Multiple sequence alignment - TraesCS7D01G401400

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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 TraesCS7D01G401400 chr7D 100.000 2708 0 0 1 2708 518622820 518625527 0.000000e+00 5001.0
1 TraesCS7D01G401400 chr7D 98.168 655 12 0 2054 2708 582180433 582179779 0.000000e+00 1144.0
2 TraesCS7D01G401400 chr7D 83.066 809 85 28 750 1555 519148627 519147868 0.000000e+00 688.0
3 TraesCS7D01G401400 chr7D 84.778 519 59 13 1340 1839 518879071 518878554 1.120000e-138 503.0
4 TraesCS7D01G401400 chr7D 84.096 459 45 15 1591 2026 519147861 519147408 4.170000e-113 418.0
5 TraesCS7D01G401400 chr7D 86.462 325 37 6 444 763 518885467 518885145 1.540000e-92 350.0
6 TraesCS7D01G401400 chr7D 77.796 599 64 28 750 1344 518884997 518884464 3.390000e-79 305.0
7 TraesCS7D01G401400 chr7D 83.237 173 21 4 599 764 519148933 519148762 4.670000e-33 152.0
8 TraesCS7D01G401400 chr7B 91.377 1902 73 30 176 2029 551930466 551932324 0.000000e+00 2519.0
9 TraesCS7D01G401400 chr7B 81.489 1048 112 35 961 1983 552133982 552132992 0.000000e+00 785.0
10 TraesCS7D01G401400 chr7B 84.694 98 8 5 860 955 552140358 552140266 1.030000e-14 91.6
11 TraesCS7D01G401400 chr7A 89.153 1475 63 42 537 1923 593445817 593447282 0.000000e+00 1748.0
12 TraesCS7D01G401400 chr7A 81.873 1153 131 34 924 2053 594599745 594598648 0.000000e+00 900.0
13 TraesCS7D01G401400 chr1A 93.072 664 34 5 2054 2708 459189374 459190034 0.000000e+00 961.0
14 TraesCS7D01G401400 chr2B 93.906 640 32 5 2073 2708 748871218 748871854 0.000000e+00 959.0
15 TraesCS7D01G401400 chr6B 93.417 638 35 4 2075 2708 683497215 683496581 0.000000e+00 939.0
16 TraesCS7D01G401400 chr6B 92.846 643 37 5 2072 2708 683499170 683498531 0.000000e+00 924.0
17 TraesCS7D01G401400 chr6B 91.581 677 39 4 2050 2708 523507216 523506540 0.000000e+00 918.0
18 TraesCS7D01G401400 chr6B 89.940 666 55 11 2045 2708 101199593 101200248 0.000000e+00 848.0
19 TraesCS7D01G401400 chr6B 92.662 586 33 5 2129 2708 633850228 633850809 0.000000e+00 835.0
20 TraesCS7D01G401400 chr2A 90.090 666 40 13 2048 2708 686873149 686872505 0.000000e+00 841.0
21 TraesCS7D01G401400 chr1B 83.562 146 21 3 2052 2196 567969449 567969306 1.690000e-27 134.0


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 TraesCS7D01G401400 chr7D 518622820 518625527 2707 False 5001.000000 5001 100.000000 1 2708 1 chr7D.!!$F1 2707
1 TraesCS7D01G401400 chr7D 582179779 582180433 654 True 1144.000000 1144 98.168000 2054 2708 1 chr7D.!!$R2 654
2 TraesCS7D01G401400 chr7D 518878554 518879071 517 True 503.000000 503 84.778000 1340 1839 1 chr7D.!!$R1 499
3 TraesCS7D01G401400 chr7D 519147408 519148933 1525 True 419.333333 688 83.466333 599 2026 3 chr7D.!!$R4 1427
4 TraesCS7D01G401400 chr7D 518884464 518885467 1003 True 327.500000 350 82.129000 444 1344 2 chr7D.!!$R3 900
5 TraesCS7D01G401400 chr7B 551930466 551932324 1858 False 2519.000000 2519 91.377000 176 2029 1 chr7B.!!$F1 1853
6 TraesCS7D01G401400 chr7B 552132992 552133982 990 True 785.000000 785 81.489000 961 1983 1 chr7B.!!$R1 1022
7 TraesCS7D01G401400 chr7A 593445817 593447282 1465 False 1748.000000 1748 89.153000 537 1923 1 chr7A.!!$F1 1386
8 TraesCS7D01G401400 chr7A 594598648 594599745 1097 True 900.000000 900 81.873000 924 2053 1 chr7A.!!$R1 1129
9 TraesCS7D01G401400 chr1A 459189374 459190034 660 False 961.000000 961 93.072000 2054 2708 1 chr1A.!!$F1 654
10 TraesCS7D01G401400 chr2B 748871218 748871854 636 False 959.000000 959 93.906000 2073 2708 1 chr2B.!!$F1 635
11 TraesCS7D01G401400 chr6B 683496581 683499170 2589 True 931.500000 939 93.131500 2072 2708 2 chr6B.!!$R2 636
12 TraesCS7D01G401400 chr6B 523506540 523507216 676 True 918.000000 918 91.581000 2050 2708 1 chr6B.!!$R1 658
13 TraesCS7D01G401400 chr6B 101199593 101200248 655 False 848.000000 848 89.940000 2045 2708 1 chr6B.!!$F1 663
14 TraesCS7D01G401400 chr6B 633850228 633850809 581 False 835.000000 835 92.662000 2129 2708 1 chr6B.!!$F2 579
15 TraesCS7D01G401400 chr2A 686872505 686873149 644 True 841.000000 841 90.090000 2048 2708 1 chr2A.!!$R1 660

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
132 133 0.107654 AAGCGCCGCTTCTCCTAATT 60.108 50.0 20.26 0.0 46.77 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2374 0.249398 GTGGCAGTTATCGGTGTCCT 59.751 55.0 0.0 0.0 0.0 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
20 21 0.447801 ATGGCGTGAGTTTGATTCGC 59.552 50.000 0.00 0.00 44.95 4.70
21 22 4.745549 GCGTGAGTTTGATTCGCC 57.254 55.556 0.00 0.00 40.83 5.54
22 23 1.225745 GCGTGAGTTTGATTCGCCG 60.226 57.895 0.00 0.00 40.83 6.46
23 24 1.225745 CGTGAGTTTGATTCGCCGC 60.226 57.895 0.00 0.00 0.00 6.53
24 25 1.225745 GTGAGTTTGATTCGCCGCG 60.226 57.895 6.39 6.39 0.00 6.46
25 26 2.387445 TGAGTTTGATTCGCCGCGG 61.387 57.895 24.05 24.05 0.00 6.46
26 27 3.095898 GAGTTTGATTCGCCGCGGG 62.096 63.158 29.38 17.41 0.00 6.13
27 28 3.122323 GTTTGATTCGCCGCGGGA 61.122 61.111 29.38 19.62 0.00 5.14
28 29 3.122323 TTTGATTCGCCGCGGGAC 61.122 61.111 29.38 10.39 0.00 4.46
31 32 4.832608 GATTCGCCGCGGGACCTT 62.833 66.667 29.38 9.61 0.00 3.50
36 37 2.750237 GCCGCGGGACCTTGATTT 60.750 61.111 29.38 0.00 0.00 2.17
37 38 2.340328 GCCGCGGGACCTTGATTTT 61.340 57.895 29.38 0.00 0.00 1.82
38 39 1.873270 GCCGCGGGACCTTGATTTTT 61.873 55.000 29.38 0.00 0.00 1.94
65 66 9.723447 TTATTCTTTTCGCGCATTTTATTATCA 57.277 25.926 8.75 0.00 0.00 2.15
66 67 8.801715 ATTCTTTTCGCGCATTTTATTATCAT 57.198 26.923 8.75 0.00 0.00 2.45
67 68 8.627487 TTCTTTTCGCGCATTTTATTATCATT 57.373 26.923 8.75 0.00 0.00 2.57
68 69 8.627487 TCTTTTCGCGCATTTTATTATCATTT 57.373 26.923 8.75 0.00 0.00 2.32
69 70 9.081997 TCTTTTCGCGCATTTTATTATCATTTT 57.918 25.926 8.75 0.00 0.00 1.82
70 71 9.135384 CTTTTCGCGCATTTTATTATCATTTTG 57.865 29.630 8.75 0.00 0.00 2.44
71 72 7.748031 TTCGCGCATTTTATTATCATTTTGT 57.252 28.000 8.75 0.00 0.00 2.83
72 73 7.147550 TCGCGCATTTTATTATCATTTTGTG 57.852 32.000 8.75 0.00 0.00 3.33
73 74 6.198029 TCGCGCATTTTATTATCATTTTGTGG 59.802 34.615 8.75 0.00 0.00 4.17
74 75 6.128729 GCGCATTTTATTATCATTTTGTGGC 58.871 36.000 0.30 0.00 0.00 5.01
75 76 6.238049 GCGCATTTTATTATCATTTTGTGGCA 60.238 34.615 0.30 0.00 0.00 4.92
76 77 7.675870 GCGCATTTTATTATCATTTTGTGGCAA 60.676 33.333 0.30 0.00 0.00 4.52
77 78 8.336806 CGCATTTTATTATCATTTTGTGGCAAT 58.663 29.630 0.00 0.00 0.00 3.56
78 79 9.440784 GCATTTTATTATCATTTTGTGGCAATG 57.559 29.630 0.00 0.00 33.55 2.82
79 80 9.440784 CATTTTATTATCATTTTGTGGCAATGC 57.559 29.630 0.00 0.00 32.49 3.56
89 90 3.451894 GGCAATGCCCCTTCGTGG 61.452 66.667 14.47 0.00 44.06 4.94
110 111 4.752879 GGCCCAGTTCGCGCTGTA 62.753 66.667 5.56 0.00 34.84 2.74
111 112 3.188786 GCCCAGTTCGCGCTGTAG 61.189 66.667 5.56 0.00 34.84 2.74
112 113 3.188786 CCCAGTTCGCGCTGTAGC 61.189 66.667 5.56 0.00 34.84 3.58
113 114 2.432456 CCAGTTCGCGCTGTAGCA 60.432 61.111 5.56 0.00 42.21 3.49
114 115 2.027073 CCAGTTCGCGCTGTAGCAA 61.027 57.895 5.56 0.00 42.21 3.91
115 116 1.417592 CAGTTCGCGCTGTAGCAAG 59.582 57.895 5.56 0.00 42.21 4.01
116 117 2.096594 GTTCGCGCTGTAGCAAGC 59.903 61.111 5.56 0.00 42.21 4.01
124 125 3.088500 CTGTAGCAAGCGCCGCTTC 62.089 63.158 23.32 20.18 46.77 3.86
125 126 2.815647 GTAGCAAGCGCCGCTTCT 60.816 61.111 23.32 22.03 46.77 2.85
126 127 2.509336 TAGCAAGCGCCGCTTCTC 60.509 61.111 23.32 16.33 46.77 2.87
129 130 2.184322 CAAGCGCCGCTTCTCCTA 59.816 61.111 23.32 0.00 46.77 2.94
130 131 1.447838 CAAGCGCCGCTTCTCCTAA 60.448 57.895 23.32 0.00 46.77 2.69
131 132 0.811616 CAAGCGCCGCTTCTCCTAAT 60.812 55.000 23.32 0.00 46.77 1.73
132 133 0.107654 AAGCGCCGCTTCTCCTAATT 60.108 50.000 20.26 0.00 46.77 1.40
133 134 0.811616 AGCGCCGCTTCTCCTAATTG 60.812 55.000 5.39 0.00 33.89 2.32
134 135 1.776034 GCGCCGCTTCTCCTAATTGG 61.776 60.000 0.00 0.00 37.10 3.16
135 136 1.776034 CGCCGCTTCTCCTAATTGGC 61.776 60.000 0.00 0.00 37.66 4.52
136 137 1.776034 GCCGCTTCTCCTAATTGGCG 61.776 60.000 0.00 0.00 41.84 5.69
137 138 1.643832 CGCTTCTCCTAATTGGCGC 59.356 57.895 0.00 0.00 36.46 6.53
138 139 0.811616 CGCTTCTCCTAATTGGCGCT 60.812 55.000 7.64 0.00 36.46 5.92
139 140 0.659957 GCTTCTCCTAATTGGCGCTG 59.340 55.000 7.64 0.00 35.26 5.18
140 141 1.743772 GCTTCTCCTAATTGGCGCTGA 60.744 52.381 7.64 0.00 35.26 4.26
141 142 2.632377 CTTCTCCTAATTGGCGCTGAA 58.368 47.619 7.64 0.20 35.26 3.02
142 143 2.315925 TCTCCTAATTGGCGCTGAAG 57.684 50.000 7.64 0.00 35.26 3.02
143 144 1.134401 TCTCCTAATTGGCGCTGAAGG 60.134 52.381 7.64 7.89 35.26 3.46
144 145 0.748005 TCCTAATTGGCGCTGAAGGC 60.748 55.000 7.64 0.00 35.26 4.35
162 163 2.812499 GCCGAGCACCGATTAGGA 59.188 61.111 0.00 0.00 45.00 2.94
163 164 1.300233 GCCGAGCACCGATTAGGAG 60.300 63.158 0.00 0.00 45.00 3.69
169 170 1.364171 CACCGATTAGGAGCTCCCG 59.636 63.158 29.54 23.51 45.00 5.14
170 171 1.076192 ACCGATTAGGAGCTCCCGT 60.076 57.895 29.54 14.62 45.00 5.28
171 172 1.108132 ACCGATTAGGAGCTCCCGTC 61.108 60.000 29.54 21.61 45.00 4.79
172 173 1.283181 CGATTAGGAGCTCCCGTCG 59.717 63.158 29.54 28.03 40.87 5.12
173 174 1.445716 CGATTAGGAGCTCCCGTCGT 61.446 60.000 29.48 17.07 40.87 4.34
174 175 0.745468 GATTAGGAGCTCCCGTCGTT 59.255 55.000 29.54 12.24 40.87 3.85
251 252 1.065926 CATGTGGCTGGCTCTTAGTGA 60.066 52.381 2.00 0.00 0.00 3.41
252 253 1.055849 TGTGGCTGGCTCTTAGTGAA 58.944 50.000 2.00 0.00 0.00 3.18
253 254 1.630369 TGTGGCTGGCTCTTAGTGAAT 59.370 47.619 2.00 0.00 0.00 2.57
254 255 2.837591 TGTGGCTGGCTCTTAGTGAATA 59.162 45.455 2.00 0.00 0.00 1.75
255 256 3.118629 TGTGGCTGGCTCTTAGTGAATAG 60.119 47.826 2.00 0.00 0.00 1.73
256 257 3.107601 TGGCTGGCTCTTAGTGAATAGT 58.892 45.455 2.00 0.00 0.00 2.12
257 258 3.118629 TGGCTGGCTCTTAGTGAATAGTG 60.119 47.826 2.00 0.00 0.00 2.74
274 275 6.599244 TGAATAGTGATCATTGTTGGACTTCC 59.401 38.462 4.93 0.00 0.00 3.46
290 291 2.501223 TTCCGATCGACTGGCACACC 62.501 60.000 18.66 0.00 0.00 4.16
291 292 2.261361 CGATCGACTGGCACACCA 59.739 61.111 10.26 0.00 46.51 4.17
292 293 2.094659 CGATCGACTGGCACACCAC 61.095 63.158 10.26 0.00 42.67 4.16
293 294 2.048222 ATCGACTGGCACACCACG 60.048 61.111 0.00 0.00 42.67 4.94
294 295 3.589654 ATCGACTGGCACACCACGG 62.590 63.158 0.00 0.00 42.67 4.94
337 340 3.367703 GCCCATTTTGTGATCAAGGTCAG 60.368 47.826 0.00 0.00 34.88 3.51
366 369 9.736414 AATGATCAATCATATTCTCCTTACCTG 57.264 33.333 0.00 0.00 46.22 4.00
367 370 7.164122 TGATCAATCATATTCTCCTTACCTGC 58.836 38.462 0.00 0.00 0.00 4.85
374 377 6.266786 TCATATTCTCCTTACCTGCGTTATGA 59.733 38.462 0.00 0.00 0.00 2.15
378 381 1.567504 CTTACCTGCGTTATGACCCG 58.432 55.000 0.00 0.00 0.00 5.28
383 386 2.895372 GCGTTATGACCCGCCAGG 60.895 66.667 0.00 0.00 43.96 4.45
427 430 3.191162 TGCTTCGCTGAATGTAGCAAAAT 59.809 39.130 0.00 0.00 43.87 1.82
433 436 8.432110 TTCGCTGAATGTAGCAAAATTATCTA 57.568 30.769 0.00 0.00 43.87 1.98
437 440 9.443283 GCTGAATGTAGCAAAATTATCTAACAG 57.557 33.333 0.00 0.00 43.17 3.16
506 510 4.814294 GGCGGCAGGTGTACCTCG 62.814 72.222 3.07 4.28 46.65 4.63
519 523 4.344390 GGTGTACCTCGGAGGAGATTTTAT 59.656 45.833 30.13 7.87 43.27 1.40
547 551 0.665835 TTGTTGCGCTTAGTGGGTTG 59.334 50.000 9.73 0.00 0.00 3.77
568 573 4.735369 TGGTGTGGAAGGAAATGTTGTAT 58.265 39.130 0.00 0.00 0.00 2.29
569 574 4.764823 TGGTGTGGAAGGAAATGTTGTATC 59.235 41.667 0.00 0.00 0.00 2.24
588 600 6.804677 TGTATCTGAAATGCAGTTTTTGTGT 58.195 32.000 0.00 0.00 45.14 3.72
655 667 5.008712 GCTGCAACTAACCTAATTATGACCC 59.991 44.000 0.00 0.00 0.00 4.46
902 1102 1.296392 CACCGCTCCATCCAACTCA 59.704 57.895 0.00 0.00 0.00 3.41
906 1106 1.672881 CCGCTCCATCCAACTCAATTC 59.327 52.381 0.00 0.00 0.00 2.17
968 1177 3.826754 AGCTCGATCGAAGCGCCA 61.827 61.111 19.92 0.00 0.00 5.69
1024 1244 4.636435 CCGACCACCACCACCACC 62.636 72.222 0.00 0.00 0.00 4.61
1025 1245 4.980805 CGACCACCACCACCACCG 62.981 72.222 0.00 0.00 0.00 4.94
1037 1257 4.920112 CCACCGCCACCACGTGAA 62.920 66.667 19.30 0.00 35.23 3.18
1038 1258 3.645975 CACCGCCACCACGTGAAC 61.646 66.667 19.30 1.92 35.23 3.18
1039 1259 4.922026 ACCGCCACCACGTGAACC 62.922 66.667 19.30 1.16 35.23 3.62
1091 1311 3.781307 CCGCCATGGGAGGAACGA 61.781 66.667 15.13 0.00 45.77 3.85
1092 1312 2.511600 CGCCATGGGAGGAACGAC 60.512 66.667 15.13 0.00 0.00 4.34
1817 2110 8.310406 TGCTATTCATTATAGGTTCATTCGTG 57.690 34.615 0.00 0.00 37.32 4.35
1847 2148 4.270084 ACAGGAACGTACATATGCAATTCG 59.730 41.667 1.58 3.66 0.00 3.34
1855 2158 6.584942 ACGTACATATGCAATTCGTATACAGG 59.415 38.462 1.58 0.00 0.00 4.00
1887 2198 9.450807 CCGCAGAAGAAAATTACTTATAAATGG 57.549 33.333 0.00 0.00 0.00 3.16
1923 2237 5.388408 AGTAGAGTATGTAAATAGCCGCC 57.612 43.478 0.00 0.00 0.00 6.13
1941 2255 0.931005 CCGCTGCGAGGAAAACTATC 59.069 55.000 25.45 0.00 0.00 2.08
1942 2256 1.471676 CCGCTGCGAGGAAAACTATCT 60.472 52.381 25.45 0.00 0.00 1.98
1943 2257 1.590238 CGCTGCGAGGAAAACTATCTG 59.410 52.381 18.66 0.00 0.00 2.90
1993 2315 7.884816 ACAGTACATATATTGCGTATGGAAC 57.115 36.000 0.00 0.00 34.58 3.62
2029 2351 1.829222 TCCATCTCCTCCCGTTTACAC 59.171 52.381 0.00 0.00 0.00 2.90
2032 2354 3.522553 CATCTCCTCCCGTTTACACTTC 58.477 50.000 0.00 0.00 0.00 3.01
2034 2356 3.170717 TCTCCTCCCGTTTACACTTCAT 58.829 45.455 0.00 0.00 0.00 2.57
2040 2362 5.878116 CCTCCCGTTTACACTTCATTTGATA 59.122 40.000 0.00 0.00 0.00 2.15
2042 2364 7.067008 CCTCCCGTTTACACTTCATTTGATATT 59.933 37.037 0.00 0.00 0.00 1.28
2043 2365 7.757526 TCCCGTTTACACTTCATTTGATATTG 58.242 34.615 0.00 0.00 0.00 1.90
2120 2442 3.337889 CCGTGTGTGGTGTGAGCG 61.338 66.667 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.745549 GCGAATCAAACTCACGCC 57.254 55.556 0.00 0.00 42.79 5.68
4 5 1.225745 CGGCGAATCAAACTCACGC 60.226 57.895 0.00 0.00 46.79 5.34
5 6 1.225745 GCGGCGAATCAAACTCACG 60.226 57.895 12.98 0.00 0.00 4.35
6 7 1.225745 CGCGGCGAATCAAACTCAC 60.226 57.895 19.16 0.00 0.00 3.51
7 8 2.387445 CCGCGGCGAATCAAACTCA 61.387 57.895 25.92 0.00 0.00 3.41
8 9 2.399611 CCGCGGCGAATCAAACTC 59.600 61.111 25.92 0.00 0.00 3.01
9 10 3.124921 CCCGCGGCGAATCAAACT 61.125 61.111 25.92 0.00 0.00 2.66
10 11 3.122323 TCCCGCGGCGAATCAAAC 61.122 61.111 25.92 0.00 0.00 2.93
11 12 3.122323 GTCCCGCGGCGAATCAAA 61.122 61.111 25.92 0.00 0.00 2.69
14 15 4.832608 AAGGTCCCGCGGCGAATC 62.833 66.667 25.92 11.90 0.00 2.52
19 20 1.873270 AAAAATCAAGGTCCCGCGGC 61.873 55.000 22.85 6.98 0.00 6.53
20 21 2.263153 AAAAATCAAGGTCCCGCGG 58.737 52.632 21.04 21.04 0.00 6.46
39 40 9.723447 TGATAATAAAATGCGCGAAAAGAATAA 57.277 25.926 12.10 0.00 0.00 1.40
40 41 9.891828 ATGATAATAAAATGCGCGAAAAGAATA 57.108 25.926 12.10 0.00 0.00 1.75
41 42 8.801715 ATGATAATAAAATGCGCGAAAAGAAT 57.198 26.923 12.10 0.00 0.00 2.40
42 43 8.627487 AATGATAATAAAATGCGCGAAAAGAA 57.373 26.923 12.10 0.00 0.00 2.52
43 44 8.627487 AAATGATAATAAAATGCGCGAAAAGA 57.373 26.923 12.10 0.00 0.00 2.52
44 45 9.135384 CAAAATGATAATAAAATGCGCGAAAAG 57.865 29.630 12.10 0.00 0.00 2.27
45 46 8.651588 ACAAAATGATAATAAAATGCGCGAAAA 58.348 25.926 12.10 0.00 0.00 2.29
46 47 8.106956 CACAAAATGATAATAAAATGCGCGAAA 58.893 29.630 12.10 0.00 0.00 3.46
47 48 7.253917 CCACAAAATGATAATAAAATGCGCGAA 60.254 33.333 12.10 0.00 0.00 4.70
48 49 6.198029 CCACAAAATGATAATAAAATGCGCGA 59.802 34.615 12.10 0.00 0.00 5.87
49 50 6.346339 CCACAAAATGATAATAAAATGCGCG 58.654 36.000 0.00 0.00 0.00 6.86
50 51 6.128729 GCCACAAAATGATAATAAAATGCGC 58.871 36.000 0.00 0.00 0.00 6.09
51 52 7.231705 TGCCACAAAATGATAATAAAATGCG 57.768 32.000 0.00 0.00 0.00 4.73
52 53 9.440784 CATTGCCACAAAATGATAATAAAATGC 57.559 29.630 0.00 0.00 37.22 3.56
53 54 9.440784 GCATTGCCACAAAATGATAATAAAATG 57.559 29.630 0.00 0.00 37.22 2.32
95 96 3.188786 GCTACAGCGCGAACTGGG 61.189 66.667 12.10 7.40 42.21 4.45
96 97 1.959899 CTTGCTACAGCGCGAACTGG 61.960 60.000 12.10 0.00 45.83 4.00
97 98 1.417592 CTTGCTACAGCGCGAACTG 59.582 57.895 12.10 11.75 45.83 3.16
98 99 2.383527 GCTTGCTACAGCGCGAACT 61.384 57.895 12.10 0.00 45.83 3.01
99 100 2.096594 GCTTGCTACAGCGCGAAC 59.903 61.111 12.10 0.00 45.83 3.95
114 115 0.811616 CAATTAGGAGAAGCGGCGCT 60.812 55.000 31.35 31.35 42.56 5.92
115 116 1.643832 CAATTAGGAGAAGCGGCGC 59.356 57.895 26.86 26.86 0.00 6.53
116 117 1.776034 GCCAATTAGGAGAAGCGGCG 61.776 60.000 0.51 0.51 41.22 6.46
117 118 1.776034 CGCCAATTAGGAGAAGCGGC 61.776 60.000 0.00 0.00 40.01 6.53
118 119 1.776034 GCGCCAATTAGGAGAAGCGG 61.776 60.000 0.00 0.00 43.52 5.52
119 120 0.811616 AGCGCCAATTAGGAGAAGCG 60.812 55.000 2.29 0.00 45.91 4.68
120 121 0.659957 CAGCGCCAATTAGGAGAAGC 59.340 55.000 2.29 0.00 40.01 3.86
121 122 2.315925 TCAGCGCCAATTAGGAGAAG 57.684 50.000 2.29 0.00 40.01 2.85
122 123 2.632377 CTTCAGCGCCAATTAGGAGAA 58.368 47.619 2.29 0.00 40.01 2.87
123 124 1.134401 CCTTCAGCGCCAATTAGGAGA 60.134 52.381 2.29 0.00 40.01 3.71
124 125 1.303309 CCTTCAGCGCCAATTAGGAG 58.697 55.000 2.29 0.00 41.22 3.69
125 126 0.748005 GCCTTCAGCGCCAATTAGGA 60.748 55.000 2.29 0.00 41.22 2.94
126 127 1.729881 GCCTTCAGCGCCAATTAGG 59.270 57.895 2.29 5.49 41.84 2.69
143 144 3.330853 CTAATCGGTGCTCGGCGC 61.331 66.667 0.00 0.00 39.77 6.53
144 145 2.658593 CCTAATCGGTGCTCGGCG 60.659 66.667 0.00 0.00 39.77 6.46
145 146 1.300233 CTCCTAATCGGTGCTCGGC 60.300 63.158 0.70 0.00 39.77 5.54
146 147 1.300233 GCTCCTAATCGGTGCTCGG 60.300 63.158 0.00 0.00 46.33 4.63
147 148 4.327885 GCTCCTAATCGGTGCTCG 57.672 61.111 0.00 0.00 46.33 5.03
151 152 1.364171 CGGGAGCTCCTAATCGGTG 59.636 63.158 31.36 8.29 35.95 4.94
152 153 1.076192 ACGGGAGCTCCTAATCGGT 60.076 57.895 31.36 16.37 35.95 4.69
153 154 1.660917 GACGGGAGCTCCTAATCGG 59.339 63.158 31.36 15.78 35.95 4.18
154 155 1.283181 CGACGGGAGCTCCTAATCG 59.717 63.158 31.36 29.00 35.95 3.34
155 156 0.745468 AACGACGGGAGCTCCTAATC 59.255 55.000 31.36 22.97 35.95 1.75
156 157 0.460311 CAACGACGGGAGCTCCTAAT 59.540 55.000 31.36 17.34 35.95 1.73
157 158 1.888018 CAACGACGGGAGCTCCTAA 59.112 57.895 31.36 0.00 35.95 2.69
158 159 2.707849 GCAACGACGGGAGCTCCTA 61.708 63.158 31.36 0.00 35.95 2.94
159 160 4.070552 GCAACGACGGGAGCTCCT 62.071 66.667 31.36 13.94 35.95 3.69
164 165 4.096003 ATGGGGCAACGACGGGAG 62.096 66.667 0.00 0.00 37.60 4.30
165 166 4.090588 GATGGGGCAACGACGGGA 62.091 66.667 0.00 0.00 37.60 5.14
167 168 4.752879 ACGATGGGGCAACGACGG 62.753 66.667 0.00 0.00 33.96 4.79
168 169 3.186047 GACGATGGGGCAACGACG 61.186 66.667 0.00 0.00 33.96 5.12
169 170 3.186047 CGACGATGGGGCAACGAC 61.186 66.667 0.00 0.00 33.96 4.34
170 171 4.444838 CCGACGATGGGGCAACGA 62.445 66.667 0.00 0.00 33.96 3.85
171 172 3.733344 ATCCGACGATGGGGCAACG 62.733 63.158 0.00 0.00 35.82 4.10
172 173 1.029947 AAATCCGACGATGGGGCAAC 61.030 55.000 0.00 0.00 0.00 4.17
173 174 0.746563 GAAATCCGACGATGGGGCAA 60.747 55.000 0.00 0.00 0.00 4.52
174 175 1.153249 GAAATCCGACGATGGGGCA 60.153 57.895 0.00 0.00 0.00 5.36
180 181 4.730949 TTTCTAGGTGAAATCCGACGAT 57.269 40.909 0.00 0.00 39.50 3.73
210 211 6.448852 CATGAAAAATGACATGTCAGTGGAA 58.551 36.000 30.63 16.63 43.61 3.53
251 252 5.586243 CGGAAGTCCAACAATGATCACTATT 59.414 40.000 0.00 0.00 35.14 1.73
252 253 5.104941 TCGGAAGTCCAACAATGATCACTAT 60.105 40.000 0.00 0.00 35.14 2.12
253 254 4.221924 TCGGAAGTCCAACAATGATCACTA 59.778 41.667 0.00 0.00 35.14 2.74
254 255 3.007940 TCGGAAGTCCAACAATGATCACT 59.992 43.478 0.00 0.00 35.14 3.41
255 256 3.334691 TCGGAAGTCCAACAATGATCAC 58.665 45.455 0.00 0.00 35.14 3.06
256 257 3.694043 TCGGAAGTCCAACAATGATCA 57.306 42.857 0.00 0.00 35.14 2.92
257 258 3.246226 CGATCGGAAGTCCAACAATGATC 59.754 47.826 7.38 0.25 35.14 2.92
274 275 2.261361 TGGTGTGCCAGTCGATCG 59.739 61.111 9.36 9.36 40.46 3.69
304 305 1.606885 AAAATGGGCAGCATGGACGG 61.607 55.000 0.00 0.00 35.86 4.79
367 370 2.203015 CCCTGGCGGGTCATAACG 60.203 66.667 12.30 0.00 46.12 3.18
388 391 1.655484 GCATTTGTTTGCTATGCCCC 58.345 50.000 0.00 0.00 38.92 5.80
427 430 7.178274 ACCAATTGTGCCAATTCTGTTAGATAA 59.822 33.333 4.43 0.00 0.00 1.75
433 436 4.101430 AGAACCAATTGTGCCAATTCTGTT 59.899 37.500 16.41 16.41 0.00 3.16
437 440 4.630111 TGAAGAACCAATTGTGCCAATTC 58.370 39.130 4.43 2.23 0.00 2.17
499 503 4.833938 AGGATAAAATCTCCTCCGAGGTAC 59.166 45.833 14.36 0.00 38.87 3.34
506 510 6.887002 ACAAAGAACAGGATAAAATCTCCTCC 59.113 38.462 0.00 0.00 41.29 4.30
519 523 1.388547 AAGCGCAACAAAGAACAGGA 58.611 45.000 11.47 0.00 0.00 3.86
547 551 5.010282 AGATACAACATTTCCTTCCACACC 58.990 41.667 0.00 0.00 0.00 4.16
568 573 6.700960 CCATTACACAAAAACTGCATTTCAGA 59.299 34.615 0.00 0.00 45.72 3.27
588 600 4.299586 TGCATTCCAGACAACTCCATTA 57.700 40.909 0.00 0.00 0.00 1.90
902 1102 2.427095 GTGCGCATTAAGGAAGGGAATT 59.573 45.455 15.91 0.00 0.00 2.17
906 1106 1.017387 GAGTGCGCATTAAGGAAGGG 58.983 55.000 15.91 0.00 0.00 3.95
968 1177 4.923942 CCCTCATCGCATGCCGCT 62.924 66.667 13.15 0.00 39.08 5.52
977 1186 3.144120 CTGTCTCCGGCCCTCATCG 62.144 68.421 0.00 0.00 0.00 3.84
1024 1244 3.345808 CTGGTTCACGTGGTGGCG 61.346 66.667 17.00 0.00 33.87 5.69
1025 1245 1.961277 CTCTGGTTCACGTGGTGGC 60.961 63.158 17.00 3.48 33.87 5.01
1026 1246 1.301716 CCTCTGGTTCACGTGGTGG 60.302 63.158 17.00 5.61 33.87 4.61
1027 1247 1.301716 CCCTCTGGTTCACGTGGTG 60.302 63.158 17.00 0.00 34.45 4.17
1028 1248 3.148084 CCCTCTGGTTCACGTGGT 58.852 61.111 17.00 0.00 0.00 4.16
1029 1249 2.358737 GCCCTCTGGTTCACGTGG 60.359 66.667 17.00 0.00 0.00 4.94
1030 1250 2.738521 CGCCCTCTGGTTCACGTG 60.739 66.667 9.94 9.94 0.00 4.49
1031 1251 4.003788 CCGCCCTCTGGTTCACGT 62.004 66.667 0.00 0.00 0.00 4.49
1033 1253 4.021925 AGCCGCCCTCTGGTTCAC 62.022 66.667 0.00 0.00 0.00 3.18
1034 1254 4.020617 CAGCCGCCCTCTGGTTCA 62.021 66.667 0.00 0.00 0.00 3.18
1035 1255 3.672295 CTCAGCCGCCCTCTGGTTC 62.672 68.421 0.00 0.00 32.63 3.62
1036 1256 3.710722 CTCAGCCGCCCTCTGGTT 61.711 66.667 0.00 0.00 32.63 3.67
1110 1360 4.803426 CTCCGCTGCCTGTCGTCC 62.803 72.222 0.00 0.00 0.00 4.79
1131 1381 3.747976 GCCATCCACACCAACGGC 61.748 66.667 0.00 0.00 0.00 5.68
1791 2076 8.438513 CACGAATGAACCTATAATGAATAGCAG 58.561 37.037 0.00 0.00 36.92 4.24
1792 2077 7.387673 CCACGAATGAACCTATAATGAATAGCA 59.612 37.037 0.00 0.00 36.92 3.49
1793 2078 7.387948 ACCACGAATGAACCTATAATGAATAGC 59.612 37.037 0.00 0.00 36.92 2.97
1817 2110 0.523072 TGTACGTTCCTGTCGCTACC 59.477 55.000 0.00 0.00 0.00 3.18
1847 2148 0.320771 CTGCGGGGATGCCTGTATAC 60.321 60.000 14.32 0.00 0.00 1.47
1855 2158 1.106285 ATTTTCTTCTGCGGGGATGC 58.894 50.000 0.00 0.00 0.00 3.91
1887 2198 3.858247 ACTCTACTACCGGCATTGTTTC 58.142 45.455 0.00 0.00 0.00 2.78
1923 2237 1.590238 CAGATAGTTTTCCTCGCAGCG 59.410 52.381 9.06 9.06 0.00 5.18
1941 2255 2.684881 CCACAAATTAGCCTGGCTACAG 59.315 50.000 27.36 18.27 41.12 2.74
1942 2256 2.041081 ACCACAAATTAGCCTGGCTACA 59.959 45.455 27.36 18.14 41.12 2.74
1943 2257 2.723273 ACCACAAATTAGCCTGGCTAC 58.277 47.619 27.36 0.00 41.12 3.58
1993 2315 5.049129 GGAGATGGAGTTGAACTTTGAACTG 60.049 44.000 0.00 0.00 34.76 3.16
2040 2362 9.457436 AGTTATCGGTGTCCTAAATAAAACAAT 57.543 29.630 0.00 0.00 0.00 2.71
2042 2364 7.148373 GCAGTTATCGGTGTCCTAAATAAAACA 60.148 37.037 0.00 0.00 0.00 2.83
2043 2365 7.184779 GCAGTTATCGGTGTCCTAAATAAAAC 58.815 38.462 0.00 0.00 0.00 2.43
2048 2370 3.199071 TGGCAGTTATCGGTGTCCTAAAT 59.801 43.478 0.00 0.00 0.00 1.40
2052 2374 0.249398 GTGGCAGTTATCGGTGTCCT 59.751 55.000 0.00 0.00 0.00 3.85
2120 2442 3.626924 ACGTGTGGGCTGTCTCCC 61.627 66.667 0.00 0.00 46.73 4.30
2239 4550 4.142513 GCCAACAGGAAATCATTCTGTCTC 60.143 45.833 0.00 0.00 35.79 3.36
2524 4856 2.106566 TCAAACTTGTTGTGCCATGGT 58.893 42.857 14.67 0.00 0.00 3.55
2532 4864 5.590259 ACAGCAACTCTATCAAACTTGTTGT 59.410 36.000 0.00 0.00 37.62 3.32
2652 4984 8.666573 CAATATGCAGTTTTTGATTTGGCATTA 58.333 29.630 0.00 0.00 40.57 1.90


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

AutoCloner maintained by Alex Coulton.