Multiple sequence alignment - TraesCS5D01G163200

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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 TraesCS5D01G163200 chr5D 100.000 5179 0 0 1 5179 254825907 254831085 0.000000e+00 9564.0
1 TraesCS5D01G163200 chr5B 96.055 4588 131 22 617 5179 287800779 287796217 0.000000e+00 7424.0
2 TraesCS5D01G163200 chr5B 96.000 75 3 0 256 330 287801086 287801012 7.040000e-24 122.0
3 TraesCS5D01G163200 chr5B 80.189 106 14 7 521 621 561938495 561938598 7.190000e-09 73.1
4 TraesCS5D01G163200 chr5B 79.808 104 15 6 524 623 551504401 551504300 2.590000e-08 71.3
5 TraesCS5D01G163200 chr5A 93.428 3256 139 23 822 4042 338226276 338229491 0.000000e+00 4758.0
6 TraesCS5D01G163200 chr5A 95.793 1141 38 4 4045 5179 338229522 338230658 0.000000e+00 1832.0
7 TraesCS5D01G163200 chr5A 87.660 624 53 11 1 603 338221446 338222066 0.000000e+00 704.0
8 TraesCS5D01G163200 chr5A 89.231 260 19 6 566 819 338222063 338222319 3.010000e-82 316.0
9 TraesCS5D01G163200 chr2D 92.354 497 29 2 1094 1582 628363513 628364008 0.000000e+00 699.0
10 TraesCS5D01G163200 chr2D 86.275 153 18 3 86 238 196004633 196004484 4.150000e-36 163.0
11 TraesCS5D01G163200 chr7B 90.951 431 26 6 1152 1582 439316839 439316422 7.530000e-158 568.0
12 TraesCS5D01G163200 chr7B 87.770 139 12 5 83 220 188001404 188001538 1.930000e-34 158.0
13 TraesCS5D01G163200 chr7B 81.308 107 11 7 525 625 565053178 565053281 1.550000e-10 78.7
14 TraesCS5D01G163200 chr4B 88.710 434 32 7 1149 1582 68649645 68650061 9.940000e-142 514.0
15 TraesCS5D01G163200 chr4B 80.992 242 25 9 17 239 396716025 396716264 6.890000e-39 172.0
16 TraesCS5D01G163200 chr4B 78.899 109 17 6 522 626 575684629 575684523 9.310000e-08 69.4
17 TraesCS5D01G163200 chr4B 93.182 44 2 1 1084 1127 68649607 68649649 4.330000e-06 63.9
18 TraesCS5D01G163200 chr2B 89.474 285 23 5 1089 1373 653684685 653684962 2.290000e-93 353.0
19 TraesCS5D01G163200 chr2B 91.189 227 13 3 1359 1578 653685953 653686179 8.430000e-78 302.0
20 TraesCS5D01G163200 chr4D 88.387 155 16 2 86 239 87959722 87959875 8.860000e-43 185.0
21 TraesCS5D01G163200 chr4A 85.366 164 17 5 80 237 554921939 554922101 4.150000e-36 163.0
22 TraesCS5D01G163200 chr3D 86.765 136 16 2 83 217 554331310 554331444 3.230000e-32 150.0
23 TraesCS5D01G163200 chr3D 82.828 99 12 5 524 618 36979663 36979760 3.320000e-12 84.2
24 TraesCS5D01G163200 chr7A 85.135 148 18 2 94 239 519170971 519171116 1.160000e-31 148.0
25 TraesCS5D01G163200 chr7A 83.766 154 23 2 86 239 281552312 281552463 1.500000e-30 145.0
26 TraesCS5D01G163200 chr7A 81.000 100 12 7 525 620 443957903 443957807 7.190000e-09 73.1
27 TraesCS5D01G163200 chr1B 80.583 103 13 7 524 621 458380425 458380325 7.190000e-09 73.1


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 TraesCS5D01G163200 chr5D 254825907 254831085 5178 False 9564.0 9564 100.0000 1 5179 1 chr5D.!!$F1 5178
1 TraesCS5D01G163200 chr5B 287796217 287801086 4869 True 3773.0 7424 96.0275 256 5179 2 chr5B.!!$R2 4923
2 TraesCS5D01G163200 chr5A 338221446 338230658 9212 False 1902.5 4758 91.5280 1 5179 4 chr5A.!!$F1 5178
3 TraesCS5D01G163200 chr2B 653684685 653686179 1494 False 327.5 353 90.3315 1089 1578 2 chr2B.!!$F1 489

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
708 779 0.109342 GATGGGAGCGGATTGGACAT 59.891 55.0 0.00 0.0 0.0 3.06 F
1043 5079 0.445436 CTTCTCACTTCGCATGCACC 59.555 55.0 19.57 0.0 0.0 5.01 F
1522 6566 0.536687 CGCTGGGGCAGATCATCATT 60.537 55.0 0.00 0.0 38.6 2.57 F
2746 7818 0.035317 CAAGACTACCACCTGCAGCA 59.965 55.0 8.66 0.0 0.0 4.41 F
3572 8665 0.388649 CTGCTGAAGAAGTACGCGGT 60.389 55.0 12.47 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 6821 0.703488 TGTTTCCTGGCCATCATCCA 59.297 50.0 5.51 0.00 0.00 3.41 R
1888 6939 0.728542 AAATTACCTTAACGGCGGCG 59.271 50.0 31.06 31.06 35.61 6.46 R
3294 8375 0.107456 GTCCCACGATGATGATGCCT 59.893 55.0 0.00 0.00 0.00 4.75 R
3618 8711 0.320771 CCTTGTCGTAGCAGCTGGTT 60.321 55.0 25.47 0.42 0.00 3.67 R
4973 10105 0.257328 TGTTGGTCCTTGTTGCCTCA 59.743 50.0 0.00 0.00 0.00 3.86 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
31 32 5.473273 TCTGCCTATTAGGACCCTGATAAA 58.527 41.667 14.16 0.00 37.67 1.40
37 38 7.162082 CCTATTAGGACCCTGATAAATGTCAC 58.838 42.308 3.41 0.00 37.67 3.67
41 42 2.351726 GACCCTGATAAATGTCACACGC 59.648 50.000 0.00 0.00 0.00 5.34
44 45 3.183754 CCTGATAAATGTCACACGCGTA 58.816 45.455 13.44 0.00 0.00 4.42
45 46 3.615056 CCTGATAAATGTCACACGCGTAA 59.385 43.478 13.44 0.00 0.00 3.18
62 63 3.363575 GCGTAACACGAACACATGACAAT 60.364 43.478 0.00 0.00 46.05 2.71
64 65 5.201910 CGTAACACGAACACATGACAATTT 58.798 37.500 0.00 0.00 46.05 1.82
74 75 4.967575 ACACATGACAATTTCGAACGTTTC 59.032 37.500 0.46 0.00 0.00 2.78
79 80 7.533900 ACATGACAATTTCGAACGTTTCTTATG 59.466 33.333 0.46 0.92 0.00 1.90
80 81 6.367421 TGACAATTTCGAACGTTTCTTATGG 58.633 36.000 0.46 0.00 0.00 2.74
83 84 4.398549 TTTCGAACGTTTCTTATGGCAG 57.601 40.909 0.46 0.00 0.00 4.85
84 85 3.306917 TCGAACGTTTCTTATGGCAGA 57.693 42.857 0.46 0.00 0.00 4.26
85 86 3.655486 TCGAACGTTTCTTATGGCAGAA 58.345 40.909 0.46 0.00 0.00 3.02
87 88 4.092821 TCGAACGTTTCTTATGGCAGAATG 59.907 41.667 0.46 0.00 40.87 2.67
124 140 5.273170 TCAAGCATGACAACTTTCTTTTCG 58.727 37.500 0.00 0.00 0.00 3.46
127 143 4.023707 AGCATGACAACTTTCTTTTCGGAG 60.024 41.667 0.00 0.00 0.00 4.63
144 160 2.543653 CGGAGGGCAAGTTTCAGTTTTG 60.544 50.000 0.00 0.00 0.00 2.44
145 161 2.693074 GGAGGGCAAGTTTCAGTTTTGA 59.307 45.455 0.00 0.00 0.00 2.69
146 162 3.321968 GGAGGGCAAGTTTCAGTTTTGAT 59.678 43.478 0.00 0.00 32.27 2.57
148 164 5.010617 GGAGGGCAAGTTTCAGTTTTGATTA 59.989 40.000 0.00 0.00 32.27 1.75
149 165 6.089249 AGGGCAAGTTTCAGTTTTGATTAG 57.911 37.500 0.00 0.00 32.27 1.73
150 166 5.598417 AGGGCAAGTTTCAGTTTTGATTAGT 59.402 36.000 0.00 0.00 32.27 2.24
153 169 7.254421 GGGCAAGTTTCAGTTTTGATTAGTTTG 60.254 37.037 0.00 0.00 32.27 2.93
154 170 7.277760 GGCAAGTTTCAGTTTTGATTAGTTTGT 59.722 33.333 0.00 0.00 32.27 2.83
238 254 5.624900 CCACACGTTTGACACTTATCATTTG 59.375 40.000 2.58 0.00 0.00 2.32
239 255 6.198687 CACACGTTTGACACTTATCATTTGT 58.801 36.000 0.00 0.00 0.00 2.83
240 256 6.140580 CACACGTTTGACACTTATCATTTGTG 59.859 38.462 0.00 0.00 37.67 3.33
243 259 7.219917 CACGTTTGACACTTATCATTTGTGTTT 59.780 33.333 0.00 0.00 43.81 2.83
339 359 8.807948 AGCTACATGATTTACACATACCTTTT 57.192 30.769 0.00 0.00 0.00 2.27
440 460 4.900635 AATTTGGCTGCTCTTATTACGG 57.099 40.909 0.00 0.00 0.00 4.02
463 483 5.132144 GGTTCTTATGTCCCTCCTATTTCCA 59.868 44.000 0.00 0.00 0.00 3.53
508 541 7.968405 GTGTGTTTTCAGTTCTCTGTTTTGTAT 59.032 33.333 0.00 0.00 41.91 2.29
530 564 5.963214 TTCCTACATAAACTTCTACCCCC 57.037 43.478 0.00 0.00 0.00 5.40
537 571 0.616964 AACTTCTACCCCCTCGTCCC 60.617 60.000 0.00 0.00 0.00 4.46
541 575 0.906282 TCTACCCCCTCGTCCCAAAC 60.906 60.000 0.00 0.00 0.00 2.93
550 584 2.612221 CCTCGTCCCAAACTAAGTGTCC 60.612 54.545 0.00 0.00 0.00 4.02
552 586 1.609841 CGTCCCAAACTAAGTGTCCCC 60.610 57.143 0.00 0.00 0.00 4.81
564 598 4.895668 AAGTGTCCCCGATTTAGTACAA 57.104 40.909 0.00 0.00 0.00 2.41
603 671 8.710835 TGCACTAATCATCGACACTTATTTTA 57.289 30.769 0.00 0.00 0.00 1.52
604 672 8.817100 TGCACTAATCATCGACACTTATTTTAG 58.183 33.333 0.00 0.00 0.00 1.85
605 673 8.276325 GCACTAATCATCGACACTTATTTTAGG 58.724 37.037 0.00 0.00 0.00 2.69
606 674 9.529325 CACTAATCATCGACACTTATTTTAGGA 57.471 33.333 0.00 0.00 0.00 2.94
607 675 9.530633 ACTAATCATCGACACTTATTTTAGGAC 57.469 33.333 0.00 0.00 0.00 3.85
609 677 5.345702 TCATCGACACTTATTTTAGGACGG 58.654 41.667 0.00 0.00 0.00 4.79
610 678 5.125900 TCATCGACACTTATTTTAGGACGGA 59.874 40.000 0.00 0.00 0.00 4.69
613 681 4.439968 GACACTTATTTTAGGACGGAGGG 58.560 47.826 0.00 0.00 0.00 4.30
614 682 4.098894 ACACTTATTTTAGGACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
615 683 4.161754 ACACTTATTTTAGGACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
671 742 1.669604 TGCGGTTTTGTAAGTCTGCA 58.330 45.000 0.00 0.00 39.41 4.41
706 777 0.181350 AAGATGGGAGCGGATTGGAC 59.819 55.000 0.00 0.00 0.00 4.02
708 779 0.109342 GATGGGAGCGGATTGGACAT 59.891 55.000 0.00 0.00 0.00 3.06
810 887 2.685897 TCATCCATGCATGTGTGATGTG 59.314 45.455 28.50 16.15 35.47 3.21
825 4856 4.991687 TGTGATGTGTCTTTGTATACGCAA 59.008 37.500 0.00 0.00 39.36 4.85
1043 5079 0.445436 CTTCTCACTTCGCATGCACC 59.555 55.000 19.57 0.00 0.00 5.01
1522 6566 0.536687 CGCTGGGGCAGATCATCATT 60.537 55.000 0.00 0.00 38.60 2.57
1531 6576 5.127194 GGGGCAGATCATCATTATCTACGTA 59.873 44.000 0.00 0.00 32.40 3.57
1693 6744 2.270527 GAGGACAAGAGCAGGGCC 59.729 66.667 0.00 0.00 0.00 5.80
1708 6759 2.109181 GCCTACATGGAGACCGCC 59.891 66.667 6.48 0.00 38.35 6.13
1967 7018 8.527810 TCTTTCTTTTTAACAAAGTGGTCATGT 58.472 29.630 0.00 0.00 0.00 3.21
2088 7150 2.742589 GCCAAAAGTAGACCAGCACTAC 59.257 50.000 0.00 0.00 40.04 2.73
2523 7595 0.107703 CTACACATCGCCACCACCAT 60.108 55.000 0.00 0.00 0.00 3.55
2709 7781 2.033757 CTGCAGCAGTTGGCCTCT 59.966 61.111 14.90 0.00 46.50 3.69
2744 7816 0.687354 ACCAAGACTACCACCTGCAG 59.313 55.000 6.78 6.78 0.00 4.41
2745 7817 0.674895 CCAAGACTACCACCTGCAGC 60.675 60.000 8.66 0.00 0.00 5.25
2746 7818 0.035317 CAAGACTACCACCTGCAGCA 59.965 55.000 8.66 0.00 0.00 4.41
2760 7832 4.404098 AGCAAGGTAACCCCGGCG 62.404 66.667 0.00 0.00 41.56 6.46
2906 7984 0.976641 AAGACTGGCGACATGGAGAA 59.023 50.000 0.00 0.00 41.51 2.87
2925 8003 3.007398 AGAAGACGTCCAAGAAGCAGAAT 59.993 43.478 13.01 0.00 0.00 2.40
2927 8005 4.744795 AGACGTCCAAGAAGCAGAATAT 57.255 40.909 13.01 0.00 0.00 1.28
2941 8022 3.119849 GCAGAATATGAAAAGCGTGTGGT 60.120 43.478 0.00 0.00 0.00 4.16
3150 8231 4.573162 GCCATCGGCTCCGTATAC 57.427 61.111 8.28 0.00 46.69 1.47
3387 8468 1.604308 CATTGGCCTGTCCTGCACA 60.604 57.895 3.32 0.00 35.26 4.57
3572 8665 0.388649 CTGCTGAAGAAGTACGCGGT 60.389 55.000 12.47 0.00 0.00 5.68
3757 8850 0.955428 GGACATGAAGCGCTTCCACA 60.955 55.000 39.25 26.34 38.77 4.17
3789 8882 1.821061 CGTCCCTGGAGACACTGCTT 61.821 60.000 13.40 0.00 36.52 3.91
3798 8891 1.830477 GAGACACTGCTTGAGGAGGAT 59.170 52.381 4.53 0.00 37.85 3.24
3810 8906 1.825474 GAGGAGGATGTCGACCTTGAA 59.175 52.381 14.12 0.00 37.93 2.69
3864 8960 0.178944 TGGTCAAGTCCTTCCTCGGA 60.179 55.000 0.00 0.00 0.00 4.55
4018 9114 2.370189 CTGAACCTCAGTCTCCAACCTT 59.630 50.000 0.00 0.00 39.58 3.50
4113 9237 7.117523 TGTTCAAAGGAAAAACAAACACTCATG 59.882 33.333 0.00 0.00 34.13 3.07
4391 9519 0.744414 TTTAGCTGGTCTGCATCGCC 60.744 55.000 0.00 0.00 34.99 5.54
4439 9567 3.557595 CGTCTAGATCATTGGCAGAAACC 59.442 47.826 0.00 0.00 0.00 3.27
4783 9912 4.040217 ACAAGCATATTTGGTTCCTTTGCA 59.960 37.500 0.00 0.00 41.48 4.08
4797 9926 2.809696 CCTTTGCAAGCCCAAGAAATTG 59.190 45.455 0.00 0.00 0.00 2.32
4806 9935 2.769893 CCCAAGAAATTGGCAAGGTTG 58.230 47.619 5.96 6.39 40.74 3.77
4887 10019 1.067295 TGGCTATCCCTATGGGCAAG 58.933 55.000 0.00 0.00 44.53 4.01
4892 10024 2.815357 ATCCCTATGGGCAAGGTCTA 57.185 50.000 0.00 0.00 43.94 2.59
4936 10068 1.616628 GGTCCTGGTCCTGGTCCAT 60.617 63.158 21.28 0.00 32.81 3.41
4973 10105 2.744202 CACGCACTCATTTTAAGCTCCT 59.256 45.455 0.00 0.00 0.00 3.69
4974 10106 2.744202 ACGCACTCATTTTAAGCTCCTG 59.256 45.455 0.00 0.00 0.00 3.86
4981 10113 3.758554 TCATTTTAAGCTCCTGAGGCAAC 59.241 43.478 0.00 0.00 0.00 4.17
5092 10224 7.185453 GCAAATAAACAAAACAATGCTGAACA 58.815 30.769 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.711704 TCAGGGTCCTAATAGGCAGAAAG 59.288 47.826 0.34 0.00 34.61 2.62
10 11 5.610982 ACATTTATCAGGGTCCTAATAGGCA 59.389 40.000 0.34 0.00 34.61 4.75
19 20 2.936498 CGTGTGACATTTATCAGGGTCC 59.064 50.000 0.00 0.00 0.00 4.46
31 32 0.318022 TCGTGTTACGCGTGTGACAT 60.318 50.000 26.44 0.00 45.03 3.06
37 38 0.505231 ATGTGTTCGTGTTACGCGTG 59.495 50.000 24.59 4.25 42.21 5.34
41 42 3.845231 TTGTCATGTGTTCGTGTTACG 57.155 42.857 0.00 0.00 44.19 3.18
44 45 4.034626 TCGAAATTGTCATGTGTTCGTGTT 59.965 37.500 13.98 0.00 41.30 3.32
45 46 3.558006 TCGAAATTGTCATGTGTTCGTGT 59.442 39.130 13.98 0.00 41.30 4.49
62 63 4.059511 TCTGCCATAAGAAACGTTCGAAA 58.940 39.130 0.00 0.00 34.02 3.46
64 65 3.306917 TCTGCCATAAGAAACGTTCGA 57.693 42.857 0.00 0.00 34.02 3.71
74 75 7.383102 ACTAAAGTTGTCATTCTGCCATAAG 57.617 36.000 0.00 0.00 0.00 1.73
123 139 1.318576 AAACTGAAACTTGCCCTCCG 58.681 50.000 0.00 0.00 0.00 4.63
124 140 2.693074 TCAAAACTGAAACTTGCCCTCC 59.307 45.455 0.00 0.00 0.00 4.30
127 143 5.842907 ACTAATCAAAACTGAAACTTGCCC 58.157 37.500 0.00 0.00 0.00 5.36
211 227 4.682306 GTGTCAAACGTGTGGCAC 57.318 55.556 26.39 26.39 46.00 5.01
357 377 5.419542 CAGGTCCTCATCGAGTTTTTCATA 58.580 41.667 0.00 0.00 0.00 2.15
440 460 6.056236 GTGGAAATAGGAGGGACATAAGAAC 58.944 44.000 0.00 0.00 0.00 3.01
463 483 8.547967 AACACACATGAATTTCGTAGATTAGT 57.452 30.769 0.00 0.00 35.04 2.24
508 541 5.606761 AGGGGGTAGAAGTTTATGTAGGAA 58.393 41.667 0.00 0.00 0.00 3.36
530 564 2.612221 GGGACACTTAGTTTGGGACGAG 60.612 54.545 0.00 0.00 0.00 4.18
537 571 5.243207 ACTAAATCGGGGACACTTAGTTTG 58.757 41.667 0.00 0.00 30.50 2.93
541 575 5.587388 TGTACTAAATCGGGGACACTTAG 57.413 43.478 0.00 0.00 0.00 2.18
575 643 5.940192 AAGTGTCGATGATTAGTGCAAAA 57.060 34.783 0.00 0.00 0.00 2.44
579 647 8.276325 CCTAAAATAAGTGTCGATGATTAGTGC 58.724 37.037 0.00 0.00 0.00 4.40
585 653 5.983720 CCGTCCTAAAATAAGTGTCGATGAT 59.016 40.000 0.00 0.00 0.00 2.45
603 671 5.735733 ATGATATATACTCCCTCCGTCCT 57.264 43.478 0.00 0.00 0.00 3.85
604 672 6.603224 ACTATGATATATACTCCCTCCGTCC 58.397 44.000 0.00 0.00 0.00 4.79
605 673 9.275398 CTAACTATGATATATACTCCCTCCGTC 57.725 40.741 0.00 0.00 0.00 4.79
606 674 8.219178 CCTAACTATGATATATACTCCCTCCGT 58.781 40.741 0.00 0.00 0.00 4.69
607 675 8.219178 ACCTAACTATGATATATACTCCCTCCG 58.781 40.741 0.00 0.00 0.00 4.63
609 677 9.924010 ACACCTAACTATGATATATACTCCCTC 57.076 37.037 0.00 0.00 0.00 4.30
640 711 3.320541 ACAAAACCGCATGAATGGAAGAA 59.679 39.130 0.00 0.00 0.00 2.52
646 717 4.853196 CAGACTTACAAAACCGCATGAATG 59.147 41.667 0.00 0.00 0.00 2.67
650 721 2.031245 TGCAGACTTACAAAACCGCATG 60.031 45.455 0.00 0.00 0.00 4.06
653 724 2.766970 TTGCAGACTTACAAAACCGC 57.233 45.000 0.00 0.00 0.00 5.68
671 742 7.502060 TCCCATCTTGAGAGTTCTTAGATTT 57.498 36.000 5.48 0.00 30.36 2.17
697 768 6.421202 GCTCTAGTTAACTTATGTCCAATCCG 59.579 42.308 14.49 0.00 0.00 4.18
706 777 3.061139 GCGCGTGCTCTAGTTAACTTATG 60.061 47.826 14.49 5.13 38.39 1.90
708 779 2.523015 GCGCGTGCTCTAGTTAACTTA 58.477 47.619 14.49 1.78 38.39 2.24
776 853 4.141665 TGCATGGATGATACTGTGATGTCA 60.142 41.667 0.00 0.00 0.00 3.58
825 4856 2.028876 CCATGGATGTGACATGCATGT 58.971 47.619 39.08 31.82 43.45 3.21
969 5001 6.751888 CATGTACGCATGTGCTTATATAGCTA 59.248 38.462 6.08 0.00 45.26 3.32
970 5002 5.578336 CATGTACGCATGTGCTTATATAGCT 59.422 40.000 6.08 0.00 45.26 3.32
1043 5079 1.869574 CTCGACTGGATCACGCACG 60.870 63.158 0.00 0.00 0.00 5.34
1087 5123 2.341168 GCTCACGTTGTTGTTGTTGTTG 59.659 45.455 0.00 0.00 0.00 3.33
1522 6566 3.067742 GCCTGAACTTGGCTACGTAGATA 59.932 47.826 26.53 10.74 46.38 1.98
1693 6744 2.279517 GCGGCGGTCTCCATGTAG 60.280 66.667 9.78 0.00 0.00 2.74
1770 6821 0.703488 TGTTTCCTGGCCATCATCCA 59.297 50.000 5.51 0.00 0.00 3.41
1884 6935 2.632136 TACCTTAACGGCGGCGATGG 62.632 60.000 38.93 29.96 35.61 3.51
1888 6939 0.728542 AAATTACCTTAACGGCGGCG 59.271 50.000 31.06 31.06 35.61 6.46
1967 7018 9.305925 GAATGAATCTATGATACGCATGACATA 57.694 33.333 0.00 0.00 37.87 2.29
2088 7150 2.985745 GGTAGCACTAGCGCTGCATTG 61.986 57.143 22.90 12.35 45.38 2.82
2203 7273 3.348647 TGCATGCTTCTACTGCCTAAA 57.651 42.857 20.33 0.00 35.02 1.85
2709 7781 2.159179 TGGTCTGATCCGGATGAGAA 57.841 50.000 31.62 17.06 33.01 2.87
2760 7832 3.858868 TTCGTCGGCTGCTGTGACC 62.859 63.158 8.55 0.00 0.00 4.02
2762 7834 1.446099 GATTCGTCGGCTGCTGTGA 60.446 57.895 8.55 5.28 0.00 3.58
2763 7835 1.291184 TTGATTCGTCGGCTGCTGTG 61.291 55.000 8.55 2.85 0.00 3.66
2906 7984 4.160439 TCATATTCTGCTTCTTGGACGTCT 59.840 41.667 16.46 0.00 0.00 4.18
2925 8003 2.811431 CCTCAACCACACGCTTTTCATA 59.189 45.455 0.00 0.00 0.00 2.15
2927 8005 1.021202 CCTCAACCACACGCTTTTCA 58.979 50.000 0.00 0.00 0.00 2.69
2941 8022 1.856873 ATTCCAGCCCCCACCTCAA 60.857 57.895 0.00 0.00 0.00 3.02
3024 8105 1.537348 CCGTGGTCGTTGTTGAAGAGA 60.537 52.381 0.00 0.00 35.01 3.10
3147 8228 4.838152 CAGCCCAGCACGCCGTAT 62.838 66.667 0.00 0.00 0.00 3.06
3294 8375 0.107456 GTCCCACGATGATGATGCCT 59.893 55.000 0.00 0.00 0.00 4.75
3480 8561 2.194597 GGTGCCAGTCCAACCACA 59.805 61.111 0.00 0.00 0.00 4.17
3591 8684 1.283793 CGCCAGCCACAGAAAGTTG 59.716 57.895 0.00 0.00 0.00 3.16
3618 8711 0.320771 CCTTGTCGTAGCAGCTGGTT 60.321 55.000 25.47 0.42 0.00 3.67
3698 8791 4.873129 CGGCGGTGTCGATGAGGG 62.873 72.222 0.00 0.00 39.00 4.30
3729 8822 1.141881 CTTCATGTCCGCGCCTAGT 59.858 57.895 0.00 0.00 0.00 2.57
3781 8874 1.277557 GACATCCTCCTCAAGCAGTGT 59.722 52.381 0.00 0.00 0.00 3.55
3789 8882 1.186200 CAAGGTCGACATCCTCCTCA 58.814 55.000 18.91 0.00 33.76 3.86
3798 8891 2.342279 CCGGCTTCAAGGTCGACA 59.658 61.111 18.91 0.00 36.31 4.35
3810 8906 0.329596 AGAAGATTCCTTTGCCGGCT 59.670 50.000 29.70 4.49 31.62 5.52
3864 8960 3.005539 AGTGCCTCCCTCGCATGT 61.006 61.111 0.00 0.00 38.76 3.21
4113 9237 7.545965 ACATTTGCTGTCTGTTGATAGTAGTAC 59.454 37.037 0.00 0.00 34.46 2.73
4176 9300 1.228657 GCAGTTGAGACGGTTGGACC 61.229 60.000 0.00 0.00 34.05 4.46
4343 9471 4.790962 CTGCCGCACCTGCATCCT 62.791 66.667 0.00 0.00 42.21 3.24
4391 9519 1.254026 TGGACAAGTACCACTCGGAG 58.746 55.000 2.83 2.83 35.59 4.63
4797 9926 0.681243 CCTAAGCTCCCAACCTTGCC 60.681 60.000 0.00 0.00 0.00 4.52
4872 10004 4.389841 AAGTAGACCTTGCCCATAGGGATA 60.390 45.833 6.20 0.00 46.48 2.59
4873 10005 3.636325 AAGTAGACCTTGCCCATAGGGAT 60.636 47.826 6.20 0.00 46.48 3.85
4887 10019 2.355209 CCAAAGGGAGAGCAAGTAGACC 60.355 54.545 0.00 0.00 35.59 3.85
4892 10024 1.140312 TGACCAAAGGGAGAGCAAGT 58.860 50.000 0.00 0.00 38.05 3.16
4973 10105 0.257328 TGTTGGTCCTTGTTGCCTCA 59.743 50.000 0.00 0.00 0.00 3.86
4974 10106 0.668535 GTGTTGGTCCTTGTTGCCTC 59.331 55.000 0.00 0.00 0.00 4.70
4981 10113 2.819608 CAAGGGTATGTGTTGGTCCTTG 59.180 50.000 0.00 0.00 43.17 3.61
5092 10224 6.149129 TCTAATGCATTACTGTGTCTCGAT 57.851 37.500 15.21 0.00 0.00 3.59
5150 10282 2.094078 GCATGAATTACCTTTGCCTGCA 60.094 45.455 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.