGTCACAC 59.386 50.000 0.00 0.00 44.28 3.82
3974 4339 2.139917 GTGACGTTGTAGCATGGTTGA 58.860 47.619 1.12 0.00 0.00 3.18
4004 4369 2.902705 TGCTGGGTATATCGGTGAAC 57.097 50.000 0.00 0.00 0.00 3.18
4026 4564 6.798427 ACTTCATCATCTTAAGAGCCTACA 57.202 37.500 11.53 0.00 0.00 2.74
4045 4583 1.200716 CAAATGTGCGCCAGTTCATCT 59.799 47.619 4.18 0.00 0.00 2.90
4074 4612 3.764237 ATGTCAGTTACTCCGTGGTTT 57.236 42.857 0.00 0.00 0.00 3.27
4091 4629 3.496884 TGGTTTAGTGCAGAATTGTCGTC 59.503 43.478 0.00 0.00 0.00 4.20
4099 4637 1.320555 CAGAATTGTCGTCGCCGTTAG 59.679 52.381 0.00 0.00 35.01 2.34
4109 4647 2.071540 GTCGCCGTTAGCCTACTTTTT 58.928 47.619 0.00 0.00 38.78 1.94
4110 4648 2.093310 GTCGCCGTTAGCCTACTTTTTC 59.907 50.000 0.00 0.00 38.78 2.29
4121 4662 4.523558 AGCCTACTTTTTCTCTGTCGTAGT 59.476 41.667 0.00 0.00 0.00 2.73
4158 4699 2.979814 ATGTGCACTAATCCAGCGTA 57.020 45.000 19.41 0.00 0.00 4.42
4175 4716 2.322161 CGTAACCTGGTGTCAGTTACG 58.678 52.381 16.99 16.99 44.17 3.18
4219 4783 3.938963 CCGTAAATGTGCACTAATCCAGT 59.061 43.478 19.41 0.00 38.32 4.00
4249 4813 0.034337 GCCAGTTACTCCGTGGTTCA 59.966 55.000 0.00 0.00 33.51 3.18
4322 4886 1.476085 CTGATCCGCACTGAGAGAACT 59.524 52.381 0.00 0.00 0.00 3.01
4351 4921 1.599518 TCGCACCCACGCTTTTGAT 60.600 52.632 0.00 0.00 0.00 2.57
4510 5094 6.683715 CAAAATAAAACAGGTATGGAACGGT 58.316 36.000 0.00 0.00 0.00 4.83
4562 5147 7.575365 CCATTTTTCATGGCAACTCTTTAAAC 58.425 34.615 0.00 0.00 37.61 2.01
4573 5158 6.262601 GCAACTCTTTAAACTTGTTGTGCTA 58.737 36.000 17.19 0.00 39.81 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 71 4.142708 CCGAAATCGATGTTTGTTGATGGA 60.143 41.667 0.00 0.00 43.02 3.41
79 85 2.627945 CTGTCATTTCCCCGAAATCGA 58.372 47.619 4.04 0.00 39.82 3.59
136 142 2.865598 CGGGGTTGTTGGCAATGCA 61.866 57.895 7.79 0.00 36.92 3.96
137 143 1.528292 TACGGGGTTGTTGGCAATGC 61.528 55.000 1.92 0.00 36.92 3.56
138 144 1.134175 GATACGGGGTTGTTGGCAATG 59.866 52.381 1.92 0.00 36.92 2.82
139 145 1.005450 AGATACGGGGTTGTTGGCAAT 59.995 47.619 1.92 0.00 36.92 3.56
140 146 0.402504 AGATACGGGGTTGTTGGCAA 59.597 50.000 0.00 0.00 0.00 4.52
173 179 1.535636 GACGATCTCATGCGTCGCAG 61.536 60.000 25.78 16.70 45.81 5.18
174 180 1.586303 GACGATCTCATGCGTCGCA 60.586 57.895 24.05 24.05 45.81 5.10
183 189 2.355445 GATGGCCGCAGACGATCTCA 62.355 60.000 0.00 0.00 43.93 3.27
199 205 4.730949 ATTTGAAGCAACAGGGATGATG 57.269 40.909 0.00 0.00 0.00 3.07
206 212 5.086888 GCTTTTGAATTTGAAGCAACAGG 57.913 39.130 13.30 0.00 43.89 4.00
234 240 3.622163 GCCTGTTGACAGATTCAGATCAG 59.378 47.826 12.54 0.00 46.59 2.90
235 241 3.262660 AGCCTGTTGACAGATTCAGATCA 59.737 43.478 12.54 0.00 46.59 2.92
237 243 3.996921 AGCCTGTTGACAGATTCAGAT 57.003 42.857 12.54 0.00 46.59 2.90
238 245 3.834813 AGTAGCCTGTTGACAGATTCAGA 59.165 43.478 12.54 0.00 46.59 3.27
252 259 2.697751 AGAGTAGCATTGGAGTAGCCTG 59.302 50.000 0.00 0.00 37.63 4.85
253 260 2.697751 CAGAGTAGCATTGGAGTAGCCT 59.302 50.000 0.00 0.00 37.63 4.58
254 261 2.695666 TCAGAGTAGCATTGGAGTAGCC 59.304 50.000 0.00 0.00 37.10 3.93
255 262 4.116238 GTTCAGAGTAGCATTGGAGTAGC 58.884 47.826 0.00 0.00 0.00 3.58
256 263 5.330455 TGTTCAGAGTAGCATTGGAGTAG 57.670 43.478 0.00 0.00 0.00 2.57
257 264 5.450550 CGATGTTCAGAGTAGCATTGGAGTA 60.451 44.000 0.00 0.00 0.00 2.59
267 275 2.656085 GCGATCCGATGTTCAGAGTAG 58.344 52.381 0.00 0.00 0.00 2.57
324 332 3.586039 CGTGCCACGAATCATGTTC 57.414 52.632 12.85 0.00 46.05 3.18
406 414 2.029844 GAACTCCACACAGCCGCTC 61.030 63.158 0.00 0.00 0.00 5.03
407 415 2.031163 GAACTCCACACAGCCGCT 59.969 61.111 0.00 0.00 0.00 5.52
408 416 3.414700 CGAACTCCACACAGCCGC 61.415 66.667 0.00 0.00 0.00 6.53
409 417 2.738521 CCGAACTCCACACAGCCG 60.739 66.667 0.00 0.00 0.00 5.52
410 418 3.050275 GCCGAACTCCACACAGCC 61.050 66.667 0.00 0.00 0.00 4.85
411 419 2.031163 AGCCGAACTCCACACAGC 59.969 61.111 0.00 0.00 0.00 4.40
412 420 1.069765 ACAGCCGAACTCCACACAG 59.930 57.895 0.00 0.00 0.00 3.66
413 421 1.227527 CACAGCCGAACTCCACACA 60.228 57.895 0.00 0.00 0.00 3.72
414 422 1.227556 ACACAGCCGAACTCCACAC 60.228 57.895 0.00 0.00 0.00 3.82
415 423 1.227527 CACACAGCCGAACTCCACA 60.228 57.895 0.00 0.00 0.00 4.17
416 424 0.946221 CTCACACAGCCGAACTCCAC 60.946 60.000 0.00 0.00 0.00 4.02
417 425 1.112916 TCTCACACAGCCGAACTCCA 61.113 55.000 0.00 0.00 0.00 3.86
418 426 0.247736 ATCTCACACAGCCGAACTCC 59.752 55.000 0.00 0.00 0.00 3.85
419 427 1.354040 CATCTCACACAGCCGAACTC 58.646 55.000 0.00 0.00 0.00 3.01
420 428 0.036952 CCATCTCACACAGCCGAACT 60.037 55.000 0.00 0.00 0.00 3.01
421 429 1.021390 CCCATCTCACACAGCCGAAC 61.021 60.000 0.00 0.00 0.00 3.95
422 430 1.296392 CCCATCTCACACAGCCGAA 59.704 57.895 0.00 0.00 0.00 4.30
423 431 2.659063 CCCCATCTCACACAGCCGA 61.659 63.158 0.00 0.00 0.00 5.54
424 432 2.124983 CCCCATCTCACACAGCCG 60.125 66.667 0.00 0.00 0.00 5.52
425 433 1.222936 CTCCCCATCTCACACAGCC 59.777 63.158 0.00 0.00 0.00 4.85
426 434 1.451028 GCTCCCCATCTCACACAGC 60.451 63.158 0.00 0.00 0.00 4.40
427 435 0.392193 GTGCTCCCCATCTCACACAG 60.392 60.000 0.00 0.00 0.00 3.66
428 436 1.679311 GTGCTCCCCATCTCACACA 59.321 57.895 0.00 0.00 0.00 3.72
429 437 1.448540 CGTGCTCCCCATCTCACAC 60.449 63.158 0.00 0.00 0.00 3.82
430 438 0.613572 TACGTGCTCCCCATCTCACA 60.614 55.000 0.00 0.00 0.00 3.58
431 439 0.535335 TTACGTGCTCCCCATCTCAC 59.465 55.000 0.00 0.00 0.00 3.51
432 440 1.271856 TTTACGTGCTCCCCATCTCA 58.728 50.000 0.00 0.00 0.00 3.27
433 441 2.213499 CATTTACGTGCTCCCCATCTC 58.787 52.381 0.00 0.00 0.00 2.75
434 442 1.134098 CCATTTACGTGCTCCCCATCT 60.134 52.381 0.00 0.00 0.00 2.90
435 443 1.308998 CCATTTACGTGCTCCCCATC 58.691 55.000 0.00 0.00 0.00 3.51
442 450 2.009774 CTTGCTAGCCATTTACGTGCT 58.990 47.619 13.29 0.00 39.10 4.40
506 539 3.827898 GACTGGGTCTCCGCTCCG 61.828 72.222 0.00 0.00 35.24 4.63
507 540 3.462678 GGACTGGGTCTCCGCTCC 61.463 72.222 0.00 0.00 35.24 4.70
508 541 3.462678 GGGACTGGGTCTCCGCTC 61.463 72.222 0.00 0.00 35.24 5.03
752 799 2.095415 GCAACCCACACGATAAAAGACC 60.095 50.000 0.00 0.00 0.00 3.85
794 841 8.084073 CGTATATCCGTATCTAACAAAAAGGGA 58.916 37.037 0.00 0.00 0.00 4.20
896 950 4.767255 GAGGGGAGTGTGCGCAGG 62.767 72.222 12.22 0.00 0.00 4.85
897 951 4.767255 GGAGGGGAGTGTGCGCAG 62.767 72.222 12.22 0.00 0.00 5.18
899 953 3.628646 AATGGAGGGGAGTGTGCGC 62.629 63.158 0.00 0.00 0.00 6.09
905 959 3.011517 AGCGCAATGGAGGGGAGT 61.012 61.111 11.47 0.00 0.00 3.85
971 1025 4.675303 TGGGGAGTGGAGTGGGGG 62.675 72.222 0.00 0.00 0.00 5.40
972 1026 3.330720 GTGGGGAGTGGAGTGGGG 61.331 72.222 0.00 0.00 0.00 4.96
973 1027 2.203998 AGTGGGGAGTGGAGTGGG 60.204 66.667 0.00 0.00 0.00 4.61
974 1028 2.294078 GGAGTGGGGAGTGGAGTGG 61.294 68.421 0.00 0.00 0.00 4.00
975 1029 2.294078 GGGAGTGGGGAGTGGAGTG 61.294 68.421 0.00 0.00 0.00 3.51
976 1030 2.122954 GGGAGTGGGGAGTGGAGT 59.877 66.667 0.00 0.00 0.00 3.85
977 1031 2.689034 GGGGAGTGGGGAGTGGAG 60.689 72.222 0.00 0.00 0.00 3.86
978 1032 3.537506 TGGGGAGTGGGGAGTGGA 61.538 66.667 0.00 0.00 0.00 4.02
979 1033 3.330720 GTGGGGAGTGGGGAGTGG 61.331 72.222 0.00 0.00 0.00 4.00
980 1034 3.706373 CGTGGGGAGTGGGGAGTG 61.706 72.222 0.00 0.00 0.00 3.51
1037 1091 3.798954 CTCCCTTCATCTCGCCGGC 62.799 68.421 19.07 19.07 0.00 6.13
1038 1092 2.419198 CTCCCTTCATCTCGCCGG 59.581 66.667 0.00 0.00 0.00 6.13
1039 1093 2.279784 GCTCCCTTCATCTCGCCG 60.280 66.667 0.00 0.00 0.00 6.46
1040 1094 0.179034 ATTGCTCCCTTCATCTCGCC 60.179 55.000 0.00 0.00 0.00 5.54
1041 1095 0.942962 CATTGCTCCCTTCATCTCGC 59.057 55.000 0.00 0.00 0.00 5.03
1042 1096 0.942962 GCATTGCTCCCTTCATCTCG 59.057 55.000 0.16 0.00 0.00 4.04
1043 1097 1.948145 CTGCATTGCTCCCTTCATCTC 59.052 52.381 10.49 0.00 0.00 2.75
1044 1098 2.022754 GCTGCATTGCTCCCTTCATCT 61.023 52.381 10.49 0.00 0.00 2.90
1216 1506 2.110006 GAGGAGATCTTGCCGGCC 59.890 66.667 26.77 7.94 0.00 6.13
1249 1539 3.723235 GAGGAAGCGCATCGGCTCA 62.723 63.158 11.47 0.00 43.93 4.26
2035 2327 1.503542 CTTGCCGAAGTGGTCATGC 59.496 57.895 0.00 0.00 41.21 4.06
2197 2489 2.538512 TTGATGATGGCTGGAGATCG 57.461 50.000 0.00 0.00 0.00 3.69
2263 2555 0.169009 GAATCAAGTTGCGAGCACCC 59.831 55.000 0.00 0.00 0.00 4.61
2269 2561 2.488204 TCATGGGAATCAAGTTGCGA 57.512 45.000 0.00 0.00 0.00 5.10
2383 2675 4.214971 CAGGTATACTGCTCATTCCATTGC 59.785 45.833 2.25 0.00 40.97 3.56
2386 2678 3.328931 CCCAGGTATACTGCTCATTCCAT 59.671 47.826 2.25 0.00 46.14 3.41
2416 2708 0.530431 TGATCACGGTGCATGGATCG 60.530 55.000 19.05 19.05 39.14 3.69
2452 2744 3.716353 TCTTGCTCCCAATCTGGCTATTA 59.284 43.478 0.00 0.00 35.79 0.98
2479 2771 2.546494 GCTTTCATCCCGGGCATCG 61.546 63.158 18.49 3.46 38.88 3.84
2698 2990 3.243301 CCAACTGCATCACTGATATTGGC 60.243 47.826 9.14 2.76 0.00 4.52
2788 3080 0.252103 TGTACTCCACCACCTCCCTC 60.252 60.000 0.00 0.00 0.00 4.30
2800 3092 0.525668 CCACATCGAGCGTGTACTCC 60.526 60.000 14.60 0.00 32.79 3.85
2824 3116 0.037326 GCCGGAGACTGAACATGTGA 60.037 55.000 5.05 0.00 0.00 3.58
3004 3296 7.861629 TCATAAACATGTAGAGGAAGATGGTT 58.138 34.615 0.00 0.00 34.68 3.67
3031 3323 1.557099 AGCGATAGTTCCACAGTCCA 58.443 50.000 0.00 0.00 39.35 4.02
3103 3395 2.256306 TCAAGCTCATCAGGGTGTGTA 58.744 47.619 0.00 0.00 0.00 2.90
3292 3584 7.062957 CCACCAGGGACAAGAATATAAAGATT 58.937 38.462 0.00 0.00 40.01 2.40
3298 3590 3.458118 CCACCACCAGGGACAAGAATATA 59.542 47.826 0.00 0.00 41.15 0.86
3493 3785 4.235372 TGTTACAACCATCCCCCATTTTT 58.765 39.130 0.00 0.00 0.00 1.94
3505 3797 1.783979 AGGGGGACAATGTTACAACCA 59.216 47.619 0.00 0.00 0.00 3.67
3507 3799 3.009143 AGAGAGGGGGACAATGTTACAAC 59.991 47.826 0.00 0.00 0.00 3.32
3597 3889 0.825840 TTACAGGGCCACCAAACTGC 60.826 55.000 6.18 0.00 40.13 4.40
3601 3893 2.380590 ACCTTATTACAGGGCCACCAAA 59.619 45.455 6.18 0.00 38.42 3.28
3602 3894 1.997040 ACCTTATTACAGGGCCACCAA 59.003 47.619 6.18 0.00 38.42 3.67
3638 3933 2.010145 TTTGCCTAGCTAAGCAGACG 57.990 50.000 16.24 0.00 40.73 4.18
3656 3951 1.883926 CCGGTCATTCCCTTCGTTTTT 59.116 47.619 0.00 0.00 0.00 1.94
3850 4145 4.434520 GGAAGGAACAGCACATACTAGAC 58.565 47.826 0.00 0.00 0.00 2.59
3891 4190 5.520649 GCCTCAGAACAAATACAGTAGTAGC 59.479 44.000 0.00 0.00 32.86 3.58
3923 4282 2.238646 ACCAGTGTGACCTCTGAAACAA 59.761 45.455 6.48 0.00 34.78 2.83
3925 4284 2.622064 ACCAGTGTGACCTCTGAAAC 57.378 50.000 6.48 0.00 34.78 2.78
3929 4288 3.069586 TGAAACTACCAGTGTGACCTCTG 59.930 47.826 0.00 0.00 33.06 3.35
3930 4289 3.069729 GTGAAACTACCAGTGTGACCTCT 59.930 47.826 0.00 0.00 0.00 3.69
3931 4290 3.391049 GTGAAACTACCAGTGTGACCTC 58.609 50.000 0.00 0.00 0.00 3.85
3932 4291 3.470645 GTGAAACTACCAGTGTGACCT 57.529 47.619 0.00 0.00 0.00 3.85
4004 4369 8.557864 CATTTGTAGGCTCTTAAGATGATGAAG 58.442 37.037 5.44 0.00 0.00 3.02
4026 4564 1.200716 CAGATGAACTGGCGCACATTT 59.799 47.619 10.83 5.42 42.39 2.32
4045 4583 4.509970 CGGAGTAACTGACATTCAACAACA 59.490 41.667 0.00 0.00 0.00 3.33
4074 4612 1.346365 GCGACGACAATTCTGCACTA 58.654 50.000 0.00 0.00 0.00 2.74
4091 4629 2.344025 AGAAAAAGTAGGCTAACGGCG 58.656 47.619 4.80 4.80 42.94 6.46
4099 4637 4.621886 CACTACGACAGAGAAAAAGTAGGC 59.378 45.833 0.00 0.00 36.74 3.93
4109 4647 3.418047 TGATCAACCACTACGACAGAGA 58.582 45.455 0.00 0.00 0.00 3.10
4110 4648 3.763902 CTGATCAACCACTACGACAGAG 58.236 50.000 0.00 0.00 0.00 3.35
4121 4662 4.256110 CACATTCAGTAGCTGATCAACCA 58.744 43.478 0.00 0.00 40.39 3.67
4158 4699 0.250166 GGCGTAACTGACACCAGGTT 60.250 55.000 0.00 0.00 44.60 3.50
4175 4716 1.237285 ATTCTGCACTGAACCACGGC 61.237 55.000 0.00 0.00 0.00 5.68
4219 4783 1.977854 AGTAACTGGCACCAGATCACA 59.022 47.619 23.30 0.64 46.30 3.58
4249 4813 1.607628 CTGCTGCTTCTTTTCTGCACT 59.392 47.619 0.00 0.00 34.32 4.40
4336 4900 1.883021 GGGATCAAAAGCGTGGGTG 59.117 57.895 0.00 0.00 0.00 4.61
4510 5094 1.191489 TCCCTTGATGGCAGACGACA 61.191 55.000 0.00 0.00 0.00 4.35
4519 5103 1.817099 GCGCTGTCTCCCTTGATGG 60.817 63.158 0.00 0.00 0.00 3.51
4562 5147 0.593128 GGCACCACTAGCACAACAAG 59.407 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.