Multiple sequence alignment - TraesCS4D01G013000

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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 TraesCS4D01G013000 chr4D 100.000 3096 0 0 1 3096 6040256 6037161 0.000000e+00 5718
1 TraesCS4D01G013000 chr4A 87.283 3161 207 69 1 3094 597675934 597678966 0.000000e+00 3430
2 TraesCS4D01G013000 chr4B 86.281 1538 85 31 715 2226 10594625 10593188 0.000000e+00 1555
3 TraesCS4D01G013000 chr4B 95.390 846 27 11 2252 3095 10592818 10591983 0.000000e+00 1336
4 TraesCS4D01G013000 chr4B 80.444 496 58 15 27 499 10597166 10596687 2.960000e-90 342
5 TraesCS4D01G013000 chr4B 90.164 122 7 3 490 607 10596280 10596160 1.490000e-33 154
6 TraesCS4D01G013000 chr5B 84.007 594 76 12 2287 2866 21181194 21181782 1.250000e-153 553
7 TraesCS4D01G013000 chr6B 81.962 693 82 18 727 1399 225626319 225625650 5.840000e-152 547
8 TraesCS4D01G013000 chr5D 82.765 586 85 10 2287 2866 28666921 28667496 2.750000e-140 508
9 TraesCS4D01G013000 chr5A 82.765 586 85 12 2287 2866 19268613 19269188 2.750000e-140 508
10 TraesCS4D01G013000 chr5A 80.609 361 61 8 2 354 568001495 568001136 1.410000e-68 270
11 TraesCS4D01G013000 chr7B 81.034 348 55 9 6 349 659734240 659733900 1.830000e-67 267
12 TraesCS4D01G013000 chr7A 81.362 279 46 6 3 278 681954579 681954304 4.020000e-54 222


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 TraesCS4D01G013000 chr4D 6037161 6040256 3095 True 5718.00 5718 100.00000 1 3096 1 chr4D.!!$R1 3095
1 TraesCS4D01G013000 chr4A 597675934 597678966 3032 False 3430.00 3430 87.28300 1 3094 1 chr4A.!!$F1 3093
2 TraesCS4D01G013000 chr4B 10591983 10597166 5183 True 846.75 1555 88.06975 27 3095 4 chr4B.!!$R1 3068
3 TraesCS4D01G013000 chr5B 21181194 21181782 588 False 553.00 553 84.00700 2287 2866 1 chr5B.!!$F1 579
4 TraesCS4D01G013000 chr6B 225625650 225626319 669 True 547.00 547 81.96200 727 1399 1 chr6B.!!$R1 672
5 TraesCS4D01G013000 chr5D 28666921 28667496 575 False 508.00 508 82.76500 2287 2866 1 chr5D.!!$F1 579
6 TraesCS4D01G013000 chr5A 19268613 19269188 575 False 508.00 508 82.76500 2287 2866 1 chr5A.!!$F1 579

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
166 171 0.034574 TTGATTGGATGACGTGGGGG 60.035 55.0 0.0 0.0 0.00 5.40 F
1059 3003 0.035056 CGCTCAAAGATCCCAAGGGT 60.035 55.0 4.8 0.0 36.47 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 4034 0.801067 GCTTATGTCTCGTCGCGGTT 60.801 55.0 6.13 0.0 0.00 4.44 R
2928 5277 0.586319 GCGCTTTAGCTGTGTTGTCA 59.414 50.0 0.00 0.0 39.32 3.58 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
22 23 3.730061 CGCTCCATCAAAATCAGCTTCAC 60.730 47.826 0.00 0.00 0.00 3.18
23 24 3.192001 GCTCCATCAAAATCAGCTTCACA 59.808 43.478 0.00 0.00 0.00 3.58
27 28 4.081862 CCATCAAAATCAGCTTCACACCAT 60.082 41.667 0.00 0.00 0.00 3.55
35 36 2.821378 CAGCTTCACACCATCAAATCCA 59.179 45.455 0.00 0.00 0.00 3.41
62 63 9.273016 CTTTGAAGAAGTTTCATACAGGAGTTA 57.727 33.333 0.00 0.00 0.00 2.24
94 95 7.309133 CCACCAAAGAGCACTTTATCATGTTTA 60.309 37.037 8.88 0.00 43.41 2.01
103 104 6.678900 GCACTTTATCATGTTTAGCTTCCAGG 60.679 42.308 0.00 0.00 0.00 4.45
119 122 4.008074 TCCAGGTAGCTTCAACTTCAAG 57.992 45.455 0.00 0.00 0.00 3.02
122 125 5.006386 CCAGGTAGCTTCAACTTCAAGAAT 58.994 41.667 0.00 0.00 0.00 2.40
141 146 7.879160 TCAAGAATGGAAATTTGATGGAAAAGG 59.121 33.333 0.00 0.00 0.00 3.11
166 171 0.034574 TTGATTGGATGACGTGGGGG 60.035 55.000 0.00 0.00 0.00 5.40
182 187 0.691332 GGGGGATTCGAAGGGGTATC 59.309 60.000 3.35 0.00 0.00 2.24
186 191 1.071857 GGATTCGAAGGGGTATCCACC 59.928 57.143 3.35 0.00 44.96 4.61
193 198 0.400093 AGGGGTATCCACCTACTGGC 60.400 60.000 0.00 0.00 45.04 4.85
197 202 1.108776 GTATCCACCTACTGGCGTCA 58.891 55.000 0.00 0.00 40.39 4.35
212 217 0.240945 CGTCAGTGGTGGGCAATTTC 59.759 55.000 0.00 0.00 0.00 2.17
224 229 1.001974 GGCAATTTCCCCAAACTCCAC 59.998 52.381 0.00 0.00 0.00 4.02
233 238 2.642807 CCCCAAACTCCACCTTCTAGAA 59.357 50.000 4.81 4.81 0.00 2.10
237 242 5.416013 CCCAAACTCCACCTTCTAGAATTTC 59.584 44.000 5.44 0.00 0.00 2.17
248 253 1.933853 CTAGAATTTCCGAAGCACCCG 59.066 52.381 0.00 0.00 0.00 5.28
316 324 3.804786 TTTTCGGAGCGGTATGTCATA 57.195 42.857 0.00 0.00 0.00 2.15
317 325 3.804786 TTTCGGAGCGGTATGTCATAA 57.195 42.857 0.00 0.00 0.00 1.90
337 345 0.036306 AGCTACCCCGTTTGACTTGG 59.964 55.000 0.00 0.00 0.00 3.61
342 371 1.752498 ACCCCGTTTGACTTGGTTTTC 59.248 47.619 0.00 0.00 0.00 2.29
343 372 2.028876 CCCCGTTTGACTTGGTTTTCT 58.971 47.619 0.00 0.00 0.00 2.52
344 373 3.215975 CCCCGTTTGACTTGGTTTTCTA 58.784 45.455 0.00 0.00 0.00 2.10
349 378 4.272504 CGTTTGACTTGGTTTTCTAGAGCA 59.727 41.667 0.00 0.00 0.00 4.26
356 385 2.899900 TGGTTTTCTAGAGCAGAGCAGA 59.100 45.455 0.00 0.00 33.83 4.26
366 395 1.627329 AGCAGAGCAGATCCAAACAGA 59.373 47.619 0.00 0.00 0.00 3.41
429 458 8.735315 TGTAATAGTGTTTAATCAATGTGTGGG 58.265 33.333 0.00 0.00 0.00 4.61
441 470 0.321210 TGTGTGGGTGTGCTTATCGG 60.321 55.000 0.00 0.00 0.00 4.18
442 471 1.024579 GTGTGGGTGTGCTTATCGGG 61.025 60.000 0.00 0.00 0.00 5.14
443 472 2.112815 GTGGGTGTGCTTATCGGGC 61.113 63.158 0.00 0.00 0.00 6.13
446 475 3.573491 GTGTGCTTATCGGGCGGC 61.573 66.667 0.00 0.00 0.00 6.53
447 476 4.089239 TGTGCTTATCGGGCGGCA 62.089 61.111 12.47 0.00 0.00 5.69
449 478 3.781307 TGCTTATCGGGCGGCACT 61.781 61.111 12.47 0.00 0.00 4.40
525 973 8.440833 ACATTTCTTCGTAAATAAAGAAGTCCG 58.559 33.333 4.65 0.00 41.22 4.79
569 1017 0.603439 GCATGCTTTTGGGTTGGGTG 60.603 55.000 11.37 0.00 0.00 4.61
607 1055 7.912949 TCAAAAACATCATTCGTCTCAAAAG 57.087 32.000 0.00 0.00 0.00 2.27
609 1057 6.633500 AAAACATCATTCGTCTCAAAAGGA 57.367 33.333 0.00 0.00 0.00 3.36
610 1058 5.613358 AACATCATTCGTCTCAAAAGGAC 57.387 39.130 0.00 0.00 0.00 3.85
611 1059 4.641396 ACATCATTCGTCTCAAAAGGACA 58.359 39.130 0.00 0.00 33.73 4.02
613 1061 5.530915 ACATCATTCGTCTCAAAAGGACAAA 59.469 36.000 0.00 0.00 33.73 2.83
646 2546 4.787882 GCTCAGAAAAGTGAGTGAACTTGC 60.788 45.833 3.00 0.00 45.07 4.01
650 2553 4.816925 AGAAAAGTGAGTGAACTTGCTACC 59.183 41.667 0.00 0.00 40.28 3.18
668 2571 4.089923 GCTACCGAAATTTGTGAATGTTGC 59.910 41.667 0.00 0.00 0.00 4.17
673 2576 5.570973 CCGAAATTTGTGAATGTTGCGATAA 59.429 36.000 0.00 0.00 0.00 1.75
675 2578 7.159644 CGAAATTTGTGAATGTTGCGATAAAG 58.840 34.615 0.00 0.00 0.00 1.85
682 2585 8.667987 TGTGAATGTTGCGATAAAGTAAATTC 57.332 30.769 0.00 0.00 0.00 2.17
685 2588 9.340695 TGAATGTTGCGATAAAGTAAATTCTTG 57.659 29.630 0.00 0.00 0.00 3.02
691 2594 6.123441 GCGATAAAGTAAATTCTTGCTCTCG 58.877 40.000 0.00 0.00 32.19 4.04
698 2601 8.859517 AAGTAAATTCTTGCTCTCGACTATAC 57.140 34.615 0.00 0.00 0.00 1.47
703 2606 6.374565 TTCTTGCTCTCGACTATACCTTAC 57.625 41.667 0.00 0.00 0.00 2.34
713 2616 8.622157 TCTCGACTATACCTTACAATCTCTTTG 58.378 37.037 0.00 0.00 41.36 2.77
742 2645 1.866601 TGTGTGCATGACTCTGAAACG 59.133 47.619 0.00 0.00 0.00 3.60
751 2657 4.913335 TGACTCTGAAACGTCTTACAGT 57.087 40.909 0.00 0.00 0.00 3.55
774 2680 9.774742 CAGTACCTTCTTTCATTTATGCTAAAC 57.225 33.333 0.00 0.00 0.00 2.01
842 2754 6.293955 GCTGACTGGTGCTTCTATTAACAAAA 60.294 38.462 0.00 0.00 0.00 2.44
974 2906 3.349006 CCATCACCGCCGCATAGC 61.349 66.667 0.00 0.00 0.00 2.97
996 2928 6.010850 AGCTATATCGTGTCATCTTCCCTAA 58.989 40.000 0.00 0.00 0.00 2.69
997 2929 6.665680 AGCTATATCGTGTCATCTTCCCTAAT 59.334 38.462 0.00 0.00 0.00 1.73
998 2930 6.975772 GCTATATCGTGTCATCTTCCCTAATC 59.024 42.308 0.00 0.00 0.00 1.75
999 2931 4.608948 ATCGTGTCATCTTCCCTAATCC 57.391 45.455 0.00 0.00 0.00 3.01
1000 2932 2.698797 TCGTGTCATCTTCCCTAATCCC 59.301 50.000 0.00 0.00 0.00 3.85
1001 2933 2.700897 CGTGTCATCTTCCCTAATCCCT 59.299 50.000 0.00 0.00 0.00 4.20
1002 2934 3.895656 CGTGTCATCTTCCCTAATCCCTA 59.104 47.826 0.00 0.00 0.00 3.53
1010 2942 6.374417 TCTTCCCTAATCCCTATAATGCAC 57.626 41.667 0.00 0.00 0.00 4.57
1011 2943 5.849475 TCTTCCCTAATCCCTATAATGCACA 59.151 40.000 0.00 0.00 0.00 4.57
1012 2944 5.499004 TCCCTAATCCCTATAATGCACAC 57.501 43.478 0.00 0.00 0.00 3.82
1013 2945 4.288626 TCCCTAATCCCTATAATGCACACC 59.711 45.833 0.00 0.00 0.00 4.16
1014 2946 4.289672 CCCTAATCCCTATAATGCACACCT 59.710 45.833 0.00 0.00 0.00 4.00
1015 2947 5.222130 CCCTAATCCCTATAATGCACACCTT 60.222 44.000 0.00 0.00 0.00 3.50
1016 2948 6.306987 CCTAATCCCTATAATGCACACCTTT 58.693 40.000 0.00 0.00 0.00 3.11
1017 2949 6.431234 CCTAATCCCTATAATGCACACCTTTC 59.569 42.308 0.00 0.00 0.00 2.62
1018 2950 4.164843 TCCCTATAATGCACACCTTTCC 57.835 45.455 0.00 0.00 0.00 3.13
1019 2951 3.785887 TCCCTATAATGCACACCTTTCCT 59.214 43.478 0.00 0.00 0.00 3.36
1020 2952 3.885297 CCCTATAATGCACACCTTTCCTG 59.115 47.826 0.00 0.00 0.00 3.86
1021 2953 4.526970 CCTATAATGCACACCTTTCCTGT 58.473 43.478 0.00 0.00 0.00 4.00
1029 2961 1.132495 ACACCTTTCCTGTCCCCTACT 60.132 52.381 0.00 0.00 0.00 2.57
1044 2988 2.482142 CCCTACTCAATCCTTGTCGCTC 60.482 54.545 0.00 0.00 0.00 5.03
1054 2998 1.339055 CCTTGTCGCTCAAAGATCCCA 60.339 52.381 0.00 0.00 35.48 4.37
1059 3003 0.035056 CGCTCAAAGATCCCAAGGGT 60.035 55.000 4.80 0.00 36.47 4.34
1104 3057 1.275010 TCTATCAACAGCAGTTCGGCA 59.725 47.619 0.00 0.00 35.28 5.69
1230 3183 3.106407 GACGTCTCAGGTGCGCAC 61.106 66.667 32.15 32.15 0.00 5.34
1294 3249 3.243873 ACTTGCGTGTCTTCTGAAGATGA 60.244 43.478 21.86 10.12 40.18 2.92
1439 3395 0.251297 TCCTCAAGTCGTTCCCGGTA 60.251 55.000 0.00 0.00 33.95 4.02
1490 3446 3.231734 CGTGATGGACAAGGAGCAA 57.768 52.632 0.00 0.00 0.00 3.91
1528 3484 2.141011 CTGCCCAAGGGGTCATCACA 62.141 60.000 7.36 0.00 46.51 3.58
1728 3693 3.347077 ACAGGGCTGAAGAGAAGAATG 57.653 47.619 0.00 0.00 0.00 2.67
1736 3704 1.021390 AAGAGAAGAATGCGGCACCG 61.021 55.000 4.03 4.30 43.09 4.94
1774 3745 3.577848 CAGATACAGGAGGAGGAGATTGG 59.422 52.174 0.00 0.00 0.00 3.16
1807 3778 0.881118 CCAAGAAACGATGGTGGTGG 59.119 55.000 0.00 0.00 31.84 4.61
1811 3782 1.351017 AGAAACGATGGTGGTGGTGAT 59.649 47.619 0.00 0.00 0.00 3.06
1812 3783 1.468520 GAAACGATGGTGGTGGTGATG 59.531 52.381 0.00 0.00 0.00 3.07
1838 3809 0.474660 AGAGGTGGTGGGAGAAGCTT 60.475 55.000 0.00 0.00 0.00 3.74
1853 3824 2.730672 GCTTACGCCTCTGCACGTG 61.731 63.158 12.28 12.28 43.44 4.49
1944 3915 8.988934 TCTGAATCATGTGTAAAAGACTACAAC 58.011 33.333 0.00 0.00 33.66 3.32
1952 3923 9.826574 ATGTGTAAAAGACTACAACTTCTGTAA 57.173 29.630 0.00 0.00 40.06 2.41
2027 4007 2.544721 AGGAGGAACTGAGAGATGCAA 58.455 47.619 0.00 0.00 41.55 4.08
2028 4008 2.500910 AGGAGGAACTGAGAGATGCAAG 59.499 50.000 0.00 0.00 41.55 4.01
2069 4049 2.202440 CGAACCGCGACGAGACAT 60.202 61.111 8.23 0.00 44.57 3.06
2139 4119 5.063438 ACATAGATACAACATGTCAACACGC 59.937 40.000 0.00 0.00 0.00 5.34
2141 4121 3.186409 AGATACAACATGTCAACACGCAC 59.814 43.478 0.00 0.00 0.00 5.34
2178 4158 2.093075 GGACTAACCCTAGCCAAACTCC 60.093 54.545 0.00 0.00 0.00 3.85
2181 4161 0.838987 AACCCTAGCCAAACTCCGGA 60.839 55.000 2.93 2.93 0.00 5.14
2658 4998 2.627699 TGTGAATCTGCCCAGGAAAAAC 59.372 45.455 0.00 0.00 0.00 2.43
2901 5250 4.788690 CGTATTTGTTACACATGCCACAA 58.211 39.130 0.00 0.00 0.00 3.33
2906 5255 1.196808 GTTACACATGCCACAAGGACG 59.803 52.381 0.00 0.00 36.89 4.79
2908 5257 1.165907 ACACATGCCACAAGGACGTG 61.166 55.000 0.00 0.00 36.89 4.49
2938 5287 2.355197 TGGTGACAACTGACAACACAG 58.645 47.619 0.00 0.00 38.56 3.66
2941 5290 3.194861 GTGACAACTGACAACACAGCTA 58.805 45.455 0.00 0.00 41.06 3.32
2943 5292 4.094294 GTGACAACTGACAACACAGCTAAA 59.906 41.667 0.00 0.00 41.06 1.85
2944 5293 4.332543 TGACAACTGACAACACAGCTAAAG 59.667 41.667 0.00 0.00 41.06 1.85
2945 5294 3.065371 ACAACTGACAACACAGCTAAAGC 59.935 43.478 0.00 0.00 41.06 3.51
2975 5324 1.818674 CAAACCTGAATACCACCAGCC 59.181 52.381 0.00 0.00 0.00 4.85
3048 5397 5.875359 GTCTCAAACCTGTATACCAAGAAGG 59.125 44.000 0.00 2.56 45.67 3.46
3082 5432 4.910458 AGTAGCAGTTAAACACCTCCAT 57.090 40.909 0.00 0.00 0.00 3.41
3089 5439 5.063204 CAGTTAAACACCTCCATGTGAAGA 58.937 41.667 0.00 0.00 39.57 2.87
3095 5445 0.458543 CCTCCATGTGAAGACCGTCG 60.459 60.000 0.00 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.507233 GGTGTGAAGCTGATTTTGATGGA 59.493 43.478 0.00 0.00 0.00 3.41
6 7 4.768448 TGATGGTGTGAAGCTGATTTTGAT 59.232 37.500 0.00 0.00 0.00 2.57
16 17 2.821969 AGTGGATTTGATGGTGTGAAGC 59.178 45.455 0.00 0.00 0.00 3.86
35 36 7.283329 ACTCCTGTATGAAACTTCTTCAAAGT 58.717 34.615 0.00 0.00 31.55 2.66
44 45 6.115448 AGCTGTAACTCCTGTATGAAACTT 57.885 37.500 0.00 0.00 0.00 2.66
103 104 6.560253 TTCCATTCTTGAAGTTGAAGCTAC 57.440 37.500 0.00 0.00 0.00 3.58
119 122 7.389232 AGACCTTTTCCATCAAATTTCCATTC 58.611 34.615 0.00 0.00 0.00 2.67
122 125 8.434589 AATAGACCTTTTCCATCAAATTTCCA 57.565 30.769 0.00 0.00 0.00 3.53
141 146 4.273480 CCCACGTCATCCAATCAAATAGAC 59.727 45.833 0.00 0.00 0.00 2.59
166 171 1.071857 GGTGGATACCCCTTCGAATCC 59.928 57.143 0.00 1.89 41.36 3.01
193 198 0.240945 GAAATTGCCCACCACTGACG 59.759 55.000 0.00 0.00 0.00 4.35
206 211 2.608623 AGGTGGAGTTTGGGGAAATTG 58.391 47.619 0.00 0.00 0.00 2.32
212 217 2.266279 TCTAGAAGGTGGAGTTTGGGG 58.734 52.381 0.00 0.00 0.00 4.96
216 221 5.012768 TCGGAAATTCTAGAAGGTGGAGTTT 59.987 40.000 11.53 4.63 29.61 2.66
224 229 3.623510 GGTGCTTCGGAAATTCTAGAAGG 59.376 47.826 22.39 11.65 40.11 3.46
271 276 7.707467 AAATAGAATATGGGGTACAAGTCCT 57.293 36.000 0.00 0.00 0.00 3.85
316 324 2.227194 CAAGTCAAACGGGGTAGCTTT 58.773 47.619 0.00 0.00 0.00 3.51
317 325 1.544759 CCAAGTCAAACGGGGTAGCTT 60.545 52.381 0.00 0.00 0.00 3.74
337 345 4.119136 GGATCTGCTCTGCTCTAGAAAAC 58.881 47.826 0.00 0.00 34.32 2.43
342 371 3.118847 TGTTTGGATCTGCTCTGCTCTAG 60.119 47.826 0.00 0.00 0.00 2.43
343 372 2.833943 TGTTTGGATCTGCTCTGCTCTA 59.166 45.455 0.00 0.00 0.00 2.43
344 373 1.627329 TGTTTGGATCTGCTCTGCTCT 59.373 47.619 0.00 0.00 0.00 4.09
349 378 1.280421 GGGTCTGTTTGGATCTGCTCT 59.720 52.381 0.00 0.00 0.00 4.09
356 385 4.664688 AAGAATGAGGGTCTGTTTGGAT 57.335 40.909 0.00 0.00 0.00 3.41
366 395 7.405292 TCTTGTCAATATCAAAGAATGAGGGT 58.595 34.615 0.00 0.00 42.53 4.34
408 437 6.016693 CACACCCACACATTGATTAAACACTA 60.017 38.462 0.00 0.00 0.00 2.74
424 453 1.298340 CCCGATAAGCACACCCACA 59.702 57.895 0.00 0.00 0.00 4.17
429 458 3.573491 GCCGCCCGATAAGCACAC 61.573 66.667 0.00 0.00 0.00 3.82
446 475 1.399440 CACAATCATTCTCGGCCAGTG 59.601 52.381 2.24 0.00 0.00 3.66
447 476 1.278985 TCACAATCATTCTCGGCCAGT 59.721 47.619 2.24 0.00 0.00 4.00
449 478 1.554617 TCTCACAATCATTCTCGGCCA 59.445 47.619 2.24 0.00 0.00 5.36
525 973 5.841810 TGTTTCATTTTCACCTTCATCCAC 58.158 37.500 0.00 0.00 0.00 4.02
618 1066 7.615403 AGTTCACTCACTTTTCTGAGCATATA 58.385 34.615 0.00 0.00 41.38 0.86
619 1067 6.471146 AGTTCACTCACTTTTCTGAGCATAT 58.529 36.000 0.00 0.00 41.38 1.78
646 2546 4.320690 CGCAACATTCACAAATTTCGGTAG 59.679 41.667 0.00 0.00 0.00 3.18
650 2553 6.609907 TTATCGCAACATTCACAAATTTCG 57.390 33.333 0.00 0.00 0.00 3.46
668 2571 7.221067 AGTCGAGAGCAAGAATTTACTTTATCG 59.779 37.037 0.00 0.00 0.00 2.92
673 2576 7.921745 GGTATAGTCGAGAGCAAGAATTTACTT 59.078 37.037 0.00 0.00 0.00 2.24
675 2578 7.427214 AGGTATAGTCGAGAGCAAGAATTTAC 58.573 38.462 0.00 0.00 0.00 2.01
682 2585 5.752892 TGTAAGGTATAGTCGAGAGCAAG 57.247 43.478 0.00 0.00 0.00 4.01
685 2588 6.428771 AGAGATTGTAAGGTATAGTCGAGAGC 59.571 42.308 0.00 0.00 0.00 4.09
697 2600 8.954350 CATTGAAGATCAAAGAGATTGTAAGGT 58.046 33.333 0.00 0.00 40.12 3.50
698 2601 8.954350 ACATTGAAGATCAAAGAGATTGTAAGG 58.046 33.333 0.00 0.00 40.12 2.69
703 2606 6.527023 GCACACATTGAAGATCAAAGAGATTG 59.473 38.462 0.00 0.00 40.12 2.67
713 2616 4.634883 AGAGTCATGCACACATTGAAGATC 59.365 41.667 0.00 0.00 32.87 2.75
781 2687 6.458751 CCACGCAGCAGAGTTAATAAATGAAT 60.459 38.462 0.00 0.00 0.00 2.57
782 2688 5.163764 CCACGCAGCAGAGTTAATAAATGAA 60.164 40.000 0.00 0.00 0.00 2.57
783 2689 4.332543 CCACGCAGCAGAGTTAATAAATGA 59.667 41.667 0.00 0.00 0.00 2.57
784 2690 4.094887 ACCACGCAGCAGAGTTAATAAATG 59.905 41.667 0.00 0.00 0.00 2.32
791 2697 1.341852 TGTTACCACGCAGCAGAGTTA 59.658 47.619 0.00 0.00 0.00 2.24
956 2884 3.349006 CTATGCGGCGGTGATGGC 61.349 66.667 9.78 0.00 0.00 4.40
974 2906 7.416890 GGGATTAGGGAAGATGACACGATATAG 60.417 44.444 0.00 0.00 0.00 1.31
996 2928 4.416848 AGGAAAGGTGTGCATTATAGGGAT 59.583 41.667 0.00 0.00 0.00 3.85
997 2929 3.785887 AGGAAAGGTGTGCATTATAGGGA 59.214 43.478 0.00 0.00 0.00 4.20
998 2930 3.885297 CAGGAAAGGTGTGCATTATAGGG 59.115 47.826 0.00 0.00 0.00 3.53
999 2931 4.526970 ACAGGAAAGGTGTGCATTATAGG 58.473 43.478 0.00 0.00 0.00 2.57
1000 2932 4.576463 GGACAGGAAAGGTGTGCATTATAG 59.424 45.833 0.00 0.00 36.35 1.31
1001 2933 4.523083 GGACAGGAAAGGTGTGCATTATA 58.477 43.478 0.00 0.00 36.35 0.98
1002 2934 3.356290 GGACAGGAAAGGTGTGCATTAT 58.644 45.455 0.00 0.00 36.35 1.28
1010 2942 1.555533 GAGTAGGGGACAGGAAAGGTG 59.444 57.143 0.00 0.00 0.00 4.00
1011 2943 1.151413 TGAGTAGGGGACAGGAAAGGT 59.849 52.381 0.00 0.00 0.00 3.50
1012 2944 1.952621 TGAGTAGGGGACAGGAAAGG 58.047 55.000 0.00 0.00 0.00 3.11
1013 2945 3.118223 GGATTGAGTAGGGGACAGGAAAG 60.118 52.174 0.00 0.00 0.00 2.62
1014 2946 2.844348 GGATTGAGTAGGGGACAGGAAA 59.156 50.000 0.00 0.00 0.00 3.13
1015 2947 2.045885 AGGATTGAGTAGGGGACAGGAA 59.954 50.000 0.00 0.00 0.00 3.36
1016 2948 1.651770 AGGATTGAGTAGGGGACAGGA 59.348 52.381 0.00 0.00 0.00 3.86
1017 2949 2.182516 AGGATTGAGTAGGGGACAGG 57.817 55.000 0.00 0.00 0.00 4.00
1044 2988 1.180029 CTGCACCCTTGGGATCTTTG 58.820 55.000 13.39 0.71 0.00 2.77
1054 2998 2.033757 CTGCTGCTCTGCACCCTT 59.966 61.111 0.00 0.00 38.12 3.95
1059 3003 3.928966 GAGACGCTGCTGCTCTGCA 62.929 63.158 17.61 1.66 39.31 4.41
1076 3025 3.756963 ACTGCTGTTGATAGACGTACAGA 59.243 43.478 16.14 3.06 40.24 3.41
1230 3183 3.691342 TGAAGGAGGACGCGGTGG 61.691 66.667 12.47 0.00 0.00 4.61
1240 3195 2.389020 CGCAGCAGCAGTGAAGGAG 61.389 63.158 0.82 0.00 42.27 3.69
1267 3222 7.689619 TCTTCAGAAGACACGCAAGTCACAT 62.690 44.000 8.95 0.00 40.32 3.21
1294 3249 1.672356 GCGACCATGGCAAGACAGT 60.672 57.895 13.04 0.00 0.00 3.55
1439 3395 4.719369 GCACGGACGCTCTTCGGT 62.719 66.667 0.00 0.00 43.86 4.69
1524 3480 3.748370 ACCTGGTGGTGGTTGTGA 58.252 55.556 0.00 0.00 46.51 3.58
1562 3521 4.430765 GCCATGGACGACGACGGT 62.431 66.667 18.40 0.00 44.46 4.83
1622 3584 2.815647 CCTTTCCGCTCTCCGTGC 60.816 66.667 0.00 0.00 34.38 5.34
1655 3617 4.492160 CCATTGCTGCTGCTGCCG 62.492 66.667 25.44 15.06 40.48 5.69
1702 3667 1.625818 TCTCTTCAGCCCTGTTCTTCC 59.374 52.381 0.00 0.00 0.00 3.46
1736 3704 4.651503 TGTATCTGAATCCTGGTCTCCTTC 59.348 45.833 0.00 0.00 0.00 3.46
1774 3745 0.890542 TCTTGGTGCATCTGGTGTGC 60.891 55.000 0.00 0.00 42.81 4.57
1807 3778 1.072331 ACCACCTCTTGTCACCATCAC 59.928 52.381 0.00 0.00 0.00 3.06
1811 3782 1.705002 CCCACCACCTCTTGTCACCA 61.705 60.000 0.00 0.00 0.00 4.17
1812 3783 1.073199 CCCACCACCTCTTGTCACC 59.927 63.158 0.00 0.00 0.00 4.02
1838 3809 2.863346 AACCACGTGCAGAGGCGTA 61.863 57.895 10.91 0.00 45.35 4.42
1853 3824 3.181500 GGACGATAACAATGAAGCCAACC 60.181 47.826 0.00 0.00 0.00 3.77
1944 3915 4.021016 AGTTAGTCAGGCAGGTTACAGAAG 60.021 45.833 0.00 0.00 0.00 2.85
1952 3923 2.037772 CTGTTCAGTTAGTCAGGCAGGT 59.962 50.000 0.00 0.00 0.00 4.00
2053 4033 1.189403 CTTATGTCTCGTCGCGGTTC 58.811 55.000 6.13 0.00 0.00 3.62
2054 4034 0.801067 GCTTATGTCTCGTCGCGGTT 60.801 55.000 6.13 0.00 0.00 4.44
2055 4035 1.226603 GCTTATGTCTCGTCGCGGT 60.227 57.895 6.13 0.00 0.00 5.68
2056 4036 0.930742 GAGCTTATGTCTCGTCGCGG 60.931 60.000 6.13 0.00 0.00 6.46
2060 4040 3.440228 GGTCTTGAGCTTATGTCTCGTC 58.560 50.000 0.00 0.00 33.41 4.20
2069 4049 1.079127 GGCTGCGGTCTTGAGCTTA 60.079 57.895 0.00 0.00 33.03 3.09
2139 4119 3.055094 AGTCCTGCTATGGTAAACTGGTG 60.055 47.826 0.00 0.00 0.00 4.17
2141 4121 3.914426 AGTCCTGCTATGGTAAACTGG 57.086 47.619 0.00 0.00 0.00 4.00
2178 4158 0.931662 CTTTATCGTACCGCCGTCCG 60.932 60.000 0.00 0.00 0.00 4.79
2181 4161 2.735823 GATTCTTTATCGTACCGCCGT 58.264 47.619 0.00 0.00 0.00 5.68
2234 4214 1.398692 TTGTTTTGTGGGGACAGAGC 58.601 50.000 0.00 0.00 44.46 4.09
2658 4998 5.557576 TCATCCATCCCTTATGAGACTTG 57.442 43.478 0.00 0.00 37.86 3.16
2901 5250 3.964688 TCACCATATCATTACCACGTCCT 59.035 43.478 0.00 0.00 0.00 3.85
2906 5255 6.037172 GTCAGTTGTCACCATATCATTACCAC 59.963 42.308 0.00 0.00 0.00 4.16
2908 5257 6.112734 TGTCAGTTGTCACCATATCATTACC 58.887 40.000 0.00 0.00 0.00 2.85
2927 5276 1.398960 GCGCTTTAGCTGTGTTGTCAG 60.399 52.381 0.00 0.00 39.32 3.51
2928 5277 0.586319 GCGCTTTAGCTGTGTTGTCA 59.414 50.000 0.00 0.00 39.32 3.58
2929 5278 3.368046 GCGCTTTAGCTGTGTTGTC 57.632 52.632 0.00 0.00 39.32 3.18
2938 5287 6.202188 TCAGGTTTGTATATAAGCGCTTTAGC 59.798 38.462 30.13 14.38 37.78 3.09
2941 5290 6.995511 TTCAGGTTTGTATATAAGCGCTTT 57.004 33.333 30.13 17.85 0.00 3.51
2943 5292 6.649557 GGTATTCAGGTTTGTATATAAGCGCT 59.350 38.462 2.64 2.64 0.00 5.92
2944 5293 6.425721 TGGTATTCAGGTTTGTATATAAGCGC 59.574 38.462 0.00 0.00 0.00 5.92
2945 5294 7.095355 GGTGGTATTCAGGTTTGTATATAAGCG 60.095 40.741 0.00 0.00 0.00 4.68
2952 5301 4.270008 GCTGGTGGTATTCAGGTTTGTAT 58.730 43.478 0.00 0.00 0.00 2.29
2975 5324 2.065899 AGGAGGTTGAGGATCTCGAG 57.934 55.000 5.93 5.93 34.92 4.04


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

AutoCloner maintained by Alex Coulton.