Multiple sequence alignment - TraesCS5B01G564900

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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 TraesCS5B01G564900 chr5B 100.000 2543 0 0 1 2543 710199779 710202321 0.000000e+00 4697
1 TraesCS5B01G564900 chr5B 76.168 214 43 7 244 450 320380001 320380213 3.460000e-19 106
2 TraesCS5B01G564900 chr5D 92.045 2577 143 30 4 2543 556848188 556845637 0.000000e+00 3567
3 TraesCS5B01G564900 chr5D 90.361 83 8 0 2003 2085 556846243 556846161 2.670000e-20 110
4 TraesCS5B01G564900 chr4D 91.916 1002 76 5 738 1738 72053107 72054104 0.000000e+00 1397
5 TraesCS5B01G564900 chr4D 91.098 337 19 3 155 480 71987090 71987426 1.790000e-121 446
6 TraesCS5B01G564900 chr4D 90.438 251 16 6 494 741 72002793 72003038 8.780000e-85 324
7 TraesCS5B01G564900 chr4A 89.318 337 24 4 155 480 527311308 527311643 1.820000e-111 412
8 TraesCS5B01G564900 chr1D 77.778 207 41 4 248 450 7983450 7983655 3.440000e-24 122
9 TraesCS5B01G564900 chr1D 77.895 190 40 2 263 450 58874650 58874461 1.600000e-22 117
10 TraesCS5B01G564900 chr2A 77.723 202 37 6 247 443 379152450 379152252 1.600000e-22 117
11 TraesCS5B01G564900 chr2A 76.961 204 43 4 243 443 161631442 161631240 2.070000e-21 113
12 TraesCS5B01G564900 chr3A 76.654 257 30 15 1585 1816 7214708 7214457 5.750000e-22 115
13 TraesCS5B01G564900 chr3A 79.470 151 24 5 679 823 7215729 7215580 1.610000e-17 100
14 TraesCS5B01G564900 chr4B 76.471 204 42 6 244 443 471312094 471312295 3.460000e-19 106


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 TraesCS5B01G564900 chr5B 710199779 710202321 2542 False 4697.0 4697 100.000 1 2543 1 chr5B.!!$F2 2542
1 TraesCS5B01G564900 chr5D 556845637 556848188 2551 True 1838.5 3567 91.203 4 2543 2 chr5D.!!$R1 2539
2 TraesCS5B01G564900 chr4D 72053107 72054104 997 False 1397.0 1397 91.916 738 1738 1 chr4D.!!$F3 1000

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
440 488 0.107848 GGGGCCAATATATCCGGACG 60.108 60.0 6.12 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2340 0.918983 ATGGTGTCATTGACGGGGAT 59.081 50.0 11.97 0.0 34.95 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
67 68 5.646360 TGGTTTTGGTGCTAAGAACTATAGC 59.354 40.000 0.00 0.00 44.77 2.97
150 188 9.973450 GGAGCACTATGATATAGTATAACATGG 57.027 37.037 18.41 17.72 0.00 3.66
151 189 9.973450 GAGCACTATGATATAGTATAACATGGG 57.027 37.037 20.52 15.33 0.00 4.00
152 190 8.928448 AGCACTATGATATAGTATAACATGGGG 58.072 37.037 20.52 18.77 0.00 4.96
153 191 7.657761 GCACTATGATATAGTATAACATGGGGC 59.342 40.741 24.97 24.97 40.33 5.80
154 192 8.704668 CACTATGATATAGTATAACATGGGGCA 58.295 37.037 20.52 4.93 0.00 5.36
155 193 8.705594 ACTATGATATAGTATAACATGGGGCAC 58.294 37.037 20.52 0.00 0.00 5.01
156 194 7.755666 ATGATATAGTATAACATGGGGCACT 57.244 36.000 11.08 0.00 0.00 4.40
157 195 8.854237 ATGATATAGTATAACATGGGGCACTA 57.146 34.615 11.08 0.00 0.00 2.74
180 218 8.457757 ACTAGGACTACCCTTATGTATCAAGAT 58.542 37.037 0.00 0.00 44.85 2.40
188 226 8.095452 ACCCTTATGTATCAAGATCTGTCTTT 57.905 34.615 0.00 0.00 41.92 2.52
190 228 7.383572 CCCTTATGTATCAAGATCTGTCTTTCG 59.616 40.741 0.00 0.00 41.92 3.46
195 233 5.793026 ATCAAGATCTGTCTTTCGCTTTC 57.207 39.130 0.00 0.00 41.92 2.62
337 385 5.011090 TGTTGGATCTGTATTCGGAAGAG 57.989 43.478 0.00 0.00 43.69 2.85
421 469 8.186163 GGTAAAAATTCAACCCTAAATACGAGG 58.814 37.037 0.00 0.00 0.00 4.63
440 488 0.107848 GGGGCCAATATATCCGGACG 60.108 60.000 6.12 0.00 0.00 4.79
489 537 0.605319 TCTTGTGACATCGGTTGGGC 60.605 55.000 0.00 0.00 0.00 5.36
498 546 2.439553 ATCGGTTGGGCCAATGTGGT 62.440 55.000 23.95 8.78 40.46 4.16
519 579 5.104941 TGGTTCCATATGTAGTGTTCCTCTG 60.105 44.000 1.24 0.00 0.00 3.35
535 595 1.761784 CTCTGGCCATCTCTTGCTACT 59.238 52.381 5.51 0.00 0.00 2.57
539 599 1.269517 GGCCATCTCTTGCTACTCTCG 60.270 57.143 0.00 0.00 0.00 4.04
541 601 2.159170 GCCATCTCTTGCTACTCTCGTT 60.159 50.000 0.00 0.00 0.00 3.85
542 602 3.701241 CCATCTCTTGCTACTCTCGTTC 58.299 50.000 0.00 0.00 0.00 3.95
543 603 3.358775 CATCTCTTGCTACTCTCGTTCG 58.641 50.000 0.00 0.00 0.00 3.95
544 604 1.738350 TCTCTTGCTACTCTCGTTCGG 59.262 52.381 0.00 0.00 0.00 4.30
545 605 1.469308 CTCTTGCTACTCTCGTTCGGT 59.531 52.381 0.00 0.00 0.00 4.69
546 606 1.199327 TCTTGCTACTCTCGTTCGGTG 59.801 52.381 0.00 0.00 0.00 4.94
548 608 0.240145 TGCTACTCTCGTTCGGTGTG 59.760 55.000 0.00 0.00 0.00 3.82
549 609 0.240411 GCTACTCTCGTTCGGTGTGT 59.760 55.000 0.00 0.00 0.00 3.72
550 610 1.728502 GCTACTCTCGTTCGGTGTGTC 60.729 57.143 0.00 0.00 0.00 3.67
551 611 0.877071 TACTCTCGTTCGGTGTGTCC 59.123 55.000 0.00 0.00 0.00 4.02
552 612 0.822532 ACTCTCGTTCGGTGTGTCCT 60.823 55.000 0.00 0.00 0.00 3.85
553 613 1.162698 CTCTCGTTCGGTGTGTCCTA 58.837 55.000 0.00 0.00 0.00 2.94
554 614 1.130749 CTCTCGTTCGGTGTGTCCTAG 59.869 57.143 0.00 0.00 0.00 3.02
555 615 0.879765 CTCGTTCGGTGTGTCCTAGT 59.120 55.000 0.00 0.00 0.00 2.57
566 627 5.390885 CGGTGTGTCCTAGTTTTCATGATTG 60.391 44.000 0.00 0.00 0.00 2.67
579 640 4.458256 TCATGATTGGCCAATCCACTAT 57.542 40.909 41.86 30.36 46.55 2.12
582 643 6.005823 TCATGATTGGCCAATCCACTATTAG 58.994 40.000 41.86 26.21 46.55 1.73
673 735 7.500141 GGCAACTCATTTATTATTGGGTTCAT 58.500 34.615 0.00 0.00 34.35 2.57
674 736 7.986889 GGCAACTCATTTATTATTGGGTTCATT 59.013 33.333 0.00 0.00 34.35 2.57
678 740 9.936329 ACTCATTTATTATTGGGTTCATTAGGT 57.064 29.630 0.00 0.00 0.00 3.08
926 988 2.154854 TTCTCTGGCACGAAGTCTTG 57.845 50.000 0.00 0.00 41.61 3.02
946 1008 9.398538 AGTCTTGTATATAGAAGAAAGAGTCGT 57.601 33.333 20.55 0.63 37.34 4.34
957 1019 0.247736 AAGAGTCGTCATGTCCTGCC 59.752 55.000 0.00 0.00 0.00 4.85
1024 1086 1.308998 GGGCACTCCAACAATATCCG 58.691 55.000 0.00 0.00 35.00 4.18
1077 1139 1.307778 TTATGGGCTCCCCTCAGCA 60.308 57.895 1.89 0.00 45.70 4.41
1080 1142 3.415087 GGGCTCCCCTCAGCACAT 61.415 66.667 0.00 0.00 42.97 3.21
1092 1154 4.241999 GCACATGCCGATGTCGCC 62.242 66.667 0.00 0.00 41.12 5.54
1156 1218 0.249238 CGAGGATGTGCTGAGCTACC 60.249 60.000 5.83 3.93 0.00 3.18
1162 1224 2.857186 TGTGCTGAGCTACCATGAAA 57.143 45.000 5.83 0.00 0.00 2.69
1301 1363 3.062466 CGTGGAGGACGCTCTGGA 61.062 66.667 0.00 0.00 42.21 3.86
1305 1367 2.637383 GGAGGACGCTCTGGACGTT 61.637 63.158 0.00 0.00 45.24 3.99
1312 1374 2.035442 GCTCTGGACGTTTGCCTCC 61.035 63.158 0.00 0.00 0.00 4.30
1313 1375 1.371183 CTCTGGACGTTTGCCTCCA 59.629 57.895 0.00 0.00 35.20 3.86
1342 1404 7.283354 CCTACGATGATGCTATAGATAACCTCA 59.717 40.741 3.21 0.00 0.00 3.86
1371 1433 3.346315 TGCCAAACATAGTCTCCATGTG 58.654 45.455 0.00 0.00 36.74 3.21
1518 1580 0.319555 GTGGCGTCACTGCTGAACTA 60.320 55.000 14.12 0.00 40.58 2.24
1858 1921 3.795688 AGGAGGTTCACATTGACACAT 57.204 42.857 0.00 0.00 0.00 3.21
1935 1998 3.538591 CATATCAGCATGGTCGCCATAT 58.461 45.455 10.44 4.65 43.15 1.78
1936 1999 4.443315 CCATATCAGCATGGTCGCCATATA 60.443 45.833 10.44 6.37 43.15 0.86
1969 2032 5.730296 TTATGGAGATTTTGGCCGAAAAA 57.270 34.783 22.09 12.60 37.10 1.94
1986 2049 5.220228 CCGAAAAATCACTGTAGCTAAGTCG 60.220 44.000 0.00 0.63 0.00 4.18
1995 2058 0.466739 TAGCTAAGTCGCCATCCCGA 60.467 55.000 0.00 0.00 34.40 5.14
2016 2079 4.929211 CGACCTTGATCGCCATAATAATCA 59.071 41.667 0.00 0.00 34.90 2.57
2017 2080 5.582269 CGACCTTGATCGCCATAATAATCAT 59.418 40.000 0.00 0.00 34.90 2.45
2086 2149 0.954452 GCCCTTCCTCGCCATAATTG 59.046 55.000 0.00 0.00 0.00 2.32
2087 2150 1.476833 GCCCTTCCTCGCCATAATTGA 60.477 52.381 0.00 0.00 0.00 2.57
2106 2169 1.820519 GATGGAGCATGCTGAAAACCA 59.179 47.619 28.27 25.10 0.00 3.67
2108 2171 2.037901 TGGAGCATGCTGAAAACCAAA 58.962 42.857 28.27 1.32 0.00 3.28
2148 2211 0.988832 GCGGATGGGGGTATATGGAA 59.011 55.000 0.00 0.00 0.00 3.53
2177 2240 3.455543 CCATTGGGAAATAGGTTTGGCAT 59.544 43.478 0.00 0.00 35.59 4.40
2251 2314 1.337821 CTTCCTCGTTGTAGTGTCGC 58.662 55.000 0.00 0.00 0.00 5.19
2269 2332 0.108472 GCCTTTGAATGCTTCTGGCC 60.108 55.000 0.00 0.00 40.92 5.36
2277 2340 0.627451 ATGCTTCTGGCCATCCTCAA 59.373 50.000 5.51 0.00 40.92 3.02
2288 2351 1.143684 CCATCCTCAATCCCCGTCAAT 59.856 52.381 0.00 0.00 0.00 2.57
2315 2378 4.475527 GTTGCAAACTCGACCCCT 57.524 55.556 0.00 0.00 45.32 4.79
2320 2383 0.818040 GCAAACTCGACCCCTGTGTT 60.818 55.000 0.00 0.00 0.00 3.32
2321 2384 1.541670 GCAAACTCGACCCCTGTGTTA 60.542 52.381 0.00 0.00 0.00 2.41
2322 2385 2.413837 CAAACTCGACCCCTGTGTTAG 58.586 52.381 0.00 0.00 0.00 2.34
2328 2391 1.762957 CGACCCCTGTGTTAGATCCAT 59.237 52.381 0.00 0.00 0.00 3.41
2332 2395 2.170607 CCCCTGTGTTAGATCCATTCGT 59.829 50.000 0.00 0.00 0.00 3.85
2334 2397 3.871594 CCCTGTGTTAGATCCATTCGTTC 59.128 47.826 0.00 0.00 0.00 3.95
2335 2398 3.551890 CCTGTGTTAGATCCATTCGTTCG 59.448 47.826 0.00 0.00 0.00 3.95
2336 2399 4.421058 CTGTGTTAGATCCATTCGTTCGA 58.579 43.478 0.00 0.00 0.00 3.71
2337 2400 4.811908 TGTGTTAGATCCATTCGTTCGAA 58.188 39.130 9.97 9.97 0.00 3.71
2338 2401 4.862574 TGTGTTAGATCCATTCGTTCGAAG 59.137 41.667 12.86 5.83 0.00 3.79
2339 2402 4.863131 GTGTTAGATCCATTCGTTCGAAGT 59.137 41.667 12.86 0.46 0.00 3.01
2340 2403 5.004535 GTGTTAGATCCATTCGTTCGAAGTC 59.995 44.000 12.86 8.40 0.00 3.01
2341 2404 2.798680 AGATCCATTCGTTCGAAGTCG 58.201 47.619 12.86 0.00 41.45 4.18
2365 2428 8.957466 TCGGATACATCGAATTCTACTATCATT 58.043 33.333 3.52 0.00 33.42 2.57
2373 2436 9.632807 ATCGAATTCTACTATCATTACTCTTGC 57.367 33.333 3.52 0.00 0.00 4.01
2379 2442 7.265673 TCTACTATCATTACTCTTGCGCTTTT 58.734 34.615 9.73 0.00 0.00 2.27
2481 2544 1.528309 CGGTGCAACAAGGGTCCTT 60.528 57.895 0.98 0.00 39.98 3.36
2508 2571 5.803237 AAGGGAACGAAGAAGACTAGAAA 57.197 39.130 0.00 0.00 0.00 2.52
2532 2595 3.451894 CATCCGTGCCTTTGCCCC 61.452 66.667 0.00 0.00 36.33 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 5.473504 AGCACCAAAACCAACACTAAGATAG 59.526 40.000 0.00 0.00 0.00 2.08
32 33 5.381757 AGCACCAAAACCAACACTAAGATA 58.618 37.500 0.00 0.00 0.00 1.98
33 34 4.215109 AGCACCAAAACCAACACTAAGAT 58.785 39.130 0.00 0.00 0.00 2.40
35 36 5.298276 TCTTAGCACCAAAACCAACACTAAG 59.702 40.000 0.00 0.00 37.67 2.18
36 37 5.194432 TCTTAGCACCAAAACCAACACTAA 58.806 37.500 0.00 0.00 0.00 2.24
75 76 8.610248 TGAGGAAAGAGAGAGTTACTATATCG 57.390 38.462 0.00 0.00 0.00 2.92
133 171 7.344612 CCTAGTGCCCCATGTTATACTATATCA 59.655 40.741 0.00 0.00 0.00 2.15
134 172 7.563924 TCCTAGTGCCCCATGTTATACTATATC 59.436 40.741 0.00 0.00 0.00 1.63
135 173 7.344871 GTCCTAGTGCCCCATGTTATACTATAT 59.655 40.741 0.00 0.00 0.00 0.86
136 174 6.666546 GTCCTAGTGCCCCATGTTATACTATA 59.333 42.308 0.00 0.00 0.00 1.31
137 175 5.484290 GTCCTAGTGCCCCATGTTATACTAT 59.516 44.000 0.00 0.00 0.00 2.12
138 176 4.836736 GTCCTAGTGCCCCATGTTATACTA 59.163 45.833 0.00 0.00 0.00 1.82
139 177 3.646637 GTCCTAGTGCCCCATGTTATACT 59.353 47.826 0.00 0.00 0.00 2.12
140 178 3.646637 AGTCCTAGTGCCCCATGTTATAC 59.353 47.826 0.00 0.00 0.00 1.47
141 179 3.936461 AGTCCTAGTGCCCCATGTTATA 58.064 45.455 0.00 0.00 0.00 0.98
142 180 2.776665 AGTCCTAGTGCCCCATGTTAT 58.223 47.619 0.00 0.00 0.00 1.89
143 181 2.263895 AGTCCTAGTGCCCCATGTTA 57.736 50.000 0.00 0.00 0.00 2.41
144 182 1.838077 GTAGTCCTAGTGCCCCATGTT 59.162 52.381 0.00 0.00 0.00 2.71
145 183 1.497161 GTAGTCCTAGTGCCCCATGT 58.503 55.000 0.00 0.00 0.00 3.21
146 184 0.759346 GGTAGTCCTAGTGCCCCATG 59.241 60.000 0.00 0.00 0.00 3.66
147 185 0.400093 GGGTAGTCCTAGTGCCCCAT 60.400 60.000 0.00 0.00 37.48 4.00
148 186 1.002533 GGGTAGTCCTAGTGCCCCA 59.997 63.158 0.00 0.00 37.48 4.96
149 187 1.313822 AGGGTAGTCCTAGTGCCCC 59.686 63.158 4.46 0.00 43.71 5.80
180 218 8.771920 TTAATTATGAGAAAGCGAAAGACAGA 57.228 30.769 0.00 0.00 0.00 3.41
337 385 9.353999 GTCACAAAAATTATACAGTGGAAATCC 57.646 33.333 0.00 0.00 0.00 3.01
417 465 0.178068 CGGATATATTGGCCCCCTCG 59.822 60.000 0.00 0.00 0.00 4.63
421 469 0.107848 CGTCCGGATATATTGGCCCC 60.108 60.000 7.81 0.00 0.00 5.80
440 488 8.221766 CGAGTAAATTTCTTGAGTACTTTGTCC 58.778 37.037 0.00 0.00 0.00 4.02
450 498 6.202954 ACAAGACACCGAGTAAATTTCTTGAG 59.797 38.462 14.51 6.69 40.51 3.02
480 528 2.282816 CCACATTGGCCCAACCGA 60.283 61.111 0.00 0.00 43.94 4.69
481 529 2.153547 GAACCACATTGGCCCAACCG 62.154 60.000 0.00 0.00 42.67 4.44
489 537 5.192927 ACACTACATATGGAACCACATTGG 58.807 41.667 7.80 0.00 45.02 3.16
498 546 4.141711 GCCAGAGGAACACTACATATGGAA 60.142 45.833 7.80 0.00 0.00 3.53
519 579 1.269517 CGAGAGTAGCAAGAGATGGCC 60.270 57.143 0.00 0.00 0.00 5.36
535 595 1.162698 CTAGGACACACCGAACGAGA 58.837 55.000 0.00 0.00 44.74 4.04
539 599 3.460103 TGAAAACTAGGACACACCGAAC 58.540 45.455 0.00 0.00 44.74 3.95
541 601 3.322541 TCATGAAAACTAGGACACACCGA 59.677 43.478 0.00 0.00 44.74 4.69
542 602 3.659786 TCATGAAAACTAGGACACACCG 58.340 45.455 0.00 0.00 44.74 4.94
543 603 5.106157 CCAATCATGAAAACTAGGACACACC 60.106 44.000 0.00 0.00 39.35 4.16
544 604 5.619981 GCCAATCATGAAAACTAGGACACAC 60.620 44.000 0.00 0.00 0.00 3.82
545 605 4.458989 GCCAATCATGAAAACTAGGACACA 59.541 41.667 0.00 0.00 0.00 3.72
546 606 4.142381 GGCCAATCATGAAAACTAGGACAC 60.142 45.833 0.00 0.00 0.00 3.67
548 608 4.016444 TGGCCAATCATGAAAACTAGGAC 58.984 43.478 0.61 0.00 0.00 3.85
549 609 4.314522 TGGCCAATCATGAAAACTAGGA 57.685 40.909 0.61 0.00 0.00 2.94
550 610 5.452356 GGATTGGCCAATCATGAAAACTAGG 60.452 44.000 43.88 0.00 46.77 3.02
551 611 5.127519 TGGATTGGCCAATCATGAAAACTAG 59.872 40.000 43.88 0.00 45.87 2.57
552 612 5.022122 TGGATTGGCCAATCATGAAAACTA 58.978 37.500 43.88 21.84 45.87 2.24
553 613 3.839490 TGGATTGGCCAATCATGAAAACT 59.161 39.130 43.88 19.05 45.87 2.66
554 614 4.205065 TGGATTGGCCAATCATGAAAAC 57.795 40.909 43.88 30.50 45.87 2.43
730 792 6.142320 CGTTGCTTTTGGTGAGTTTAGAATTC 59.858 38.462 0.00 0.00 0.00 2.17
814 876 9.385902 CAAATCAAATGAATAATAGTACCAGCG 57.614 33.333 0.00 0.00 0.00 5.18
926 988 9.601971 GACATGACGACTCTTTCTTCTATATAC 57.398 37.037 0.00 0.00 0.00 1.47
946 1008 1.074775 GTGTTGGGGCAGGACATGA 59.925 57.895 0.00 0.00 0.00 3.07
957 1019 1.336755 GCTAGGTGTTGTTGTGTTGGG 59.663 52.381 0.00 0.00 0.00 4.12
1024 1086 1.654105 CACGACGAGAACCATAGCAAC 59.346 52.381 0.00 0.00 0.00 4.17
1092 1154 5.823209 TCTTGCATGTGTTGGATATGAAG 57.177 39.130 0.00 0.00 0.00 3.02
1156 1218 1.410153 GGCCTGGGTGCTATTTTCATG 59.590 52.381 0.00 0.00 0.00 3.07
1162 1224 1.619363 TGGAGGCCTGGGTGCTATT 60.619 57.895 12.00 0.00 0.00 1.73
1203 1265 2.501128 GTGGCTATCTCCAGCGCA 59.499 61.111 11.47 0.00 42.76 6.09
1289 1351 1.006102 CAAACGTCCAGAGCGTCCT 60.006 57.895 0.00 0.00 42.10 3.85
1312 1374 3.696548 TCTATAGCATCATCGTAGGCCTG 59.303 47.826 17.99 0.00 0.00 4.85
1313 1375 3.969553 TCTATAGCATCATCGTAGGCCT 58.030 45.455 11.78 11.78 0.00 5.19
1320 1382 6.977502 CCTTGAGGTTATCTATAGCATCATCG 59.022 42.308 2.72 0.00 35.01 3.84
1342 1404 3.074538 AGACTATGTTTGGCAAGGACCTT 59.925 43.478 0.00 0.00 0.00 3.50
1371 1433 2.032681 GCATCGGCATAGTCCCCC 59.967 66.667 0.00 0.00 40.72 5.40
1518 1580 3.054361 ACTTGTGGATAAGAAGCCCGATT 60.054 43.478 0.00 0.00 32.33 3.34
1662 1724 4.895836 TGAGAGGGATTCTAGGATTCCAA 58.104 43.478 11.32 0.00 35.87 3.53
1709 1772 7.052873 CCCATGAATGTTTAGAGTCTGAGATT 58.947 38.462 1.86 1.85 0.00 2.40
1836 1899 4.698201 TGTGTCAATGTGAACCTCCTTA 57.302 40.909 0.00 0.00 0.00 2.69
1858 1921 5.247337 TCATCTATGGGCATTGGACGTAATA 59.753 40.000 0.00 0.00 0.00 0.98
1936 1999 8.299570 GCCAAAATCTCCATAATGTCGATTATT 58.700 33.333 0.00 0.00 33.21 1.40
1969 2032 2.100197 TGGCGACTTAGCTACAGTGAT 58.900 47.619 11.68 0.00 37.29 3.06
1986 2049 1.595382 CGATCAAGGTCGGGATGGC 60.595 63.158 0.00 0.00 37.94 4.40
1995 2058 6.475504 TGATGATTATTATGGCGATCAAGGT 58.524 36.000 0.00 0.00 32.80 3.50
2016 2079 4.728772 TCGGCCAAAATCTCCATAATGAT 58.271 39.130 2.24 0.00 0.00 2.45
2017 2080 4.163441 TCGGCCAAAATCTCCATAATGA 57.837 40.909 2.24 0.00 0.00 2.57
2086 2149 1.820519 TGGTTTTCAGCATGCTCCATC 59.179 47.619 19.68 7.51 34.76 3.51
2087 2150 1.927487 TGGTTTTCAGCATGCTCCAT 58.073 45.000 19.68 0.00 34.76 3.41
2106 2169 2.572333 ATATGGGGCGCTGCTGGTTT 62.572 55.000 7.64 0.00 0.00 3.27
2108 2171 2.572333 AAATATGGGGCGCTGCTGGT 62.572 55.000 7.64 0.00 0.00 4.00
2131 2194 3.009143 GTGAGTTCCATATACCCCCATCC 59.991 52.174 0.00 0.00 0.00 3.51
2148 2211 3.852578 ACCTATTTCCCAATGGAGTGAGT 59.147 43.478 0.00 0.00 43.07 3.41
2269 2332 2.158769 TCATTGACGGGGATTGAGGATG 60.159 50.000 0.00 0.00 0.00 3.51
2277 2340 0.918983 ATGGTGTCATTGACGGGGAT 59.081 50.000 11.97 0.00 34.95 3.85
2288 2351 2.805671 CGAGTTTGCAACTATGGTGTCA 59.194 45.455 0.00 0.00 43.03 3.58
2315 2378 4.443913 TCGAACGAATGGATCTAACACA 57.556 40.909 0.00 0.00 0.00 3.72
2320 2383 3.242969 CCGACTTCGAACGAATGGATCTA 60.243 47.826 9.97 0.00 43.02 1.98
2321 2384 2.479730 CCGACTTCGAACGAATGGATCT 60.480 50.000 9.97 0.00 43.02 2.75
2322 2385 1.852895 CCGACTTCGAACGAATGGATC 59.147 52.381 9.97 5.64 43.02 3.36
2328 2391 3.688272 GATGTATCCGACTTCGAACGAA 58.312 45.455 9.49 9.22 43.02 3.85
2335 2398 6.670233 AGTAGAATTCGATGTATCCGACTTC 58.330 40.000 0.00 0.00 42.29 3.01
2336 2399 6.636562 AGTAGAATTCGATGTATCCGACTT 57.363 37.500 0.00 0.00 35.61 3.01
2337 2400 7.606839 TGATAGTAGAATTCGATGTATCCGACT 59.393 37.037 13.56 0.00 35.61 4.18
2338 2401 7.749808 TGATAGTAGAATTCGATGTATCCGAC 58.250 38.462 13.56 0.00 35.61 4.79
2339 2402 7.916914 TGATAGTAGAATTCGATGTATCCGA 57.083 36.000 13.56 0.00 0.00 4.55
2356 2419 7.010183 GTCAAAAGCGCAAGAGTAATGATAGTA 59.990 37.037 11.47 0.00 43.02 1.82
2365 2428 1.144969 CCGTCAAAAGCGCAAGAGTA 58.855 50.000 11.47 0.00 43.02 2.59
2373 2436 4.084888 GGTCGGCCGTCAAAAGCG 62.085 66.667 27.15 0.00 0.00 4.68
2379 2442 3.998672 GGTTGAGGTCGGCCGTCA 61.999 66.667 27.15 19.21 40.50 4.35
2481 2544 3.134081 AGTCTTCTTCGTTCCCTTTGTCA 59.866 43.478 0.00 0.00 0.00 3.58
2482 2545 3.729966 AGTCTTCTTCGTTCCCTTTGTC 58.270 45.455 0.00 0.00 0.00 3.18
2496 2559 4.161377 GGATGTGGCTCTTTCTAGTCTTCT 59.839 45.833 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.