Multiple sequence alignment - TraesCS7A01G061700

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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 TraesCS7A01G061700 chr7A 100.000 3010 0 0 1 3010 30660821 30657812 0.000000e+00 5559
1 TraesCS7A01G061700 chr4A 93.283 2918 176 8 109 3010 698905662 698908575 0.000000e+00 4285
2 TraesCS7A01G061700 chr4A 92.953 2611 161 10 412 3010 698133135 698135734 0.000000e+00 3781
3 TraesCS7A01G061700 chr4A 94.949 99 4 1 4 101 729882862 729882960 1.450000e-33 154
4 TraesCS7A01G061700 chr7D 95.022 1587 76 3 873 2458 30270251 30268667 0.000000e+00 2490
5 TraesCS7A01G061700 chr7D 94.660 206 11 0 2805 3010 30268664 30268459 1.350000e-83 320
6 TraesCS7A01G061700 chr7D 94.118 102 5 1 1 101 329047411 329047310 1.450000e-33 154
7 TraesCS7A01G061700 chr3D 80.176 2159 340 62 599 2703 462862137 462860013 0.000000e+00 1535
8 TraesCS7A01G061700 chr3D 81.550 1897 290 34 594 2447 463185030 463186909 0.000000e+00 1509
9 TraesCS7A01G061700 chr3D 94.118 102 4 2 1 101 395903986 395904086 1.450000e-33 154
10 TraesCS7A01G061700 chr3A 80.379 2110 328 61 594 2647 606431117 606433196 0.000000e+00 1524
11 TraesCS7A01G061700 chr3B 79.925 2142 331 72 594 2677 616260691 616262791 0.000000e+00 1482
12 TraesCS7A01G061700 chr3B 77.778 1233 201 47 1356 2543 615778252 615777048 0.000000e+00 691
13 TraesCS7A01G061700 chr2D 83.380 1071 163 7 806 1865 29068986 29070052 0.000000e+00 977
14 TraesCS7A01G061700 chr6D 73.491 928 199 35 794 1706 468089145 468088250 1.050000e-79 307
15 TraesCS7A01G061700 chr6D 95.918 98 3 1 4 100 269564468 269564565 1.120000e-34 158
16 TraesCS7A01G061700 chr1D 96.939 98 2 1 4 100 481697914 481698011 2.400000e-36 163
17 TraesCS7A01G061700 chr4B 95.960 99 3 1 4 101 362138007 362137909 3.110000e-35 159
18 TraesCS7A01G061700 chr5B 94.949 99 4 1 4 101 521134673 521134771 1.450000e-33 154
19 TraesCS7A01G061700 chr5B 93.137 102 6 1 1 101 270633656 270633757 6.720000e-32 148
20 TraesCS7A01G061700 chr2A 88.430 121 8 4 4 120 240457962 240457844 1.120000e-29 141


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 TraesCS7A01G061700 chr7A 30657812 30660821 3009 True 5559 5559 100.000 1 3010 1 chr7A.!!$R1 3009
1 TraesCS7A01G061700 chr4A 698905662 698908575 2913 False 4285 4285 93.283 109 3010 1 chr4A.!!$F2 2901
2 TraesCS7A01G061700 chr4A 698133135 698135734 2599 False 3781 3781 92.953 412 3010 1 chr4A.!!$F1 2598
3 TraesCS7A01G061700 chr7D 30268459 30270251 1792 True 1405 2490 94.841 873 3010 2 chr7D.!!$R2 2137
4 TraesCS7A01G061700 chr3D 462860013 462862137 2124 True 1535 1535 80.176 599 2703 1 chr3D.!!$R1 2104
5 TraesCS7A01G061700 chr3D 463185030 463186909 1879 False 1509 1509 81.550 594 2447 1 chr3D.!!$F2 1853
6 TraesCS7A01G061700 chr3A 606431117 606433196 2079 False 1524 1524 80.379 594 2647 1 chr3A.!!$F1 2053
7 TraesCS7A01G061700 chr3B 616260691 616262791 2100 False 1482 1482 79.925 594 2677 1 chr3B.!!$F1 2083
8 TraesCS7A01G061700 chr3B 615777048 615778252 1204 True 691 691 77.778 1356 2543 1 chr3B.!!$R1 1187
9 TraesCS7A01G061700 chr2D 29068986 29070052 1066 False 977 977 83.380 806 1865 1 chr2D.!!$F1 1059
10 TraesCS7A01G061700 chr6D 468088250 468089145 895 True 307 307 73.491 794 1706 1 chr6D.!!$R1 912

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
84 85 0.035056 CACCTCCCCTAAGCACCTTG 60.035 60.0 0.00 0.00 0.00 3.61 F
865 884 0.601558 CCATTTTGCTGCAGCTCTGT 59.398 50.0 36.61 18.98 42.66 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1246 1265 3.428534 GCAGTTTGCCGTTTCTTATTTGG 59.571 43.478 0.0 0.0 37.42 3.28 R
2079 2115 3.910568 ATGTGGCCCAAACAAATATGG 57.089 42.857 0.0 0.0 36.42 2.74 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 2.211250 ACTAAGCGTCTACCCTGACA 57.789 50.000 0.00 0.00 36.82 3.58
21 22 2.522185 ACTAAGCGTCTACCCTGACAA 58.478 47.619 0.00 0.00 36.82 3.18
22 23 2.895404 ACTAAGCGTCTACCCTGACAAA 59.105 45.455 0.00 0.00 36.82 2.83
23 24 3.514309 ACTAAGCGTCTACCCTGACAAAT 59.486 43.478 0.00 0.00 36.82 2.32
24 25 4.708421 ACTAAGCGTCTACCCTGACAAATA 59.292 41.667 0.00 0.00 36.82 1.40
25 26 3.521947 AGCGTCTACCCTGACAAATAC 57.478 47.619 0.00 0.00 36.82 1.89
26 27 2.159282 AGCGTCTACCCTGACAAATACG 60.159 50.000 0.00 0.00 36.82 3.06
27 28 2.190981 CGTCTACCCTGACAAATACGC 58.809 52.381 0.00 0.00 36.82 4.42
28 29 2.416296 CGTCTACCCTGACAAATACGCA 60.416 50.000 0.00 0.00 36.82 5.24
29 30 2.928116 GTCTACCCTGACAAATACGCAC 59.072 50.000 0.00 0.00 36.97 5.34
30 31 2.093869 TCTACCCTGACAAATACGCACC 60.094 50.000 0.00 0.00 0.00 5.01
31 32 0.672401 ACCCTGACAAATACGCACCG 60.672 55.000 0.00 0.00 0.00 4.94
32 33 1.366111 CCCTGACAAATACGCACCGG 61.366 60.000 0.00 0.00 0.00 5.28
33 34 0.672401 CCTGACAAATACGCACCGGT 60.672 55.000 0.00 0.00 0.00 5.28
34 35 0.442310 CTGACAAATACGCACCGGTG 59.558 55.000 30.66 30.66 0.00 4.94
47 48 3.537793 CACCGGTGCTTAAGAAAAGTC 57.462 47.619 24.02 0.00 0.00 3.01
48 49 3.139077 CACCGGTGCTTAAGAAAAGTCT 58.861 45.455 24.02 0.00 34.72 3.24
49 50 3.058914 CACCGGTGCTTAAGAAAAGTCTG 60.059 47.826 24.02 0.00 33.05 3.51
50 51 2.484264 CCGGTGCTTAAGAAAAGTCTGG 59.516 50.000 6.67 0.00 33.05 3.86
51 52 3.139077 CGGTGCTTAAGAAAAGTCTGGT 58.861 45.455 6.67 0.00 33.05 4.00
52 53 3.564225 CGGTGCTTAAGAAAAGTCTGGTT 59.436 43.478 6.67 0.00 33.05 3.67
53 54 4.036380 CGGTGCTTAAGAAAAGTCTGGTTT 59.964 41.667 6.67 0.00 33.05 3.27
54 55 5.237779 CGGTGCTTAAGAAAAGTCTGGTTTA 59.762 40.000 6.67 0.00 33.05 2.01
55 56 6.072673 CGGTGCTTAAGAAAAGTCTGGTTTAT 60.073 38.462 6.67 0.00 33.05 1.40
56 57 7.521585 CGGTGCTTAAGAAAAGTCTGGTTTATT 60.522 37.037 6.67 0.00 33.05 1.40
57 58 8.141909 GGTGCTTAAGAAAAGTCTGGTTTATTT 58.858 33.333 6.67 0.00 33.05 1.40
58 59 9.181805 GTGCTTAAGAAAAGTCTGGTTTATTTC 57.818 33.333 6.67 0.00 33.05 2.17
59 60 9.131791 TGCTTAAGAAAAGTCTGGTTTATTTCT 57.868 29.630 6.67 0.00 40.90 2.52
60 61 9.613957 GCTTAAGAAAAGTCTGGTTTATTTCTC 57.386 33.333 6.67 0.00 38.89 2.87
65 66 9.004717 AGAAAAGTCTGGTTTATTTCTCTAAGC 57.995 33.333 0.00 0.00 35.96 3.09
66 67 8.691661 AAAAGTCTGGTTTATTTCTCTAAGCA 57.308 30.769 0.00 0.00 0.00 3.91
67 68 7.674471 AAGTCTGGTTTATTTCTCTAAGCAC 57.326 36.000 0.00 0.00 0.00 4.40
68 69 6.174049 AGTCTGGTTTATTTCTCTAAGCACC 58.826 40.000 0.00 0.00 0.00 5.01
69 70 6.013293 AGTCTGGTTTATTTCTCTAAGCACCT 60.013 38.462 0.00 0.00 0.00 4.00
70 71 6.314152 GTCTGGTTTATTTCTCTAAGCACCTC 59.686 42.308 0.00 0.00 0.00 3.85
71 72 5.497474 TGGTTTATTTCTCTAAGCACCTCC 58.503 41.667 0.00 0.00 0.00 4.30
72 73 4.882427 GGTTTATTTCTCTAAGCACCTCCC 59.118 45.833 0.00 0.00 0.00 4.30
73 74 4.772886 TTATTTCTCTAAGCACCTCCCC 57.227 45.455 0.00 0.00 0.00 4.81
74 75 2.344093 TTTCTCTAAGCACCTCCCCT 57.656 50.000 0.00 0.00 0.00 4.79
75 76 3.484953 TTTCTCTAAGCACCTCCCCTA 57.515 47.619 0.00 0.00 0.00 3.53
76 77 3.484953 TTCTCTAAGCACCTCCCCTAA 57.515 47.619 0.00 0.00 0.00 2.69
77 78 3.033659 TCTCTAAGCACCTCCCCTAAG 57.966 52.381 0.00 0.00 0.00 2.18
78 79 1.414550 CTCTAAGCACCTCCCCTAAGC 59.585 57.143 0.00 0.00 0.00 3.09
79 80 1.204146 CTAAGCACCTCCCCTAAGCA 58.796 55.000 0.00 0.00 0.00 3.91
80 81 0.909623 TAAGCACCTCCCCTAAGCAC 59.090 55.000 0.00 0.00 0.00 4.40
81 82 1.853250 AAGCACCTCCCCTAAGCACC 61.853 60.000 0.00 0.00 0.00 5.01
82 83 2.301738 GCACCTCCCCTAAGCACCT 61.302 63.158 0.00 0.00 0.00 4.00
83 84 1.853250 GCACCTCCCCTAAGCACCTT 61.853 60.000 0.00 0.00 0.00 3.50
84 85 0.035056 CACCTCCCCTAAGCACCTTG 60.035 60.000 0.00 0.00 0.00 3.61
85 86 1.077429 CCTCCCCTAAGCACCTTGC 60.077 63.158 0.00 0.00 45.46 4.01
101 102 2.950433 CTTGCATTGTACAAGGCCTTG 58.050 47.619 38.30 38.30 46.35 3.61
102 103 1.255882 TGCATTGTACAAGGCCTTGG 58.744 50.000 41.04 26.42 46.35 3.61
103 104 1.256812 GCATTGTACAAGGCCTTGGT 58.743 50.000 41.04 29.77 44.45 3.67
104 105 2.224892 TGCATTGTACAAGGCCTTGGTA 60.225 45.455 41.04 28.85 46.35 3.25
105 106 2.423538 GCATTGTACAAGGCCTTGGTAG 59.576 50.000 41.04 26.60 44.45 3.18
106 107 3.686016 CATTGTACAAGGCCTTGGTAGT 58.314 45.455 41.04 26.51 44.45 2.73
107 108 3.868619 TTGTACAAGGCCTTGGTAGTT 57.131 42.857 41.04 26.17 44.45 2.24
158 159 2.159240 TGCTGAACTACATGTCGGCTAG 60.159 50.000 14.94 4.62 0.00 3.42
183 184 5.125578 TCAAGCACTAATCGTGACTAGTCAT 59.874 40.000 27.54 14.63 46.81 3.06
214 215 3.181486 TGTCTATGAGTCGGCATTCTGAC 60.181 47.826 0.00 0.00 46.54 3.51
220 221 1.078759 GTCGGCATTCTGACCACTCG 61.079 60.000 0.00 0.00 41.64 4.18
245 246 5.651530 CTTGACTCGTAATTCTTGCTCCTA 58.348 41.667 0.00 0.00 0.00 2.94
273 274 5.403897 TGTTCGTATTAGCAATAGCAAGC 57.596 39.130 0.00 0.00 45.49 4.01
277 278 3.981416 CGTATTAGCAATAGCAAGCGAGA 59.019 43.478 0.00 0.00 45.49 4.04
354 355 4.918810 TTGTTCTGCTTCTCCCTTTTTC 57.081 40.909 0.00 0.00 0.00 2.29
362 363 3.885901 GCTTCTCCCTTTTTCTGTTGTCT 59.114 43.478 0.00 0.00 0.00 3.41
366 367 1.001378 CCCTTTTTCTGTTGTCTGCCG 60.001 52.381 0.00 0.00 0.00 5.69
368 369 1.065401 CTTTTTCTGTTGTCTGCCGCA 59.935 47.619 0.00 0.00 0.00 5.69
376 377 5.606505 TCTGTTGTCTGCCGCATAAATATA 58.393 37.500 0.00 0.00 0.00 0.86
380 381 6.094186 TGTTGTCTGCCGCATAAATATACAAA 59.906 34.615 0.00 0.00 0.00 2.83
382 383 5.586643 TGTCTGCCGCATAAATATACAAACA 59.413 36.000 0.00 0.00 0.00 2.83
399 400 5.120399 ACAAACATCACTCTTTCCGTTGTA 58.880 37.500 0.00 0.00 0.00 2.41
410 411 1.249407 TCCGTTGTATTTTGTGCCCC 58.751 50.000 0.00 0.00 0.00 5.80
431 432 7.825761 TGCCCCTCTTTATAGTGTTTTACTTAC 59.174 37.037 0.00 0.00 40.89 2.34
455 456 0.816825 ATAAGAGCGCATGCACCTGG 60.817 55.000 19.57 1.33 46.23 4.45
470 471 1.153289 CTGGCTGCGCTACATCCTT 60.153 57.895 9.73 0.00 35.46 3.36
714 731 6.071463 GCTTGCCGATTATAATTTAGTGTCG 58.929 40.000 0.00 0.00 0.00 4.35
716 735 6.758593 TGCCGATTATAATTTAGTGTCGTC 57.241 37.500 0.00 0.00 0.00 4.20
718 737 7.650890 TGCCGATTATAATTTAGTGTCGTCTA 58.349 34.615 0.00 0.00 0.00 2.59
719 738 7.806487 TGCCGATTATAATTTAGTGTCGTCTAG 59.194 37.037 0.00 0.00 0.00 2.43
780 799 9.844257 AAGAAATATCTATTTGCAGAGCTTACT 57.156 29.630 0.05 0.00 36.13 2.24
865 884 0.601558 CCATTTTGCTGCAGCTCTGT 59.398 50.000 36.61 18.98 42.66 3.41
1130 1149 2.408032 GCAGAAATCGATCGCTCTCATC 59.592 50.000 11.09 2.89 0.00 2.92
1246 1265 8.988747 GTAATCGGCAAATACGTTTAAACTTAC 58.011 33.333 16.01 9.13 30.32 2.34
1331 1353 9.817809 TTTTGATGATCAGGTAATGTACTCTAC 57.182 33.333 0.09 0.00 0.00 2.59
1370 1392 2.165030 CTGCCCTTGATGCGAAAGAAAT 59.835 45.455 0.00 0.00 0.00 2.17
1518 1544 5.689383 TGAAGAAAACTACAATGACCAGC 57.311 39.130 0.00 0.00 0.00 4.85
1589 1615 6.437928 ACAAACATTGTGTATTGCTGTAGTG 58.562 36.000 0.00 0.00 43.48 2.74
1715 1741 5.916320 TGCTTTTGATGCATTCATAATAGCG 59.084 36.000 0.00 0.00 35.31 4.26
1798 1833 4.370364 ACTCACACAGTCGCAAAATTTT 57.630 36.364 0.00 0.00 0.00 1.82
1900 1935 0.097674 GCGCCAGTTGCTCATAAGTG 59.902 55.000 0.00 0.00 38.05 3.16
1904 1939 2.430465 CCAGTTGCTCATAAGTGTGCT 58.570 47.619 4.44 0.00 43.42 4.40
1929 1964 5.305644 GTCACTATCTGTGTCATTATCCCCT 59.694 44.000 0.00 0.00 46.27 4.79
1972 2007 8.681806 CAAAATTGAATTTTTGGTAAAGTGGGT 58.318 29.630 12.81 0.00 40.27 4.51
1982 2017 2.160205 GTAAAGTGGGTTCTTCTGGCC 58.840 52.381 0.00 0.00 0.00 5.36
2079 2115 5.750352 ATGGAATTTTGGCCCATCATATC 57.250 39.130 0.00 0.00 35.95 1.63
2103 2139 7.015680 TCCATATTTGTTTGGGCCACATATAT 58.984 34.615 5.23 9.76 32.26 0.86
2237 2288 6.457799 CGTTGGGTATTTAGGATTTACTGTGC 60.458 42.308 0.00 0.00 0.00 4.57
2333 2400 7.121611 TGCTCATCATCATGTAAACACTGATTT 59.878 33.333 0.00 0.00 0.00 2.17
2594 2665 5.410924 TGTTCTCGTAGATGGAGTTTCATG 58.589 41.667 0.00 0.00 33.89 3.07
2685 2758 4.997395 CGCTAGAAGGTTTATGCACCATAT 59.003 41.667 0.00 0.00 39.62 1.78
2800 2874 4.438608 GCAATTCATTAGTCGTGAATGCCA 60.439 41.667 2.48 0.00 43.49 4.92
2807 2881 3.845781 AGTCGTGAATGCCATCCTAAT 57.154 42.857 0.00 0.00 0.00 1.73
2895 2969 3.056678 CCTTGTAGGAAATTGCATGTGCA 60.057 43.478 3.09 3.09 43.72 4.57
2924 2998 6.978343 TGTCATGTTTATGTTACCTAGTGC 57.022 37.500 0.00 0.00 35.73 4.40
2956 3030 3.939592 GGTTAGTTGCTTCAGTGGTATCC 59.060 47.826 0.00 0.00 0.00 2.59
2973 3047 6.537301 GTGGTATCCGATATGTGAACAAGAAA 59.463 38.462 0.00 0.00 0.00 2.52
2986 3060 6.183360 TGTGAACAAGAAACTTCATCATGCTT 60.183 34.615 0.00 0.00 0.00 3.91
2994 3068 8.114331 AGAAACTTCATCATGCTTGTATTTGA 57.886 30.769 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.522185 TGTCAGGGTAGACGCTTAGTT 58.478 47.619 0.00 0.00 41.41 2.24
2 3 3.587797 TTTGTCAGGGTAGACGCTTAG 57.412 47.619 0.00 0.00 41.41 2.18
3 4 4.439153 CGTATTTGTCAGGGTAGACGCTTA 60.439 45.833 0.00 0.00 41.41 3.09
5 6 2.159282 CGTATTTGTCAGGGTAGACGCT 60.159 50.000 0.00 0.00 41.41 5.07
6 7 2.190981 CGTATTTGTCAGGGTAGACGC 58.809 52.381 0.00 0.00 41.41 5.19
7 8 2.190981 GCGTATTTGTCAGGGTAGACG 58.809 52.381 0.00 0.00 41.41 4.18
8 9 2.928116 GTGCGTATTTGTCAGGGTAGAC 59.072 50.000 0.00 0.00 38.99 2.59
9 10 2.093869 GGTGCGTATTTGTCAGGGTAGA 60.094 50.000 0.00 0.00 0.00 2.59
10 11 2.277084 GGTGCGTATTTGTCAGGGTAG 58.723 52.381 0.00 0.00 0.00 3.18
11 12 1.404449 CGGTGCGTATTTGTCAGGGTA 60.404 52.381 0.00 0.00 0.00 3.69
12 13 0.672401 CGGTGCGTATTTGTCAGGGT 60.672 55.000 0.00 0.00 0.00 4.34
13 14 1.366111 CCGGTGCGTATTTGTCAGGG 61.366 60.000 0.00 0.00 0.00 4.45
14 15 0.672401 ACCGGTGCGTATTTGTCAGG 60.672 55.000 6.12 0.00 0.00 3.86
15 16 0.442310 CACCGGTGCGTATTTGTCAG 59.558 55.000 24.02 0.00 0.00 3.51
16 17 2.534452 CACCGGTGCGTATTTGTCA 58.466 52.632 24.02 0.00 0.00 3.58
27 28 3.058914 CAGACTTTTCTTAAGCACCGGTG 60.059 47.826 30.66 30.66 0.00 4.94
28 29 3.139077 CAGACTTTTCTTAAGCACCGGT 58.861 45.455 0.00 0.00 0.00 5.28
29 30 2.484264 CCAGACTTTTCTTAAGCACCGG 59.516 50.000 0.00 0.00 0.00 5.28
30 31 3.139077 ACCAGACTTTTCTTAAGCACCG 58.861 45.455 0.00 0.00 0.00 4.94
31 32 5.515797 AAACCAGACTTTTCTTAAGCACC 57.484 39.130 0.00 0.00 0.00 5.01
32 33 9.181805 GAAATAAACCAGACTTTTCTTAAGCAC 57.818 33.333 0.00 0.00 0.00 4.40
33 34 9.131791 AGAAATAAACCAGACTTTTCTTAAGCA 57.868 29.630 0.00 0.00 33.97 3.91
34 35 9.613957 GAGAAATAAACCAGACTTTTCTTAAGC 57.386 33.333 0.00 0.00 36.91 3.09
39 40 9.004717 GCTTAGAGAAATAAACCAGACTTTTCT 57.995 33.333 0.00 0.00 38.86 2.52
40 41 8.784043 TGCTTAGAGAAATAAACCAGACTTTTC 58.216 33.333 0.00 0.00 0.00 2.29
41 42 8.568794 GTGCTTAGAGAAATAAACCAGACTTTT 58.431 33.333 0.00 0.00 0.00 2.27
42 43 7.175119 GGTGCTTAGAGAAATAAACCAGACTTT 59.825 37.037 0.00 0.00 0.00 2.66
43 44 6.655425 GGTGCTTAGAGAAATAAACCAGACTT 59.345 38.462 0.00 0.00 0.00 3.01
44 45 6.013293 AGGTGCTTAGAGAAATAAACCAGACT 60.013 38.462 0.00 0.00 0.00 3.24
45 46 6.174049 AGGTGCTTAGAGAAATAAACCAGAC 58.826 40.000 0.00 0.00 0.00 3.51
46 47 6.374417 AGGTGCTTAGAGAAATAAACCAGA 57.626 37.500 0.00 0.00 0.00 3.86
47 48 5.586643 GGAGGTGCTTAGAGAAATAAACCAG 59.413 44.000 0.00 0.00 0.00 4.00
48 49 5.497474 GGAGGTGCTTAGAGAAATAAACCA 58.503 41.667 0.00 0.00 0.00 3.67
49 50 4.882427 GGGAGGTGCTTAGAGAAATAAACC 59.118 45.833 0.00 0.00 0.00 3.27
50 51 4.882427 GGGGAGGTGCTTAGAGAAATAAAC 59.118 45.833 0.00 0.00 0.00 2.01
51 52 4.788617 AGGGGAGGTGCTTAGAGAAATAAA 59.211 41.667 0.00 0.00 0.00 1.40
52 53 4.371681 AGGGGAGGTGCTTAGAGAAATAA 58.628 43.478 0.00 0.00 0.00 1.40
53 54 4.008916 AGGGGAGGTGCTTAGAGAAATA 57.991 45.455 0.00 0.00 0.00 1.40
54 55 2.852130 AGGGGAGGTGCTTAGAGAAAT 58.148 47.619 0.00 0.00 0.00 2.17
55 56 2.344093 AGGGGAGGTGCTTAGAGAAA 57.656 50.000 0.00 0.00 0.00 2.52
56 57 3.375699 CTTAGGGGAGGTGCTTAGAGAA 58.624 50.000 0.00 0.00 0.00 2.87
57 58 2.955461 GCTTAGGGGAGGTGCTTAGAGA 60.955 54.545 0.00 0.00 0.00 3.10
58 59 1.414550 GCTTAGGGGAGGTGCTTAGAG 59.585 57.143 0.00 0.00 0.00 2.43
59 60 1.273609 TGCTTAGGGGAGGTGCTTAGA 60.274 52.381 0.00 0.00 0.00 2.10
60 61 1.134371 GTGCTTAGGGGAGGTGCTTAG 60.134 57.143 0.00 0.00 0.00 2.18
61 62 0.909623 GTGCTTAGGGGAGGTGCTTA 59.090 55.000 0.00 0.00 0.00 3.09
62 63 1.685820 GTGCTTAGGGGAGGTGCTT 59.314 57.895 0.00 0.00 0.00 3.91
63 64 2.301738 GGTGCTTAGGGGAGGTGCT 61.302 63.158 0.00 0.00 0.00 4.40
64 65 1.853250 AAGGTGCTTAGGGGAGGTGC 61.853 60.000 0.00 0.00 0.00 5.01
65 66 0.035056 CAAGGTGCTTAGGGGAGGTG 60.035 60.000 0.00 0.00 0.00 4.00
66 67 1.853250 GCAAGGTGCTTAGGGGAGGT 61.853 60.000 0.00 0.00 40.96 3.85
67 68 1.077429 GCAAGGTGCTTAGGGGAGG 60.077 63.158 0.00 0.00 40.96 4.30
68 69 0.257039 ATGCAAGGTGCTTAGGGGAG 59.743 55.000 0.00 0.00 45.31 4.30
69 70 0.704076 AATGCAAGGTGCTTAGGGGA 59.296 50.000 0.00 0.00 45.31 4.81
70 71 0.819582 CAATGCAAGGTGCTTAGGGG 59.180 55.000 0.00 0.00 45.31 4.79
71 72 1.549203 ACAATGCAAGGTGCTTAGGG 58.451 50.000 0.00 0.00 45.31 3.53
72 73 3.081061 TGTACAATGCAAGGTGCTTAGG 58.919 45.455 9.81 0.00 45.31 2.69
73 74 4.726416 CTTGTACAATGCAAGGTGCTTAG 58.274 43.478 9.13 4.87 45.31 2.18
74 75 4.764679 CTTGTACAATGCAAGGTGCTTA 57.235 40.909 9.13 0.00 45.31 3.09
75 76 3.648339 CTTGTACAATGCAAGGTGCTT 57.352 42.857 9.13 0.00 45.31 3.91
81 82 2.353011 CCAAGGCCTTGTACAATGCAAG 60.353 50.000 37.09 18.32 42.00 4.01
82 83 1.617850 CCAAGGCCTTGTACAATGCAA 59.382 47.619 37.09 1.35 38.85 4.08
83 84 1.255882 CCAAGGCCTTGTACAATGCA 58.744 50.000 37.09 1.72 38.85 3.96
84 85 1.256812 ACCAAGGCCTTGTACAATGC 58.743 50.000 37.09 23.06 38.85 3.56
85 86 3.686016 ACTACCAAGGCCTTGTACAATG 58.314 45.455 37.09 25.24 38.85 2.82
86 87 4.382386 AACTACCAAGGCCTTGTACAAT 57.618 40.909 37.09 21.04 38.85 2.71
87 88 3.868619 AACTACCAAGGCCTTGTACAA 57.131 42.857 37.09 21.11 38.85 2.41
88 89 4.348754 ACTTAACTACCAAGGCCTTGTACA 59.651 41.667 37.09 23.02 38.85 2.90
89 90 4.903054 ACTTAACTACCAAGGCCTTGTAC 58.097 43.478 37.09 0.00 38.85 2.90
90 91 5.781818 AGTACTTAACTACCAAGGCCTTGTA 59.218 40.000 37.09 27.53 36.33 2.41
91 92 4.596212 AGTACTTAACTACCAAGGCCTTGT 59.404 41.667 37.09 27.85 36.33 3.16
92 93 5.161943 AGTACTTAACTACCAAGGCCTTG 57.838 43.478 34.60 34.60 36.36 3.61
93 94 7.843252 ACTATAGTACTTAACTACCAAGGCCTT 59.157 37.037 13.78 13.78 43.47 4.35
94 95 7.360643 ACTATAGTACTTAACTACCAAGGCCT 58.639 38.462 0.00 0.00 43.47 5.19
95 96 7.594351 ACTATAGTACTTAACTACCAAGGCC 57.406 40.000 2.75 0.00 43.47 5.19
136 137 1.002366 GCCGACATGTAGTTCAGCAG 58.998 55.000 0.00 0.00 0.00 4.24
138 139 2.159226 ACTAGCCGACATGTAGTTCAGC 60.159 50.000 0.00 0.00 0.00 4.26
140 141 3.086282 TGACTAGCCGACATGTAGTTCA 58.914 45.455 0.00 0.00 0.00 3.18
169 170 8.948631 ACAAATTAATCATGACTAGTCACGAT 57.051 30.769 24.87 24.87 43.37 3.73
183 184 6.345298 TGCCGACTCATAGACAAATTAATCA 58.655 36.000 0.00 0.00 0.00 2.57
185 186 7.716998 AGAATGCCGACTCATAGACAAATTAAT 59.283 33.333 0.00 0.00 0.00 1.40
203 204 1.811266 CCGAGTGGTCAGAATGCCG 60.811 63.158 0.00 0.00 35.46 5.69
214 215 0.242825 TTACGAGTCAAGCCGAGTGG 59.757 55.000 0.00 0.00 38.77 4.00
215 216 2.279582 ATTACGAGTCAAGCCGAGTG 57.720 50.000 0.00 0.00 0.00 3.51
220 221 3.003480 AGCAAGAATTACGAGTCAAGCC 58.997 45.455 0.00 0.00 0.00 4.35
245 246 8.657074 TGCTATTGCTAATACGAACATTAACT 57.343 30.769 0.00 0.00 40.48 2.24
273 274 6.273825 AGTAATGTGTAATACAAGGCTCTCG 58.726 40.000 0.00 0.00 43.77 4.04
277 278 5.190925 TGGGAGTAATGTGTAATACAAGGCT 59.809 40.000 0.00 0.00 43.77 4.58
279 280 9.621629 TTATTGGGAGTAATGTGTAATACAAGG 57.378 33.333 0.00 0.00 43.77 3.61
290 291 8.877864 TCTGTGAAAATTATTGGGAGTAATGT 57.122 30.769 0.00 0.00 0.00 2.71
354 355 4.818534 ATATTTATGCGGCAGACAACAG 57.181 40.909 9.25 0.00 0.00 3.16
362 363 6.262049 AGTGATGTTTGTATATTTATGCGGCA 59.738 34.615 4.58 4.58 0.00 5.69
376 377 3.945285 ACAACGGAAAGAGTGATGTTTGT 59.055 39.130 0.00 0.00 0.00 2.83
380 381 6.262273 ACAAAATACAACGGAAAGAGTGATGT 59.738 34.615 0.00 0.00 0.00 3.06
382 383 6.668323 CACAAAATACAACGGAAAGAGTGAT 58.332 36.000 0.00 0.00 0.00 3.06
394 395 4.600692 AAAGAGGGGCACAAAATACAAC 57.399 40.909 0.00 0.00 0.00 3.32
399 400 5.580022 ACACTATAAAGAGGGGCACAAAAT 58.420 37.500 0.00 0.00 0.00 1.82
460 461 5.080969 TGTACACCAAGTAAGGATGTAGC 57.919 43.478 0.00 0.00 33.72 3.58
503 504 4.160065 CCCCACATCTTGCACATTTGATTA 59.840 41.667 0.00 0.00 0.00 1.75
505 506 2.498481 CCCCACATCTTGCACATTTGAT 59.502 45.455 0.00 0.00 0.00 2.57
707 724 7.821359 ACAACAACTACTATCTAGACGACACTA 59.179 37.037 0.00 0.00 0.00 2.74
714 731 7.969508 GGTGAGAACAACAACTACTATCTAGAC 59.030 40.741 0.00 0.00 33.34 2.59
716 735 8.057536 AGGTGAGAACAACAACTACTATCTAG 57.942 38.462 0.00 0.00 35.97 2.43
718 737 6.919775 AGGTGAGAACAACAACTACTATCT 57.080 37.500 0.00 0.00 35.97 1.98
719 738 7.152645 TCAAGGTGAGAACAACAACTACTATC 58.847 38.462 0.00 0.00 33.95 2.08
780 799 6.040391 CACTGTTCCATTCCAAGACCTTTTTA 59.960 38.462 0.00 0.00 0.00 1.52
865 884 2.344592 TCCTTGGAGACTTTGCCCTAA 58.655 47.619 0.00 0.00 0.00 2.69
1130 1149 7.838771 TCATTATCCTGCATATTCAGAATCG 57.161 36.000 3.72 0.00 36.19 3.34
1246 1265 3.428534 GCAGTTTGCCGTTTCTTATTTGG 59.571 43.478 0.00 0.00 37.42 3.28
1331 1353 4.929211 GGGCAGTGCTTAAAAATAAACTGG 59.071 41.667 16.11 0.00 36.41 4.00
1370 1392 4.039004 CCAAACCACACAAATCTCCATTGA 59.961 41.667 0.00 0.00 0.00 2.57
1589 1615 4.793216 CCAAACGTCATAGTTGCAATTAGC 59.207 41.667 0.59 0.00 45.96 3.09
1715 1741 4.314121 ACAAGATGAAAGAGAGTGTGCTC 58.686 43.478 0.00 0.00 41.94 4.26
1798 1833 6.071221 TCCAAAATACAAGGCTACGAGTAAGA 60.071 38.462 0.00 0.00 0.00 2.10
1972 2007 4.524802 ACATAATGATGGGCCAGAAGAA 57.475 40.909 13.78 0.00 37.39 2.52
1982 2017 5.106555 GCCCAATTCGAGTACATAATGATGG 60.107 44.000 0.00 0.00 37.39 3.51
2079 2115 3.910568 ATGTGGCCCAAACAAATATGG 57.089 42.857 0.00 0.00 36.42 2.74
2103 2139 8.999895 AGTTCCATTTATAAGCCTAGTTCCTTA 58.000 33.333 0.00 0.00 0.00 2.69
2333 2400 7.847096 TCAAAGAAGTTGTATATAGCACTGGA 58.153 34.615 0.00 0.00 38.47 3.86
2685 2758 4.583073 CCATCATGCATCCTTTCTCATCAA 59.417 41.667 0.00 0.00 0.00 2.57
2725 2799 5.278463 CCCTGACTCAACTTAACCATGTTTG 60.278 44.000 0.00 0.00 0.00 2.93
2800 2874 4.756564 TCTCTCATGCCACCTATTAGGAT 58.243 43.478 16.80 0.00 37.67 3.24
2807 2881 4.033009 TCATTTCTCTCTCATGCCACCTA 58.967 43.478 0.00 0.00 0.00 3.08
2816 2890 4.687948 CGCTTTCACTTCATTTCTCTCTCA 59.312 41.667 0.00 0.00 0.00 3.27
2895 2969 9.383519 CTAGGTAACATAAACATGACAAGTGAT 57.616 33.333 0.00 0.00 41.41 3.06
2956 3030 7.742151 TGATGAAGTTTCTTGTTCACATATCG 58.258 34.615 0.00 0.00 35.55 2.92
2973 3047 7.833786 ACAATCAAATACAAGCATGATGAAGT 58.166 30.769 0.00 0.00 33.06 3.01


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

AutoCloner maintained by Alex Coulton.