Multiple sequence alignment - TraesCS2D01G361800

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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 TraesCS2D01G361800 chr2D 100.000 2943 0 0 812 3754 467057753 467060695 0.000000e+00 5435.0
1 TraesCS2D01G361800 chr2D 100.000 555 0 0 1 555 467056942 467057496 0.000000e+00 1026.0
2 TraesCS2D01G361800 chr2A 90.287 2440 129 36 812 3201 607908193 607910574 0.000000e+00 3094.0
3 TraesCS2D01G361800 chr2A 87.008 508 37 17 1 505 607907303 607907784 2.550000e-151 545.0
4 TraesCS2D01G361800 chr2A 82.373 573 52 21 3220 3754 607911653 607912214 1.590000e-123 453.0
5 TraesCS2D01G361800 chr2B 89.559 2289 150 42 977 3201 545755410 545757673 0.000000e+00 2820.0
6 TraesCS2D01G361800 chr2B 94.513 565 25 3 3196 3754 545758021 545758585 0.000000e+00 867.0
7 TraesCS2D01G361800 chr2B 79.661 590 71 18 3196 3745 110483346 110482766 2.740000e-101 379.0
8 TraesCS2D01G361800 chr2B 81.174 409 49 16 1391 1772 9921605 9922012 1.690000e-78 303.0
9 TraesCS2D01G361800 chr2B 87.352 253 20 2 315 555 545754688 545754940 2.860000e-71 279.0
10 TraesCS2D01G361800 chr2B 97.059 34 1 0 2957 2990 545757507 545757540 1.460000e-04 58.4
11 TraesCS2D01G361800 chr6D 87.990 841 59 23 962 1772 451098664 451099492 0.000000e+00 955.0
12 TraesCS2D01G361800 chr6D 84.030 526 66 14 2276 2786 451099872 451100394 1.210000e-134 490.0
13 TraesCS2D01G361800 chr6A 87.161 849 71 23 955 1772 596744651 596745492 0.000000e+00 929.0
14 TraesCS2D01G361800 chr6A 82.609 529 59 18 2276 2786 596745869 596746382 1.600000e-118 436.0
15 TraesCS2D01G361800 chr6A 83.226 310 36 7 3433 3728 539181514 539181821 1.720000e-68 270.0
16 TraesCS2D01G361800 chr6B 87.396 841 60 29 944 1756 685151335 685152157 0.000000e+00 924.0
17 TraesCS2D01G361800 chr6B 84.130 523 62 11 2276 2782 685152556 685153073 1.570000e-133 486.0
18 TraesCS2D01G361800 chr5A 82.519 389 51 12 1212 1585 639311731 639311345 3.620000e-85 326.0
19 TraesCS2D01G361800 chr1B 81.491 389 54 11 1212 1585 490598163 490598548 1.690000e-78 303.0
20 TraesCS2D01G361800 chr5D 77.491 582 62 29 3196 3728 496980446 496981007 6.140000e-73 285.0
21 TraesCS2D01G361800 chr7B 92.466 146 9 1 1629 1772 348045196 348045341 1.370000e-49 207.0
22 TraesCS2D01G361800 chr7B 91.096 146 11 1 1629 1772 27649283 27649428 2.960000e-46 196.0
23 TraesCS2D01G361800 chr4A 89.933 149 13 1 1629 1775 665985576 665985428 1.380000e-44 191.0
24 TraesCS2D01G361800 chr5B 86.471 170 18 4 1629 1793 37927588 37927757 8.280000e-42 182.0
25 TraesCS2D01G361800 chr4B 78.916 166 16 13 815 976 69135844 69135694 1.110000e-15 95.3
26 TraesCS2D01G361800 chrUn 91.111 45 3 1 852 896 117191537 117191494 4.050000e-05 60.2


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 TraesCS2D01G361800 chr2D 467056942 467060695 3753 False 3230.5 5435 100.00000 1 3754 2 chr2D.!!$F1 3753
1 TraesCS2D01G361800 chr2A 607907303 607912214 4911 False 1364.0 3094 86.55600 1 3754 3 chr2A.!!$F1 3753
2 TraesCS2D01G361800 chr2B 545754688 545758585 3897 False 1006.1 2820 92.12075 315 3754 4 chr2B.!!$F2 3439
3 TraesCS2D01G361800 chr2B 110482766 110483346 580 True 379.0 379 79.66100 3196 3745 1 chr2B.!!$R1 549
4 TraesCS2D01G361800 chr6D 451098664 451100394 1730 False 722.5 955 86.01000 962 2786 2 chr6D.!!$F1 1824
5 TraesCS2D01G361800 chr6A 596744651 596746382 1731 False 682.5 929 84.88500 955 2786 2 chr6A.!!$F2 1831
6 TraesCS2D01G361800 chr6B 685151335 685153073 1738 False 705.0 924 85.76300 944 2782 2 chr6B.!!$F1 1838
7 TraesCS2D01G361800 chr5D 496980446 496981007 561 False 285.0 285 77.49100 3196 3728 1 chr5D.!!$F1 532

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
239 241 0.039978 CAGGCGAGCGATCGAGTATT 60.040 55.0 29.29 3.22 34.64 1.89 F
310 312 0.249398 TAGCGCTTCTTGAACTCCCC 59.751 55.0 18.68 0.00 0.00 4.81 F
313 315 0.391793 CGCTTCTTGAACTCCCCCTC 60.392 60.0 0.00 0.00 0.00 4.30 F
1564 2041 0.178068 ATCGGTGACACTGGTATGCC 59.822 55.0 14.44 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1053 1481 0.036010 CCGTCACCAGCTCCTTGATT 60.036 55.000 0.00 0.0 0.00 2.57 R
1369 1826 0.597568 ACGACGGTTACCATCGACAA 59.402 50.000 26.45 0.0 39.16 3.18 R
1622 2101 0.801067 GACCGCCGTCAGACATGTAC 60.801 60.000 0.00 0.0 38.99 2.90 R
3398 5147 1.199789 CACAAACACAGGCATACGCAT 59.800 47.619 0.00 0.0 41.24 4.73 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
42 43 5.408880 TCCATATACGCCATTAAATCCGA 57.591 39.130 0.00 0.00 0.00 4.55
116 117 8.538409 AATCTGTGAAAATGTTGCTTTTATCC 57.462 30.769 0.00 0.00 0.00 2.59
135 136 1.873591 CCTGAAACAAAGACCAGTCCG 59.126 52.381 0.00 0.00 0.00 4.79
148 149 3.881089 GACCAGTCCGGAAGAAAGAAAAA 59.119 43.478 5.23 0.00 38.63 1.94
149 150 4.470602 ACCAGTCCGGAAGAAAGAAAAAT 58.529 39.130 5.23 0.00 38.63 1.82
155 156 4.216257 TCCGGAAGAAAGAAAAATGAGCAG 59.784 41.667 0.00 0.00 0.00 4.24
161 162 6.949352 AGAAAGAAAAATGAGCAGACAGAA 57.051 33.333 0.00 0.00 0.00 3.02
188 190 2.760634 TAGCCAAATGAGCGAACAGA 57.239 45.000 0.00 0.00 34.64 3.41
189 191 2.119801 AGCCAAATGAGCGAACAGAT 57.880 45.000 0.00 0.00 34.64 2.90
200 202 0.179073 CGAACAGATCAGGGGCGAAT 60.179 55.000 0.00 0.00 0.00 3.34
225 227 1.064946 CTAGCGGAGAGAACAGGCG 59.935 63.158 0.00 0.00 0.00 5.52
232 234 0.593773 GAGAGAACAGGCGAGCGATC 60.594 60.000 0.00 0.00 0.00 3.69
239 241 0.039978 CAGGCGAGCGATCGAGTATT 60.040 55.000 29.29 3.22 34.64 1.89
251 253 3.380479 TCGAGTATTAATGGGCTTCGG 57.620 47.619 0.00 0.00 0.00 4.30
266 268 1.027792 TTCGGCCCAGTAAAATCGGC 61.028 55.000 0.00 0.00 40.85 5.54
268 270 1.714899 CGGCCCAGTAAAATCGGCTG 61.715 60.000 0.00 0.00 41.35 4.85
269 271 0.679960 GGCCCAGTAAAATCGGCTGT 60.680 55.000 0.00 0.00 41.35 4.40
272 274 1.094785 CCAGTAAAATCGGCTGTGGG 58.905 55.000 0.00 0.00 0.00 4.61
288 290 1.118356 TGGGCGCCAGGAACAAAAAT 61.118 50.000 30.85 0.00 0.00 1.82
289 291 0.892063 GGGCGCCAGGAACAAAAATA 59.108 50.000 30.85 0.00 0.00 1.40
290 292 1.403647 GGGCGCCAGGAACAAAAATAC 60.404 52.381 30.85 0.45 0.00 1.89
291 293 1.544246 GGCGCCAGGAACAAAAATACT 59.456 47.619 24.80 0.00 0.00 2.12
292 294 2.750712 GGCGCCAGGAACAAAAATACTA 59.249 45.455 24.80 0.00 0.00 1.82
293 295 3.181500 GGCGCCAGGAACAAAAATACTAG 60.181 47.826 24.80 0.00 0.00 2.57
294 296 3.730963 GCGCCAGGAACAAAAATACTAGC 60.731 47.826 0.00 0.00 0.00 3.42
295 297 3.485216 CGCCAGGAACAAAAATACTAGCG 60.485 47.826 0.00 0.00 0.00 4.26
296 298 3.730963 GCCAGGAACAAAAATACTAGCGC 60.731 47.826 0.00 0.00 0.00 5.92
297 299 3.689649 CCAGGAACAAAAATACTAGCGCT 59.310 43.478 17.26 17.26 0.00 5.92
298 300 4.156008 CCAGGAACAAAAATACTAGCGCTT 59.844 41.667 18.68 0.00 0.00 4.68
299 301 5.324697 CAGGAACAAAAATACTAGCGCTTC 58.675 41.667 18.68 1.20 0.00 3.86
300 302 5.122396 CAGGAACAAAAATACTAGCGCTTCT 59.878 40.000 18.68 2.94 0.00 2.85
301 303 5.705905 AGGAACAAAAATACTAGCGCTTCTT 59.294 36.000 18.68 2.19 0.00 2.52
302 304 5.795441 GGAACAAAAATACTAGCGCTTCTTG 59.205 40.000 18.68 11.19 0.00 3.02
303 305 6.348213 GGAACAAAAATACTAGCGCTTCTTGA 60.348 38.462 18.68 0.00 0.00 3.02
304 306 6.554334 ACAAAAATACTAGCGCTTCTTGAA 57.446 33.333 18.68 0.00 0.00 2.69
305 307 6.371389 ACAAAAATACTAGCGCTTCTTGAAC 58.629 36.000 18.68 0.00 0.00 3.18
306 308 6.204882 ACAAAAATACTAGCGCTTCTTGAACT 59.795 34.615 18.68 0.00 0.00 3.01
307 309 6.410243 AAAATACTAGCGCTTCTTGAACTC 57.590 37.500 18.68 0.00 0.00 3.01
308 310 2.371910 ACTAGCGCTTCTTGAACTCC 57.628 50.000 18.68 0.00 0.00 3.85
309 311 1.066787 ACTAGCGCTTCTTGAACTCCC 60.067 52.381 18.68 0.00 0.00 4.30
310 312 0.249398 TAGCGCTTCTTGAACTCCCC 59.751 55.000 18.68 0.00 0.00 4.81
311 313 2.041115 GCGCTTCTTGAACTCCCCC 61.041 63.158 0.00 0.00 0.00 5.40
312 314 1.679898 CGCTTCTTGAACTCCCCCT 59.320 57.895 0.00 0.00 0.00 4.79
313 315 0.391793 CGCTTCTTGAACTCCCCCTC 60.392 60.000 0.00 0.00 0.00 4.30
400 403 1.969589 CCCTTTCCCAAACCGACCG 60.970 63.158 0.00 0.00 0.00 4.79
431 434 4.722700 ACATGTGGGACCGCAGCC 62.723 66.667 10.65 0.00 39.95 4.85
466 470 2.001803 CAGGCCAATCTTCCAGGGA 58.998 57.895 5.01 0.00 0.00 4.20
470 474 1.272704 GGCCAATCTTCCAGGGAAAGT 60.273 52.381 0.00 0.00 33.34 2.66
532 547 4.256180 GCTCCGCATCCCCCGAAT 62.256 66.667 0.00 0.00 0.00 3.34
533 548 2.281070 CTCCGCATCCCCCGAATG 60.281 66.667 0.00 0.00 0.00 2.67
534 549 3.087253 TCCGCATCCCCCGAATGT 61.087 61.111 0.00 0.00 0.00 2.71
535 550 2.124320 CCGCATCCCCCGAATGTT 60.124 61.111 0.00 0.00 0.00 2.71
536 551 2.186826 CCGCATCCCCCGAATGTTC 61.187 63.158 0.00 0.00 0.00 3.18
1098 1526 2.282958 TTCGACTGCTCCGGGACT 60.283 61.111 0.00 0.00 0.00 3.85
1218 1646 1.077501 CATGGGCATGAACCTCGGT 60.078 57.895 0.00 0.00 41.20 4.69
1308 1736 2.218603 GACACCGTCACCTTCATGTTT 58.781 47.619 0.00 0.00 32.09 2.83
1349 1803 2.561373 CGCCCCTCTTTTCGTTGC 59.439 61.111 0.00 0.00 0.00 4.17
1365 1822 1.819288 GTTGCTCCTTTTCCTTAGCCC 59.181 52.381 0.00 0.00 33.99 5.19
1369 1826 1.636003 CTCCTTTTCCTTAGCCCTGGT 59.364 52.381 0.00 0.00 0.00 4.00
1386 1843 1.337074 TGGTTGTCGATGGTAACCGTC 60.337 52.381 14.75 0.00 45.27 4.79
1550 2027 1.418334 AGGATCTTAGCAGCATCGGT 58.582 50.000 0.00 0.00 0.00 4.69
1564 2041 0.178068 ATCGGTGACACTGGTATGCC 59.822 55.000 14.44 0.00 0.00 4.40
1586 2065 3.569701 CGAATCCCCCATTTCCTGTAATG 59.430 47.826 0.00 0.00 35.70 1.90
1589 2068 3.976015 TCCCCCATTTCCTGTAATGTTC 58.024 45.455 0.00 0.00 34.42 3.18
1599 2078 4.093743 TCCTGTAATGTTCTGGTCTGCTA 58.906 43.478 0.00 0.00 0.00 3.49
1603 2082 2.770164 ATGTTCTGGTCTGCTACACC 57.230 50.000 0.00 0.00 0.00 4.16
1609 2088 0.679505 TGGTCTGCTACACCTGTCAC 59.320 55.000 1.71 0.00 34.66 3.67
1622 2101 4.202264 ACACCTGTCACCTCTGTTTCTTAG 60.202 45.833 0.00 0.00 0.00 2.18
1623 2102 3.967987 ACCTGTCACCTCTGTTTCTTAGT 59.032 43.478 0.00 0.00 0.00 2.24
1624 2103 5.010719 CACCTGTCACCTCTGTTTCTTAGTA 59.989 44.000 0.00 0.00 0.00 1.82
1758 2245 3.594603 AGACCGTTGACAAGGTATCTG 57.405 47.619 7.09 0.00 41.51 2.90
1785 2272 8.893727 GCATTGTTTCTCCACTAGTTTGTATAT 58.106 33.333 0.00 0.00 0.00 0.86
1852 2345 7.994911 TGTATTGCATAATGAGAGTCAGGAATT 59.005 33.333 0.00 0.00 0.00 2.17
1903 2396 8.458052 TGTCAATACCTTAATTGTAGCAACATG 58.542 33.333 0.00 0.00 37.94 3.21
1936 2441 5.727791 GCTGCACCAGATTGTTTACTAATCG 60.728 44.000 0.00 0.00 39.07 3.34
2026 2543 3.249320 CCCAACATGTCTTCATAGATGCG 59.751 47.826 0.00 0.00 31.86 4.73
2034 2551 2.035961 TCTTCATAGATGCGCACTACCC 59.964 50.000 14.90 0.00 0.00 3.69
2035 2552 1.408969 TCATAGATGCGCACTACCCA 58.591 50.000 14.90 0.00 0.00 4.51
2070 2590 6.981559 TGTTTTGTTCCTTTACATGGCTTAAC 59.018 34.615 0.00 0.00 0.00 2.01
2181 2704 8.126700 GTGTTGTTAGTTGTACATAGCTTTGTT 58.873 33.333 15.18 0.00 0.00 2.83
2223 2746 4.097741 ACAGATCTACTAGAACTGCAGCTG 59.902 45.833 15.27 10.11 45.59 4.24
2273 2805 2.181975 CCAAGTGATTTTGATGGCCCT 58.818 47.619 0.00 0.00 0.00 5.19
2303 2845 1.673665 CTGGTGAGCCTGGCAACTC 60.674 63.158 22.65 10.52 35.27 3.01
2335 2877 6.389906 AGTTGCAAGTGTAAAATATTGGAGC 58.610 36.000 5.84 0.00 0.00 4.70
2666 3225 2.027377 CCTCTCATCTGAACTGCCAGTT 60.027 50.000 10.45 10.45 41.95 3.16
2711 3270 6.260271 GTGAGATGGGCTACATTAGGTTTTAC 59.740 42.308 0.00 0.00 40.72 2.01
2791 3350 3.470709 TGCTGATCTTGCCTACAATAGC 58.529 45.455 8.39 0.00 34.61 2.97
2995 3563 3.191371 GTGACTGTTGGTCCATGGATTTC 59.809 47.826 19.62 11.41 43.89 2.17
3067 3679 3.818210 TGTTACACCAGTGCTGTTATTGG 59.182 43.478 0.00 0.00 36.76 3.16
3100 3748 6.814644 TGACTTGGATTGATTGAATGCATTTC 59.185 34.615 14.33 8.01 41.56 2.17
3101 3749 6.942976 ACTTGGATTGATTGAATGCATTTCT 58.057 32.000 14.33 1.07 41.56 2.52
3102 3750 8.070034 ACTTGGATTGATTGAATGCATTTCTA 57.930 30.769 14.33 4.85 41.56 2.10
3104 3752 7.046292 TGGATTGATTGAATGCATTTCTAGG 57.954 36.000 14.33 0.00 37.46 3.02
3105 3753 6.608405 TGGATTGATTGAATGCATTTCTAGGT 59.392 34.615 14.33 0.00 37.46 3.08
3106 3754 7.779326 TGGATTGATTGAATGCATTTCTAGGTA 59.221 33.333 14.33 0.00 37.46 3.08
3108 3756 9.837525 GATTGATTGAATGCATTTCTAGGTATC 57.162 33.333 14.33 8.13 35.23 2.24
3109 3757 7.425577 TGATTGAATGCATTTCTAGGTATCG 57.574 36.000 14.33 0.00 35.23 2.92
3110 3758 5.673337 TTGAATGCATTTCTAGGTATCGC 57.327 39.130 14.33 0.00 35.23 4.58
3113 3761 4.607293 ATGCATTTCTAGGTATCGCAGA 57.393 40.909 0.00 0.00 45.75 4.26
3122 3770 2.076863 AGGTATCGCAGAGTGTTTTGC 58.923 47.619 0.00 0.00 43.63 3.68
3130 3778 2.813754 GCAGAGTGTTTTGCATCAGGTA 59.186 45.455 0.00 0.00 40.02 3.08
3320 5050 9.535878 TTAACATTTAAGTCATTTTCCAACCAC 57.464 29.630 0.00 0.00 0.00 4.16
3563 5354 7.041372 TGTTCTATGCTTTGTGGTTAGTTTCTC 60.041 37.037 0.00 0.00 0.00 2.87
3659 5454 1.139058 AGTCACTCCTTTGCGTCTTGT 59.861 47.619 0.00 0.00 0.00 3.16
3686 5481 9.548208 GCAGTCTCAAGATATTTTTAACTGAAC 57.452 33.333 12.67 0.00 34.89 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.062991 GGTTCTCGGATTTAATGGCGTAT 58.937 43.478 0.00 0.00 0.00 3.06
106 107 5.596361 TGGTCTTTGTTTCAGGATAAAAGCA 59.404 36.000 0.00 0.00 0.00 3.91
108 109 7.277174 ACTGGTCTTTGTTTCAGGATAAAAG 57.723 36.000 0.00 0.00 0.00 2.27
116 117 1.873591 CCGGACTGGTCTTTGTTTCAG 59.126 52.381 0.00 0.00 0.00 3.02
135 136 6.016777 TCTGTCTGCTCATTTTTCTTTCTTCC 60.017 38.462 0.00 0.00 0.00 3.46
177 179 1.900351 CCCCTGATCTGTTCGCTCA 59.100 57.895 0.00 0.00 0.00 4.26
179 181 2.586792 GCCCCTGATCTGTTCGCT 59.413 61.111 0.00 0.00 0.00 4.93
188 190 1.668294 CTCGCTATTCGCCCCTGAT 59.332 57.895 0.00 0.00 38.27 2.90
189 191 3.129300 CTCGCTATTCGCCCCTGA 58.871 61.111 0.00 0.00 38.27 3.86
200 202 0.179054 TTCTCTCCGCTAGCTCGCTA 60.179 55.000 13.93 0.00 0.00 4.26
208 210 1.377366 CTCGCCTGTTCTCTCCGCTA 61.377 60.000 0.00 0.00 0.00 4.26
225 227 2.924290 GCCCATTAATACTCGATCGCTC 59.076 50.000 11.09 0.00 0.00 5.03
232 234 1.798813 GCCGAAGCCCATTAATACTCG 59.201 52.381 0.00 0.00 0.00 4.18
251 253 0.451783 CACAGCCGATTTTACTGGGC 59.548 55.000 0.00 0.00 45.91 5.36
255 257 1.024579 CGCCCACAGCCGATTTTACT 61.025 55.000 0.00 0.00 38.78 2.24
266 268 4.641645 TGTTCCTGGCGCCCACAG 62.642 66.667 26.77 15.21 35.74 3.66
268 270 2.022240 TTTTTGTTCCTGGCGCCCAC 62.022 55.000 26.77 15.76 0.00 4.61
269 271 1.118356 ATTTTTGTTCCTGGCGCCCA 61.118 50.000 26.77 11.66 0.00 5.36
272 274 3.730963 GCTAGTATTTTTGTTCCTGGCGC 60.731 47.826 0.00 0.00 0.00 6.53
274 276 3.730963 GCGCTAGTATTTTTGTTCCTGGC 60.731 47.826 0.00 0.00 0.00 4.85
275 277 3.689649 AGCGCTAGTATTTTTGTTCCTGG 59.310 43.478 8.99 0.00 0.00 4.45
278 280 5.547181 AGAAGCGCTAGTATTTTTGTTCC 57.453 39.130 12.05 0.00 0.00 3.62
279 281 6.599437 TCAAGAAGCGCTAGTATTTTTGTTC 58.401 36.000 12.05 0.00 0.00 3.18
282 284 6.603095 AGTTCAAGAAGCGCTAGTATTTTTG 58.397 36.000 12.05 6.66 0.00 2.44
288 290 2.165845 GGGAGTTCAAGAAGCGCTAGTA 59.834 50.000 12.05 0.00 0.00 1.82
289 291 1.066787 GGGAGTTCAAGAAGCGCTAGT 60.067 52.381 12.05 0.00 0.00 2.57
290 292 1.646189 GGGAGTTCAAGAAGCGCTAG 58.354 55.000 12.05 0.83 0.00 3.42
291 293 0.249398 GGGGAGTTCAAGAAGCGCTA 59.751 55.000 12.05 0.00 0.00 4.26
292 294 1.003233 GGGGAGTTCAAGAAGCGCT 60.003 57.895 2.64 2.64 0.00 5.92
293 295 2.041115 GGGGGAGTTCAAGAAGCGC 61.041 63.158 0.00 0.00 0.00 5.92
294 296 0.391793 GAGGGGGAGTTCAAGAAGCG 60.392 60.000 0.00 0.00 0.00 4.68
295 297 0.034960 GGAGGGGGAGTTCAAGAAGC 60.035 60.000 0.00 0.00 0.00 3.86
296 298 0.621082 GGGAGGGGGAGTTCAAGAAG 59.379 60.000 0.00 0.00 0.00 2.85
297 299 0.845102 GGGGAGGGGGAGTTCAAGAA 60.845 60.000 0.00 0.00 0.00 2.52
298 300 1.229853 GGGGAGGGGGAGTTCAAGA 60.230 63.158 0.00 0.00 0.00 3.02
299 301 1.541368 TGGGGAGGGGGAGTTCAAG 60.541 63.158 0.00 0.00 0.00 3.02
300 302 1.850755 GTGGGGAGGGGGAGTTCAA 60.851 63.158 0.00 0.00 0.00 2.69
301 303 2.204090 GTGGGGAGGGGGAGTTCA 60.204 66.667 0.00 0.00 0.00 3.18
302 304 3.400054 CGTGGGGAGGGGGAGTTC 61.400 72.222 0.00 0.00 0.00 3.01
400 403 3.083997 ATGTCGGTGGAGGGGAGC 61.084 66.667 0.00 0.00 0.00 4.70
470 474 4.673298 TTTTCCCGCTCGCGCTCA 62.673 61.111 5.56 0.00 38.24 4.26
488 492 2.897350 GGGAGGGAGCGCGAAATG 60.897 66.667 12.10 0.00 0.00 2.32
849 967 5.070047 GTGGATCGAGAAACCCTAGGATTTA 59.930 44.000 11.48 0.00 0.00 1.40
930 1048 1.223763 GGGTGGATCGAGAAACCCC 59.776 63.158 17.47 7.41 45.63 4.95
1053 1481 0.036010 CCGTCACCAGCTCCTTGATT 60.036 55.000 0.00 0.00 0.00 2.57
1218 1646 1.746861 CGGAGCATCTTGGCCATGTTA 60.747 52.381 17.54 0.53 33.73 2.41
1308 1736 0.685097 GGTGCTTACTGGGTGACTCA 59.315 55.000 0.00 0.00 0.00 3.41
1349 1803 1.636003 ACCAGGGCTAAGGAAAAGGAG 59.364 52.381 0.00 0.00 0.00 3.69
1365 1822 1.337447 ACGGTTACCATCGACAACCAG 60.337 52.381 16.03 12.10 41.52 4.00
1369 1826 0.597568 ACGACGGTTACCATCGACAA 59.402 50.000 26.45 0.00 39.16 3.18
1386 1843 0.953471 TCTGTTCGCCCATCCAAACG 60.953 55.000 0.00 0.00 0.00 3.60
1398 1871 4.149571 CGCAATCTTATCCTGATCTGTTCG 59.850 45.833 0.00 0.00 0.00 3.95
1550 2027 1.134521 GGATTCGGCATACCAGTGTCA 60.135 52.381 0.00 0.00 34.57 3.58
1564 2041 3.290948 TTACAGGAAATGGGGGATTCG 57.709 47.619 0.00 0.00 0.00 3.34
1586 2065 1.344763 ACAGGTGTAGCAGACCAGAAC 59.655 52.381 5.51 0.00 35.76 3.01
1589 2068 0.969149 TGACAGGTGTAGCAGACCAG 59.031 55.000 5.51 0.70 35.76 4.00
1599 2078 2.119495 AGAAACAGAGGTGACAGGTGT 58.881 47.619 0.00 0.00 0.00 4.16
1603 2082 6.085555 TGTACTAAGAAACAGAGGTGACAG 57.914 41.667 0.00 0.00 0.00 3.51
1609 2088 6.809196 GTCAGACATGTACTAAGAAACAGAGG 59.191 42.308 0.00 0.00 0.00 3.69
1622 2101 0.801067 GACCGCCGTCAGACATGTAC 60.801 60.000 0.00 0.00 38.99 2.90
1623 2102 0.963856 AGACCGCCGTCAGACATGTA 60.964 55.000 0.00 0.00 41.87 2.29
1624 2103 2.261671 GACCGCCGTCAGACATGT 59.738 61.111 0.00 0.00 38.99 3.21
1758 2245 4.278419 ACAAACTAGTGGAGAAACAATGCC 59.722 41.667 0.00 0.00 0.00 4.40
1803 2293 7.158021 ACACCACAAAACCACAATATAAATGG 58.842 34.615 0.00 0.00 39.57 3.16
1852 2345 1.212688 ACAATCATCCCTGCAATCGGA 59.787 47.619 0.00 0.00 0.00 4.55
1903 2396 2.680312 TCTGGTGCAGCTGACTATTC 57.320 50.000 20.43 0.00 0.00 1.75
1936 2441 9.599322 CAAATCGTCCAAATATAATAACTGAGC 57.401 33.333 0.00 0.00 0.00 4.26
1998 2503 3.663995 TGAAGACATGTTGGGCAAATG 57.336 42.857 0.00 0.00 0.00 2.32
2026 2543 1.376037 GCAGGACTGTGGGTAGTGC 60.376 63.158 0.82 0.00 39.07 4.40
2070 2590 5.836347 TGTAGCTAACTGCAGACTATCATG 58.164 41.667 23.35 2.57 45.94 3.07
2254 2783 3.007182 ACAAGGGCCATCAAAATCACTTG 59.993 43.478 6.18 7.30 39.76 3.16
2273 2805 1.273606 GCTCACCAGCTCAGAGTACAA 59.726 52.381 0.00 0.00 43.09 2.41
2335 2877 6.765512 ACCTCAACCACAATTTTAAAATGGTG 59.234 34.615 29.96 29.96 45.66 4.17
2666 3225 5.432645 TCACCAATCTTGTACTCAACAACA 58.567 37.500 0.00 0.00 43.22 3.33
2791 3350 2.787473 TCTTGGGTGCCAGATAACAG 57.213 50.000 0.00 0.00 33.81 3.16
2995 3563 6.532657 GCTAAAAGACCAACATTCATCAATGG 59.467 38.462 0.00 0.00 43.47 3.16
3067 3679 5.357878 TCAATCAATCCAAGTCATTGCCTAC 59.642 40.000 0.00 0.00 34.91 3.18
3100 3748 3.307242 GCAAAACACTCTGCGATACCTAG 59.693 47.826 0.00 0.00 0.00 3.02
3101 3749 3.259064 GCAAAACACTCTGCGATACCTA 58.741 45.455 0.00 0.00 0.00 3.08
3102 3750 2.076863 GCAAAACACTCTGCGATACCT 58.923 47.619 0.00 0.00 0.00 3.08
3104 3752 3.125146 TGATGCAAAACACTCTGCGATAC 59.875 43.478 0.00 0.00 41.63 2.24
3105 3753 3.333804 TGATGCAAAACACTCTGCGATA 58.666 40.909 0.00 0.00 41.63 2.92
3106 3754 2.153645 TGATGCAAAACACTCTGCGAT 58.846 42.857 0.00 0.00 41.63 4.58
3108 3756 1.400629 CCTGATGCAAAACACTCTGCG 60.401 52.381 0.00 0.00 41.63 5.18
3109 3757 1.610522 ACCTGATGCAAAACACTCTGC 59.389 47.619 0.00 0.00 39.09 4.26
3110 3758 4.318332 TCTACCTGATGCAAAACACTCTG 58.682 43.478 0.00 0.00 0.00 3.35
3358 5088 9.491675 ACAATCACAATGAGATTTTTGCAAATA 57.508 25.926 13.65 8.92 33.64 1.40
3359 5089 8.385898 ACAATCACAATGAGATTTTTGCAAAT 57.614 26.923 13.65 0.00 33.64 2.32
3360 5090 7.789273 ACAATCACAATGAGATTTTTGCAAA 57.211 28.000 8.05 8.05 33.64 3.68
3397 5146 1.885887 ACAAACACAGGCATACGCATT 59.114 42.857 0.00 0.00 41.24 3.56
3398 5147 1.199789 CACAAACACAGGCATACGCAT 59.800 47.619 0.00 0.00 41.24 4.73
3563 5354 3.964031 ACTCTAAAGATGTAGCCTGGGAG 59.036 47.826 0.00 0.00 0.00 4.30
3659 5454 8.846943 TCAGTTAAAAATATCTTGAGACTGCA 57.153 30.769 0.00 0.00 33.78 4.41


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

AutoCloner maintained by Alex Coulton.