Multiple sequence alignment - TraesCS6A01G271600

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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 TraesCS6A01G271600 chr6A 100.000 3920 0 0 1 3920 498531852 498527933 0.000000e+00 7239.0
1 TraesCS6A01G271600 chr6D 94.157 3320 112 32 630 3920 355859843 355856577 0.000000e+00 4981.0
2 TraesCS6A01G271600 chr6D 88.158 456 31 7 176 612 355860399 355859948 4.490000e-144 521.0
3 TraesCS6A01G271600 chr6D 93.617 47 3 0 643 689 358433256 358433302 1.950000e-08 71.3
4 TraesCS6A01G271600 chr6B 93.937 3216 132 22 741 3904 536816838 536813634 0.000000e+00 4800.0
5 TraesCS6A01G271600 chr6B 93.617 47 3 0 643 689 86516835 86516881 1.950000e-08 71.3
6 TraesCS6A01G271600 chr2A 77.465 142 28 3 20 160 18883849 18883711 9.030000e-12 82.4
7 TraesCS6A01G271600 chr2A 95.745 47 2 0 643 689 569779416 569779370 4.200000e-10 76.8
8 TraesCS6A01G271600 chr2D 77.692 130 27 2 20 148 17467489 17467361 1.170000e-10 78.7
9 TraesCS6A01G271600 chr5B 95.745 47 2 0 643 689 125082904 125082950 4.200000e-10 76.8
10 TraesCS6A01G271600 chr5B 79.268 82 11 5 1543 1621 29337928 29338006 7.000000e-03 52.8
11 TraesCS6A01G271600 chr4D 85.915 71 7 2 643 712 24395761 24395829 5.430000e-09 73.1
12 TraesCS6A01G271600 chr4D 93.617 47 3 0 643 689 472750920 472750874 1.950000e-08 71.3
13 TraesCS6A01G271600 chr7D 93.617 47 3 0 643 689 442989008 442988962 1.950000e-08 71.3
14 TraesCS6A01G271600 chr1A 93.617 47 3 0 643 689 403320955 403321001 1.950000e-08 71.3
15 TraesCS6A01G271600 chr5D 81.818 88 10 4 1543 1627 38724308 38724392 7.030000e-08 69.4
16 TraesCS6A01G271600 chr5A 81.818 88 10 4 1543 1627 27516506 27516590 7.030000e-08 69.4


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 TraesCS6A01G271600 chr6A 498527933 498531852 3919 True 7239 7239 100.0000 1 3920 1 chr6A.!!$R1 3919
1 TraesCS6A01G271600 chr6D 355856577 355860399 3822 True 2751 4981 91.1575 176 3920 2 chr6D.!!$R1 3744
2 TraesCS6A01G271600 chr6B 536813634 536816838 3204 True 4800 4800 93.9370 741 3904 1 chr6B.!!$R1 3163

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
122 123 0.476771 TGGAGAGTGGTTTTGGGGAC 59.523 55.000 0.00 0.0 0.00 4.46 F
410 411 0.739561 AGACCGTTCGATGGCTACTC 59.260 55.000 4.23 0.0 0.00 2.59 F
792 899 0.949105 GTCGCTGTGATCCAACGGTT 60.949 55.000 0.00 0.0 33.51 4.44 F
1147 1273 1.218316 CCGAACCCCAGCTACAGAC 59.782 63.158 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1059 1185 0.393402 TCGGAGCATGAGCAGCATTT 60.393 50.000 0.00 0.00 45.49 2.32 R
1230 1356 1.016653 GGTGCTCTTCCGTCTCTTGC 61.017 60.000 0.00 0.00 0.00 4.01 R
1950 2088 2.967397 CCACCGAAGTCGCACCTA 59.033 61.111 0.00 0.00 38.18 3.08 R
2937 3075 0.606401 CGGAAACATCTGGCAGTGGT 60.606 55.000 15.27 10.98 0.00 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
20 21 3.719173 GAACGGAGGGAGTAGATGAAG 57.281 52.381 0.00 0.00 0.00 3.02
21 22 3.288964 GAACGGAGGGAGTAGATGAAGA 58.711 50.000 0.00 0.00 0.00 2.87
22 23 3.603965 ACGGAGGGAGTAGATGAAGAT 57.396 47.619 0.00 0.00 0.00 2.40
23 24 3.226777 ACGGAGGGAGTAGATGAAGATG 58.773 50.000 0.00 0.00 0.00 2.90
24 25 2.029470 CGGAGGGAGTAGATGAAGATGC 60.029 54.545 0.00 0.00 0.00 3.91
25 26 2.968574 GGAGGGAGTAGATGAAGATGCA 59.031 50.000 0.00 0.00 0.00 3.96
26 27 3.389329 GGAGGGAGTAGATGAAGATGCAA 59.611 47.826 0.00 0.00 0.00 4.08
27 28 4.141620 GGAGGGAGTAGATGAAGATGCAAA 60.142 45.833 0.00 0.00 0.00 3.68
28 29 5.455899 GGAGGGAGTAGATGAAGATGCAAAT 60.456 44.000 0.00 0.00 0.00 2.32
29 30 6.011122 AGGGAGTAGATGAAGATGCAAATT 57.989 37.500 0.00 0.00 0.00 1.82
30 31 6.430007 AGGGAGTAGATGAAGATGCAAATTT 58.570 36.000 0.00 0.00 0.00 1.82
31 32 6.320672 AGGGAGTAGATGAAGATGCAAATTTG 59.679 38.462 14.03 14.03 0.00 2.32
44 45 3.976468 CAAATTTGCATCGCGAAATGT 57.024 38.095 15.24 0.00 35.42 2.71
45 46 4.310675 CAAATTTGCATCGCGAAATGTT 57.689 36.364 15.24 0.59 35.42 2.71
46 47 3.976468 AATTTGCATCGCGAAATGTTG 57.024 38.095 15.24 7.74 35.42 3.33
47 48 2.414058 TTTGCATCGCGAAATGTTGT 57.586 40.000 15.24 0.00 0.00 3.32
48 49 3.544356 TTTGCATCGCGAAATGTTGTA 57.456 38.095 15.24 2.47 0.00 2.41
49 50 3.755965 TTGCATCGCGAAATGTTGTAT 57.244 38.095 15.24 0.00 0.00 2.29
50 51 3.755965 TGCATCGCGAAATGTTGTATT 57.244 38.095 15.24 0.00 0.00 1.89
51 52 4.090138 TGCATCGCGAAATGTTGTATTT 57.910 36.364 15.24 0.00 0.00 1.40
52 53 4.480541 TGCATCGCGAAATGTTGTATTTT 58.519 34.783 15.24 0.00 0.00 1.82
53 54 5.631992 TGCATCGCGAAATGTTGTATTTTA 58.368 33.333 15.24 0.00 0.00 1.52
54 55 5.509972 TGCATCGCGAAATGTTGTATTTTAC 59.490 36.000 15.24 0.00 0.00 2.01
55 56 5.509972 GCATCGCGAAATGTTGTATTTTACA 59.490 36.000 15.24 0.00 36.79 2.41
56 57 6.196353 GCATCGCGAAATGTTGTATTTTACAT 59.804 34.615 15.24 0.00 38.68 2.29
57 58 7.563296 GCATCGCGAAATGTTGTATTTTACATC 60.563 37.037 15.24 0.00 38.68 3.06
58 59 7.067532 TCGCGAAATGTTGTATTTTACATCT 57.932 32.000 6.20 0.00 38.68 2.90
59 60 7.177407 TCGCGAAATGTTGTATTTTACATCTC 58.823 34.615 6.20 0.00 38.68 2.75
60 61 6.410914 CGCGAAATGTTGTATTTTACATCTCC 59.589 38.462 0.00 0.00 38.68 3.71
61 62 6.410914 GCGAAATGTTGTATTTTACATCTCCG 59.589 38.462 0.00 0.00 38.68 4.63
62 63 6.905076 CGAAATGTTGTATTTTACATCTCCGG 59.095 38.462 0.00 0.00 38.68 5.14
63 64 7.201574 CGAAATGTTGTATTTTACATCTCCGGA 60.202 37.037 2.93 2.93 38.68 5.14
64 65 7.931578 AATGTTGTATTTTACATCTCCGGAA 57.068 32.000 5.23 0.00 38.68 4.30
65 66 6.978343 TGTTGTATTTTACATCTCCGGAAG 57.022 37.500 5.23 0.46 38.68 3.46
66 67 5.878116 TGTTGTATTTTACATCTCCGGAAGG 59.122 40.000 5.23 0.83 45.94 3.46
67 68 5.687166 TGTATTTTACATCTCCGGAAGGT 57.313 39.130 5.23 7.37 42.76 3.50
68 69 6.057321 TGTATTTTACATCTCCGGAAGGTT 57.943 37.500 5.23 0.00 42.76 3.50
69 70 5.878116 TGTATTTTACATCTCCGGAAGGTTG 59.122 40.000 5.23 2.77 42.76 3.77
70 71 6.295973 TGTATTTTACATCTCCGGAAGGTTGA 60.296 38.462 5.23 0.00 42.76 3.18
71 72 8.061237 TGTATTTTACATCTCCGGAAGGTTGAG 61.061 40.741 5.23 0.00 42.76 3.02
82 83 5.447624 CGGAAGGTTGAGGTGTAATTTTT 57.552 39.130 0.00 0.00 0.00 1.94
110 111 9.593565 TTATATCTACATCATCTGTTGGAGAGT 57.406 33.333 8.68 3.99 37.92 3.24
111 112 5.588958 TCTACATCATCTGTTGGAGAGTG 57.411 43.478 0.00 0.00 39.39 3.51
112 113 3.623906 ACATCATCTGTTGGAGAGTGG 57.376 47.619 0.00 0.00 32.90 4.00
113 114 2.909006 ACATCATCTGTTGGAGAGTGGT 59.091 45.455 0.00 0.00 32.90 4.16
114 115 3.328931 ACATCATCTGTTGGAGAGTGGTT 59.671 43.478 0.00 0.00 32.90 3.67
115 116 4.202503 ACATCATCTGTTGGAGAGTGGTTT 60.203 41.667 0.00 0.00 32.90 3.27
116 117 4.437682 TCATCTGTTGGAGAGTGGTTTT 57.562 40.909 0.00 0.00 32.80 2.43
117 118 4.136796 TCATCTGTTGGAGAGTGGTTTTG 58.863 43.478 0.00 0.00 32.80 2.44
118 119 2.930950 TCTGTTGGAGAGTGGTTTTGG 58.069 47.619 0.00 0.00 0.00 3.28
119 120 1.956477 CTGTTGGAGAGTGGTTTTGGG 59.044 52.381 0.00 0.00 0.00 4.12
120 121 1.328279 GTTGGAGAGTGGTTTTGGGG 58.672 55.000 0.00 0.00 0.00 4.96
121 122 1.133606 GTTGGAGAGTGGTTTTGGGGA 60.134 52.381 0.00 0.00 0.00 4.81
122 123 0.476771 TGGAGAGTGGTTTTGGGGAC 59.523 55.000 0.00 0.00 0.00 4.46
123 124 0.771755 GGAGAGTGGTTTTGGGGACT 59.228 55.000 0.00 0.00 0.00 3.85
124 125 1.271434 GGAGAGTGGTTTTGGGGACTC 60.271 57.143 0.00 0.00 35.97 3.36
125 126 1.420138 GAGAGTGGTTTTGGGGACTCA 59.580 52.381 0.00 0.00 37.83 3.41
126 127 1.421646 AGAGTGGTTTTGGGGACTCAG 59.578 52.381 0.00 0.00 37.83 3.35
127 128 1.420138 GAGTGGTTTTGGGGACTCAGA 59.580 52.381 0.00 0.00 35.82 3.27
128 129 1.850345 AGTGGTTTTGGGGACTCAGAA 59.150 47.619 0.00 0.00 0.00 3.02
129 130 2.158608 AGTGGTTTTGGGGACTCAGAAG 60.159 50.000 0.00 0.00 0.00 2.85
130 131 1.850345 TGGTTTTGGGGACTCAGAAGT 59.150 47.619 0.00 0.00 38.88 3.01
131 132 2.230660 GGTTTTGGGGACTCAGAAGTG 58.769 52.381 0.00 0.00 35.28 3.16
132 133 2.158667 GGTTTTGGGGACTCAGAAGTGA 60.159 50.000 0.00 0.00 35.28 3.41
133 134 3.551846 GTTTTGGGGACTCAGAAGTGAA 58.448 45.455 0.00 0.00 35.28 3.18
134 135 3.943671 TTTGGGGACTCAGAAGTGAAA 57.056 42.857 0.00 0.00 35.28 2.69
135 136 3.943671 TTGGGGACTCAGAAGTGAAAA 57.056 42.857 0.00 0.00 35.28 2.29
136 137 3.943671 TGGGGACTCAGAAGTGAAAAA 57.056 42.857 0.00 0.00 35.28 1.94
189 190 7.042797 ACCAAAGCATGTAATTTATAGCAGG 57.957 36.000 0.00 0.00 0.00 4.85
193 194 7.502120 AAGCATGTAATTTATAGCAGGACTG 57.498 36.000 0.00 0.00 0.00 3.51
216 217 2.618709 ACAGTTGCCTAGCACTTCAAAC 59.381 45.455 0.00 0.00 38.71 2.93
227 228 4.104776 AGCACTTCAAACGAAATTGTGTG 58.895 39.130 0.00 7.05 38.06 3.82
233 234 2.834574 AACGAAATTGTGTGAACGCA 57.165 40.000 0.00 0.00 34.11 5.24
245 246 1.285950 GAACGCACCCTTTCCAAGC 59.714 57.895 0.00 0.00 0.00 4.01
250 251 1.648467 GCACCCTTTCCAAGCTAGCG 61.648 60.000 9.55 0.00 0.00 4.26
263 264 3.127425 AGCTAGCGACTTGAAAACCTT 57.873 42.857 9.55 0.00 0.00 3.50
264 265 3.067833 AGCTAGCGACTTGAAAACCTTC 58.932 45.455 9.55 0.00 0.00 3.46
268 269 2.018717 CGACTTGAAAACCTTCGCAC 57.981 50.000 0.00 0.00 33.94 5.34
269 270 1.597663 CGACTTGAAAACCTTCGCACT 59.402 47.619 0.00 0.00 33.94 4.40
270 271 2.031683 CGACTTGAAAACCTTCGCACTT 59.968 45.455 0.00 0.00 33.94 3.16
274 275 4.157840 ACTTGAAAACCTTCGCACTTCTTT 59.842 37.500 0.00 0.00 33.94 2.52
285 286 5.295431 TCGCACTTCTTTTTCATACATGG 57.705 39.130 0.00 0.00 0.00 3.66
291 292 6.430925 CACTTCTTTTTCATACATGGTCCAGA 59.569 38.462 0.00 0.00 0.00 3.86
301 302 3.240670 TGGTCCAGACACCAGTTCT 57.759 52.632 0.00 0.00 41.84 3.01
341 342 9.775854 ATCTTCCTAGATCACATCAACAATAAG 57.224 33.333 0.00 0.00 36.34 1.73
342 343 8.762645 TCTTCCTAGATCACATCAACAATAAGT 58.237 33.333 0.00 0.00 0.00 2.24
399 400 1.342174 TGTTGGGAGTGTAGACCGTTC 59.658 52.381 0.00 0.00 0.00 3.95
410 411 0.739561 AGACCGTTCGATGGCTACTC 59.260 55.000 4.23 0.00 0.00 2.59
426 427 4.333926 GGCTACTCACAAATTCACCATCTC 59.666 45.833 0.00 0.00 0.00 2.75
431 432 4.326826 TCACAAATTCACCATCTCAGTCC 58.673 43.478 0.00 0.00 0.00 3.85
480 481 2.706890 TCGGGCCAAAAGAAGTATGAC 58.293 47.619 4.39 0.00 0.00 3.06
482 483 3.016736 CGGGCCAAAAGAAGTATGACAT 58.983 45.455 4.39 0.00 0.00 3.06
483 484 3.065371 CGGGCCAAAAGAAGTATGACATC 59.935 47.826 4.39 0.00 0.00 3.06
484 485 4.016444 GGGCCAAAAGAAGTATGACATCA 58.984 43.478 4.39 0.00 0.00 3.07
492 512 9.695526 CAAAAGAAGTATGACATCAAAAATCCA 57.304 29.630 0.00 0.00 0.00 3.41
592 612 1.676006 GGCGAACCCAATCACCTAATG 59.324 52.381 0.00 0.00 0.00 1.90
595 615 3.683281 GCGAACCCAATCACCTAATGGTA 60.683 47.826 0.00 0.00 46.60 3.25
599 619 6.239487 CGAACCCAATCACCTAATGGTATCTA 60.239 42.308 0.00 0.00 46.60 1.98
603 623 7.778382 ACCCAATCACCTAATGGTATCTAAAAC 59.222 37.037 0.00 0.00 46.60 2.43
618 638 9.959749 GGTATCTAAAACTTGATGAAACACAAA 57.040 29.630 0.00 0.00 0.00 2.83
664 771 9.387123 CTAACAACTCTAGTTCATTTTTCTTGC 57.613 33.333 0.00 0.00 35.83 4.01
750 857 1.169661 CCAAACACCCTAGCGCAACA 61.170 55.000 11.47 0.00 0.00 3.33
792 899 0.949105 GTCGCTGTGATCCAACGGTT 60.949 55.000 0.00 0.00 33.51 4.44
892 999 2.646930 AGCATAGCATACAAGCAGCAA 58.353 42.857 0.00 0.00 36.85 3.91
918 1026 2.967076 AGCGTGCGAACTGGTGTG 60.967 61.111 0.00 0.00 0.00 3.82
953 1079 6.086871 GCTACTCAACAAAGAAATTGCTACC 58.913 40.000 0.00 0.00 43.13 3.18
1059 1185 1.271840 ATCTCTACCCCGCCAAAGCA 61.272 55.000 0.00 0.00 39.83 3.91
1147 1273 1.218316 CCGAACCCCAGCTACAGAC 59.782 63.158 0.00 0.00 0.00 3.51
1315 1441 2.048222 CGAGAACGAGCAGGGCAA 60.048 61.111 0.00 0.00 42.66 4.52
1950 2088 3.681835 GAGGTGACCACGCTCGGT 61.682 66.667 3.63 0.00 43.91 4.69
2547 2685 3.645268 GATCAACCCGGGCTGCCTT 62.645 63.158 24.08 3.28 0.00 4.35
2890 3028 3.598715 ACGGCCTGTTCGTCACGA 61.599 61.111 0.00 0.00 35.87 4.35
2913 3051 2.581354 GAGCTCCGGTCACAGCAT 59.419 61.111 14.64 0.87 38.18 3.79
2933 3071 5.707764 AGCATCAATGATCATCAGATTCAGG 59.292 40.000 9.06 5.48 33.72 3.86
2937 3075 3.918294 TGATCATCAGATTCAGGCACA 57.082 42.857 0.00 0.00 33.72 4.57
2941 3079 1.741706 CATCAGATTCAGGCACACCAC 59.258 52.381 0.00 0.00 39.06 4.16
2942 3080 1.059098 TCAGATTCAGGCACACCACT 58.941 50.000 0.00 0.00 39.06 4.00
2943 3081 1.162698 CAGATTCAGGCACACCACTG 58.837 55.000 0.00 0.00 39.06 3.66
2963 3103 1.063006 CAGATGTTTCCGCGCCATG 59.937 57.895 0.00 0.00 0.00 3.66
2969 3109 1.377856 TTTCCGCGCCATGGATTGA 60.378 52.632 18.40 2.48 34.91 2.57
2970 3110 0.751277 TTTCCGCGCCATGGATTGAT 60.751 50.000 18.40 0.00 34.91 2.57
3048 3189 4.287067 GGATCCCATGACATACACATAGGT 59.713 45.833 0.00 0.00 30.74 3.08
3080 3222 7.992608 TGGTATCTCATGTGTAGCATTTACATT 59.007 33.333 0.00 0.00 35.19 2.71
3152 3300 2.228822 AGCCTGGAAAATACTTGCAACG 59.771 45.455 0.00 0.00 0.00 4.10
3156 3304 2.359214 TGGAAAATACTTGCAACGCACA 59.641 40.909 0.00 0.00 38.71 4.57
3215 3363 6.088824 AGTACGAAACAAGGTATGAACTACG 58.911 40.000 0.00 0.00 0.00 3.51
3228 3378 5.707242 ATGAACTACGAGAACTTCACAGA 57.293 39.130 0.00 0.00 0.00 3.41
3269 3421 6.821160 TCTCTCAAAGTTTTACACACATGACA 59.179 34.615 0.00 0.00 0.00 3.58
3332 3484 7.123847 AGGGATTTCACGGGATATACATACTAC 59.876 40.741 2.58 0.00 0.00 2.73
3380 3535 8.217799 AGCTACCTTGCATTTGGTTATAGAATA 58.782 33.333 11.02 0.00 37.74 1.75
3399 3554 7.747155 AGAATAATCAATTCAGCATCCTCAG 57.253 36.000 1.01 0.00 45.58 3.35
3402 3557 3.708403 TCAATTCAGCATCCTCAGTGT 57.292 42.857 0.00 0.00 0.00 3.55
3403 3558 3.340928 TCAATTCAGCATCCTCAGTGTG 58.659 45.455 0.00 0.00 0.00 3.82
3411 3566 2.160417 GCATCCTCAGTGTGTTGTTAGC 59.840 50.000 0.00 0.00 0.00 3.09
3424 3579 5.212934 GTGTTGTTAGCCTAGAAAAACAGC 58.787 41.667 0.00 1.51 33.70 4.40
3500 3655 7.070447 AGGTATGAGAGTATGATTTTCTGCAGA 59.930 37.037 13.74 13.74 0.00 4.26
3501 3656 7.384660 GGTATGAGAGTATGATTTTCTGCAGAG 59.615 40.741 17.43 0.00 0.00 3.35
3601 3756 7.009907 GCATTCTGTATTTTTCCTCATCAAAGC 59.990 37.037 0.00 0.00 0.00 3.51
3606 3761 7.541162 TGTATTTTTCCTCATCAAAGCAGATG 58.459 34.615 7.30 7.30 45.28 2.90
3659 3825 3.433343 AGATTCATGTGGCACATTCCAA 58.567 40.909 29.57 21.25 44.52 3.53
3776 3942 1.338200 GGTACTCCAGTGGCAGTCAAG 60.338 57.143 15.02 4.90 0.00 3.02
3880 4046 7.599621 CAGAGCAGATTATACCTCAGATCAAAG 59.400 40.741 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.288964 TCTTCATCTACTCCCTCCGTTC 58.711 50.000 0.00 0.00 0.00 3.95
1 2 3.383698 TCTTCATCTACTCCCTCCGTT 57.616 47.619 0.00 0.00 0.00 4.44
2 3 3.226777 CATCTTCATCTACTCCCTCCGT 58.773 50.000 0.00 0.00 0.00 4.69
3 4 2.029470 GCATCTTCATCTACTCCCTCCG 60.029 54.545 0.00 0.00 0.00 4.63
4 5 2.968574 TGCATCTTCATCTACTCCCTCC 59.031 50.000 0.00 0.00 0.00 4.30
5 6 4.679373 TTGCATCTTCATCTACTCCCTC 57.321 45.455 0.00 0.00 0.00 4.30
6 7 5.643421 ATTTGCATCTTCATCTACTCCCT 57.357 39.130 0.00 0.00 0.00 4.20
7 8 6.501781 CAAATTTGCATCTTCATCTACTCCC 58.498 40.000 5.01 0.00 0.00 4.30
24 25 3.976468 ACATTTCGCGATGCAAATTTG 57.024 38.095 10.88 14.03 0.00 2.32
25 26 3.740321 ACAACATTTCGCGATGCAAATTT 59.260 34.783 10.88 0.00 0.00 1.82
26 27 3.316283 ACAACATTTCGCGATGCAAATT 58.684 36.364 10.88 0.00 0.00 1.82
27 28 2.945278 ACAACATTTCGCGATGCAAAT 58.055 38.095 10.88 3.31 0.00 2.32
28 29 2.414058 ACAACATTTCGCGATGCAAA 57.586 40.000 10.88 0.25 0.00 3.68
29 30 3.755965 ATACAACATTTCGCGATGCAA 57.244 38.095 10.88 0.72 0.00 4.08
30 31 3.755965 AATACAACATTTCGCGATGCA 57.244 38.095 10.88 0.00 0.00 3.96
31 32 5.509972 TGTAAAATACAACATTTCGCGATGC 59.490 36.000 10.88 0.00 35.38 3.91
32 33 7.639850 AGATGTAAAATACAACATTTCGCGATG 59.360 33.333 10.88 9.25 42.76 3.84
33 34 7.693952 AGATGTAAAATACAACATTTCGCGAT 58.306 30.769 10.88 0.00 42.76 4.58
34 35 7.067532 AGATGTAAAATACAACATTTCGCGA 57.932 32.000 3.71 3.71 42.76 5.87
35 36 6.410914 GGAGATGTAAAATACAACATTTCGCG 59.589 38.462 0.00 0.00 42.76 5.87
36 37 6.410914 CGGAGATGTAAAATACAACATTTCGC 59.589 38.462 0.00 0.00 42.76 4.70
37 38 6.905076 CCGGAGATGTAAAATACAACATTTCG 59.095 38.462 0.00 0.00 42.76 3.46
38 39 7.981142 TCCGGAGATGTAAAATACAACATTTC 58.019 34.615 0.00 0.00 42.76 2.17
39 40 7.931578 TCCGGAGATGTAAAATACAACATTT 57.068 32.000 0.00 0.00 42.76 2.32
40 41 7.067008 CCTTCCGGAGATGTAAAATACAACATT 59.933 37.037 3.34 0.00 42.76 2.71
41 42 6.542370 CCTTCCGGAGATGTAAAATACAACAT 59.458 38.462 3.34 0.00 42.76 2.71
42 43 5.878116 CCTTCCGGAGATGTAAAATACAACA 59.122 40.000 3.34 0.00 42.76 3.33
43 44 5.878669 ACCTTCCGGAGATGTAAAATACAAC 59.121 40.000 3.34 0.00 42.76 3.32
44 45 6.057321 ACCTTCCGGAGATGTAAAATACAA 57.943 37.500 3.34 0.00 42.76 2.41
45 46 5.687166 ACCTTCCGGAGATGTAAAATACA 57.313 39.130 3.34 0.00 43.80 2.29
46 47 6.110707 TCAACCTTCCGGAGATGTAAAATAC 58.889 40.000 3.34 0.00 0.00 1.89
47 48 6.302535 TCAACCTTCCGGAGATGTAAAATA 57.697 37.500 3.34 0.00 0.00 1.40
48 49 5.174037 TCAACCTTCCGGAGATGTAAAAT 57.826 39.130 3.34 0.00 0.00 1.82
49 50 4.564821 CCTCAACCTTCCGGAGATGTAAAA 60.565 45.833 3.34 0.00 0.00 1.52
50 51 3.055385 CCTCAACCTTCCGGAGATGTAAA 60.055 47.826 3.34 0.00 0.00 2.01
51 52 2.500098 CCTCAACCTTCCGGAGATGTAA 59.500 50.000 3.34 0.00 0.00 2.41
52 53 2.108168 CCTCAACCTTCCGGAGATGTA 58.892 52.381 3.34 0.00 0.00 2.29
53 54 0.905357 CCTCAACCTTCCGGAGATGT 59.095 55.000 3.34 0.00 0.00 3.06
54 55 0.905357 ACCTCAACCTTCCGGAGATG 59.095 55.000 3.34 0.00 0.00 2.90
55 56 0.905357 CACCTCAACCTTCCGGAGAT 59.095 55.000 3.34 0.00 0.00 2.75
56 57 0.471211 ACACCTCAACCTTCCGGAGA 60.471 55.000 3.34 0.00 0.00 3.71
57 58 1.263356 TACACCTCAACCTTCCGGAG 58.737 55.000 3.34 0.00 0.00 4.63
58 59 1.719529 TTACACCTCAACCTTCCGGA 58.280 50.000 0.00 0.00 0.00 5.14
59 60 2.781681 ATTACACCTCAACCTTCCGG 57.218 50.000 0.00 0.00 0.00 5.14
60 61 5.447624 AAAAATTACACCTCAACCTTCCG 57.552 39.130 0.00 0.00 0.00 4.30
84 85 9.593565 ACTCTCCAACAGATGATGTAGATATAA 57.406 33.333 0.00 0.00 43.00 0.98
85 86 9.018582 CACTCTCCAACAGATGATGTAGATATA 57.981 37.037 0.00 0.00 43.00 0.86
86 87 7.039152 CCACTCTCCAACAGATGATGTAGATAT 60.039 40.741 0.00 0.00 43.00 1.63
87 88 6.266330 CCACTCTCCAACAGATGATGTAGATA 59.734 42.308 0.00 0.00 43.00 1.98
88 89 5.070180 CCACTCTCCAACAGATGATGTAGAT 59.930 44.000 0.00 0.00 43.00 1.98
89 90 4.403752 CCACTCTCCAACAGATGATGTAGA 59.596 45.833 0.00 0.00 43.00 2.59
90 91 4.161189 ACCACTCTCCAACAGATGATGTAG 59.839 45.833 0.00 0.00 43.00 2.74
91 92 4.096681 ACCACTCTCCAACAGATGATGTA 58.903 43.478 0.00 0.00 43.00 2.29
92 93 2.909006 ACCACTCTCCAACAGATGATGT 59.091 45.455 0.00 0.00 46.97 3.06
93 94 3.623906 ACCACTCTCCAACAGATGATG 57.376 47.619 0.00 0.00 0.00 3.07
94 95 4.647564 AAACCACTCTCCAACAGATGAT 57.352 40.909 0.00 0.00 0.00 2.45
95 96 4.136796 CAAAACCACTCTCCAACAGATGA 58.863 43.478 0.00 0.00 0.00 2.92
96 97 3.254166 CCAAAACCACTCTCCAACAGATG 59.746 47.826 0.00 0.00 0.00 2.90
97 98 3.490348 CCAAAACCACTCTCCAACAGAT 58.510 45.455 0.00 0.00 0.00 2.90
98 99 2.422803 CCCAAAACCACTCTCCAACAGA 60.423 50.000 0.00 0.00 0.00 3.41
99 100 1.956477 CCCAAAACCACTCTCCAACAG 59.044 52.381 0.00 0.00 0.00 3.16
100 101 1.410932 CCCCAAAACCACTCTCCAACA 60.411 52.381 0.00 0.00 0.00 3.33
101 102 1.133606 TCCCCAAAACCACTCTCCAAC 60.134 52.381 0.00 0.00 0.00 3.77
102 103 1.133606 GTCCCCAAAACCACTCTCCAA 60.134 52.381 0.00 0.00 0.00 3.53
103 104 0.476771 GTCCCCAAAACCACTCTCCA 59.523 55.000 0.00 0.00 0.00 3.86
104 105 0.771755 AGTCCCCAAAACCACTCTCC 59.228 55.000 0.00 0.00 0.00 3.71
105 106 1.420138 TGAGTCCCCAAAACCACTCTC 59.580 52.381 0.00 0.00 36.91 3.20
106 107 1.421646 CTGAGTCCCCAAAACCACTCT 59.578 52.381 0.00 0.00 36.91 3.24
107 108 1.420138 TCTGAGTCCCCAAAACCACTC 59.580 52.381 0.00 0.00 36.57 3.51
108 109 1.518367 TCTGAGTCCCCAAAACCACT 58.482 50.000 0.00 0.00 0.00 4.00
109 110 2.230660 CTTCTGAGTCCCCAAAACCAC 58.769 52.381 0.00 0.00 0.00 4.16
110 111 1.850345 ACTTCTGAGTCCCCAAAACCA 59.150 47.619 0.00 0.00 0.00 3.67
111 112 2.158667 TCACTTCTGAGTCCCCAAAACC 60.159 50.000 0.00 0.00 32.54 3.27
112 113 3.208747 TCACTTCTGAGTCCCCAAAAC 57.791 47.619 0.00 0.00 32.54 2.43
113 114 3.943671 TTCACTTCTGAGTCCCCAAAA 57.056 42.857 0.00 0.00 32.54 2.44
114 115 3.943671 TTTCACTTCTGAGTCCCCAAA 57.056 42.857 0.00 0.00 32.54 3.28
115 116 3.943671 TTTTCACTTCTGAGTCCCCAA 57.056 42.857 0.00 0.00 32.54 4.12
116 117 3.943671 TTTTTCACTTCTGAGTCCCCA 57.056 42.857 0.00 0.00 32.54 4.96
150 151 8.660435 ACATGCTTTGGTTATAGGTAGATGTAT 58.340 33.333 0.00 0.00 0.00 2.29
151 152 8.029782 ACATGCTTTGGTTATAGGTAGATGTA 57.970 34.615 0.00 0.00 0.00 2.29
152 153 6.900194 ACATGCTTTGGTTATAGGTAGATGT 58.100 36.000 0.00 0.00 0.00 3.06
153 154 8.902540 TTACATGCTTTGGTTATAGGTAGATG 57.097 34.615 0.00 0.00 0.00 2.90
155 156 9.914834 AAATTACATGCTTTGGTTATAGGTAGA 57.085 29.630 0.00 0.00 0.00 2.59
163 164 8.629158 CCTGCTATAAATTACATGCTTTGGTTA 58.371 33.333 0.00 0.00 0.00 2.85
164 165 7.341769 TCCTGCTATAAATTACATGCTTTGGTT 59.658 33.333 0.00 0.00 0.00 3.67
165 166 6.833416 TCCTGCTATAAATTACATGCTTTGGT 59.167 34.615 0.00 0.00 0.00 3.67
166 167 7.013655 AGTCCTGCTATAAATTACATGCTTTGG 59.986 37.037 0.00 0.00 0.00 3.28
167 168 7.859377 CAGTCCTGCTATAAATTACATGCTTTG 59.141 37.037 0.00 0.00 0.00 2.77
168 169 7.013655 CCAGTCCTGCTATAAATTACATGCTTT 59.986 37.037 0.00 0.00 0.00 3.51
169 170 6.488006 CCAGTCCTGCTATAAATTACATGCTT 59.512 38.462 0.00 0.00 0.00 3.91
170 171 6.000219 CCAGTCCTGCTATAAATTACATGCT 59.000 40.000 0.00 0.00 0.00 3.79
171 172 5.997746 TCCAGTCCTGCTATAAATTACATGC 59.002 40.000 0.00 0.00 0.00 4.06
172 173 6.992123 TGTCCAGTCCTGCTATAAATTACATG 59.008 38.462 0.00 0.00 0.00 3.21
173 174 7.136822 TGTCCAGTCCTGCTATAAATTACAT 57.863 36.000 0.00 0.00 0.00 2.29
174 175 6.156256 ACTGTCCAGTCCTGCTATAAATTACA 59.844 38.462 0.00 0.00 36.92 2.41
216 217 1.394697 GGTGCGTTCACACAATTTCG 58.605 50.000 0.00 0.00 44.87 3.46
227 228 1.172812 AGCTTGGAAAGGGTGCGTTC 61.173 55.000 0.00 0.00 46.35 3.95
233 234 0.036294 GTCGCTAGCTTGGAAAGGGT 60.036 55.000 13.93 0.00 46.35 4.34
245 246 3.706994 CGAAGGTTTTCAAGTCGCTAG 57.293 47.619 0.00 0.00 32.67 3.42
250 251 3.312697 AGAAGTGCGAAGGTTTTCAAGTC 59.687 43.478 0.00 0.00 32.67 3.01
263 264 4.759693 ACCATGTATGAAAAAGAAGTGCGA 59.240 37.500 0.00 0.00 0.00 5.10
264 265 5.046910 ACCATGTATGAAAAAGAAGTGCG 57.953 39.130 0.00 0.00 0.00 5.34
268 269 6.430925 TGTCTGGACCATGTATGAAAAAGAAG 59.569 38.462 0.00 0.00 0.00 2.85
269 270 6.206634 GTGTCTGGACCATGTATGAAAAAGAA 59.793 38.462 0.00 0.00 0.00 2.52
270 271 5.705441 GTGTCTGGACCATGTATGAAAAAGA 59.295 40.000 0.00 0.00 0.00 2.52
274 275 3.329225 TGGTGTCTGGACCATGTATGAAA 59.671 43.478 0.00 0.00 41.30 2.69
285 286 2.526432 TCCTAGAACTGGTGTCTGGAC 58.474 52.381 0.00 0.00 0.00 4.02
291 292 9.084533 GATAAGATAGAATCCTAGAACTGGTGT 57.915 37.037 0.00 0.00 0.00 4.16
384 385 1.202268 CCATCGAACGGTCTACACTCC 60.202 57.143 0.00 0.00 0.00 3.85
399 400 3.063997 GGTGAATTTGTGAGTAGCCATCG 59.936 47.826 0.00 0.00 0.00 3.84
410 411 4.330250 AGGACTGAGATGGTGAATTTGTG 58.670 43.478 0.00 0.00 0.00 3.33
426 427 0.543749 GAGGGTCATTGGGAGGACTG 59.456 60.000 0.00 0.00 36.82 3.51
431 432 1.635487 TCTTTGGAGGGTCATTGGGAG 59.365 52.381 0.00 0.00 0.00 4.30
492 512 6.998968 TTCATCAAATTGTGCCAAAACTTT 57.001 29.167 0.00 0.00 0.00 2.66
562 582 0.391927 TGGGTTCGCCGGAATTACAG 60.392 55.000 5.05 0.00 38.45 2.74
565 585 1.065345 TGATTGGGTTCGCCGGAATTA 60.065 47.619 5.05 0.00 38.45 1.40
592 612 9.959749 TTTGTGTTTCATCAAGTTTTAGATACC 57.040 29.630 0.00 0.00 0.00 2.73
639 746 8.349983 GGCAAGAAAAATGAACTAGAGTTGTTA 58.650 33.333 0.00 0.00 38.56 2.41
664 771 2.231964 CCCATGAGTTGGTCAACAATGG 59.768 50.000 25.52 25.52 46.41 3.16
750 857 2.881403 GCACAATGTGGGAGGATGAAGT 60.881 50.000 15.78 0.00 33.64 3.01
871 978 3.473923 TGCTGCTTGTATGCTATGCTA 57.526 42.857 0.00 0.00 0.00 3.49
872 979 2.336945 TGCTGCTTGTATGCTATGCT 57.663 45.000 0.00 0.00 0.00 3.79
873 980 3.425577 TTTGCTGCTTGTATGCTATGC 57.574 42.857 0.00 0.00 0.00 3.14
874 981 4.357142 CCTTTTGCTGCTTGTATGCTATG 58.643 43.478 0.00 0.00 0.00 2.23
875 982 3.181483 GCCTTTTGCTGCTTGTATGCTAT 60.181 43.478 0.00 0.00 36.87 2.97
900 1008 2.967076 ACACCAGTTCGCACGCTG 60.967 61.111 0.00 0.00 0.00 5.18
918 1026 1.136224 GTTGAGTAGCAGCAAACGCTC 60.136 52.381 0.00 0.00 40.96 5.03
953 1079 3.881688 CTCTTTGGATTGCTAGTGGATGG 59.118 47.826 0.00 0.00 0.00 3.51
1059 1185 0.393402 TCGGAGCATGAGCAGCATTT 60.393 50.000 0.00 0.00 45.49 2.32
1147 1273 4.796231 CGACGTGCCCTTCCTCCG 62.796 72.222 0.00 0.00 0.00 4.63
1230 1356 1.016653 GGTGCTCTTCCGTCTCTTGC 61.017 60.000 0.00 0.00 0.00 4.01
1266 1392 2.946329 TCGTGTACCAGTTGCATTGTTT 59.054 40.909 0.00 0.00 0.00 2.83
1950 2088 2.967397 CCACCGAAGTCGCACCTA 59.033 61.111 0.00 0.00 38.18 3.08
2913 3051 4.820173 GTGCCTGAATCTGATGATCATTGA 59.180 41.667 10.14 11.66 31.51 2.57
2933 3071 1.174712 AACATCTGGCAGTGGTGTGC 61.175 55.000 15.27 0.00 43.19 4.57
2937 3075 0.606401 CGGAAACATCTGGCAGTGGT 60.606 55.000 15.27 10.98 0.00 4.16
2941 3079 2.787249 CGCGGAAACATCTGGCAG 59.213 61.111 8.58 8.58 0.00 4.85
2942 3080 3.430862 GCGCGGAAACATCTGGCA 61.431 61.111 8.83 0.00 0.00 4.92
2943 3081 4.179579 GGCGCGGAAACATCTGGC 62.180 66.667 8.83 0.00 0.00 4.85
2945 3083 1.063006 CATGGCGCGGAAACATCTG 59.937 57.895 8.83 0.00 0.00 2.90
2946 3084 2.114670 CCATGGCGCGGAAACATCT 61.115 57.895 8.83 0.00 0.00 2.90
2963 3103 1.350193 ATACATCGCGCGATCAATCC 58.650 50.000 40.03 0.00 31.62 3.01
2969 3109 5.499935 GTCTACTATTATACATCGCGCGAT 58.500 41.667 37.68 37.68 34.81 4.58
2970 3110 4.201753 GGTCTACTATTATACATCGCGCGA 60.202 45.833 36.65 36.65 0.00 5.87
3048 3189 6.413892 TGCTACACATGAGATACCAATTTCA 58.586 36.000 0.00 0.00 31.37 2.69
3054 3195 6.883744 TGTAAATGCTACACATGAGATACCA 58.116 36.000 0.00 0.00 39.60 3.25
3080 3222 8.665643 TTCACCGATAGTTCTTTCTTGTAAAA 57.334 30.769 0.00 0.00 0.00 1.52
3099 3241 2.552315 ACTGCAGGTATGTTTTTCACCG 59.448 45.455 19.93 0.00 37.42 4.94
3152 3300 1.035932 ATTCTGCAGGCTGGATGTGC 61.036 55.000 17.64 1.38 37.73 4.57
3215 3363 8.085296 TGAAACTCTCTTATCTGTGAAGTTCTC 58.915 37.037 4.17 0.83 0.00 2.87
3269 3421 6.239217 TGTATGAACTCTGTAGCCATTGAT 57.761 37.500 0.00 0.00 0.00 2.57
3332 3484 1.726791 CACCGACTTCGTGAAATCCAG 59.273 52.381 0.00 0.00 37.74 3.86
3380 3535 4.398358 CACACTGAGGATGCTGAATTGATT 59.602 41.667 0.00 0.00 0.00 2.57
3399 3554 6.126568 TGTTTTTCTAGGCTAACAACACAC 57.873 37.500 0.00 0.00 0.00 3.82
3402 3557 4.884744 TGCTGTTTTTCTAGGCTAACAACA 59.115 37.500 0.00 0.00 30.87 3.33
3403 3558 5.432885 TGCTGTTTTTCTAGGCTAACAAC 57.567 39.130 0.00 0.00 30.87 3.32
3411 3566 5.404946 CCATGTTCATGCTGTTTTTCTAGG 58.595 41.667 7.21 0.00 0.00 3.02
3424 3579 5.048224 AGACAAAAGAGAAGCCATGTTCATG 60.048 40.000 5.88 5.88 0.00 3.07
3500 3655 1.676916 CGATGTTGGCATCTGTGTCCT 60.677 52.381 6.11 0.00 46.96 3.85
3501 3656 0.729116 CGATGTTGGCATCTGTGTCC 59.271 55.000 6.11 0.00 46.96 4.02
3520 3675 7.588512 AGAAGATTGCACTGAAGATTGTTAAC 58.411 34.615 0.00 0.00 0.00 2.01
3590 3745 2.054232 AGGCATCTGCTTTGATGAGG 57.946 50.000 15.46 0.00 44.71 3.86
3622 3785 6.876257 ACATGAATCTTGAGAAGTTGGTCTAC 59.124 38.462 0.00 0.00 0.00 2.59
3659 3825 5.222151 GCCCTTTATATCCCTTTCTAGGCTT 60.222 44.000 0.00 0.00 40.50 4.35
3776 3942 1.681025 GGGCGCGACGTAGAGAAAAC 61.681 60.000 12.10 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.