Multiple sequence alignment - TraesCS4A01G122700

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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 TraesCS4A01G122700 chr4A 100.000 3745 0 0 1 3745 152649024 152652768 0.000000e+00 6916.0
1 TraesCS4A01G122700 chr4B 89.318 2743 120 80 325 2977 400396520 400399179 0.000000e+00 3282.0
2 TraesCS4A01G122700 chr4B 93.711 159 10 0 1 159 400395965 400396123 4.830000e-59 239.0
3 TraesCS4A01G122700 chr4B 95.294 85 4 0 179 263 400396418 400396502 6.520000e-28 135.0
4 TraesCS4A01G122700 chr4D 92.591 2092 74 37 873 2924 320213123 320211073 0.000000e+00 2929.0
5 TraesCS4A01G122700 chr4D 93.410 698 31 5 140 836 320215020 320214337 0.000000e+00 1020.0
6 TraesCS4A01G122700 chr4D 90.390 770 61 9 2981 3745 293366250 293367011 0.000000e+00 1000.0
7 TraesCS4A01G122700 chr1B 91.173 1824 68 34 1009 2755 638034428 638036235 0.000000e+00 2390.0
8 TraesCS4A01G122700 chr1B 89.538 411 17 12 551 961 638034045 638034429 7.220000e-137 497.0
9 TraesCS4A01G122700 chr2A 92.095 759 56 3 2988 3745 727960200 727960955 0.000000e+00 1066.0
10 TraesCS4A01G122700 chr2D 91.590 761 50 10 2988 3745 243653438 243652689 0.000000e+00 1038.0
11 TraesCS4A01G122700 chr5D 91.436 759 55 7 2988 3744 445866815 445866065 0.000000e+00 1033.0
12 TraesCS4A01G122700 chr5D 90.013 761 62 8 2988 3745 521405597 521406346 0.000000e+00 972.0
13 TraesCS4A01G122700 chr5A 91.219 763 62 5 2986 3745 666717557 666718317 0.000000e+00 1033.0
14 TraesCS4A01G122700 chr7A 91.064 761 66 2 2986 3745 281567096 281566337 0.000000e+00 1027.0
15 TraesCS4A01G122700 chr7A 91.667 48 4 0 1419 1466 145462193 145462240 2.410000e-07 67.6
16 TraesCS4A01G122700 chr7D 91.173 759 57 7 2988 3744 599081639 599082389 0.000000e+00 1022.0
17 TraesCS4A01G122700 chr7D 93.333 45 3 0 1422 1466 144147703 144147659 2.410000e-07 67.6
18 TraesCS4A01G122700 chr3A 90.658 760 62 6 2982 3739 449732460 449733212 0.000000e+00 1002.0


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 TraesCS4A01G122700 chr4A 152649024 152652768 3744 False 6916.000000 6916 100.000000 1 3745 1 chr4A.!!$F1 3744
1 TraesCS4A01G122700 chr4B 400395965 400399179 3214 False 1218.666667 3282 92.774333 1 2977 3 chr4B.!!$F1 2976
2 TraesCS4A01G122700 chr4D 320211073 320215020 3947 True 1974.500000 2929 93.000500 140 2924 2 chr4D.!!$R1 2784
3 TraesCS4A01G122700 chr4D 293366250 293367011 761 False 1000.000000 1000 90.390000 2981 3745 1 chr4D.!!$F1 764
4 TraesCS4A01G122700 chr1B 638034045 638036235 2190 False 1443.500000 2390 90.355500 551 2755 2 chr1B.!!$F1 2204
5 TraesCS4A01G122700 chr2A 727960200 727960955 755 False 1066.000000 1066 92.095000 2988 3745 1 chr2A.!!$F1 757
6 TraesCS4A01G122700 chr2D 243652689 243653438 749 True 1038.000000 1038 91.590000 2988 3745 1 chr2D.!!$R1 757
7 TraesCS4A01G122700 chr5D 445866065 445866815 750 True 1033.000000 1033 91.436000 2988 3744 1 chr5D.!!$R1 756
8 TraesCS4A01G122700 chr5D 521405597 521406346 749 False 972.000000 972 90.013000 2988 3745 1 chr5D.!!$F1 757
9 TraesCS4A01G122700 chr5A 666717557 666718317 760 False 1033.000000 1033 91.219000 2986 3745 1 chr5A.!!$F1 759
10 TraesCS4A01G122700 chr7A 281566337 281567096 759 True 1027.000000 1027 91.064000 2986 3745 1 chr7A.!!$R1 759
11 TraesCS4A01G122700 chr7D 599081639 599082389 750 False 1022.000000 1022 91.173000 2988 3744 1 chr7D.!!$F1 756
12 TraesCS4A01G122700 chr3A 449732460 449733212 752 False 1002.000000 1002 90.658000 2982 3739 1 chr3A.!!$F1 757

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
855 1136 0.107214 TTTAGATGCAGAAGCCGGGG 60.107 55.0 2.18 0.0 41.13 5.73 F
1726 3227 0.246757 CGAAACGACGATTCCGCTTG 60.247 55.0 11.65 0.0 39.95 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2723 4318 0.244994 AAGCATCGTCGAAGAGCAGT 59.755 50.0 18.84 8.42 36.95 4.40 R
3348 4962 0.171455 GTGCGGAGTGAAGATCGACT 59.829 55.0 0.00 0.00 0.00 4.18 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
25 26 2.266055 CCTGCGGTTCACCCTCTC 59.734 66.667 0.00 0.00 0.00 3.20
32 33 1.484444 GGTTCACCCTCTCACAGGCT 61.484 60.000 0.00 0.00 41.80 4.58
102 103 3.403038 CATCGACTTCTCAACCCTTTGT 58.597 45.455 0.00 0.00 34.02 2.83
106 107 3.492656 CGACTTCTCAACCCTTTGTGAGA 60.493 47.826 0.00 0.00 36.76 3.27
372 648 1.670406 CTGCAGCCTGTGTCCTGAC 60.670 63.158 0.00 0.00 0.00 3.51
389 665 5.119588 GTCCTGACAAAAATGAATGCACATG 59.880 40.000 0.00 0.00 0.00 3.21
391 667 4.958509 TGACAAAAATGAATGCACATGGT 58.041 34.783 0.00 0.00 0.00 3.55
471 747 2.524306 CTGAACCCTGCCCAAAATACA 58.476 47.619 0.00 0.00 0.00 2.29
473 749 1.204704 GAACCCTGCCCAAAATACAGC 59.795 52.381 0.00 0.00 0.00 4.40
501 777 2.362632 CTCGTCCCCTTCTCCGGT 60.363 66.667 0.00 0.00 0.00 5.28
635 911 2.918712 AACCTTCAGAGACCACACAG 57.081 50.000 0.00 0.00 0.00 3.66
798 1075 4.681942 CGGTTCGTCTCCATTATCTCAATC 59.318 45.833 0.00 0.00 0.00 2.67
799 1076 5.601662 GGTTCGTCTCCATTATCTCAATCA 58.398 41.667 0.00 0.00 0.00 2.57
800 1077 6.226787 GGTTCGTCTCCATTATCTCAATCAT 58.773 40.000 0.00 0.00 0.00 2.45
801 1078 6.708054 GGTTCGTCTCCATTATCTCAATCATT 59.292 38.462 0.00 0.00 0.00 2.57
802 1079 7.095439 GGTTCGTCTCCATTATCTCAATCATTC 60.095 40.741 0.00 0.00 0.00 2.67
803 1080 6.152379 TCGTCTCCATTATCTCAATCATTCG 58.848 40.000 0.00 0.00 0.00 3.34
804 1081 5.923114 CGTCTCCATTATCTCAATCATTCGT 59.077 40.000 0.00 0.00 0.00 3.85
805 1082 6.088749 CGTCTCCATTATCTCAATCATTCGTC 59.911 42.308 0.00 0.00 0.00 4.20
831 1112 7.769507 CCATTCATATACTCCATCAGATTCTGG 59.230 40.741 13.59 0.00 31.51 3.86
836 1117 3.113824 ACTCCATCAGATTCTGGCTCTT 58.886 45.455 13.59 0.00 32.30 2.85
837 1118 3.522750 ACTCCATCAGATTCTGGCTCTTT 59.477 43.478 13.59 0.00 32.30 2.52
838 1119 4.018597 ACTCCATCAGATTCTGGCTCTTTT 60.019 41.667 13.59 0.00 32.30 2.27
839 1120 5.190528 ACTCCATCAGATTCTGGCTCTTTTA 59.809 40.000 13.59 0.00 32.30 1.52
840 1121 5.678583 TCCATCAGATTCTGGCTCTTTTAG 58.321 41.667 13.59 0.00 32.30 1.85
841 1122 5.426509 TCCATCAGATTCTGGCTCTTTTAGA 59.573 40.000 13.59 0.00 32.30 2.10
842 1123 6.100859 TCCATCAGATTCTGGCTCTTTTAGAT 59.899 38.462 13.59 0.00 32.30 1.98
843 1124 6.205076 CCATCAGATTCTGGCTCTTTTAGATG 59.795 42.308 13.59 5.91 31.51 2.90
844 1125 5.121811 TCAGATTCTGGCTCTTTTAGATGC 58.878 41.667 13.59 0.00 31.51 3.91
845 1126 4.880120 CAGATTCTGGCTCTTTTAGATGCA 59.120 41.667 5.73 0.00 0.00 3.96
846 1127 5.007823 CAGATTCTGGCTCTTTTAGATGCAG 59.992 44.000 5.73 0.00 0.00 4.41
847 1128 4.558226 TTCTGGCTCTTTTAGATGCAGA 57.442 40.909 0.00 0.00 0.00 4.26
851 1132 2.357323 GGCTCTTTTAGATGCAGAAGCC 59.643 50.000 0.00 0.00 41.13 4.35
853 1134 2.611292 CTCTTTTAGATGCAGAAGCCGG 59.389 50.000 0.00 0.00 41.13 6.13
855 1136 0.107214 TTTAGATGCAGAAGCCGGGG 60.107 55.000 2.18 0.00 41.13 5.73
857 1138 4.115199 GATGCAGAAGCCGGGGGT 62.115 66.667 2.18 0.00 41.13 4.95
858 1139 2.690881 ATGCAGAAGCCGGGGGTA 60.691 61.111 2.18 0.00 41.13 3.69
965 2434 5.648092 CGTAGGATCTTTTGACATTTTCCCT 59.352 40.000 0.00 0.00 0.00 4.20
978 2447 4.963628 ACATTTTCCCTCTCCTAGTCCTAC 59.036 45.833 0.00 0.00 0.00 3.18
1213 2682 2.046314 ATTTCGACGGCCACCAGG 60.046 61.111 2.24 0.00 38.23 4.45
1269 2738 5.907945 CGTCGACATACTAGGTGATAAACAG 59.092 44.000 17.16 0.00 0.00 3.16
1271 2740 6.911511 GTCGACATACTAGGTGATAAACAGTC 59.088 42.308 11.55 0.00 0.00 3.51
1273 2742 6.039493 CGACATACTAGGTGATAAACAGTCCT 59.961 42.308 4.61 0.00 0.00 3.85
1274 2743 7.416438 CGACATACTAGGTGATAAACAGTCCTT 60.416 40.741 4.61 0.00 0.00 3.36
1315 2784 4.081642 ACGCTGCCTCTGTTCTCTATTTAA 60.082 41.667 0.00 0.00 0.00 1.52
1316 2785 4.870426 CGCTGCCTCTGTTCTCTATTTAAA 59.130 41.667 0.00 0.00 0.00 1.52
1317 2786 5.006165 CGCTGCCTCTGTTCTCTATTTAAAG 59.994 44.000 0.00 0.00 0.00 1.85
1318 2787 6.109359 GCTGCCTCTGTTCTCTATTTAAAGA 58.891 40.000 0.00 0.00 0.00 2.52
1319 2788 6.595716 GCTGCCTCTGTTCTCTATTTAAAGAA 59.404 38.462 0.00 0.00 0.00 2.52
1377 2846 2.116125 GCTGGGAGGGTTTGTGCT 59.884 61.111 0.00 0.00 0.00 4.40
1493 2962 7.336161 AGCATCTTCGTCAGTATACTTACTT 57.664 36.000 13.84 0.00 36.50 2.24
1602 3073 1.683917 TGAAGCCTTCTCCGATAGCTC 59.316 52.381 5.96 0.00 32.19 4.09
1707 3184 3.190535 TCCGGCAGTAATTTCTCTTTTGC 59.809 43.478 0.00 0.00 0.00 3.68
1726 3227 0.246757 CGAAACGACGATTCCGCTTG 60.247 55.000 11.65 0.00 39.95 4.01
1886 3388 1.353609 CGCGACATGATGACACAGCA 61.354 55.000 0.00 0.00 33.25 4.41
2445 4033 5.556355 GACATCAAGTCATCAAGCATGAA 57.444 39.130 0.00 0.00 43.52 2.57
2446 4034 5.562506 ACATCAAGTCATCAAGCATGAAG 57.437 39.130 0.00 0.00 43.52 3.02
2447 4035 4.142447 ACATCAAGTCATCAAGCATGAAGC 60.142 41.667 0.00 0.00 43.52 3.86
2448 4036 8.274259 GACATCAAGTCATCAAGCATGAAGCA 62.274 42.308 0.00 0.00 46.19 3.91
2449 4037 9.488128 GACATCAAGTCATCAAGCATGAAGCAT 62.488 40.741 0.00 0.00 46.19 3.79
2495 4088 3.764049 GTGACTCGGCGTTGCGTC 61.764 66.667 6.85 10.22 0.00 5.19
2670 4265 3.630148 CCAACGCGCTCATAGCCG 61.630 66.667 5.73 7.81 38.18 5.52
2671 4266 4.285149 CAACGCGCTCATAGCCGC 62.285 66.667 5.73 7.40 38.18 6.53
2723 4318 3.276091 CCTGTCAACGTGCGCCAA 61.276 61.111 4.18 0.00 0.00 4.52
2756 4351 3.375299 ACGATGCTTAGCTTGGAATCAAC 59.625 43.478 5.60 0.00 0.00 3.18
2757 4352 3.544834 CGATGCTTAGCTTGGAATCAACG 60.545 47.826 5.60 0.00 0.00 4.10
2759 4354 2.290008 TGCTTAGCTTGGAATCAACGGA 60.290 45.455 5.60 0.00 0.00 4.69
2760 4355 2.096013 GCTTAGCTTGGAATCAACGGAC 59.904 50.000 0.00 0.00 0.00 4.79
2762 4357 2.568623 AGCTTGGAATCAACGGACTT 57.431 45.000 0.00 0.00 0.00 3.01
2763 4358 3.695830 AGCTTGGAATCAACGGACTTA 57.304 42.857 0.00 0.00 0.00 2.24
2766 4361 3.938963 GCTTGGAATCAACGGACTTATGA 59.061 43.478 0.00 0.00 0.00 2.15
2767 4362 4.394920 GCTTGGAATCAACGGACTTATGAA 59.605 41.667 0.00 0.00 0.00 2.57
2768 4363 5.066505 GCTTGGAATCAACGGACTTATGAAT 59.933 40.000 0.00 0.00 0.00 2.57
2769 4364 6.677781 TTGGAATCAACGGACTTATGAATC 57.322 37.500 0.00 0.00 0.00 2.52
2770 4365 5.739959 TGGAATCAACGGACTTATGAATCA 58.260 37.500 0.00 0.00 0.00 2.57
2771 4366 6.176896 TGGAATCAACGGACTTATGAATCAA 58.823 36.000 0.00 0.00 0.00 2.57
2772 4367 6.657117 TGGAATCAACGGACTTATGAATCAAA 59.343 34.615 0.00 0.00 0.00 2.69
2773 4368 6.967199 GGAATCAACGGACTTATGAATCAAAC 59.033 38.462 0.00 0.00 0.00 2.93
2774 4369 7.361713 GGAATCAACGGACTTATGAATCAAACA 60.362 37.037 0.00 0.00 0.00 2.83
2775 4370 6.480524 TCAACGGACTTATGAATCAAACAG 57.519 37.500 0.00 0.00 0.00 3.16
2776 4371 5.411361 TCAACGGACTTATGAATCAAACAGG 59.589 40.000 0.00 0.00 0.00 4.00
2777 4372 4.261801 ACGGACTTATGAATCAAACAGGG 58.738 43.478 0.00 0.00 0.00 4.45
2778 4373 4.261801 CGGACTTATGAATCAAACAGGGT 58.738 43.478 0.00 0.00 0.00 4.34
2783 4378 7.775561 GGACTTATGAATCAAACAGGGTCTTAT 59.224 37.037 0.00 0.00 0.00 1.73
2807 4405 1.722034 TCTCAGAGGCTGTTGTTCCT 58.278 50.000 0.00 0.00 34.90 3.36
2810 4408 1.072331 TCAGAGGCTGTTGTTCCTTCC 59.928 52.381 0.00 0.00 31.71 3.46
2815 4413 0.586802 GCTGTTGTTCCTTCCGTGAC 59.413 55.000 0.00 0.00 0.00 3.67
2823 4421 2.342279 CTTCCGTGACTTCCCGCA 59.658 61.111 0.00 0.00 0.00 5.69
2850 4449 0.929824 CGCGTGCTGTTTTGGAAGTG 60.930 55.000 0.00 0.00 0.00 3.16
2878 4477 5.652452 GGTCCTATTTGTTCAGTTTGCCTAT 59.348 40.000 0.00 0.00 0.00 2.57
2970 4581 6.985117 AGTTGTTGATGATTGCAGTATTGTT 58.015 32.000 0.00 0.00 0.00 2.83
2973 4584 6.979465 TGTTGATGATTGCAGTATTGTTGAA 58.021 32.000 0.00 0.00 0.00 2.69
2977 4588 5.281693 TGATTGCAGTATTGTTGAACTCG 57.718 39.130 0.00 0.00 0.00 4.18
2978 4589 4.754618 TGATTGCAGTATTGTTGAACTCGT 59.245 37.500 0.00 0.00 0.00 4.18
2979 4590 5.929415 TGATTGCAGTATTGTTGAACTCGTA 59.071 36.000 0.00 0.00 0.00 3.43
2980 4591 6.425417 TGATTGCAGTATTGTTGAACTCGTAA 59.575 34.615 0.00 0.00 0.00 3.18
2981 4592 6.795098 TTGCAGTATTGTTGAACTCGTAAT 57.205 33.333 0.00 0.00 0.00 1.89
2982 4593 6.795098 TGCAGTATTGTTGAACTCGTAATT 57.205 33.333 0.00 0.00 0.00 1.40
2983 4594 7.197071 TGCAGTATTGTTGAACTCGTAATTT 57.803 32.000 0.00 0.00 0.00 1.82
2984 4595 7.075121 TGCAGTATTGTTGAACTCGTAATTTG 58.925 34.615 0.00 0.00 0.00 2.32
3001 4612 6.237861 CGTAATTTGTTAGAGCAACTCTAGCC 60.238 42.308 13.69 6.33 42.92 3.93
3054 4665 5.460646 CATTTGCAAGTCATAGAAAACCGT 58.539 37.500 0.00 0.00 0.00 4.83
3059 4670 7.028926 TGCAAGTCATAGAAAACCGTTTTTA 57.971 32.000 10.53 6.05 34.94 1.52
3103 4714 1.072505 GCAGACCCCTCAAACGGAA 59.927 57.895 0.00 0.00 0.00 4.30
3252 4865 8.977505 CCACAAATAAGTTCAAATTCAAACGAT 58.022 29.630 0.00 0.00 0.00 3.73
3275 4889 7.161900 CGATATAACACAGTTTACGTGCAAATG 59.838 37.037 0.00 3.10 37.93 2.32
3287 4901 2.219216 CGTGCAAATGAAAGCCAAGTTG 59.781 45.455 0.00 0.00 0.00 3.16
3348 4962 0.251916 CCAAGTCCGGCACCATCTTA 59.748 55.000 0.00 0.00 0.00 2.10
3372 4992 1.137872 GATCTTCACTCCGCACCATCT 59.862 52.381 0.00 0.00 0.00 2.90
3373 4993 0.976641 TCTTCACTCCGCACCATCTT 59.023 50.000 0.00 0.00 0.00 2.40
3374 4994 2.176045 TCTTCACTCCGCACCATCTTA 58.824 47.619 0.00 0.00 0.00 2.10
3375 4995 2.565391 TCTTCACTCCGCACCATCTTAA 59.435 45.455 0.00 0.00 0.00 1.85
3376 4996 3.197766 TCTTCACTCCGCACCATCTTAAT 59.802 43.478 0.00 0.00 0.00 1.40
3377 4997 3.179443 TCACTCCGCACCATCTTAATC 57.821 47.619 0.00 0.00 0.00 1.75
3378 4998 2.499693 TCACTCCGCACCATCTTAATCA 59.500 45.455 0.00 0.00 0.00 2.57
3487 5108 6.100279 ACCATATGGAGCAGAGAAAACATCTA 59.900 38.462 28.77 0.00 37.27 1.98
3500 5122 5.812642 AGAAAACATCTATGGAACTGTAGCG 59.187 40.000 0.00 0.00 36.32 4.26
3550 5172 4.288105 TCTTCAAGATTTCTCTCCTTGCCT 59.712 41.667 0.00 0.00 37.71 4.75
3714 5338 2.758979 CTCTTCCTTGAGCAATTGCCAT 59.241 45.455 26.45 9.54 43.38 4.40
3739 5363 1.198637 CTTGCTTCTCCTTTGCCTTCG 59.801 52.381 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.703703 GCCTGTGAGAGGGTGAAC 57.296 61.111 0.00 0.00 43.07 3.18
114 115 4.991687 GTCTGTTCTCGAGGATCTTTTTGT 59.008 41.667 13.56 0.00 0.00 2.83
115 116 4.090642 CGTCTGTTCTCGAGGATCTTTTTG 59.909 45.833 13.56 0.00 0.00 2.44
121 122 3.119779 AGTTTCGTCTGTTCTCGAGGATC 60.120 47.826 13.56 4.14 37.38 3.36
130 131 2.031944 GGCAGGAAAGTTTCGTCTGTTC 60.032 50.000 17.75 10.38 0.00 3.18
204 480 1.135774 TGGTCTCGTCTCGTGATTTCG 60.136 52.381 0.00 0.00 32.30 3.46
372 648 7.537715 TCTAGTACCATGTGCATTCATTTTTG 58.462 34.615 0.00 0.00 0.00 2.44
389 665 5.229469 CGTGTCGTCAATCAATTCTAGTACC 59.771 44.000 0.00 0.00 0.00 3.34
391 667 4.796830 GCGTGTCGTCAATCAATTCTAGTA 59.203 41.667 0.00 0.00 0.00 1.82
490 766 1.228429 TTTTGCCACCGGAGAAGGG 60.228 57.895 9.46 2.12 35.02 3.95
493 769 1.679153 GAAACTTTTGCCACCGGAGAA 59.321 47.619 9.46 0.00 0.00 2.87
501 777 1.950909 CTACCCGTGAAACTTTTGCCA 59.049 47.619 0.00 0.00 31.75 4.92
569 845 3.538591 TGGCATTGTTTTTGCATGAACA 58.461 36.364 10.36 10.36 41.95 3.18
598 874 9.438291 CTGAAGGTTTTCGCACATATATAAAAG 57.562 33.333 0.00 0.00 36.04 2.27
603 879 6.480320 GTCTCTGAAGGTTTTCGCACATATAT 59.520 38.462 0.00 0.00 36.04 0.86
635 911 7.971183 ACAAGAATAAACAAGGAGAGAAGAC 57.029 36.000 0.00 0.00 0.00 3.01
798 1075 7.099120 TGATGGAGTATATGAATGGACGAATG 58.901 38.462 0.00 0.00 0.00 2.67
799 1076 7.179160 TCTGATGGAGTATATGAATGGACGAAT 59.821 37.037 0.00 0.00 0.00 3.34
800 1077 6.493458 TCTGATGGAGTATATGAATGGACGAA 59.507 38.462 0.00 0.00 0.00 3.85
801 1078 6.010219 TCTGATGGAGTATATGAATGGACGA 58.990 40.000 0.00 0.00 0.00 4.20
802 1079 6.272822 TCTGATGGAGTATATGAATGGACG 57.727 41.667 0.00 0.00 0.00 4.79
803 1080 8.538701 AGAATCTGATGGAGTATATGAATGGAC 58.461 37.037 0.00 0.00 0.00 4.02
804 1081 8.537858 CAGAATCTGATGGAGTATATGAATGGA 58.462 37.037 3.77 0.00 32.44 3.41
805 1082 7.769507 CCAGAATCTGATGGAGTATATGAATGG 59.230 40.741 12.53 0.00 39.02 3.16
831 1112 2.031437 CGGCTTCTGCATCTAAAAGAGC 59.969 50.000 0.00 0.00 41.91 4.09
836 1117 0.107214 CCCCGGCTTCTGCATCTAAA 60.107 55.000 0.00 0.00 41.91 1.85
837 1118 1.526887 CCCCGGCTTCTGCATCTAA 59.473 57.895 0.00 0.00 41.91 2.10
838 1119 2.443394 CCCCCGGCTTCTGCATCTA 61.443 63.158 0.00 0.00 41.91 1.98
839 1120 3.801997 CCCCCGGCTTCTGCATCT 61.802 66.667 0.00 0.00 41.91 2.90
840 1121 2.265467 TTACCCCCGGCTTCTGCATC 62.265 60.000 0.00 0.00 41.91 3.91
841 1122 1.645402 ATTACCCCCGGCTTCTGCAT 61.645 55.000 0.00 0.00 41.91 3.96
842 1123 0.983905 TATTACCCCCGGCTTCTGCA 60.984 55.000 0.00 0.00 41.91 4.41
843 1124 0.400594 ATATTACCCCCGGCTTCTGC 59.599 55.000 0.00 0.00 38.76 4.26
844 1125 4.070009 GTTTATATTACCCCCGGCTTCTG 58.930 47.826 0.00 0.00 0.00 3.02
845 1126 3.717913 TGTTTATATTACCCCCGGCTTCT 59.282 43.478 0.00 0.00 0.00 2.85
846 1127 4.070009 CTGTTTATATTACCCCCGGCTTC 58.930 47.826 0.00 0.00 0.00 3.86
847 1128 3.181437 CCTGTTTATATTACCCCCGGCTT 60.181 47.826 0.00 0.00 0.00 4.35
851 1132 3.495434 TGCCTGTTTATATTACCCCCG 57.505 47.619 0.00 0.00 0.00 5.73
853 1134 3.566742 CCGTTGCCTGTTTATATTACCCC 59.433 47.826 0.00 0.00 0.00 4.95
855 1136 5.823209 AACCGTTGCCTGTTTATATTACC 57.177 39.130 0.00 0.00 0.00 2.85
857 1138 8.967664 AAGATAACCGTTGCCTGTTTATATTA 57.032 30.769 0.00 0.00 0.00 0.98
858 1139 7.012989 GGAAGATAACCGTTGCCTGTTTATATT 59.987 37.037 0.00 0.00 0.00 1.28
949 2418 6.241645 ACTAGGAGAGGGAAAATGTCAAAAG 58.758 40.000 0.00 0.00 0.00 2.27
965 2434 1.911357 TGTCACGGTAGGACTAGGAGA 59.089 52.381 0.00 0.00 36.26 3.71
978 2447 1.737735 TGAGCGAGCAATGTCACGG 60.738 57.895 0.00 0.00 0.00 4.94
1269 2738 7.674240 GCGTGACAGTAAAATTCAGATAAGGAC 60.674 40.741 0.00 0.00 0.00 3.85
1271 2740 6.313905 AGCGTGACAGTAAAATTCAGATAAGG 59.686 38.462 0.00 0.00 0.00 2.69
1273 2742 6.402118 GCAGCGTGACAGTAAAATTCAGATAA 60.402 38.462 0.00 0.00 0.00 1.75
1274 2743 5.063438 GCAGCGTGACAGTAAAATTCAGATA 59.937 40.000 0.00 0.00 0.00 1.98
1377 2846 0.039035 GTTTGGGTCCATGTAGGGCA 59.961 55.000 0.00 0.00 46.80 5.36
1493 2962 4.124238 ACACAAAAGCGAGCAGTTTAGTA 58.876 39.130 0.00 0.00 0.00 1.82
1521 2991 3.304829 TGAAAAGGGGAAACAAGAAGGG 58.695 45.455 0.00 0.00 0.00 3.95
1647 3118 3.251479 ACTATGAAATGTGCTGCGAGA 57.749 42.857 0.00 0.00 0.00 4.04
1648 3119 3.371898 TCAACTATGAAATGTGCTGCGAG 59.628 43.478 0.00 0.00 30.99 5.03
1681 3158 4.015872 AGAGAAATTACTGCCGGAACAA 57.984 40.909 5.05 0.00 0.00 2.83
1682 3159 3.695830 AGAGAAATTACTGCCGGAACA 57.304 42.857 5.05 0.00 0.00 3.18
1707 3184 0.246757 CAAGCGGAATCGTCGTTTCG 60.247 55.000 9.35 6.86 38.89 3.46
1738 3239 2.487762 CACAAGCAGCTTATCGGGAAAA 59.512 45.455 7.52 0.00 0.00 2.29
1745 3246 4.130286 AGTACTCCACAAGCAGCTTATC 57.870 45.455 7.52 0.00 0.00 1.75
1923 3425 1.186200 CCATGGTGACCGAGAAGAGA 58.814 55.000 2.57 0.00 0.00 3.10
2382 3953 1.654105 CGACTTGTAGTTGGCGATGAC 59.346 52.381 0.00 0.00 0.00 3.06
2444 4032 4.851843 TGTTTCTCCATCTGATCATGCTT 58.148 39.130 0.00 0.00 0.00 3.91
2445 4033 4.452825 CTGTTTCTCCATCTGATCATGCT 58.547 43.478 0.00 0.00 0.00 3.79
2446 4034 3.564644 CCTGTTTCTCCATCTGATCATGC 59.435 47.826 0.00 0.00 0.00 4.06
2447 4035 5.032327 TCCTGTTTCTCCATCTGATCATG 57.968 43.478 0.00 0.00 0.00 3.07
2448 4036 4.720773 ACTCCTGTTTCTCCATCTGATCAT 59.279 41.667 0.00 0.00 0.00 2.45
2449 4037 4.099633 ACTCCTGTTTCTCCATCTGATCA 58.900 43.478 0.00 0.00 0.00 2.92
2450 4038 4.751767 ACTCCTGTTTCTCCATCTGATC 57.248 45.455 0.00 0.00 0.00 2.92
2476 4068 4.059459 CGCAACGCCGAGTCACAC 62.059 66.667 0.00 0.00 0.00 3.82
2495 4088 2.416027 CCCTACACACAGACACAGATCG 60.416 54.545 0.00 0.00 0.00 3.69
2723 4318 0.244994 AAGCATCGTCGAAGAGCAGT 59.755 50.000 18.84 8.42 36.95 4.40
2756 4351 4.261801 ACCCTGTTTGATTCATAAGTCCG 58.738 43.478 0.00 0.00 0.00 4.79
2757 4352 5.501156 AGACCCTGTTTGATTCATAAGTCC 58.499 41.667 0.00 0.00 0.00 3.85
2759 4354 8.960591 CAATAAGACCCTGTTTGATTCATAAGT 58.039 33.333 0.00 0.00 0.00 2.24
2760 4355 8.960591 ACAATAAGACCCTGTTTGATTCATAAG 58.039 33.333 0.00 0.00 0.00 1.73
2763 4358 9.125026 GATACAATAAGACCCTGTTTGATTCAT 57.875 33.333 0.00 0.00 0.00 2.57
2766 4361 8.328758 TGAGATACAATAAGACCCTGTTTGATT 58.671 33.333 0.00 0.00 0.00 2.57
2767 4362 7.861629 TGAGATACAATAAGACCCTGTTTGAT 58.138 34.615 0.00 0.00 0.00 2.57
2768 4363 7.180229 TCTGAGATACAATAAGACCCTGTTTGA 59.820 37.037 0.00 0.00 0.00 2.69
2769 4364 7.331026 TCTGAGATACAATAAGACCCTGTTTG 58.669 38.462 0.00 0.00 0.00 2.93
2770 4365 7.365117 CCTCTGAGATACAATAAGACCCTGTTT 60.365 40.741 6.17 0.00 0.00 2.83
2771 4366 6.098982 CCTCTGAGATACAATAAGACCCTGTT 59.901 42.308 6.17 0.00 0.00 3.16
2772 4367 5.600484 CCTCTGAGATACAATAAGACCCTGT 59.400 44.000 6.17 0.00 0.00 4.00
2773 4368 5.510520 GCCTCTGAGATACAATAAGACCCTG 60.511 48.000 6.17 0.00 0.00 4.45
2774 4369 4.591072 GCCTCTGAGATACAATAAGACCCT 59.409 45.833 6.17 0.00 0.00 4.34
2775 4370 4.591072 AGCCTCTGAGATACAATAAGACCC 59.409 45.833 6.17 0.00 0.00 4.46
2776 4371 5.069781 ACAGCCTCTGAGATACAATAAGACC 59.930 44.000 6.17 0.00 35.18 3.85
2777 4372 6.155475 ACAGCCTCTGAGATACAATAAGAC 57.845 41.667 6.17 0.00 35.18 3.01
2778 4373 6.155221 ACAACAGCCTCTGAGATACAATAAGA 59.845 38.462 6.17 0.00 35.18 2.10
2783 4378 4.563580 GGAACAACAGCCTCTGAGATACAA 60.564 45.833 6.17 0.00 35.18 2.41
2807 4405 2.154798 CTCTGCGGGAAGTCACGGAA 62.155 60.000 4.94 0.00 43.89 4.30
2815 4413 2.125912 CGGACACTCTGCGGGAAG 60.126 66.667 0.00 0.00 0.00 3.46
2823 4421 2.644555 AAACAGCACGCGGACACTCT 62.645 55.000 12.47 0.00 0.00 3.24
2850 4449 5.222631 CAAACTGAACAAATAGGACCAAGC 58.777 41.667 0.00 0.00 0.00 4.01
2878 4477 0.178068 GAAGCGTGGCTAGAATGGGA 59.822 55.000 0.00 0.00 38.25 4.37
2948 4559 6.979465 TCAACAATACTGCAATCATCAACAA 58.021 32.000 0.00 0.00 0.00 2.83
2949 4560 6.572167 TCAACAATACTGCAATCATCAACA 57.428 33.333 0.00 0.00 0.00 3.33
2970 4581 6.704493 AGTTGCTCTAACAAATTACGAGTTCA 59.296 34.615 0.00 0.00 41.88 3.18
2973 4584 6.456501 AGAGTTGCTCTAACAAATTACGAGT 58.543 36.000 0.00 0.00 39.28 4.18
2977 4588 6.237861 CGGCTAGAGTTGCTCTAACAAATTAC 60.238 42.308 7.22 0.00 41.74 1.89
2978 4589 5.810587 CGGCTAGAGTTGCTCTAACAAATTA 59.189 40.000 7.22 0.00 41.74 1.40
2979 4590 4.631813 CGGCTAGAGTTGCTCTAACAAATT 59.368 41.667 7.22 0.00 41.74 1.82
2980 4591 4.081642 TCGGCTAGAGTTGCTCTAACAAAT 60.082 41.667 7.22 0.00 41.74 2.32
2981 4592 3.257375 TCGGCTAGAGTTGCTCTAACAAA 59.743 43.478 7.22 0.00 41.74 2.83
2982 4593 2.823747 TCGGCTAGAGTTGCTCTAACAA 59.176 45.455 7.22 0.00 41.74 2.83
2983 4594 2.163815 GTCGGCTAGAGTTGCTCTAACA 59.836 50.000 7.22 0.00 41.74 2.41
2984 4595 2.479901 GGTCGGCTAGAGTTGCTCTAAC 60.480 54.545 7.22 3.33 41.74 2.34
3023 4634 2.886081 TGACTTGCAAATGCGTTTTGT 58.114 38.095 0.00 0.00 45.41 2.83
3054 4665 1.673009 CCGAGCCAGCCCGTAAAAA 60.673 57.895 0.00 0.00 0.00 1.94
3185 4796 5.508200 AGAATTACCGTTTTCTGTTTGCA 57.492 34.783 0.00 0.00 31.15 4.08
3201 4814 9.321562 GGAAACCTATGTCAAATACGAGAATTA 57.678 33.333 0.00 0.00 0.00 1.40
3252 4865 7.422878 TCATTTGCACGTAAACTGTGTTATA 57.577 32.000 0.00 0.00 39.53 0.98
3275 4889 3.128349 TGTCGTACTCAACTTGGCTTTC 58.872 45.455 0.00 0.00 0.00 2.62
3287 4901 3.362693 CCTCTTTTGCGTTTGTCGTACTC 60.363 47.826 0.00 0.00 42.13 2.59
3332 4946 0.824759 GACTAAGATGGTGCCGGACT 59.175 55.000 5.05 0.00 0.00 3.85
3348 4962 0.171455 GTGCGGAGTGAAGATCGACT 59.829 55.000 0.00 0.00 0.00 4.18
3378 4998 3.686726 GCGATGAACTTCAAGATGGACTT 59.313 43.478 0.00 0.00 39.70 3.01
3428 5048 2.725203 TTTCGGTGCGGGAGTTGGAG 62.725 60.000 0.00 0.00 0.00 3.86
3487 5108 2.100631 GTGCGCGCTACAGTTCCAT 61.101 57.895 33.29 0.00 0.00 3.41
3578 5200 3.080319 TCAATGAACCGCAATGACATGA 58.920 40.909 0.00 0.00 31.61 3.07
3714 5338 3.706086 AGGCAAAGGAGAAGCAAGAAAAA 59.294 39.130 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.