Multiple sequence alignment - TraesCS4B01G209500

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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 TraesCS4B01G209500 chr4B 100.000 4802 0 0 1 4802 446858516 446853715 0.000000e+00 8868
1 TraesCS4B01G209500 chr4D 93.909 3464 154 26 151 3575 361600424 361596979 0.000000e+00 5175
2 TraesCS4B01G209500 chr4D 92.821 989 41 16 3814 4802 361596651 361595693 0.000000e+00 1406
3 TraesCS4B01G209500 chr4D 97.610 251 4 1 3571 3819 361596933 361596683 3.430000e-116 429
4 TraesCS4B01G209500 chr4A 93.111 2874 151 25 720 3575 103386612 103389456 0.000000e+00 4167
5 TraesCS4B01G209500 chr4A 93.168 966 45 10 3847 4802 103389850 103390804 0.000000e+00 1399
6 TraesCS4B01G209500 chr4A 92.323 508 18 6 118 613 103385724 103386222 0.000000e+00 702
7 TraesCS4B01G209500 chr4A 96.386 249 9 0 3571 3819 103389502 103389750 1.240000e-110 411
8 TraesCS4B01G209500 chr4A 91.398 93 5 2 1620 1710 103387558 103387649 1.810000e-24 124
9 TraesCS4B01G209500 chr5A 82.237 1368 162 25 2103 3435 9324614 9325935 0.000000e+00 1105
10 TraesCS4B01G209500 chr5D 81.858 1367 169 22 2103 3435 10898609 10899930 0.000000e+00 1077
11 TraesCS4B01G209500 chr5B 82.008 1295 162 18 2103 3358 11456010 11457272 0.000000e+00 1035


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 TraesCS4B01G209500 chr4B 446853715 446858516 4801 True 8868.000000 8868 100.0000 1 4802 1 chr4B.!!$R1 4801
1 TraesCS4B01G209500 chr4D 361595693 361600424 4731 True 2336.666667 5175 94.7800 151 4802 3 chr4D.!!$R1 4651
2 TraesCS4B01G209500 chr4A 103385724 103390804 5080 False 1360.600000 4167 93.2772 118 4802 5 chr4A.!!$F1 4684
3 TraesCS4B01G209500 chr5A 9324614 9325935 1321 False 1105.000000 1105 82.2370 2103 3435 1 chr5A.!!$F1 1332
4 TraesCS4B01G209500 chr5D 10898609 10899930 1321 False 1077.000000 1077 81.8580 2103 3435 1 chr5D.!!$F1 1332
5 TraesCS4B01G209500 chr5B 11456010 11457272 1262 False 1035.000000 1035 82.0080 2103 3358 1 chr5B.!!$F1 1255

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
635 655 0.107116 TCCCTCCTGTAGTCGAGCTC 60.107 60.0 2.73 2.73 0.00 4.09 F
2049 2370 0.106719 ACCAATAACCGGCAGGATGG 60.107 55.0 10.86 14.02 41.02 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 2488 1.322442 GACAAGCCAGGAAAACAGCT 58.678 50.0 0.00 0.0 37.10 4.24 R
4019 4530 0.248012 TCATTGCTCGGGCTAACGAA 59.752 50.0 9.62 0.0 42.98 3.85 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
45 46 3.870723 TTTTTCTCGTGTTCCGTCATG 57.129 42.857 0.00 0.00 37.94 3.07
46 47 2.804697 TTTCTCGTGTTCCGTCATGA 57.195 45.000 0.00 0.00 37.94 3.07
47 48 3.313012 TTTCTCGTGTTCCGTCATGAT 57.687 42.857 0.00 0.00 37.94 2.45
48 49 4.443913 TTTCTCGTGTTCCGTCATGATA 57.556 40.909 0.00 0.00 37.94 2.15
49 50 4.649088 TTCTCGTGTTCCGTCATGATAT 57.351 40.909 0.00 0.00 37.94 1.63
50 51 4.649088 TCTCGTGTTCCGTCATGATATT 57.351 40.909 0.00 0.00 37.94 1.28
51 52 5.006153 TCTCGTGTTCCGTCATGATATTT 57.994 39.130 0.00 0.00 37.94 1.40
52 53 4.803613 TCTCGTGTTCCGTCATGATATTTG 59.196 41.667 0.00 0.00 37.94 2.32
53 54 4.749976 TCGTGTTCCGTCATGATATTTGA 58.250 39.130 0.00 0.00 37.94 2.69
54 55 5.356426 TCGTGTTCCGTCATGATATTTGAT 58.644 37.500 0.00 0.00 37.94 2.57
55 56 5.234116 TCGTGTTCCGTCATGATATTTGATG 59.766 40.000 0.00 3.11 37.94 3.07
56 57 5.234116 CGTGTTCCGTCATGATATTTGATGA 59.766 40.000 0.00 0.00 32.89 2.92
57 58 6.238076 CGTGTTCCGTCATGATATTTGATGAA 60.238 38.462 0.00 5.82 32.89 2.57
58 59 7.518848 CGTGTTCCGTCATGATATTTGATGAAT 60.519 37.037 0.00 0.00 32.89 2.57
59 60 8.773645 GTGTTCCGTCATGATATTTGATGAATA 58.226 33.333 0.00 4.81 32.89 1.75
60 61 8.992073 TGTTCCGTCATGATATTTGATGAATAG 58.008 33.333 0.00 0.00 33.87 1.73
61 62 8.993121 GTTCCGTCATGATATTTGATGAATAGT 58.007 33.333 0.00 0.00 33.87 2.12
63 64 9.639601 TCCGTCATGATATTTGATGAATAGTAC 57.360 33.333 0.00 0.00 33.87 2.73
64 65 9.645059 CCGTCATGATATTTGATGAATAGTACT 57.355 33.333 0.00 0.00 33.87 2.73
74 75 9.698309 ATTTGATGAATAGTACTCGTAGATTGG 57.302 33.333 0.00 0.00 33.89 3.16
75 76 8.459911 TTGATGAATAGTACTCGTAGATTGGA 57.540 34.615 0.00 0.00 33.89 3.53
76 77 8.459911 TGATGAATAGTACTCGTAGATTGGAA 57.540 34.615 0.00 0.00 33.89 3.53
77 78 9.078990 TGATGAATAGTACTCGTAGATTGGAAT 57.921 33.333 0.00 0.00 33.89 3.01
78 79 9.915629 GATGAATAGTACTCGTAGATTGGAATT 57.084 33.333 0.00 0.00 33.89 2.17
85 86 9.939802 AGTACTCGTAGATTGGAATTTTTAACT 57.060 29.630 0.00 0.00 33.89 2.24
88 89 8.936864 ACTCGTAGATTGGAATTTTTAACTCTG 58.063 33.333 0.00 0.00 33.89 3.35
89 90 9.151471 CTCGTAGATTGGAATTTTTAACTCTGA 57.849 33.333 0.00 0.00 33.89 3.27
90 91 9.151471 TCGTAGATTGGAATTTTTAACTCTGAG 57.849 33.333 2.45 2.45 0.00 3.35
91 92 7.905493 CGTAGATTGGAATTTTTAACTCTGAGC 59.095 37.037 4.19 0.00 0.00 4.26
92 93 7.765695 AGATTGGAATTTTTAACTCTGAGCA 57.234 32.000 4.19 0.00 0.00 4.26
93 94 7.597386 AGATTGGAATTTTTAACTCTGAGCAC 58.403 34.615 4.19 0.00 0.00 4.40
94 95 5.705609 TGGAATTTTTAACTCTGAGCACC 57.294 39.130 4.19 0.00 0.00 5.01
95 96 5.136828 TGGAATTTTTAACTCTGAGCACCA 58.863 37.500 4.19 0.00 0.00 4.17
96 97 5.241506 TGGAATTTTTAACTCTGAGCACCAG 59.758 40.000 4.19 0.22 44.27 4.00
97 98 5.335976 GGAATTTTTAACTCTGAGCACCAGG 60.336 44.000 4.19 0.00 43.12 4.45
99 100 2.024176 TTAACTCTGAGCACCAGGGA 57.976 50.000 12.24 0.00 46.52 4.20
100 101 2.024176 TAACTCTGAGCACCAGGGAA 57.976 50.000 12.24 0.00 46.52 3.97
101 102 1.140312 AACTCTGAGCACCAGGGAAA 58.860 50.000 12.24 0.00 46.52 3.13
102 103 0.689623 ACTCTGAGCACCAGGGAAAG 59.310 55.000 12.24 2.89 46.52 2.62
103 104 0.979665 CTCTGAGCACCAGGGAAAGA 59.020 55.000 0.11 0.00 46.52 2.52
104 105 0.687354 TCTGAGCACCAGGGAAAGAC 59.313 55.000 6.33 0.00 43.12 3.01
105 106 0.322008 CTGAGCACCAGGGAAAGACC 60.322 60.000 0.00 0.00 39.23 3.85
106 107 1.059584 TGAGCACCAGGGAAAGACCA 61.060 55.000 0.00 0.00 41.20 4.02
107 108 0.110486 GAGCACCAGGGAAAGACCAA 59.890 55.000 0.00 0.00 41.20 3.67
108 109 0.779997 AGCACCAGGGAAAGACCAAT 59.220 50.000 0.00 0.00 41.20 3.16
109 110 1.992557 AGCACCAGGGAAAGACCAATA 59.007 47.619 0.00 0.00 41.20 1.90
110 111 2.378547 AGCACCAGGGAAAGACCAATAA 59.621 45.455 0.00 0.00 41.20 1.40
111 112 3.011708 AGCACCAGGGAAAGACCAATAAT 59.988 43.478 0.00 0.00 41.20 1.28
112 113 4.229582 AGCACCAGGGAAAGACCAATAATA 59.770 41.667 0.00 0.00 41.20 0.98
113 114 4.580580 GCACCAGGGAAAGACCAATAATAG 59.419 45.833 0.00 0.00 41.20 1.73
114 115 4.580580 CACCAGGGAAAGACCAATAATAGC 59.419 45.833 0.00 0.00 41.20 2.97
115 116 4.145052 CCAGGGAAAGACCAATAATAGCC 58.855 47.826 0.00 0.00 41.20 3.93
116 117 4.145052 CAGGGAAAGACCAATAATAGCCC 58.855 47.826 0.00 0.00 41.20 5.19
141 142 1.006832 AAATCATCGAACCGGAAGCG 58.993 50.000 9.46 8.91 0.00 4.68
152 153 3.339253 ACCGGAAGCGGTTTTATTAGT 57.661 42.857 9.46 0.00 39.56 2.24
153 154 4.470334 ACCGGAAGCGGTTTTATTAGTA 57.530 40.909 9.46 0.00 39.56 1.82
154 155 4.436332 ACCGGAAGCGGTTTTATTAGTAG 58.564 43.478 9.46 0.00 39.56 2.57
155 156 4.081476 ACCGGAAGCGGTTTTATTAGTAGT 60.081 41.667 9.46 0.00 39.56 2.73
160 166 7.167136 CGGAAGCGGTTTTATTAGTAGTAGAAG 59.833 40.741 0.00 0.00 0.00 2.85
162 168 7.651027 AGCGGTTTTATTAGTAGTAGAAGGA 57.349 36.000 0.00 0.00 0.00 3.36
300 306 4.803426 GGCCAGACGACAGCCGAG 62.803 72.222 0.00 0.00 41.76 4.63
635 655 0.107116 TCCCTCCTGTAGTCGAGCTC 60.107 60.000 2.73 2.73 0.00 4.09
811 1115 7.268586 TGAGCTTCTAATCATCCAGAAACTAC 58.731 38.462 0.00 0.00 29.59 2.73
821 1125 7.496346 TCATCCAGAAACTACTAAACCTCAT 57.504 36.000 0.00 0.00 0.00 2.90
854 1158 2.707529 AATTTTGGGCGTGCCGGTTG 62.708 55.000 1.90 0.00 36.85 3.77
945 1249 0.695924 TCCAGGGATCCAAAAGCGAA 59.304 50.000 15.23 0.00 0.00 4.70
999 1303 3.997021 AGCAACTACGGTTTCATTCAGAG 59.003 43.478 0.00 0.00 32.73 3.35
1087 1391 2.445274 GTCAATTCTGCTGCGACGA 58.555 52.632 0.00 0.00 0.00 4.20
1116 1420 3.924507 GCCAACGCCAGATTCCAT 58.075 55.556 0.00 0.00 0.00 3.41
1134 1438 2.632028 CCATTCCCAACAACCACATCAA 59.368 45.455 0.00 0.00 0.00 2.57
1136 1440 3.304911 TTCCCAACAACCACATCAAGA 57.695 42.857 0.00 0.00 0.00 3.02
1137 1441 2.582052 TCCCAACAACCACATCAAGAC 58.418 47.619 0.00 0.00 0.00 3.01
1157 1461 0.465824 AGGGTATACTCGTGCGCTCT 60.466 55.000 9.73 0.00 0.00 4.09
1163 1467 4.083643 GGTATACTCGTGCGCTCTATTACA 60.084 45.833 9.73 0.00 0.00 2.41
1166 1470 4.768130 ACTCGTGCGCTCTATTACATAT 57.232 40.909 9.73 0.00 0.00 1.78
1178 1482 7.971168 CGCTCTATTACATATGCTTAGCTAGTT 59.029 37.037 5.60 0.00 0.00 2.24
1317 1623 2.237143 AGTAGTGGCTGCTTGCTTCATA 59.763 45.455 0.00 0.00 42.39 2.15
1368 1678 3.524095 TCATCTTGGTGTTGGTCCATT 57.476 42.857 0.00 0.00 34.75 3.16
1411 1721 8.172352 TGCACTAGTTTGGTAATTTTGTACAT 57.828 30.769 0.00 0.00 0.00 2.29
1435 1745 4.018415 ACCACATACCTTTTCCTGCTACAT 60.018 41.667 0.00 0.00 0.00 2.29
1511 1821 6.354938 TCAGTATATAGGTATAGCTGGTCGG 58.645 44.000 14.72 2.51 30.85 4.79
1519 1829 3.869832 GGTATAGCTGGTCGGTTTTTCTC 59.130 47.826 0.00 0.00 0.00 2.87
1545 1860 4.751767 TCCACATTTTGCTTTGAGGTTT 57.248 36.364 0.00 0.00 0.00 3.27
1557 1872 4.583073 GCTTTGAGGTTTGGGAAAAGTAGA 59.417 41.667 0.00 0.00 31.86 2.59
1568 1884 8.761497 GTTTGGGAAAAGTAGATTTTACTTTGC 58.239 33.333 11.78 10.18 44.27 3.68
1584 1900 5.169836 ACTTTGCAAAGCACTTACTGTAC 57.830 39.130 33.72 0.00 38.71 2.90
1585 1901 3.870723 TTGCAAAGCACTTACTGTACG 57.129 42.857 0.00 0.00 38.71 3.67
1586 1902 2.139917 TGCAAAGCACTTACTGTACGG 58.860 47.619 0.00 0.00 31.71 4.02
1587 1903 2.140717 GCAAAGCACTTACTGTACGGT 58.859 47.619 12.92 12.92 0.00 4.83
1588 1904 3.243805 TGCAAAGCACTTACTGTACGGTA 60.244 43.478 10.61 10.61 31.71 4.02
1589 1905 3.122445 GCAAAGCACTTACTGTACGGTAC 59.878 47.826 14.23 11.33 0.00 3.34
1691 2010 3.449018 ACGCTGTGATCAGTTAGGATCTT 59.551 43.478 0.00 0.00 43.27 2.40
1710 2029 8.801299 AGGATCTTTTTCCTTCTGAAGATTTTC 58.199 33.333 18.68 4.79 43.88 2.29
1728 2047 9.525826 AAGATTTTCCAGACTCTTGTGAAATAT 57.474 29.630 0.00 0.00 0.00 1.28
1755 2074 6.360844 CTGTGATCAGCTAGGATCTTTTTG 57.639 41.667 13.51 0.00 43.27 2.44
1759 2078 6.540189 GTGATCAGCTAGGATCTTTTTGCTTA 59.460 38.462 13.51 0.00 43.27 3.09
1787 2106 9.794685 GAAGATTTTTCACTTTTTCAGACTCTT 57.205 29.630 0.00 0.00 0.00 2.85
1789 2108 8.960591 AGATTTTTCACTTTTTCAGACTCTTGA 58.039 29.630 0.00 0.00 0.00 3.02
1864 2183 3.875884 GCATTTTGCGCTTGTGAATTTT 58.124 36.364 9.73 0.00 31.71 1.82
1890 2209 9.688091 TGGTCTAATTTACTTGCATGGTTATTA 57.312 29.630 4.44 4.16 0.00 0.98
1977 2296 8.999431 CATTGACCTAACTAGTACATTGTGTTT 58.001 33.333 0.00 0.00 0.00 2.83
2024 2343 2.035066 AGCTGTGGAGTCAATTTTGTGC 59.965 45.455 0.00 0.00 0.00 4.57
2038 2359 8.279800 GTCAATTTTGTGCCTTTTACCAATAAC 58.720 33.333 0.00 0.00 0.00 1.89
2039 2360 7.442666 TCAATTTTGTGCCTTTTACCAATAACC 59.557 33.333 0.00 0.00 0.00 2.85
2040 2361 4.506886 TTGTGCCTTTTACCAATAACCG 57.493 40.909 0.00 0.00 0.00 4.44
2049 2370 0.106719 ACCAATAACCGGCAGGATGG 60.107 55.000 10.86 14.02 41.02 3.51
2087 2408 5.852827 TCCAGGAACAACCAAATTCATTTC 58.147 37.500 0.00 0.00 42.04 2.17
2126 2447 8.673626 AAAATTCATTTACTTGCACTGATACG 57.326 30.769 0.00 0.00 0.00 3.06
2127 2448 6.985188 ATTCATTTACTTGCACTGATACGT 57.015 33.333 0.00 0.00 0.00 3.57
2140 2461 5.220416 GCACTGATACGTTACATGTTTCTCC 60.220 44.000 2.30 0.00 0.00 3.71
2167 2488 2.461300 ACAGCAGAGTAGATGGGCTA 57.539 50.000 0.00 0.00 32.71 3.93
2176 2497 4.123506 GAGTAGATGGGCTAGCTGTTTTC 58.876 47.826 15.72 5.26 0.00 2.29
2562 2883 1.754226 CCTCCTCCTGAACTAGCTCAC 59.246 57.143 0.00 0.00 0.00 3.51
2887 3214 2.358300 CCTGAGCAAGAGGTCCCTACTA 60.358 54.545 0.00 0.00 41.53 1.82
2988 3318 1.406205 GCTGCCCCTAGAAACTGTCTC 60.406 57.143 0.00 0.00 37.84 3.36
2991 3321 1.208293 GCCCCTAGAAACTGTCTCCTG 59.792 57.143 0.00 0.00 37.84 3.86
3153 3486 2.715749 TTGGATTCAGTGCGGATGAT 57.284 45.000 0.00 0.00 0.00 2.45
3283 3637 3.135348 TGATCTGCCTAATGAGGTTCAGG 59.865 47.826 0.00 0.00 45.78 3.86
3449 3813 4.158384 CAGCCATTTTGTTGTATCGTGAC 58.842 43.478 0.00 0.00 0.00 3.67
3535 3906 5.734855 ACTATACTTGCATTTTGTAGCCG 57.265 39.130 0.00 0.00 0.00 5.52
3536 3907 5.424757 ACTATACTTGCATTTTGTAGCCGA 58.575 37.500 0.00 0.00 0.00 5.54
3562 3933 6.449698 ACACAAATGTCTTTCATCAACATCC 58.550 36.000 0.00 0.00 31.55 3.51
3568 3939 5.559770 TGTCTTTCATCAACATCCAGCTAA 58.440 37.500 0.00 0.00 0.00 3.09
3588 4009 1.004918 CTCAGGAACGAAAGCGGGT 60.005 57.895 0.00 0.00 43.17 5.28
3813 4236 0.677731 TGCAGTAATGGTGCTCTGGC 60.678 55.000 0.00 0.00 41.78 4.85
3934 4445 2.711009 TCTGGGGATTTATACAGCCAGG 59.289 50.000 0.00 0.00 0.00 4.45
3940 4451 3.565902 GGATTTATACAGCCAGGTTGCTC 59.434 47.826 2.54 0.00 40.32 4.26
3997 4508 7.643123 ACTCCCTATTTAAGATCACCATGTTT 58.357 34.615 0.00 0.00 0.00 2.83
4009 4520 8.048534 AGATCACCATGTTTCTCTTTTGTATG 57.951 34.615 0.00 0.00 0.00 2.39
4010 4521 6.012658 TCACCATGTTTCTCTTTTGTATGC 57.987 37.500 0.00 0.00 0.00 3.14
4019 4530 8.097038 TGTTTCTCTTTTGTATGCACTCTCTAT 58.903 33.333 0.00 0.00 0.00 1.98
4029 4540 2.100916 TGCACTCTCTATTCGTTAGCCC 59.899 50.000 0.00 0.00 0.00 5.19
4065 4576 6.007076 TGAAAGGGTGTGCATGATTACTTTA 58.993 36.000 0.00 0.00 0.00 1.85
4066 4577 6.150976 TGAAAGGGTGTGCATGATTACTTTAG 59.849 38.462 0.00 0.00 0.00 1.85
4156 4667 1.207593 GCAGTGCGAATTCTGCGTT 59.792 52.632 0.00 5.58 45.42 4.84
4157 4668 0.385974 GCAGTGCGAATTCTGCGTTT 60.386 50.000 0.00 3.70 45.42 3.60
4165 4676 2.754472 GAATTCTGCGTTTTTGGCCTT 58.246 42.857 3.32 0.00 0.00 4.35
4167 4678 0.030101 TTCTGCGTTTTTGGCCTTCG 59.970 50.000 3.32 2.76 0.00 3.79
4168 4679 2.016165 CTGCGTTTTTGGCCTTCGC 61.016 57.895 17.95 17.95 45.70 4.70
4195 4706 1.302033 CGTTCCTTCTGCAGCCACT 60.302 57.895 9.47 0.00 0.00 4.00
4204 4715 1.558294 TCTGCAGCCACTGATTCATCT 59.442 47.619 9.47 0.00 32.44 2.90
4205 4716 1.941294 CTGCAGCCACTGATTCATCTC 59.059 52.381 0.00 0.00 32.44 2.75
4227 4738 3.418684 AGCTTACAACGAGGGACATTT 57.581 42.857 0.00 0.00 0.00 2.32
4448 4963 3.425713 ATGCACGTCGCTGGCTTG 61.426 61.111 10.54 0.00 43.06 4.01
4584 5099 3.843240 CGACTTGAAGAGCGGCGC 61.843 66.667 26.86 26.86 0.00 6.53
4750 5271 2.279851 CCGTTGCTGACACCGTGA 60.280 61.111 5.28 0.00 28.20 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.603237 TCATCAAATATCATGACGGAACAC 57.397 37.500 0.00 0.00 0.00 3.32
34 35 7.806409 ATTCATCAAATATCATGACGGAACA 57.194 32.000 0.00 0.00 30.81 3.18
35 36 8.993121 ACTATTCATCAAATATCATGACGGAAC 58.007 33.333 0.00 0.00 30.81 3.62
37 38 9.639601 GTACTATTCATCAAATATCATGACGGA 57.360 33.333 0.00 0.00 0.00 4.69
38 39 9.645059 AGTACTATTCATCAAATATCATGACGG 57.355 33.333 0.00 0.00 0.00 4.79
48 49 9.698309 CCAATCTACGAGTACTATTCATCAAAT 57.302 33.333 0.00 0.00 0.00 2.32
49 50 8.909923 TCCAATCTACGAGTACTATTCATCAAA 58.090 33.333 0.00 0.00 0.00 2.69
50 51 8.459911 TCCAATCTACGAGTACTATTCATCAA 57.540 34.615 0.00 0.00 0.00 2.57
51 52 8.459911 TTCCAATCTACGAGTACTATTCATCA 57.540 34.615 0.00 0.00 0.00 3.07
52 53 9.915629 AATTCCAATCTACGAGTACTATTCATC 57.084 33.333 0.00 0.00 0.00 2.92
59 60 9.939802 AGTTAAAAATTCCAATCTACGAGTACT 57.060 29.630 0.00 0.00 0.00 2.73
62 63 8.936864 CAGAGTTAAAAATTCCAATCTACGAGT 58.063 33.333 0.00 0.00 0.00 4.18
63 64 9.151471 TCAGAGTTAAAAATTCCAATCTACGAG 57.849 33.333 0.00 0.00 0.00 4.18
64 65 9.151471 CTCAGAGTTAAAAATTCCAATCTACGA 57.849 33.333 0.00 0.00 0.00 3.43
65 66 7.905493 GCTCAGAGTTAAAAATTCCAATCTACG 59.095 37.037 0.00 0.00 0.00 3.51
66 67 8.730680 TGCTCAGAGTTAAAAATTCCAATCTAC 58.269 33.333 0.00 0.00 0.00 2.59
67 68 8.730680 GTGCTCAGAGTTAAAAATTCCAATCTA 58.269 33.333 0.00 0.00 0.00 1.98
68 69 7.309438 GGTGCTCAGAGTTAAAAATTCCAATCT 60.309 37.037 0.00 0.00 0.00 2.40
69 70 6.808704 GGTGCTCAGAGTTAAAAATTCCAATC 59.191 38.462 0.00 0.00 0.00 2.67
70 71 6.267471 TGGTGCTCAGAGTTAAAAATTCCAAT 59.733 34.615 0.00 0.00 0.00 3.16
71 72 5.596361 TGGTGCTCAGAGTTAAAAATTCCAA 59.404 36.000 0.00 0.00 0.00 3.53
72 73 5.136828 TGGTGCTCAGAGTTAAAAATTCCA 58.863 37.500 0.00 0.00 0.00 3.53
73 74 5.335976 CCTGGTGCTCAGAGTTAAAAATTCC 60.336 44.000 8.81 0.00 46.18 3.01
74 75 5.335976 CCCTGGTGCTCAGAGTTAAAAATTC 60.336 44.000 8.81 0.00 46.18 2.17
75 76 4.524328 CCCTGGTGCTCAGAGTTAAAAATT 59.476 41.667 8.81 0.00 46.18 1.82
76 77 4.082125 CCCTGGTGCTCAGAGTTAAAAAT 58.918 43.478 8.81 0.00 46.18 1.82
77 78 3.137544 TCCCTGGTGCTCAGAGTTAAAAA 59.862 43.478 8.81 0.00 46.18 1.94
78 79 2.708861 TCCCTGGTGCTCAGAGTTAAAA 59.291 45.455 8.81 0.00 46.18 1.52
79 80 2.334977 TCCCTGGTGCTCAGAGTTAAA 58.665 47.619 8.81 0.00 46.18 1.52
80 81 2.024176 TCCCTGGTGCTCAGAGTTAA 57.976 50.000 8.81 0.00 46.18 2.01
81 82 2.024176 TTCCCTGGTGCTCAGAGTTA 57.976 50.000 8.81 0.00 46.18 2.24
82 83 1.072965 CTTTCCCTGGTGCTCAGAGTT 59.927 52.381 8.81 0.00 46.18 3.01
83 84 0.689623 CTTTCCCTGGTGCTCAGAGT 59.310 55.000 8.81 0.00 46.18 3.24
84 85 0.979665 TCTTTCCCTGGTGCTCAGAG 59.020 55.000 8.81 0.00 46.18 3.35
85 86 0.687354 GTCTTTCCCTGGTGCTCAGA 59.313 55.000 8.81 0.00 46.18 3.27
86 87 0.322008 GGTCTTTCCCTGGTGCTCAG 60.322 60.000 0.00 1.44 43.00 3.35
87 88 1.059584 TGGTCTTTCCCTGGTGCTCA 61.060 55.000 0.00 0.00 34.77 4.26
88 89 0.110486 TTGGTCTTTCCCTGGTGCTC 59.890 55.000 0.00 0.00 34.77 4.26
89 90 0.779997 ATTGGTCTTTCCCTGGTGCT 59.220 50.000 0.00 0.00 34.77 4.40
90 91 2.507407 TATTGGTCTTTCCCTGGTGC 57.493 50.000 0.00 0.00 34.77 5.01
91 92 4.580580 GCTATTATTGGTCTTTCCCTGGTG 59.419 45.833 0.00 0.00 34.77 4.17
92 93 4.386424 GGCTATTATTGGTCTTTCCCTGGT 60.386 45.833 0.00 0.00 34.77 4.00
93 94 4.145052 GGCTATTATTGGTCTTTCCCTGG 58.855 47.826 0.00 0.00 34.77 4.45
94 95 4.145052 GGGCTATTATTGGTCTTTCCCTG 58.855 47.826 0.00 0.00 34.77 4.45
95 96 3.181443 CGGGCTATTATTGGTCTTTCCCT 60.181 47.826 0.00 0.00 34.77 4.20
96 97 3.146847 CGGGCTATTATTGGTCTTTCCC 58.853 50.000 0.00 0.00 34.77 3.97
97 98 3.146847 CCGGGCTATTATTGGTCTTTCC 58.853 50.000 0.00 0.00 0.00 3.13
98 99 3.813724 GACCGGGCTATTATTGGTCTTTC 59.186 47.826 6.32 0.00 44.47 2.62
99 100 3.434596 GGACCGGGCTATTATTGGTCTTT 60.435 47.826 7.57 0.00 46.52 2.52
100 101 2.105993 GGACCGGGCTATTATTGGTCTT 59.894 50.000 7.57 0.00 46.52 3.01
101 102 1.697982 GGACCGGGCTATTATTGGTCT 59.302 52.381 7.57 0.00 46.52 3.85
102 103 1.418637 TGGACCGGGCTATTATTGGTC 59.581 52.381 7.57 1.12 46.58 4.02
103 104 1.513858 TGGACCGGGCTATTATTGGT 58.486 50.000 7.57 0.00 35.14 3.67
104 105 2.649531 TTGGACCGGGCTATTATTGG 57.350 50.000 7.57 0.00 0.00 3.16
105 106 4.141287 TGATTTGGACCGGGCTATTATTG 58.859 43.478 7.57 0.00 0.00 1.90
106 107 4.447138 TGATTTGGACCGGGCTATTATT 57.553 40.909 7.57 0.00 0.00 1.40
107 108 4.589908 GATGATTTGGACCGGGCTATTAT 58.410 43.478 7.57 0.00 0.00 1.28
108 109 3.556213 CGATGATTTGGACCGGGCTATTA 60.556 47.826 7.57 0.00 0.00 0.98
109 110 2.810400 CGATGATTTGGACCGGGCTATT 60.810 50.000 7.57 0.00 0.00 1.73
110 111 1.270839 CGATGATTTGGACCGGGCTAT 60.271 52.381 7.57 0.00 0.00 2.97
111 112 0.105964 CGATGATTTGGACCGGGCTA 59.894 55.000 7.57 0.00 0.00 3.93
112 113 1.153168 CGATGATTTGGACCGGGCT 60.153 57.895 7.57 0.00 0.00 5.19
113 114 0.746563 TTCGATGATTTGGACCGGGC 60.747 55.000 6.32 0.21 0.00 6.13
114 115 1.014352 GTTCGATGATTTGGACCGGG 58.986 55.000 6.32 0.00 0.00 5.73
115 116 1.014352 GGTTCGATGATTTGGACCGG 58.986 55.000 0.00 0.00 0.00 5.28
116 117 0.650512 CGGTTCGATGATTTGGACCG 59.349 55.000 6.65 6.65 0.00 4.79
150 151 8.493787 TCTCTTTCCTTTTTCCTTCTACTACT 57.506 34.615 0.00 0.00 0.00 2.57
151 152 8.586744 TCTCTCTTTCCTTTTTCCTTCTACTAC 58.413 37.037 0.00 0.00 0.00 2.73
152 153 8.722622 TCTCTCTTTCCTTTTTCCTTCTACTA 57.277 34.615 0.00 0.00 0.00 1.82
153 154 7.619512 TCTCTCTTTCCTTTTTCCTTCTACT 57.380 36.000 0.00 0.00 0.00 2.57
154 155 7.934665 ACTTCTCTCTTTCCTTTTTCCTTCTAC 59.065 37.037 0.00 0.00 0.00 2.59
155 156 8.035448 ACTTCTCTCTTTCCTTTTTCCTTCTA 57.965 34.615 0.00 0.00 0.00 2.10
160 166 4.452795 CCGACTTCTCTCTTTCCTTTTTCC 59.547 45.833 0.00 0.00 0.00 3.13
162 168 3.815962 GCCGACTTCTCTCTTTCCTTTTT 59.184 43.478 0.00 0.00 0.00 1.94
811 1115 6.446781 TGTCGAGGTTAGTATGAGGTTTAG 57.553 41.667 0.00 0.00 0.00 1.85
821 1125 4.456566 GCCCAAAATTTGTCGAGGTTAGTA 59.543 41.667 4.92 0.00 0.00 1.82
854 1158 0.322456 TACATGGTGTGCAGGAAGGC 60.322 55.000 0.00 0.00 0.00 4.35
1066 1370 1.005037 TCGCAGCAGAATTGACGGT 60.005 52.632 0.00 0.00 0.00 4.83
1087 1391 4.974989 GTTGGCCGAACCGACCGT 62.975 66.667 0.00 0.00 46.16 4.83
1102 1406 0.331278 TGGGAATGGAATCTGGCGTT 59.669 50.000 0.00 0.00 0.00 4.84
1104 1408 0.740737 GTTGGGAATGGAATCTGGCG 59.259 55.000 0.00 0.00 0.00 5.69
1116 1420 2.955660 GTCTTGATGTGGTTGTTGGGAA 59.044 45.455 0.00 0.00 0.00 3.97
1134 1438 1.022735 CGCACGAGTATACCCTGTCT 58.977 55.000 0.00 0.00 0.00 3.41
1136 1440 1.035932 AGCGCACGAGTATACCCTGT 61.036 55.000 11.47 0.00 0.00 4.00
1137 1441 0.317938 GAGCGCACGAGTATACCCTG 60.318 60.000 11.47 0.00 0.00 4.45
1163 1467 6.375455 AGCACAAAACAACTAGCTAAGCATAT 59.625 34.615 0.00 0.00 0.00 1.78
1166 1470 3.882888 AGCACAAAACAACTAGCTAAGCA 59.117 39.130 0.00 0.00 0.00 3.91
1203 1507 4.039124 TCGTATGCAGTGATGGATGTACAT 59.961 41.667 8.43 8.43 0.00 2.29
1204 1508 3.383185 TCGTATGCAGTGATGGATGTACA 59.617 43.478 0.00 0.00 0.00 2.90
1206 1510 4.099419 ACTTCGTATGCAGTGATGGATGTA 59.901 41.667 0.00 0.00 0.00 2.29
1241 1545 1.593196 GTTGCAGCAACTAGTGTCCA 58.407 50.000 27.98 0.00 40.73 4.02
1411 1721 4.532916 TGTAGCAGGAAAAGGTATGTGGTA 59.467 41.667 0.00 0.00 0.00 3.25
1424 1734 2.171237 CCAGGTGATGATGTAGCAGGAA 59.829 50.000 0.00 0.00 0.00 3.36
1435 1745 3.378512 AGCAAGATACTCCAGGTGATGA 58.621 45.455 0.00 0.00 0.00 2.92
1511 1821 9.860898 AAGCAAAATGTGGATATAGAGAAAAAC 57.139 29.630 0.00 0.00 0.00 2.43
1519 1829 7.338800 ACCTCAAAGCAAAATGTGGATATAG 57.661 36.000 0.00 0.00 34.93 1.31
1545 1860 7.589958 TGCAAAGTAAAATCTACTTTTCCCA 57.410 32.000 7.08 3.73 43.00 4.37
1557 1872 7.264947 ACAGTAAGTGCTTTGCAAAGTAAAAT 58.735 30.769 33.47 22.27 41.47 1.82
1568 1884 3.362831 CGTACCGTACAGTAAGTGCTTTG 59.637 47.826 9.34 0.00 0.00 2.77
1584 1900 1.723003 GTTTGTGCTTCTACCGTACCG 59.277 52.381 0.00 0.00 0.00 4.02
1585 1901 2.991866 GAGTTTGTGCTTCTACCGTACC 59.008 50.000 0.00 0.00 0.00 3.34
1586 1902 3.645884 TGAGTTTGTGCTTCTACCGTAC 58.354 45.455 0.00 0.00 0.00 3.67
1587 1903 4.530710 ATGAGTTTGTGCTTCTACCGTA 57.469 40.909 0.00 0.00 0.00 4.02
1588 1904 2.902705 TGAGTTTGTGCTTCTACCGT 57.097 45.000 0.00 0.00 0.00 4.83
1589 1905 4.466828 CAAATGAGTTTGTGCTTCTACCG 58.533 43.478 0.00 0.00 39.85 4.02
1691 2010 7.062957 AGTCTGGAAAATCTTCAGAAGGAAAA 58.937 34.615 10.42 0.00 34.44 2.29
1710 2029 4.940046 AGCACATATTTCACAAGAGTCTGG 59.060 41.667 0.00 0.00 0.00 3.86
1759 2078 9.741647 GAGTCTGAAAAAGTGAAAAATCTTCAT 57.258 29.630 0.00 0.00 0.00 2.57
1787 2106 3.313803 GTCATCACAGCTCGTATCTCTCA 59.686 47.826 0.00 0.00 0.00 3.27
1789 2108 3.314913 CAGTCATCACAGCTCGTATCTCT 59.685 47.826 0.00 0.00 0.00 3.10
1864 2183 8.588290 AATAACCATGCAAGTAAATTAGACCA 57.412 30.769 0.00 0.00 0.00 4.02
1936 2255 5.014858 AGGTCAATGATGAAACTGCAGATT 58.985 37.500 23.35 16.10 37.30 2.40
1949 2268 8.540388 ACACAATGTACTAGTTAGGTCAATGAT 58.460 33.333 0.00 0.00 0.00 2.45
1999 2318 4.586001 ACAAAATTGACTCCACAGCTGAAT 59.414 37.500 23.35 4.59 0.00 2.57
2024 2343 2.425668 CCTGCCGGTTATTGGTAAAAGG 59.574 50.000 1.90 0.00 0.00 3.11
2038 2359 2.618709 GAGATAAAAACCATCCTGCCGG 59.381 50.000 0.00 0.00 0.00 6.13
2039 2360 3.313526 CAGAGATAAAAACCATCCTGCCG 59.686 47.826 0.00 0.00 0.00 5.69
2040 2361 3.067320 GCAGAGATAAAAACCATCCTGCC 59.933 47.826 0.00 0.00 38.91 4.85
2049 2370 5.473504 TGTTCCTGGAAGCAGAGATAAAAAC 59.526 40.000 9.92 0.00 0.00 2.43
2121 2442 5.803967 AGAACGGAGAAACATGTAACGTATC 59.196 40.000 0.00 6.74 32.35 2.24
2126 2447 7.181143 TGTTAAGAACGGAGAAACATGTAAC 57.819 36.000 0.00 0.00 0.00 2.50
2127 2448 6.073440 GCTGTTAAGAACGGAGAAACATGTAA 60.073 38.462 0.00 0.00 40.26 2.41
2140 2461 4.800993 CCATCTACTCTGCTGTTAAGAACG 59.199 45.833 0.00 0.00 0.00 3.95
2167 2488 1.322442 GACAAGCCAGGAAAACAGCT 58.678 50.000 0.00 0.00 37.10 4.24
2176 2497 1.962807 TCCAAAACATGACAAGCCAGG 59.037 47.619 0.00 0.00 0.00 4.45
2648 2969 4.297510 TGTTGTTGACAAGTAATGCATGC 58.702 39.130 11.82 11.82 36.39 4.06
2659 2980 4.133820 CCACCAGAGTATGTTGTTGACAA 58.866 43.478 0.00 0.00 42.62 3.18
3014 3344 1.484240 GGTAGAACTGAGCAGATGCCT 59.516 52.381 4.21 0.00 43.38 4.75
3105 3438 4.682859 GCTCTGTATGCTTCAACCTCATCT 60.683 45.833 0.00 0.00 0.00 2.90
3417 3780 2.507471 ACAAAATGGCTGGGGTGAAAAA 59.493 40.909 0.00 0.00 0.00 1.94
3472 3836 3.656457 TGCACAGCAGTTCATGGAT 57.344 47.368 0.00 0.00 33.32 3.41
3522 3893 3.006659 TGTGTTTCGGCTACAAAATGC 57.993 42.857 0.00 0.00 0.00 3.56
3536 3907 7.439056 GGATGTTGATGAAAGACATTTGTGTTT 59.561 33.333 5.61 5.61 43.04 2.83
3562 3933 3.120511 GCTTTCGTTCCTGAGTTTAGCTG 60.121 47.826 0.00 0.00 0.00 4.24
3568 3939 0.602905 CCCGCTTTCGTTCCTGAGTT 60.603 55.000 0.00 0.00 0.00 3.01
3588 4009 1.406898 GCGTCATCCTCAGACAGATGA 59.593 52.381 4.78 4.78 45.03 2.92
3813 4236 0.807275 TCGGCTCGACTTGATGCATG 60.807 55.000 2.46 0.00 0.00 4.06
3912 4423 3.331889 CCTGGCTGTATAAATCCCCAGAT 59.668 47.826 6.08 0.00 41.76 2.90
3913 4424 2.711009 CCTGGCTGTATAAATCCCCAGA 59.289 50.000 6.08 0.00 41.76 3.86
3934 4445 3.266510 TCATCACATACCCAGAGCAAC 57.733 47.619 0.00 0.00 0.00 4.17
3940 4451 3.272574 AGCTGTTCATCACATACCCAG 57.727 47.619 0.00 0.00 33.76 4.45
3997 4508 6.975197 CGAATAGAGAGTGCATACAAAAGAGA 59.025 38.462 0.00 0.00 0.00 3.10
4009 4520 2.745102 GGGCTAACGAATAGAGAGTGC 58.255 52.381 0.00 0.00 33.04 4.40
4010 4521 2.617308 TCGGGCTAACGAATAGAGAGTG 59.383 50.000 0.00 0.00 40.34 3.51
4019 4530 0.248012 TCATTGCTCGGGCTAACGAA 59.752 50.000 9.62 0.00 42.98 3.85
4029 4540 3.057315 ACACCCTTTCATTTCATTGCTCG 60.057 43.478 0.00 0.00 0.00 5.03
4065 4576 6.324512 ACATGAGACTTCTAGCATCAGAATCT 59.675 38.462 0.00 0.00 34.14 2.40
4066 4577 6.514947 ACATGAGACTTCTAGCATCAGAATC 58.485 40.000 0.00 0.00 34.14 2.52
4167 4678 4.368543 AAGGAACGTCGACGGGGC 62.369 66.667 37.89 25.95 44.95 5.80
4168 4679 2.126189 GAAGGAACGTCGACGGGG 60.126 66.667 37.89 14.82 44.95 5.73
4169 4680 1.443872 CAGAAGGAACGTCGACGGG 60.444 63.158 37.89 15.57 42.91 5.28
4170 4681 2.087009 GCAGAAGGAACGTCGACGG 61.087 63.158 37.89 21.83 42.91 4.79
4171 4682 1.337817 CTGCAGAAGGAACGTCGACG 61.338 60.000 34.58 34.58 42.91 5.12
4195 4706 5.478407 TCGTTGTAAGCTTGAGATGAATCA 58.522 37.500 9.86 0.00 0.00 2.57
4204 4715 1.689813 TGTCCCTCGTTGTAAGCTTGA 59.310 47.619 9.86 0.00 0.00 3.02
4205 4716 2.163818 TGTCCCTCGTTGTAAGCTTG 57.836 50.000 9.86 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.