Multiple sequence alignment - TraesCS1A01G218600

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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 TraesCS1A01G218600 chr1A 100.000 3620 0 0 1 3620 387200803 387197184 0.000000e+00 6685
1 TraesCS1A01G218600 chr1D 93.238 3623 197 25 12 3601 308086681 308083074 0.000000e+00 5289
2 TraesCS1A01G218600 chr1B 94.829 2572 114 12 288 2851 417128147 417125587 0.000000e+00 3995
3 TraesCS1A01G218600 chr1B 84.820 527 72 5 3077 3601 417124854 417124334 1.150000e-144 523
4 TraesCS1A01G218600 chr1B 95.341 279 13 0 11 289 417128518 417128240 9.220000e-121 444


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 TraesCS1A01G218600 chr1A 387197184 387200803 3619 True 6685 6685 100.000000 1 3620 1 chr1A.!!$R1 3619
1 TraesCS1A01G218600 chr1D 308083074 308086681 3607 True 5289 5289 93.238000 12 3601 1 chr1D.!!$R1 3589
2 TraesCS1A01G218600 chr1B 417124334 417128518 4184 True 1654 3995 91.663333 11 3601 3 chr1B.!!$R1 3590

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
928 1030 0.948623 TTGTGCACACGCTAGCGATT 60.949 50.000 41.33 24.66 42.83 3.34 F
1231 1333 1.229209 GACAGGGAGGAGACCACCA 60.229 63.158 6.59 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 2007 1.741770 GGCCGTCTTGTACAGGCTG 60.742 63.158 19.80 14.16 43.20 4.85 R
3068 3741 0.028505 CTATCAGCGCACAATGCACC 59.971 55.000 11.47 0.00 45.36 5.01 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
53 54 5.175491 CCACAAAACACAAGTGCATATGAAC 59.825 40.000 6.97 6.25 32.09 3.18
163 165 5.556355 TGAGTTTGAGTTGATGCATCATC 57.444 39.130 29.13 26.43 40.88 2.92
166 168 3.657398 TTGAGTTGATGCATCATCCCT 57.343 42.857 29.13 23.04 39.87 4.20
274 276 7.096023 TGCTTCGTACTACTACGTACTAATAGC 60.096 40.741 0.00 0.00 45.14 2.97
621 722 7.681939 TGGTGTAGGAACTGTAATTGATTTC 57.318 36.000 0.00 0.00 41.52 2.17
680 782 6.419710 TCACGCTGTATAAATCCAAATACTCG 59.580 38.462 0.00 0.00 34.54 4.18
684 786 7.017645 GCTGTATAAATCCAAATACTCGCATG 58.982 38.462 0.00 0.00 31.75 4.06
687 789 4.717233 AAATCCAAATACTCGCATGCAA 57.283 36.364 19.57 0.00 0.00 4.08
698 800 8.552083 AATACTCGCATGCAATCAATTCTATA 57.448 30.769 19.57 0.00 0.00 1.31
700 802 7.263100 ACTCGCATGCAATCAATTCTATAAA 57.737 32.000 19.57 0.00 0.00 1.40
732 834 4.512944 CGCACATTTTACCTCTATGAGCAT 59.487 41.667 0.00 0.00 36.20 3.79
734 836 6.369890 CGCACATTTTACCTCTATGAGCATAT 59.630 38.462 0.00 0.00 36.20 1.78
735 837 7.524912 GCACATTTTACCTCTATGAGCATATG 58.475 38.462 0.00 0.00 36.37 1.78
755 857 7.912250 GCATATGTTTCACCACAAAGAATCTAG 59.088 37.037 4.29 0.00 0.00 2.43
903 1005 2.186160 CCACCGCACTTGCACTTGA 61.186 57.895 1.48 0.00 42.21 3.02
928 1030 0.948623 TTGTGCACACGCTAGCGATT 60.949 50.000 41.33 24.66 42.83 3.34
1228 1330 2.680352 GCGACAGGGAGGAGACCA 60.680 66.667 0.00 0.00 0.00 4.02
1231 1333 1.229209 GACAGGGAGGAGACCACCA 60.229 63.158 6.59 0.00 0.00 4.17
1290 1392 2.665185 AACGCGCTGAACCTGTCC 60.665 61.111 5.73 0.00 0.00 4.02
1639 1741 1.305201 GTTTGCCACGTCTTCCTTGA 58.695 50.000 0.00 0.00 0.00 3.02
1823 1925 2.600769 AGAGAACCTCCGCACCGT 60.601 61.111 0.00 0.00 0.00 4.83
1905 2007 2.046217 GTGGCGAAGGGGTTCCTC 60.046 66.667 0.00 0.00 44.07 3.71
2602 2704 1.478510 CTGATGGACAGTACGGCTTCT 59.521 52.381 0.00 0.00 41.30 2.85
2629 2731 0.526211 TCCCTCGTGACGTTGATCAG 59.474 55.000 4.40 0.00 0.00 2.90
2674 2776 0.389817 TATCTGCAGTGCACGTGTCC 60.390 55.000 15.37 7.95 33.79 4.02
2788 2890 7.279090 TCGTGTTGTTTTGTTCAGAAGAATCTA 59.721 33.333 0.00 0.00 35.92 1.98
2790 2892 7.377131 GTGTTGTTTTGTTCAGAAGAATCTAGC 59.623 37.037 0.00 0.00 35.92 3.42
2795 2899 6.791887 TTGTTCAGAAGAATCTAGCACTTG 57.208 37.500 0.00 0.00 35.92 3.16
2916 3573 3.304458 CGCAAGGAACCTCAAAGTTAACC 60.304 47.826 0.88 0.00 0.00 2.85
2918 3575 3.851458 AGGAACCTCAAAGTTAACCGT 57.149 42.857 0.88 0.00 0.00 4.83
2922 3579 5.761726 AGGAACCTCAAAGTTAACCGTAAAG 59.238 40.000 0.88 0.00 0.00 1.85
2923 3580 5.528690 GGAACCTCAAAGTTAACCGTAAAGT 59.471 40.000 0.88 0.00 0.00 2.66
2924 3581 5.996669 ACCTCAAAGTTAACCGTAAAGTG 57.003 39.130 0.88 0.00 0.00 3.16
2925 3582 5.430886 ACCTCAAAGTTAACCGTAAAGTGT 58.569 37.500 0.88 0.00 0.00 3.55
2926 3583 5.295045 ACCTCAAAGTTAACCGTAAAGTGTG 59.705 40.000 0.88 0.00 0.00 3.82
2927 3584 5.524646 CCTCAAAGTTAACCGTAAAGTGTGA 59.475 40.000 0.88 0.00 0.00 3.58
2931 3588 7.750014 TCAAAGTTAACCGTAAAGTGTGAAAAC 59.250 33.333 0.88 0.00 0.00 2.43
2935 3592 4.870221 ACCGTAAAGTGTGAAAACAGAC 57.130 40.909 0.00 0.00 0.00 3.51
2938 3595 5.751990 ACCGTAAAGTGTGAAAACAGACTAG 59.248 40.000 0.00 0.00 0.00 2.57
2948 3607 9.419297 GTGTGAAAACAGACTAGTGTTGATATA 57.581 33.333 0.00 0.00 39.82 0.86
2957 3616 6.901300 AGACTAGTGTTGATATAAGGGGACAA 59.099 38.462 0.00 0.00 0.00 3.18
2974 3633 5.010282 GGGACAATTTAGATGTGAGGTGTT 58.990 41.667 0.00 0.00 0.00 3.32
3012 3685 1.408127 CCGGAGGCATTACAACCATGA 60.408 52.381 0.00 0.00 46.14 3.07
3018 3691 5.594317 GGAGGCATTACAACCATGAAGTAAT 59.406 40.000 0.00 3.09 38.57 1.89
3019 3692 6.770785 GGAGGCATTACAACCATGAAGTAATA 59.229 38.462 13.40 0.00 36.58 0.98
3021 3694 7.116075 AGGCATTACAACCATGAAGTAATACA 58.884 34.615 13.40 0.00 36.58 2.29
3040 3713 3.164268 ACACTTTGGGCATCTGCAATAA 58.836 40.909 4.33 0.00 44.36 1.40
3041 3714 3.770933 ACACTTTGGGCATCTGCAATAAT 59.229 39.130 4.33 0.00 44.36 1.28
3042 3715 4.955450 ACACTTTGGGCATCTGCAATAATA 59.045 37.500 4.33 0.00 44.36 0.98
3043 3716 5.163519 ACACTTTGGGCATCTGCAATAATAC 60.164 40.000 4.33 0.00 44.36 1.89
3044 3717 4.955450 ACTTTGGGCATCTGCAATAATACA 59.045 37.500 4.33 0.00 44.36 2.29
3045 3718 5.421693 ACTTTGGGCATCTGCAATAATACAA 59.578 36.000 4.33 0.00 44.36 2.41
3046 3719 6.098695 ACTTTGGGCATCTGCAATAATACAAT 59.901 34.615 4.33 0.00 44.36 2.71
3047 3720 7.287466 ACTTTGGGCATCTGCAATAATACAATA 59.713 33.333 4.33 0.00 44.36 1.90
3048 3721 7.594351 TTGGGCATCTGCAATAATACAATAA 57.406 32.000 4.33 0.00 44.36 1.40
3049 3722 7.779754 TGGGCATCTGCAATAATACAATAAT 57.220 32.000 4.33 0.00 44.36 1.28
3050 3723 8.876303 TGGGCATCTGCAATAATACAATAATA 57.124 30.769 4.33 0.00 44.36 0.98
3051 3724 9.306777 TGGGCATCTGCAATAATACAATAATAA 57.693 29.630 4.33 0.00 44.36 1.40
3072 3745 8.504812 AATAAAATGAAAATTATGTGGGGTGC 57.495 30.769 0.00 0.00 0.00 5.01
3073 3746 5.495926 AAATGAAAATTATGTGGGGTGCA 57.504 34.783 0.00 0.00 0.00 4.57
3074 3747 5.697082 AATGAAAATTATGTGGGGTGCAT 57.303 34.783 0.00 0.00 0.00 3.96
3075 3748 5.697082 ATGAAAATTATGTGGGGTGCATT 57.303 34.783 0.00 0.00 0.00 3.56
3092 3801 1.019673 ATTGTGCGCTGATAGCCAAG 58.980 50.000 9.73 0.00 38.18 3.61
3114 3823 1.803334 CCAGTGGCAAAGCTACGTAA 58.197 50.000 0.00 0.00 44.64 3.18
3123 3832 3.366985 GCAAAGCTACGTAAGGGCAAAAT 60.367 43.478 7.88 0.00 46.39 1.82
3136 3845 1.637478 GCAAAATTGTGCCATGGCCG 61.637 55.000 33.44 12.30 38.66 6.13
3151 3860 2.429930 CCGGCCCAACTCAGAACA 59.570 61.111 0.00 0.00 0.00 3.18
3169 3878 8.389779 TCAGAACAAAGACAATGCAAAGTATA 57.610 30.769 0.00 0.00 0.00 1.47
3173 3882 6.389906 ACAAAGACAATGCAAAGTATAAGCC 58.610 36.000 0.00 0.00 0.00 4.35
3175 3884 6.442513 AAGACAATGCAAAGTATAAGCCTC 57.557 37.500 0.00 0.00 0.00 4.70
3180 3889 6.884295 ACAATGCAAAGTATAAGCCTCACTAA 59.116 34.615 0.00 0.00 0.00 2.24
3220 3929 4.721776 TGGGTGATATTCTTTAGACTGGCT 59.278 41.667 0.00 0.00 0.00 4.75
3222 3931 5.071115 GGGTGATATTCTTTAGACTGGCTCT 59.929 44.000 0.00 0.00 0.00 4.09
3246 3955 3.832490 TCTGCTCTTAGTTTGTAGCTCCA 59.168 43.478 0.00 0.00 35.95 3.86
3259 3968 2.113774 CTCCACCACTGCCAGCAA 59.886 61.111 0.00 0.00 0.00 3.91
3260 3969 1.970114 CTCCACCACTGCCAGCAAG 60.970 63.158 0.00 0.00 0.00 4.01
3272 3981 2.108157 AGCAAGGCGACGTGTCAA 59.892 55.556 5.96 0.00 42.26 3.18
3282 3991 1.470805 CGACGTGTCAATGGCCATCTA 60.471 52.381 21.08 7.35 0.00 1.98
3294 4003 0.183492 GCCATCTAATCCAGTGGGCA 59.817 55.000 9.92 0.00 41.35 5.36
3306 4015 2.776526 TGGGCACTGGACAAGGGT 60.777 61.111 0.00 0.00 0.00 4.34
3309 4018 2.564721 GGCACTGGACAAGGGTTGC 61.565 63.158 0.00 0.00 0.00 4.17
3322 4031 2.526120 GGTTGCCTCGACGCTATGC 61.526 63.158 7.89 0.00 0.00 3.14
3324 4033 1.143838 TTGCCTCGACGCTATGCAT 59.856 52.632 3.79 3.79 0.00 3.96
3336 4045 2.096268 CGCTATGCATGGTGGATTAACG 60.096 50.000 15.27 2.21 29.08 3.18
3338 4047 3.563808 GCTATGCATGGTGGATTAACGAA 59.436 43.478 10.16 0.00 29.08 3.85
3340 4049 5.278463 GCTATGCATGGTGGATTAACGAATT 60.278 40.000 10.16 0.00 29.08 2.17
3357 4066 2.408271 ATTGGCTGATGATGTGTCGT 57.592 45.000 0.00 0.00 0.00 4.34
3359 4068 2.293677 TGGCTGATGATGTGTCGTAC 57.706 50.000 0.00 0.00 0.00 3.67
3395 4104 2.425143 AAATGCTCATGTCGGGTCAT 57.575 45.000 0.00 0.00 0.00 3.06
3411 4120 4.214119 CGGGTCATGGTGCTAATAGAATTG 59.786 45.833 0.00 0.00 0.00 2.32
3422 4131 5.357878 TGCTAATAGAATTGGAGGTGCAAAG 59.642 40.000 0.00 0.00 0.00 2.77
3514 4225 3.977427 AGCTTTGGTCATTTTCGGAAAC 58.023 40.909 1.96 0.00 0.00 2.78
3530 4241 2.089116 AAACCCCCTGGCTAACACCC 62.089 60.000 0.00 0.00 33.59 4.61
3566 4277 2.976185 TCTTTCCACCATCTACCACACA 59.024 45.455 0.00 0.00 0.00 3.72
3567 4278 3.587061 TCTTTCCACCATCTACCACACAT 59.413 43.478 0.00 0.00 0.00 3.21
3574 4285 5.393352 CCACCATCTACCACACATCAAATTG 60.393 44.000 0.00 0.00 0.00 2.32
3601 4312 3.733224 CGTGCACTAGAGATACAATGCTC 59.267 47.826 16.19 0.00 34.18 4.26
3602 4313 4.686972 GTGCACTAGAGATACAATGCTCA 58.313 43.478 10.32 0.00 34.18 4.26
3603 4314 4.505922 GTGCACTAGAGATACAATGCTCAC 59.494 45.833 10.32 0.00 34.18 3.51
3604 4315 4.160252 TGCACTAGAGATACAATGCTCACA 59.840 41.667 0.00 0.00 34.18 3.58
3605 4316 4.505922 GCACTAGAGATACAATGCTCACAC 59.494 45.833 0.00 0.00 33.62 3.82
3606 4317 5.046529 CACTAGAGATACAATGCTCACACC 58.953 45.833 0.00 0.00 33.62 4.16
3607 4318 4.959210 ACTAGAGATACAATGCTCACACCT 59.041 41.667 0.00 0.00 33.62 4.00
3608 4319 6.039829 CACTAGAGATACAATGCTCACACCTA 59.960 42.308 0.00 0.00 33.62 3.08
3609 4320 6.780031 ACTAGAGATACAATGCTCACACCTAT 59.220 38.462 0.00 0.00 33.62 2.57
3610 4321 6.491714 AGAGATACAATGCTCACACCTATT 57.508 37.500 0.00 0.00 33.62 1.73
3611 4322 6.893583 AGAGATACAATGCTCACACCTATTT 58.106 36.000 0.00 0.00 33.62 1.40
3612 4323 7.341805 AGAGATACAATGCTCACACCTATTTT 58.658 34.615 0.00 0.00 33.62 1.82
3613 4324 7.831193 AGAGATACAATGCTCACACCTATTTTT 59.169 33.333 0.00 0.00 33.62 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 165 3.016736 ACTGAACTGTTCACACAAAGGG 58.983 45.455 18.69 9.41 35.46 3.95
166 168 3.689161 CCTGACTGAACTGTTCACACAAA 59.311 43.478 18.69 3.42 35.46 2.83
274 276 3.788694 CGAGAAAGATCAGTAGTTCAGCG 59.211 47.826 0.00 0.00 0.00 5.18
307 403 7.709947 TCGGTTAAAGATCGTAATGTACATCT 58.290 34.615 9.23 0.00 32.08 2.90
316 412 7.592938 TCTAACAGTTCGGTTAAAGATCGTAA 58.407 34.615 0.00 0.00 33.18 3.18
318 414 6.017400 TCTAACAGTTCGGTTAAAGATCGT 57.983 37.500 0.00 0.00 33.18 3.73
320 416 8.530269 TTCTTCTAACAGTTCGGTTAAAGATC 57.470 34.615 13.99 0.00 34.40 2.75
449 549 6.095021 TGCTCTGATCCTGAATTCTTGATTTG 59.905 38.462 7.05 6.01 0.00 2.32
568 668 7.315890 GGTCAACTTGCTAAGCTATCAAAAAT 58.684 34.615 0.00 0.00 0.00 1.82
583 684 1.008538 CACCAAGCGGTCAACTTGC 60.009 57.895 0.00 0.00 44.71 4.01
659 761 6.539649 TGCGAGTATTTGGATTTATACAGC 57.460 37.500 0.00 0.00 35.57 4.40
669 771 3.277715 TGATTGCATGCGAGTATTTGGA 58.722 40.909 14.20 0.00 0.00 3.53
670 772 3.696281 TGATTGCATGCGAGTATTTGG 57.304 42.857 14.20 0.00 0.00 3.28
676 778 6.866010 TTATAGAATTGATTGCATGCGAGT 57.134 33.333 14.20 0.97 0.00 4.18
680 782 7.646446 TGCATTTATAGAATTGATTGCATGC 57.354 32.000 11.82 11.82 34.24 4.06
684 786 7.507304 GTGCATGCATTTATAGAATTGATTGC 58.493 34.615 25.64 0.00 32.12 3.56
687 789 5.860182 GCGTGCATGCATTTATAGAATTGAT 59.140 36.000 25.64 0.00 34.15 2.57
732 834 8.154203 TGACTAGATTCTTTGTGGTGAAACATA 58.846 33.333 0.00 0.00 39.98 2.29
734 836 6.353323 TGACTAGATTCTTTGTGGTGAAACA 58.647 36.000 0.00 0.00 39.98 2.83
735 837 6.861065 TGACTAGATTCTTTGTGGTGAAAC 57.139 37.500 0.00 0.00 0.00 2.78
779 881 4.982295 GGTTACCAAAATCAAGTGCAGTTC 59.018 41.667 3.08 0.00 0.00 3.01
870 972 2.743838 GCGGTGGTTTATAGCTAGGCAA 60.744 50.000 0.00 0.00 0.00 4.52
928 1030 1.070786 GAGTGGTTCGAAGGTGGCA 59.929 57.895 0.00 0.00 0.00 4.92
1082 1184 1.302192 GCGTTAGGCTTGGTGGTGA 60.302 57.895 0.00 0.00 39.11 4.02
1228 1330 2.595463 TTCGTCGGAGTCGGTGGT 60.595 61.111 0.00 0.00 39.90 4.16
1231 1333 4.395583 GCGTTCGTCGGAGTCGGT 62.396 66.667 0.00 0.00 39.90 4.69
1290 1392 1.831389 CTGTGAACGGCAGGAACGTG 61.831 60.000 0.00 0.00 44.83 4.49
1518 1620 4.164252 GAGTGGAACGCCGTGTAG 57.836 61.111 0.00 0.00 45.86 2.74
1823 1925 3.680786 CCGACACTGGCACGAGGA 61.681 66.667 0.00 0.00 0.00 3.71
1905 2007 1.741770 GGCCGTCTTGTACAGGCTG 60.742 63.158 19.80 14.16 43.20 4.85
2085 2187 1.809619 GCTGTTACTCGCCGCATCA 60.810 57.895 0.00 0.00 0.00 3.07
2270 2372 4.789075 CGGCCATCGTCGTCGGTT 62.789 66.667 2.24 0.00 37.69 4.44
2472 2574 2.038837 GCTGGTCCGCTGGTAAACC 61.039 63.158 0.00 0.00 0.00 3.27
2602 2704 2.525629 TCACGAGGGACTGGCCAA 60.526 61.111 7.01 0.00 41.55 4.52
2629 2731 2.535984 GAGTACACTACATGCATGCGAC 59.464 50.000 26.53 14.28 0.00 5.19
2674 2776 2.607635 AGTACACAAGTTTGCACGTCAG 59.392 45.455 0.00 0.00 0.00 3.51
2788 2890 5.066764 ACGTGTAACAAATTTACCAAGTGCT 59.933 36.000 0.00 0.00 35.74 4.40
2890 3547 3.547746 ACTTTGAGGTTCCTTGCGTAAA 58.452 40.909 0.00 0.00 0.00 2.01
2891 3548 3.202829 ACTTTGAGGTTCCTTGCGTAA 57.797 42.857 0.00 0.00 0.00 3.18
2916 3573 6.255020 ACACTAGTCTGTTTTCACACTTTACG 59.745 38.462 0.00 0.00 31.81 3.18
2918 3575 7.820386 TCAACACTAGTCTGTTTTCACACTTTA 59.180 33.333 0.00 0.00 31.73 1.85
2922 3579 6.604735 ATCAACACTAGTCTGTTTTCACAC 57.395 37.500 0.00 0.00 31.73 3.82
2923 3580 9.990360 TTATATCAACACTAGTCTGTTTTCACA 57.010 29.630 0.00 0.00 31.73 3.58
2925 3582 9.653287 CCTTATATCAACACTAGTCTGTTTTCA 57.347 33.333 0.00 0.00 31.73 2.69
2926 3583 9.099454 CCCTTATATCAACACTAGTCTGTTTTC 57.901 37.037 0.00 0.00 31.73 2.29
2927 3584 8.047310 CCCCTTATATCAACACTAGTCTGTTTT 58.953 37.037 0.00 0.00 31.73 2.43
2931 3588 6.323996 TGTCCCCTTATATCAACACTAGTCTG 59.676 42.308 0.00 0.00 0.00 3.51
2935 3592 8.980481 AAATTGTCCCCTTATATCAACACTAG 57.020 34.615 0.00 0.00 0.00 2.57
2938 3595 8.974060 TCTAAATTGTCCCCTTATATCAACAC 57.026 34.615 0.00 0.00 0.00 3.32
2948 3607 4.292306 ACCTCACATCTAAATTGTCCCCTT 59.708 41.667 0.00 0.00 0.00 3.95
2957 3616 3.009723 CCGCAACACCTCACATCTAAAT 58.990 45.455 0.00 0.00 0.00 1.40
2991 3664 0.106719 ATGGTTGTAATGCCTCCGGG 60.107 55.000 0.00 0.00 0.00 5.73
3009 3682 9.025425 GCAGATGCCCAAAGTGTATTACTTCAT 62.025 40.741 0.00 0.00 41.03 2.57
3012 3685 4.399303 GCAGATGCCCAAAGTGTATTACTT 59.601 41.667 0.00 0.00 42.53 2.24
3018 3691 2.284754 TTGCAGATGCCCAAAGTGTA 57.715 45.000 1.72 0.00 41.18 2.90
3019 3692 1.636148 ATTGCAGATGCCCAAAGTGT 58.364 45.000 1.72 0.00 41.18 3.55
3021 3694 4.955450 TGTATTATTGCAGATGCCCAAAGT 59.045 37.500 1.72 0.00 41.18 2.66
3046 3719 9.606631 GCACCCCACATAATTTTCATTTTATTA 57.393 29.630 0.00 0.00 0.00 0.98
3047 3720 8.105829 TGCACCCCACATAATTTTCATTTTATT 58.894 29.630 0.00 0.00 0.00 1.40
3048 3721 7.628234 TGCACCCCACATAATTTTCATTTTAT 58.372 30.769 0.00 0.00 0.00 1.40
3049 3722 7.009179 TGCACCCCACATAATTTTCATTTTA 57.991 32.000 0.00 0.00 0.00 1.52
3050 3723 5.874093 TGCACCCCACATAATTTTCATTTT 58.126 33.333 0.00 0.00 0.00 1.82
3051 3724 5.495926 TGCACCCCACATAATTTTCATTT 57.504 34.783 0.00 0.00 0.00 2.32
3052 3725 5.697082 ATGCACCCCACATAATTTTCATT 57.303 34.783 0.00 0.00 0.00 2.57
3053 3726 5.045724 ACAATGCACCCCACATAATTTTCAT 60.046 36.000 0.00 0.00 0.00 2.57
3054 3727 4.285517 ACAATGCACCCCACATAATTTTCA 59.714 37.500 0.00 0.00 0.00 2.69
3055 3728 4.630940 CACAATGCACCCCACATAATTTTC 59.369 41.667 0.00 0.00 0.00 2.29
3056 3729 4.577875 CACAATGCACCCCACATAATTTT 58.422 39.130 0.00 0.00 0.00 1.82
3057 3730 3.619487 GCACAATGCACCCCACATAATTT 60.619 43.478 0.00 0.00 44.26 1.82
3058 3731 2.093553 GCACAATGCACCCCACATAATT 60.094 45.455 0.00 0.00 44.26 1.40
3059 3732 1.481772 GCACAATGCACCCCACATAAT 59.518 47.619 0.00 0.00 44.26 1.28
3060 3733 0.894141 GCACAATGCACCCCACATAA 59.106 50.000 0.00 0.00 44.26 1.90
3061 3734 1.311651 CGCACAATGCACCCCACATA 61.312 55.000 1.20 0.00 45.36 2.29
3062 3735 2.638354 CGCACAATGCACCCCACAT 61.638 57.895 1.20 0.00 45.36 3.21
3063 3736 3.293714 CGCACAATGCACCCCACA 61.294 61.111 1.20 0.00 45.36 4.17
3064 3737 4.722855 GCGCACAATGCACCCCAC 62.723 66.667 0.30 0.00 45.36 4.61
3065 3738 4.972733 AGCGCACAATGCACCCCA 62.973 61.111 11.47 0.00 45.36 4.96
3066 3739 4.424566 CAGCGCACAATGCACCCC 62.425 66.667 11.47 0.00 45.36 4.95
3067 3740 1.375853 TATCAGCGCACAATGCACCC 61.376 55.000 11.47 0.00 45.36 4.61
3068 3741 0.028505 CTATCAGCGCACAATGCACC 59.971 55.000 11.47 0.00 45.36 5.01
3069 3742 0.590732 GCTATCAGCGCACAATGCAC 60.591 55.000 11.47 0.00 45.36 4.57
3070 3743 1.717791 GGCTATCAGCGCACAATGCA 61.718 55.000 11.47 0.00 45.36 3.96
3071 3744 1.009222 GGCTATCAGCGCACAATGC 60.009 57.895 11.47 8.23 43.62 3.56
3072 3745 0.734309 TTGGCTATCAGCGCACAATG 59.266 50.000 11.47 0.00 43.62 2.82
3073 3746 1.019673 CTTGGCTATCAGCGCACAAT 58.980 50.000 11.47 1.82 43.62 2.71
3074 3747 0.036483 TCTTGGCTATCAGCGCACAA 60.036 50.000 11.47 2.05 43.62 3.33
3075 3748 0.460811 CTCTTGGCTATCAGCGCACA 60.461 55.000 11.47 0.00 43.62 4.57
3103 3812 4.279922 ACAATTTTGCCCTTACGTAGCTTT 59.720 37.500 6.82 0.00 0.00 3.51
3136 3845 1.609072 GTCTTTGTTCTGAGTTGGGCC 59.391 52.381 0.00 0.00 0.00 5.80
3142 3851 5.126061 ACTTTGCATTGTCTTTGTTCTGAGT 59.874 36.000 0.00 0.00 0.00 3.41
3151 3860 6.434028 TGAGGCTTATACTTTGCATTGTCTTT 59.566 34.615 0.00 0.00 0.00 2.52
3196 3905 5.370880 AGCCAGTCTAAAGAATATCACCCAT 59.629 40.000 0.00 0.00 0.00 4.00
3197 3906 4.721776 AGCCAGTCTAAAGAATATCACCCA 59.278 41.667 0.00 0.00 0.00 4.51
3198 3907 5.071115 AGAGCCAGTCTAAAGAATATCACCC 59.929 44.000 0.00 0.00 31.71 4.61
3215 3924 2.378038 ACTAAGAGCAGAGAGAGCCAG 58.622 52.381 0.00 0.00 0.00 4.85
3220 3929 5.013547 AGCTACAAACTAAGAGCAGAGAGA 58.986 41.667 0.00 0.00 37.40 3.10
3222 3931 4.158764 GGAGCTACAAACTAAGAGCAGAGA 59.841 45.833 0.00 0.00 37.40 3.10
3259 3968 2.742372 GCCATTGACACGTCGCCT 60.742 61.111 0.00 0.00 0.00 5.52
3260 3969 3.799755 GGCCATTGACACGTCGCC 61.800 66.667 0.00 0.00 0.00 5.54
3272 3981 1.426598 CCCACTGGATTAGATGGCCAT 59.573 52.381 20.96 20.96 0.00 4.40
3294 4003 1.456287 GAGGCAACCCTTGTCCAGT 59.544 57.895 0.00 0.00 43.12 4.00
3306 4015 1.143838 ATGCATAGCGTCGAGGCAA 59.856 52.632 29.61 11.50 38.08 4.52
3309 4018 1.068083 ACCATGCATAGCGTCGAGG 59.932 57.895 0.00 0.00 0.00 4.63
3322 4031 3.381272 AGCCAATTCGTTAATCCACCATG 59.619 43.478 0.00 0.00 0.00 3.66
3324 4033 2.752354 CAGCCAATTCGTTAATCCACCA 59.248 45.455 0.00 0.00 0.00 4.17
3336 4045 2.679837 ACGACACATCATCAGCCAATTC 59.320 45.455 0.00 0.00 0.00 2.17
3338 4047 2.408271 ACGACACATCATCAGCCAAT 57.592 45.000 0.00 0.00 0.00 3.16
3340 4049 1.469079 CGTACGACACATCATCAGCCA 60.469 52.381 10.44 0.00 0.00 4.75
3357 4066 3.300852 TTATGCAACCAGACGAACGTA 57.699 42.857 0.00 0.00 0.00 3.57
3359 4068 3.416277 CATTTATGCAACCAGACGAACG 58.584 45.455 0.00 0.00 0.00 3.95
3391 4100 5.471456 CCTCCAATTCTATTAGCACCATGAC 59.529 44.000 0.00 0.00 0.00 3.06
3395 4104 4.780815 CACCTCCAATTCTATTAGCACCA 58.219 43.478 0.00 0.00 0.00 4.17
3411 4120 9.699703 TGTTAAAAATTTATACTTTGCACCTCC 57.300 29.630 0.00 0.00 0.00 4.30
3422 4131 9.498307 CAGACGGTCCATGTTAAAAATTTATAC 57.502 33.333 4.14 0.00 0.00 1.47
3474 4183 4.609018 CCCGGTAGCTCCCATGCG 62.609 72.222 0.00 0.00 38.13 4.73
3514 4225 2.938798 TGGGTGTTAGCCAGGGGG 60.939 66.667 0.00 0.00 41.50 5.40
3566 4277 1.608918 TGCACGGCCCCAATTTGAT 60.609 52.632 0.00 0.00 0.00 2.57
3567 4278 2.203552 TGCACGGCCCCAATTTGA 60.204 55.556 0.00 0.00 0.00 2.69
3574 4285 1.113517 TATCTCTAGTGCACGGCCCC 61.114 60.000 12.01 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.