Multiple sequence alignment - TraesCS6D01G222400

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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 TraesCS6D01G222400 chr6D 100.000 3172 0 0 1 3172 313189304 313186133 0.000000e+00 5858.0
1 TraesCS6D01G222400 chr6B 93.657 2617 97 36 1 2598 513134533 513137099 0.000000e+00 3849.0
2 TraesCS6D01G222400 chr6B 89.357 498 19 11 2592 3080 513138290 513138762 2.110000e-166 595.0
3 TraesCS6D01G222400 chr6B 100.000 42 0 0 3131 3172 513138765 513138806 9.430000e-11 78.7
4 TraesCS6D01G222400 chr6A 92.096 2657 106 41 1 2581 450109401 450106773 0.000000e+00 3648.0
5 TraesCS6D01G222400 chr6A 91.748 412 14 7 2768 3172 450098420 450098022 3.570000e-154 555.0
6 TraesCS6D01G222400 chr6A 95.031 161 8 0 2622 2782 450105106 450104946 1.460000e-63 254.0
7 TraesCS6D01G222400 chr4B 94.340 318 12 1 1015 1326 27404958 27404641 1.710000e-132 483.0
8 TraesCS6D01G222400 chr1A 78.311 438 76 16 1476 1908 319320525 319320948 6.750000e-67 265.0
9 TraesCS6D01G222400 chr1A 87.692 65 8 0 1841 1905 497504520 497504456 3.390000e-10 76.8
10 TraesCS6D01G222400 chr1D 77.677 439 79 17 1475 1908 249560541 249560965 1.890000e-62 250.0
11 TraesCS6D01G222400 chr1D 80.365 219 40 3 1144 1362 249560225 249560440 2.530000e-36 163.0
12 TraesCS6D01G222400 chr1D 87.692 65 8 0 1841 1905 401667225 401667161 3.390000e-10 76.8
13 TraesCS6D01G222400 chr5A 98.450 129 2 0 1198 1326 645412949 645412821 8.850000e-56 228.0
14 TraesCS6D01G222400 chr7A 97.674 129 3 0 1198 1326 83536322 83536450 4.120000e-54 222.0
15 TraesCS6D01G222400 chr7A 92.857 56 4 0 1841 1896 712180986 712181041 7.290000e-12 82.4
16 TraesCS6D01G222400 chr4A 95.349 129 6 0 1198 1326 21864824 21864952 4.150000e-49 206.0
17 TraesCS6D01G222400 chr1B 80.822 219 39 3 1144 1362 364919506 364919291 5.440000e-38 169.0
18 TraesCS6D01G222400 chr1B 87.692 65 8 0 1841 1905 539547535 539547471 3.390000e-10 76.8
19 TraesCS6D01G222400 chr2B 98.413 63 1 0 1264 1326 768651575 768651637 9.300000e-21 111.0
20 TraesCS6D01G222400 chr5D 91.071 56 5 0 1841 1896 368333269 368333324 3.390000e-10 76.8


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 TraesCS6D01G222400 chr6D 313186133 313189304 3171 True 5858.000000 5858 100.0000 1 3172 1 chr6D.!!$R1 3171
1 TraesCS6D01G222400 chr6B 513134533 513138806 4273 False 1507.566667 3849 94.3380 1 3172 3 chr6B.!!$F1 3171
2 TraesCS6D01G222400 chr6A 450104946 450109401 4455 True 1951.000000 3648 93.5635 1 2782 2 chr6A.!!$R2 2781
3 TraesCS6D01G222400 chr1D 249560225 249560965 740 False 206.500000 250 79.0210 1144 1908 2 chr1D.!!$F1 764

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
985 1042 0.450184 GGTGTGTGTGTGGTGTGTTC 59.55 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2887 5062 0.251922 TAGGCTGTCGGTTAGGGTGT 60.252 55.0 0.0 0.0 0.0 4.16 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
72 77 1.068748 GGCAGGATAAGATGCAATGCG 60.069 52.381 0.00 0.00 44.37 4.73
100 106 4.523083 AGTGCTCCACTGTGAAAAAGTAA 58.477 39.130 9.86 0.00 43.63 2.24
144 156 0.621571 TCTGCATTACTCCAGGGGCT 60.622 55.000 0.00 0.00 0.00 5.19
346 374 2.141517 CTCTTGTCTGCTCCACAACTG 58.858 52.381 0.00 0.00 30.49 3.16
458 486 2.963782 ACACTACACGAGGAAAAGGTCT 59.036 45.455 0.00 0.00 0.00 3.85
471 499 3.050275 GGTCTCGCCACTTGGTGC 61.050 66.667 3.77 0.00 45.04 5.01
472 500 3.050275 GTCTCGCCACTTGGTGCC 61.050 66.667 3.77 0.00 45.04 5.01
473 501 4.680237 TCTCGCCACTTGGTGCCG 62.680 66.667 3.77 0.00 45.04 5.69
477 505 2.281900 GCCACTTGGTGCCGGTTA 60.282 61.111 1.90 0.00 37.57 2.85
478 506 2.332654 GCCACTTGGTGCCGGTTAG 61.333 63.158 1.90 0.00 37.57 2.34
627 664 8.256611 TCAGGAATTCGAGAATGTTTTCTTAG 57.743 34.615 0.00 0.00 42.34 2.18
665 716 3.312421 ACACATGCCGATAAATGCAGTAC 59.688 43.478 0.00 0.00 41.46 2.73
668 719 3.260475 TGCCGATAAATGCAGTACTGT 57.740 42.857 23.44 6.84 32.77 3.55
683 734 5.699915 GCAGTACTGTATGACGATAGGAGTA 59.300 44.000 23.44 0.00 43.77 2.59
693 744 2.103771 ACGATAGGAGTACGCAGGACTA 59.896 50.000 0.00 0.00 43.77 2.59
694 745 2.479656 CGATAGGAGTACGCAGGACTAC 59.520 54.545 0.00 0.00 0.00 2.73
695 746 1.945387 TAGGAGTACGCAGGACTACG 58.055 55.000 0.00 0.00 32.55 3.51
725 778 0.524862 CACACATCTCAAAGCAGCCC 59.475 55.000 0.00 0.00 0.00 5.19
883 936 5.834204 AGAGAAATATACGCACTCCTACCTT 59.166 40.000 0.00 0.00 0.00 3.50
932 989 6.570764 GCCTTCTCGATTAGTATTCCAGTAGG 60.571 46.154 7.52 7.52 0.00 3.18
985 1042 0.450184 GGTGTGTGTGTGGTGTGTTC 59.550 55.000 0.00 0.00 0.00 3.18
1167 1230 2.876219 GAGGTCGAGTCGGTCACC 59.124 66.667 13.54 13.06 0.00 4.02
1391 1454 2.034879 CACACCCACCACGATCAGC 61.035 63.158 0.00 0.00 0.00 4.26
1392 1455 2.436646 CACCCACCACGATCAGCC 60.437 66.667 0.00 0.00 0.00 4.85
1421 1484 3.332187 TCTTGGTCAACCCATCCACATTA 59.668 43.478 0.00 0.00 44.74 1.90
1435 1501 2.097466 CCACATTACCAACGAGGCAATC 59.903 50.000 0.00 0.00 43.14 2.67
1640 1716 2.681778 CACGAGAGCCAGGACCCT 60.682 66.667 0.00 0.00 0.00 4.34
2056 2132 2.503375 GCTGCAGTGCATCAACGC 60.503 61.111 20.10 14.47 38.13 4.84
2084 2160 3.770040 CTCCGGCCGTCCATGACA 61.770 66.667 26.12 0.00 32.09 3.58
2155 2231 3.406595 GACCTAAGCCGGCCAGCAT 62.407 63.158 26.15 11.41 34.23 3.79
2211 2290 3.877508 GTGTAAATGCTTAGGTAGGGCAG 59.122 47.826 0.00 0.00 39.38 4.85
2215 2295 4.316025 AATGCTTAGGTAGGGCAGAAAA 57.684 40.909 0.00 0.00 39.38 2.29
2227 2307 2.357952 GGGCAGAAAACTTTTCGTCACT 59.642 45.455 8.32 0.00 0.00 3.41
2251 2336 9.574516 ACTTTTGTTATTGTAAAGAGGATCAGT 57.425 29.630 0.00 0.00 37.82 3.41
2343 2435 5.652994 AATCTAATCCGCCTGTAGATCTC 57.347 43.478 0.00 0.00 34.27 2.75
2431 2524 1.619654 TCCGGGTACTTTGAGACGAA 58.380 50.000 0.00 0.00 0.00 3.85
2515 2608 1.272592 TGCATGTGATCCACCATGGTT 60.273 47.619 16.84 0.00 39.03 3.67
2520 2613 4.220693 TGTGATCCACCATGGTTAGAAG 57.779 45.455 16.84 2.99 39.03 2.85
2567 2670 1.826921 CATGCATGCACTCCCCTCC 60.827 63.158 25.37 0.00 0.00 4.30
2586 2690 3.233980 CCCCGCCGATCTGATGGA 61.234 66.667 0.83 0.00 0.00 3.41
2609 4718 2.874701 ACATATCCATCTCGCTGTTTGC 59.125 45.455 0.00 0.00 38.57 3.68
2626 4795 2.981560 GCCGCCATGTCACCACTTG 61.982 63.158 0.00 0.00 0.00 3.16
2834 5009 1.135972 CGAGGCACGAAAATGACCAAG 60.136 52.381 0.00 0.00 45.77 3.61
2835 5010 1.880027 GAGGCACGAAAATGACCAAGT 59.120 47.619 0.00 0.00 0.00 3.16
2836 5011 1.880027 AGGCACGAAAATGACCAAGTC 59.120 47.619 0.00 0.00 0.00 3.01
2837 5012 1.606668 GGCACGAAAATGACCAAGTCA 59.393 47.619 0.00 0.00 46.90 3.41
2838 5013 2.604614 GGCACGAAAATGACCAAGTCAC 60.605 50.000 0.00 0.00 45.65 3.67
2839 5014 2.903678 CACGAAAATGACCAAGTCACG 58.096 47.619 0.00 2.08 45.65 4.35
2840 5015 1.871039 ACGAAAATGACCAAGTCACGG 59.129 47.619 0.00 0.00 45.65 4.94
2841 5016 1.196808 CGAAAATGACCAAGTCACGGG 59.803 52.381 0.00 0.00 45.65 5.28
2842 5017 2.500229 GAAAATGACCAAGTCACGGGA 58.500 47.619 0.00 0.00 45.65 5.14
2843 5018 2.649531 AAATGACCAAGTCACGGGAA 57.350 45.000 0.00 0.00 45.65 3.97
2844 5019 2.185004 AATGACCAAGTCACGGGAAG 57.815 50.000 0.00 0.00 45.65 3.46
2845 5020 0.324943 ATGACCAAGTCACGGGAAGG 59.675 55.000 0.00 0.00 45.65 3.46
2846 5021 0.761323 TGACCAAGTCACGGGAAGGA 60.761 55.000 8.87 0.00 37.67 3.36
2847 5022 0.395312 GACCAAGTCACGGGAAGGAA 59.605 55.000 8.87 0.00 32.09 3.36
2848 5023 1.003233 GACCAAGTCACGGGAAGGAAT 59.997 52.381 8.87 0.00 32.09 3.01
2849 5024 1.003233 ACCAAGTCACGGGAAGGAATC 59.997 52.381 8.87 0.00 0.00 2.52
2850 5025 1.359848 CAAGTCACGGGAAGGAATCG 58.640 55.000 0.00 0.00 0.00 3.34
2886 5061 4.025401 GGTTGCTGCGGTTGACGG 62.025 66.667 0.00 0.00 44.51 4.79
2887 5062 2.970324 GTTGCTGCGGTTGACGGA 60.970 61.111 0.00 0.00 44.51 4.69
2888 5063 2.970324 TTGCTGCGGTTGACGGAC 60.970 61.111 0.00 0.00 44.51 4.79
2922 5097 0.035458 CCTAATGACGGCCTGGATCC 59.965 60.000 4.20 4.20 0.00 3.36
2935 5110 3.065371 GCCTGGATCCGAATTAACAACAG 59.935 47.826 7.39 0.00 0.00 3.16
2942 5119 8.262227 TGGATCCGAATTAACAACAGTTACTAT 58.738 33.333 7.39 0.00 0.00 2.12
2944 5121 8.658499 ATCCGAATTAACAACAGTTACTATCC 57.342 34.615 0.00 0.00 0.00 2.59
2945 5122 7.613585 TCCGAATTAACAACAGTTACTATCCA 58.386 34.615 0.00 0.00 0.00 3.41
2946 5123 7.546667 TCCGAATTAACAACAGTTACTATCCAC 59.453 37.037 0.00 0.00 0.00 4.02
2947 5124 7.388712 CGAATTAACAACAGTTACTATCCACG 58.611 38.462 0.00 0.00 0.00 4.94
2958 5135 3.914426 ACTATCCACGATTGAAGCCTT 57.086 42.857 0.00 0.00 0.00 4.35
2959 5136 3.798202 ACTATCCACGATTGAAGCCTTC 58.202 45.455 0.00 0.00 0.00 3.46
2960 5137 2.044123 ATCCACGATTGAAGCCTTCC 57.956 50.000 1.21 0.00 0.00 3.46
2961 5138 0.690192 TCCACGATTGAAGCCTTCCA 59.310 50.000 1.21 0.00 0.00 3.53
2987 5164 0.244721 ACAACTACGGGAAGGCGTAC 59.755 55.000 0.00 0.00 0.00 3.67
3018 5195 2.711885 GTGCGTAACAGTTCACAAACC 58.288 47.619 0.00 0.00 35.92 3.27
3040 5217 1.139734 CTGGTCGATCAGTCACCCG 59.860 63.158 17.87 0.00 0.00 5.28
3041 5218 2.284798 CTGGTCGATCAGTCACCCGG 62.285 65.000 17.87 0.00 0.00 5.73
3050 5227 2.603776 GTCACCCGGTGGAGAGGT 60.604 66.667 17.76 0.00 31.35 3.85
3053 5230 2.283966 ACCCGGTGGAGAGGTGAG 60.284 66.667 0.00 0.00 34.81 3.51
3076 5253 7.491372 TGAGTTAGGTCGCATTCATACTTAAAG 59.509 37.037 0.00 0.00 0.00 1.85
3080 5257 4.332819 GGTCGCATTCATACTTAAAGTGCT 59.667 41.667 0.00 0.00 0.00 4.40
3081 5258 5.258622 GTCGCATTCATACTTAAAGTGCTG 58.741 41.667 0.00 0.00 0.00 4.41
3082 5259 4.332543 TCGCATTCATACTTAAAGTGCTGG 59.667 41.667 0.00 0.00 0.00 4.85
3083 5260 4.094887 CGCATTCATACTTAAAGTGCTGGT 59.905 41.667 0.00 0.00 0.00 4.00
3084 5261 5.391950 CGCATTCATACTTAAAGTGCTGGTT 60.392 40.000 0.00 0.00 0.00 3.67
3085 5262 5.801947 GCATTCATACTTAAAGTGCTGGTTG 59.198 40.000 0.00 0.00 0.00 3.77
3086 5263 5.371115 TTCATACTTAAAGTGCTGGTTGC 57.629 39.130 0.00 0.00 43.25 4.17
3087 5264 4.651778 TCATACTTAAAGTGCTGGTTGCT 58.348 39.130 0.00 0.00 43.37 3.91
3088 5265 5.800296 TCATACTTAAAGTGCTGGTTGCTA 58.200 37.500 0.00 0.00 43.37 3.49
3089 5266 5.642063 TCATACTTAAAGTGCTGGTTGCTAC 59.358 40.000 0.00 0.00 43.37 3.58
3090 5267 2.806244 ACTTAAAGTGCTGGTTGCTACG 59.194 45.455 0.00 0.00 43.37 3.51
3091 5268 1.153353 TAAAGTGCTGGTTGCTACGC 58.847 50.000 0.00 0.00 43.37 4.42
3092 5269 0.817634 AAAGTGCTGGTTGCTACGCA 60.818 50.000 0.00 0.00 43.37 5.24
3093 5270 0.606401 AAGTGCTGGTTGCTACGCAT 60.606 50.000 4.46 0.00 43.37 4.73
3094 5271 1.135315 GTGCTGGTTGCTACGCATG 59.865 57.895 4.46 0.00 43.37 4.06
3095 5272 1.003959 TGCTGGTTGCTACGCATGA 60.004 52.632 0.00 0.00 43.37 3.07
3096 5273 0.392863 TGCTGGTTGCTACGCATGAT 60.393 50.000 0.00 0.00 43.37 2.45
3097 5274 0.028505 GCTGGTTGCTACGCATGATG 59.971 55.000 0.00 0.00 38.76 3.07
3098 5275 0.659427 CTGGTTGCTACGCATGATGG 59.341 55.000 0.00 0.00 38.76 3.51
3099 5276 0.251634 TGGTTGCTACGCATGATGGA 59.748 50.000 0.00 0.00 38.76 3.41
3100 5277 1.339535 TGGTTGCTACGCATGATGGAA 60.340 47.619 0.00 0.00 38.76 3.53
3101 5278 1.949525 GGTTGCTACGCATGATGGAAT 59.050 47.619 0.00 0.00 38.76 3.01
3102 5279 2.287188 GGTTGCTACGCATGATGGAATG 60.287 50.000 0.00 0.00 38.76 2.67
3108 5285 3.734683 GCATGATGGAATGCGTACG 57.265 52.632 11.84 11.84 43.22 3.67
3109 5286 0.384725 GCATGATGGAATGCGTACGC 60.385 55.000 32.49 32.49 43.22 4.42
3110 5287 0.111134 CATGATGGAATGCGTACGCG 60.111 55.000 32.65 12.45 45.51 6.01
3111 5288 0.529773 ATGATGGAATGCGTACGCGT 60.530 50.000 32.65 30.65 45.51 6.01
3117 5294 2.701006 ATGCGTACGCGTTGCATC 59.299 55.556 32.78 16.38 45.68 3.91
3118 5295 2.097635 ATGCGTACGCGTTGCATCA 61.098 52.632 32.78 20.13 45.68 3.07
3119 5296 1.631144 ATGCGTACGCGTTGCATCAA 61.631 50.000 32.78 17.27 45.68 2.57
3120 5297 1.857426 GCGTACGCGTTGCATCAAC 60.857 57.895 26.17 12.67 40.54 3.18
3121 5298 1.779061 CGTACGCGTTGCATCAACT 59.221 52.632 20.78 0.00 41.62 3.16
3122 5299 0.162933 CGTACGCGTTGCATCAACTT 59.837 50.000 20.78 0.00 41.62 2.66
3123 5300 1.397945 CGTACGCGTTGCATCAACTTT 60.398 47.619 20.78 0.00 41.62 2.66
3124 5301 1.969256 GTACGCGTTGCATCAACTTTG 59.031 47.619 20.78 1.13 41.62 2.77
3125 5302 0.317770 ACGCGTTGCATCAACTTTGG 60.318 50.000 5.58 0.00 41.62 3.28
3126 5303 0.317770 CGCGTTGCATCAACTTTGGT 60.318 50.000 0.00 0.00 41.62 3.67
3127 5304 1.130955 GCGTTGCATCAACTTTGGTG 58.869 50.000 7.91 0.00 41.62 4.17
3128 5305 1.268999 GCGTTGCATCAACTTTGGTGA 60.269 47.619 6.40 0.00 41.81 4.02
3129 5306 2.653890 CGTTGCATCAACTTTGGTGAG 58.346 47.619 6.40 0.00 41.81 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 77 1.613925 TCACAGTGGAGCACTCAGTAC 59.386 52.381 0.00 0.00 43.43 2.73
100 106 6.136857 TCCTGCTACTACTGTCCATAGATTT 58.863 40.000 0.00 0.00 0.00 2.17
144 156 3.774528 CTGCGCACCAGAGGGCTA 61.775 66.667 5.66 0.00 46.41 3.93
346 374 0.546598 ATCCCAAACGGAGATGTCCC 59.453 55.000 2.75 0.00 46.60 4.46
473 501 1.315257 TGACGTCCTACCGGCTAACC 61.315 60.000 14.12 0.00 36.61 2.85
474 502 0.179153 GTGACGTCCTACCGGCTAAC 60.179 60.000 14.12 0.00 36.61 2.34
475 503 1.647545 CGTGACGTCCTACCGGCTAA 61.648 60.000 14.12 0.00 36.61 3.09
476 504 2.108514 CGTGACGTCCTACCGGCTA 61.109 63.158 14.12 0.00 36.61 3.93
477 505 3.437795 CGTGACGTCCTACCGGCT 61.438 66.667 14.12 0.00 36.61 5.52
642 679 2.754552 ACTGCATTTATCGGCATGTGTT 59.245 40.909 0.00 0.00 39.65 3.32
665 716 3.497262 TGCGTACTCCTATCGTCATACAG 59.503 47.826 0.00 0.00 0.00 2.74
668 719 3.072211 CCTGCGTACTCCTATCGTCATA 58.928 50.000 0.00 0.00 0.00 2.15
683 734 2.675423 TCTGCCGTAGTCCTGCGT 60.675 61.111 4.18 0.00 36.97 5.24
693 744 4.664677 GTGTGACGCCTCTGCCGT 62.665 66.667 0.00 0.00 42.31 5.68
694 745 3.939837 ATGTGTGACGCCTCTGCCG 62.940 63.158 0.00 0.00 0.00 5.69
695 746 2.046892 ATGTGTGACGCCTCTGCC 60.047 61.111 0.00 0.00 0.00 4.85
725 778 3.595709 TTGTGCGTAAAGAAAGGTTCG 57.404 42.857 0.00 0.00 34.02 3.95
853 906 3.639094 AGTGCGTATATTTCTCTCTGGCT 59.361 43.478 0.00 0.00 0.00 4.75
866 919 2.380941 TGCAAGGTAGGAGTGCGTATA 58.619 47.619 0.00 0.00 41.27 1.47
883 936 3.276091 CCCGTCGCTGTTGTTGCA 61.276 61.111 0.00 0.00 0.00 4.08
918 971 7.996788 TGATGGAGATACCTACTGGAATACTA 58.003 38.462 0.00 0.00 39.86 1.82
919 972 6.864421 TGATGGAGATACCTACTGGAATACT 58.136 40.000 0.00 0.00 39.86 2.12
920 973 7.379750 GTTGATGGAGATACCTACTGGAATAC 58.620 42.308 0.00 0.00 39.86 1.89
932 989 2.386249 GAGCGTCGTTGATGGAGATAC 58.614 52.381 0.00 0.00 0.00 2.24
1391 1454 1.607148 GGGTTGACCAAGAAACGAAGG 59.393 52.381 2.12 0.00 39.85 3.46
1435 1501 2.507992 CGCTCCAGCCAGAACTCG 60.508 66.667 0.00 0.00 37.91 4.18
2084 2160 4.280494 AGAACGCGCACCACGTCT 62.280 61.111 5.73 0.00 44.30 4.18
2155 2231 3.142951 CACCTTTACGAAACCACCATCA 58.857 45.455 0.00 0.00 0.00 3.07
2211 2290 9.670180 CAATAACAAAAGTGACGAAAAGTTTTC 57.330 29.630 16.87 16.87 29.72 2.29
2215 2295 9.843334 TTTACAATAACAAAAGTGACGAAAAGT 57.157 25.926 0.00 0.00 0.00 2.66
2243 2328 6.350277 CGGAGTTCAACTACTAAACTGATCCT 60.350 42.308 0.00 0.00 33.54 3.24
2251 2336 6.403866 TTGTACCGGAGTTCAACTACTAAA 57.596 37.500 9.46 0.00 29.37 1.85
2431 2524 6.128172 CGACTTTGATTTCCTCAGCAGTAAAT 60.128 38.462 0.00 0.00 34.68 1.40
2515 2608 4.595762 AGCCGAGTAAACAACACTTCTA 57.404 40.909 0.00 0.00 0.00 2.10
2520 2613 2.215196 TCCAAGCCGAGTAAACAACAC 58.785 47.619 0.00 0.00 0.00 3.32
2567 2670 2.341543 CATCAGATCGGCGGGGAG 59.658 66.667 7.21 0.00 0.00 4.30
2586 2690 3.827008 AACAGCGAGATGGATATGTGT 57.173 42.857 0.00 0.00 0.00 3.72
2609 4718 0.677731 ATCAAGTGGTGACATGGCGG 60.678 55.000 0.00 0.00 46.14 6.13
2626 4795 1.416813 CTCTGCTGCCACGACGAATC 61.417 60.000 0.00 0.00 0.00 2.52
2772 4947 6.077322 CCCCTTTTATAATCCACACATCCAT 58.923 40.000 0.00 0.00 0.00 3.41
2834 5009 1.079405 TGCGATTCCTTCCCGTGAC 60.079 57.895 0.00 0.00 0.00 3.67
2835 5010 1.079405 GTGCGATTCCTTCCCGTGA 60.079 57.895 0.00 0.00 0.00 4.35
2836 5011 2.452813 CGTGCGATTCCTTCCCGTG 61.453 63.158 0.00 0.00 0.00 4.94
2837 5012 2.125673 CGTGCGATTCCTTCCCGT 60.126 61.111 0.00 0.00 0.00 5.28
2838 5013 1.017177 TTTCGTGCGATTCCTTCCCG 61.017 55.000 0.00 0.00 0.00 5.14
2839 5014 1.161843 TTTTCGTGCGATTCCTTCCC 58.838 50.000 0.00 0.00 0.00 3.97
2840 5015 3.426323 GAATTTTCGTGCGATTCCTTCC 58.574 45.455 0.00 0.00 0.00 3.46
2841 5016 3.091417 CGAATTTTCGTGCGATTCCTTC 58.909 45.455 4.58 0.00 45.09 3.46
2842 5017 3.117434 CGAATTTTCGTGCGATTCCTT 57.883 42.857 4.58 0.00 45.09 3.36
2843 5018 2.806288 CGAATTTTCGTGCGATTCCT 57.194 45.000 4.58 0.00 45.09 3.36
2885 5060 1.079336 GCTGTCGGTTAGGGTGTCC 60.079 63.158 0.00 0.00 0.00 4.02
2886 5061 1.079336 GGCTGTCGGTTAGGGTGTC 60.079 63.158 0.00 0.00 0.00 3.67
2887 5062 0.251922 TAGGCTGTCGGTTAGGGTGT 60.252 55.000 0.00 0.00 0.00 4.16
2888 5063 0.899720 TTAGGCTGTCGGTTAGGGTG 59.100 55.000 0.00 0.00 0.00 4.61
2922 5097 7.274033 TCGTGGATAGTAACTGTTGTTAATTCG 59.726 37.037 2.69 0.58 39.96 3.34
2935 5110 4.694339 AGGCTTCAATCGTGGATAGTAAC 58.306 43.478 0.00 0.00 0.00 2.50
2942 5119 0.690192 TGGAAGGCTTCAATCGTGGA 59.310 50.000 27.17 0.00 0.00 4.02
2947 5124 3.185246 TCTCGATGGAAGGCTTCAATC 57.815 47.619 27.77 27.77 36.87 2.67
2958 5135 1.475280 CCCGTAGTTGTTCTCGATGGA 59.525 52.381 0.00 0.00 0.00 3.41
2959 5136 1.475280 TCCCGTAGTTGTTCTCGATGG 59.525 52.381 0.00 0.00 0.00 3.51
2960 5137 2.933495 TCCCGTAGTTGTTCTCGATG 57.067 50.000 0.00 0.00 0.00 3.84
2961 5138 2.165845 CCTTCCCGTAGTTGTTCTCGAT 59.834 50.000 0.00 0.00 0.00 3.59
2987 5164 1.461512 TGTTACGCACGGCACATTTAG 59.538 47.619 0.00 0.00 0.00 1.85
3018 5195 2.105128 GACTGATCGACCAGGGCG 59.895 66.667 12.49 9.10 38.44 6.13
3040 5217 1.826096 GACCTAACTCACCTCTCCACC 59.174 57.143 0.00 0.00 0.00 4.61
3041 5218 1.473278 CGACCTAACTCACCTCTCCAC 59.527 57.143 0.00 0.00 0.00 4.02
3050 5227 5.339008 AAGTATGAATGCGACCTAACTCA 57.661 39.130 0.00 0.00 0.00 3.41
3053 5230 7.399523 CACTTTAAGTATGAATGCGACCTAAC 58.600 38.462 0.00 0.00 0.00 2.34
3090 5267 0.384725 GCGTACGCATTCCATCATGC 60.385 55.000 33.90 0.00 45.34 4.06
3091 5268 0.111134 CGCGTACGCATTCCATCATG 60.111 55.000 36.44 14.78 42.06 3.07
3092 5269 0.529773 ACGCGTACGCATTCCATCAT 60.530 50.000 36.44 9.65 45.53 2.45
3093 5270 0.738063 AACGCGTACGCATTCCATCA 60.738 50.000 36.44 0.00 45.53 3.07
3094 5271 0.315059 CAACGCGTACGCATTCCATC 60.315 55.000 36.44 8.07 45.53 3.51
3095 5272 1.713246 CAACGCGTACGCATTCCAT 59.287 52.632 36.44 14.64 45.53 3.41
3096 5273 3.017656 GCAACGCGTACGCATTCCA 62.018 57.895 36.44 0.00 45.53 3.53
3097 5274 2.276430 GCAACGCGTACGCATTCC 60.276 61.111 36.44 18.20 45.53 3.01
3098 5275 0.919427 GATGCAACGCGTACGCATTC 60.919 55.000 35.25 26.80 46.01 2.67
3099 5276 1.060308 GATGCAACGCGTACGCATT 59.940 52.632 35.25 27.82 46.01 3.56
3101 5278 2.310966 TTGATGCAACGCGTACGCA 61.311 52.632 36.44 30.65 45.53 5.24
3102 5279 1.857426 GTTGATGCAACGCGTACGC 60.857 57.895 29.83 29.83 45.53 4.42
3110 5287 2.622942 TCCTCACCAAAGTTGATGCAAC 59.377 45.455 0.00 2.22 43.83 4.17
3111 5288 2.886523 CTCCTCACCAAAGTTGATGCAA 59.113 45.455 0.00 0.00 0.00 4.08
3112 5289 2.158623 ACTCCTCACCAAAGTTGATGCA 60.159 45.455 0.00 0.00 0.00 3.96
3113 5290 2.508526 ACTCCTCACCAAAGTTGATGC 58.491 47.619 0.00 0.00 0.00 3.91
3114 5291 4.136796 TGAACTCCTCACCAAAGTTGATG 58.863 43.478 0.00 0.00 33.54 3.07
3115 5292 4.437682 TGAACTCCTCACCAAAGTTGAT 57.562 40.909 0.00 0.00 33.54 2.57
3116 5293 3.924114 TGAACTCCTCACCAAAGTTGA 57.076 42.857 0.00 0.00 33.54 3.18
3117 5294 4.339247 ACATTGAACTCCTCACCAAAGTTG 59.661 41.667 0.00 0.00 33.54 3.16
3118 5295 4.339247 CACATTGAACTCCTCACCAAAGTT 59.661 41.667 0.00 0.00 36.00 2.66
3119 5296 3.885297 CACATTGAACTCCTCACCAAAGT 59.115 43.478 0.00 0.00 32.21 2.66
3120 5297 4.136796 TCACATTGAACTCCTCACCAAAG 58.863 43.478 0.00 0.00 32.21 2.77
3121 5298 4.136796 CTCACATTGAACTCCTCACCAAA 58.863 43.478 0.00 0.00 32.21 3.28
3122 5299 3.496692 CCTCACATTGAACTCCTCACCAA 60.497 47.826 0.00 0.00 32.21 3.67
3123 5300 2.038952 CCTCACATTGAACTCCTCACCA 59.961 50.000 0.00 0.00 32.21 4.17
3124 5301 2.616510 CCCTCACATTGAACTCCTCACC 60.617 54.545 0.00 0.00 32.21 4.02
3125 5302 2.039084 ACCCTCACATTGAACTCCTCAC 59.961 50.000 0.00 0.00 32.21 3.51
3126 5303 2.338809 ACCCTCACATTGAACTCCTCA 58.661 47.619 0.00 0.00 0.00 3.86
3127 5304 4.080863 ACATACCCTCACATTGAACTCCTC 60.081 45.833 0.00 0.00 0.00 3.71
3128 5305 3.846588 ACATACCCTCACATTGAACTCCT 59.153 43.478 0.00 0.00 0.00 3.69
3129 5306 3.941483 CACATACCCTCACATTGAACTCC 59.059 47.826 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.