Multiple sequence alignment - TraesCS2B01G318400

Loading Multiple Alignment...

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 TraesCS2B01G318400 chr2B 100.000 4673 0 0 1 4673 454324491 454329163 0.000000e+00 8630.0
1 TraesCS2B01G318400 chr2A 94.226 2338 87 20 1851 4175 519345409 519347711 0.000000e+00 3526.0
2 TraesCS2B01G318400 chr2A 98.061 980 19 0 857 1836 519344445 519345424 0.000000e+00 1705.0
3 TraesCS2B01G318400 chr2A 95.570 632 18 4 220 842 519343832 519344462 0.000000e+00 1003.0
4 TraesCS2B01G318400 chr2A 95.329 471 19 2 4206 4673 519350018 519350488 0.000000e+00 745.0
5 TraesCS2B01G318400 chr2A 89.305 187 11 5 28 211 519343602 519343782 4.700000e-55 226.0
6 TraesCS2B01G318400 chr2A 97.297 37 1 0 1 37 71586590 71586554 3.900000e-06 63.9
7 TraesCS2B01G318400 chr2A 94.286 35 2 0 1 35 23627352 23627386 2.000000e-03 54.7
8 TraesCS2B01G318400 chr2D 96.446 1829 35 10 28 1836 383845051 383846869 0.000000e+00 2990.0
9 TraesCS2B01G318400 chr2D 94.532 1591 66 11 1852 3431 383846855 383848435 0.000000e+00 2436.0
10 TraesCS2B01G318400 chr2D 93.267 1203 52 14 3322 4510 383848434 383849621 0.000000e+00 1746.0
11 TraesCS2B01G318400 chr2D 100.000 73 0 0 4601 4673 383849923 383849995 8.160000e-28 135.0
12 TraesCS2B01G318400 chrUn 100.000 31 0 0 1 31 30868603 30868633 1.820000e-04 58.4
13 TraesCS2B01G318400 chr4B 100.000 31 0 0 1 31 507956994 507956964 1.820000e-04 58.4
14 TraesCS2B01G318400 chr6B 100.000 30 0 0 1 30 565314437 565314408 6.530000e-04 56.5
15 TraesCS2B01G318400 chr6B 100.000 30 0 0 1 30 620321687 620321658 6.530000e-04 56.5
16 TraesCS2B01G318400 chr6B 92.105 38 2 1 1 38 679343707 679343743 8.000000e-03 52.8
17 TraesCS2B01G318400 chr6A 94.595 37 1 1 1 36 58154392 58154356 6.530000e-04 56.5
18 TraesCS2B01G318400 chr5A 100.000 28 0 0 1 28 19950411 19950438 8.000000e-03 52.8


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 TraesCS2B01G318400 chr2B 454324491 454329163 4672 False 8630.00 8630 100.00000 1 4673 1 chr2B.!!$F1 4672
1 TraesCS2B01G318400 chr2A 519343602 519350488 6886 False 1441.00 3526 94.49820 28 4673 5 chr2A.!!$F2 4645
2 TraesCS2B01G318400 chr2D 383845051 383849995 4944 False 1826.75 2990 96.06125 28 4673 4 chr2D.!!$F1 4645

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
160 164 0.311790 CTCGCATCAGCTCTCCTCTC 59.688 60.0 0.00 0.00 39.10 3.20 F
622 685 1.137594 CACCCCTCACCCTTTACCCA 61.138 60.0 0.00 0.00 0.00 4.51 F
623 686 1.138228 ACCCCTCACCCTTTACCCAC 61.138 60.0 0.00 0.00 0.00 4.61 F
2488 2552 0.881118 TAGCAAAGCTTTTGGGCTCG 59.119 50.0 21.74 6.01 42.24 5.03 F
3161 3227 0.178947 ATTTTTCCTGTTGCCGGGGA 60.179 50.0 2.18 0.00 37.74 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 1911 0.676782 AGCATGCTAACAACGACCCC 60.677 55.000 21.21 0.00 0.00 4.95 R
2488 2552 1.130186 GTCGTGACGTAACTCCTCTCC 59.870 57.143 4.40 0.00 0.00 3.71 R
2775 2840 6.715344 AATGCATTTCACAAGTGCTTAATG 57.285 33.333 5.99 13.35 39.52 1.90 R
3582 3772 0.603569 CATTCCCGCTACTATCGCCT 59.396 55.000 0.00 0.00 0.00 5.52 R
4186 6643 1.063266 TGCCACCAACCTCTCCTTTTT 60.063 47.619 0.00 0.00 0.00 1.94 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
25 26 7.897864 GTATGTTACTCTCCATTATGGCTAGT 58.102 38.462 17.86 17.86 37.47 2.57
26 27 6.406692 TGTTACTCTCCATTATGGCTAGTC 57.593 41.667 17.47 8.64 37.47 2.59
119 123 2.356125 CCAATTGGACGTTCTCCCTCAT 60.356 50.000 20.50 0.00 38.49 2.90
131 135 5.290386 GTTCTCCCTCATTAGTCCAATACG 58.710 45.833 0.00 0.00 0.00 3.06
157 161 2.813901 GCTCGCATCAGCTCTCCT 59.186 61.111 0.00 0.00 39.10 3.69
158 162 1.300080 GCTCGCATCAGCTCTCCTC 60.300 63.158 0.00 0.00 39.10 3.71
159 163 1.737355 GCTCGCATCAGCTCTCCTCT 61.737 60.000 0.00 0.00 39.10 3.69
160 164 0.311790 CTCGCATCAGCTCTCCTCTC 59.688 60.000 0.00 0.00 39.10 3.20
205 209 3.771216 CCCCCAAAATATCATCCTCCTG 58.229 50.000 0.00 0.00 0.00 3.86
377 430 1.897225 CTCCCTCACAGCTCCCACTG 61.897 65.000 0.00 0.00 43.59 3.66
487 550 5.941788 ACCGCTCCTAATAATTGATCCTTT 58.058 37.500 0.00 0.00 0.00 3.11
499 562 4.581309 TTGATCCTTTGCTCTCCATTCT 57.419 40.909 0.00 0.00 0.00 2.40
622 685 1.137594 CACCCCTCACCCTTTACCCA 61.138 60.000 0.00 0.00 0.00 4.51
623 686 1.138228 ACCCCTCACCCTTTACCCAC 61.138 60.000 0.00 0.00 0.00 4.61
676 739 2.564062 CACATTGCTCCCAAATCCAACT 59.436 45.455 0.00 0.00 34.05 3.16
680 743 3.243359 TGCTCCCAAATCCAACTTCTT 57.757 42.857 0.00 0.00 0.00 2.52
689 752 1.153756 CCAACTTCTTGGGCCCTGT 59.846 57.895 25.70 11.03 43.19 4.00
849 912 1.563410 CTGAGGGAATCCAGCCTTTCT 59.437 52.381 0.09 0.00 34.83 2.52
945 1008 3.769739 TCTGCAAGAAAGCCAGAGTTA 57.230 42.857 0.00 0.00 42.31 2.24
1092 1155 2.665603 GCCTTCGTGCTCCTCCTT 59.334 61.111 0.00 0.00 0.00 3.36
1838 1901 4.893424 ACAAGTCGTTGTTAGCATGTTT 57.107 36.364 0.00 0.00 45.00 2.83
1839 1902 5.243426 ACAAGTCGTTGTTAGCATGTTTT 57.757 34.783 0.00 0.00 45.00 2.43
1840 1903 5.646606 ACAAGTCGTTGTTAGCATGTTTTT 58.353 33.333 0.00 0.00 45.00 1.94
1906 1969 2.189594 TGAGAGGCTGAAATGTGTGG 57.810 50.000 0.00 0.00 0.00 4.17
2088 2151 2.237392 AGGTGCCTCCTTGAGTGATAAC 59.763 50.000 0.00 0.00 45.67 1.89
2129 2193 6.292649 CGATAAATGAGGCGCTTGTAACATAA 60.293 38.462 7.64 0.00 0.00 1.90
2313 2377 8.815189 CATGTGAGTTACTGATGATCTAACAAG 58.185 37.037 7.16 0.00 0.00 3.16
2323 2387 9.698309 ACTGATGATCTAACAAGATATTTACCG 57.302 33.333 0.00 0.00 0.00 4.02
2330 2394 9.694137 ATCTAACAAGATATTTACCGCTACTTC 57.306 33.333 0.00 0.00 0.00 3.01
2488 2552 0.881118 TAGCAAAGCTTTTGGGCTCG 59.119 50.000 21.74 6.01 42.24 5.03
2775 2840 3.134081 TGCCTCCTTATAACCAGTGCTAC 59.866 47.826 0.00 0.00 0.00 3.58
2858 2923 3.084039 TGAATGGCTGAAGACAATGGTC 58.916 45.455 0.00 0.00 44.66 4.02
3052 3117 6.051717 ACAGAGATGTAAGTCAATATGGCAC 58.948 40.000 0.00 0.00 0.00 5.01
3054 3119 5.069119 AGAGATGTAAGTCAATATGGCACGA 59.931 40.000 0.00 0.00 0.00 4.35
3160 3226 1.551452 TATTTTTCCTGTTGCCGGGG 58.449 50.000 2.18 0.00 37.74 5.73
3161 3227 0.178947 ATTTTTCCTGTTGCCGGGGA 60.179 50.000 2.18 0.00 37.74 4.81
3162 3228 0.397254 TTTTTCCTGTTGCCGGGGAA 60.397 50.000 2.18 3.98 37.74 3.97
3163 3229 0.397254 TTTTCCTGTTGCCGGGGAAA 60.397 50.000 15.44 15.44 41.54 3.13
3164 3230 0.825840 TTTCCTGTTGCCGGGGAAAG 60.826 55.000 15.44 3.26 42.10 2.62
3184 3250 6.376581 GGAAAGAAGGACATCAAGATGAACAT 59.623 38.462 16.39 5.45 41.20 2.71
3188 3254 4.186926 AGGACATCAAGATGAACATGTCG 58.813 43.478 16.39 0.00 41.20 4.35
3207 3276 8.390354 ACATGTCGAGTATCATACATTGTTTTG 58.610 33.333 0.00 0.00 38.76 2.44
3249 3318 5.876357 ACCATACACTTTCTCTTTTGCCTA 58.124 37.500 0.00 0.00 0.00 3.93
3252 3321 8.107095 ACCATACACTTTCTCTTTTGCCTATTA 58.893 33.333 0.00 0.00 0.00 0.98
3258 3327 8.233190 CACTTTCTCTTTTGCCTATTACTGAAG 58.767 37.037 0.00 0.00 0.00 3.02
3289 3358 7.507616 TCCCTTTTGGTCATTGTAAGTTACATT 59.492 33.333 16.26 10.23 36.81 2.71
3291 3360 8.141268 CCTTTTGGTCATTGTAAGTTACATTGT 58.859 33.333 25.82 11.81 39.66 2.71
3304 3373 7.448748 AAGTTACATTGTGGGTTGATACTTC 57.551 36.000 0.00 0.00 0.00 3.01
3307 3376 7.724061 AGTTACATTGTGGGTTGATACTTCTTT 59.276 33.333 0.00 0.00 0.00 2.52
3362 3544 9.748708 CATTTTCTTTCCAGTTTGAATCTGTTA 57.251 29.630 2.92 0.00 0.00 2.41
3365 3547 8.746052 TTCTTTCCAGTTTGAATCTGTTAAGA 57.254 30.769 10.60 10.60 36.69 2.10
3404 3592 6.788598 TGAAGCCATTTGCCTTTCAATATA 57.211 33.333 0.00 0.00 42.71 0.86
3405 3593 6.572519 TGAAGCCATTTGCCTTTCAATATAC 58.427 36.000 0.00 0.00 42.71 1.47
3409 3597 5.458779 GCCATTTGCCTTTCAATATACGAAC 59.541 40.000 0.00 0.00 34.12 3.95
3415 3603 6.971602 TGCCTTTCAATATACGAACAACAAA 58.028 32.000 0.00 0.00 0.00 2.83
3416 3604 7.598278 TGCCTTTCAATATACGAACAACAAAT 58.402 30.769 0.00 0.00 0.00 2.32
3435 3623 7.660030 ACAAATTTGTCCCCTCATAATTAGG 57.340 36.000 18.13 0.00 36.50 2.69
3441 3629 6.590656 TGTCCCCTCATAATTAGGTCAAAT 57.409 37.500 0.00 0.00 31.70 2.32
3568 3758 1.256812 AGCGAAATTGGGGGAAACAG 58.743 50.000 0.00 0.00 0.00 3.16
3573 3763 2.397044 AATTGGGGGAAACAGCTTCA 57.603 45.000 0.00 0.00 35.55 3.02
3576 3766 1.979155 GGGGGAAACAGCTTCAGGC 60.979 63.158 0.00 0.00 42.19 4.85
3591 3781 2.058595 AGGCGAACCAGGCGATAGT 61.059 57.895 0.00 0.00 41.99 2.12
3600 3790 0.603569 CAGGCGATAGTAGCGGGAAT 59.396 55.000 10.19 0.00 39.35 3.01
3618 3808 0.250295 ATGACACACCAAGGGACACG 60.250 55.000 0.00 0.00 0.00 4.49
3633 3823 0.958822 ACACGCCAAAAGGTCAATCC 59.041 50.000 0.00 0.00 0.00 3.01
3637 3827 2.223947 ACGCCAAAAGGTCAATCCAAAC 60.224 45.455 0.00 0.00 39.02 2.93
3639 3829 2.549992 GCCAAAAGGTCAATCCAAACCC 60.550 50.000 0.00 0.00 39.02 4.11
3663 3853 5.391310 CGACAATTCAAGGTGGAGAAATCAG 60.391 44.000 0.00 0.00 0.00 2.90
3685 3875 5.248020 CAGGAGACCTAGCTATGATGGAAAT 59.752 44.000 2.75 0.00 29.64 2.17
3705 3895 1.278127 TGGTGATTCTTCCGGACCTTC 59.722 52.381 1.83 0.00 0.00 3.46
3757 3947 4.065789 GCAGACCTACTACAAACAAGCTT 58.934 43.478 0.00 0.00 0.00 3.74
3781 3971 1.904771 CGGCTCCATGGGTTGAGTA 59.095 57.895 13.02 0.00 0.00 2.59
3808 3998 2.039216 TGGAACCATGGAAAGCGTCTAA 59.961 45.455 21.47 0.00 0.00 2.10
3996 4186 0.318955 GTTGGTGTCATGTTGCTGCC 60.319 55.000 0.00 0.00 0.00 4.85
4012 4202 2.502295 CTGCCCAGCTTATGATTCCTC 58.498 52.381 0.00 0.00 0.00 3.71
4142 4333 1.753930 TTGCATGGCATGGTACTCTG 58.246 50.000 27.48 2.71 38.76 3.35
4144 4335 0.749091 GCATGGCATGGTACTCTGCA 60.749 55.000 27.48 8.01 38.95 4.41
4145 4336 1.977056 CATGGCATGGTACTCTGCAT 58.023 50.000 19.80 9.44 38.95 3.96
4146 4337 2.304092 CATGGCATGGTACTCTGCATT 58.696 47.619 19.80 5.76 38.95 3.56
4147 4338 2.042686 TGGCATGGTACTCTGCATTC 57.957 50.000 17.79 5.65 38.95 2.67
4148 4339 1.561076 TGGCATGGTACTCTGCATTCT 59.439 47.619 17.79 0.00 38.95 2.40
4149 4340 1.945394 GGCATGGTACTCTGCATTCTG 59.055 52.381 17.79 0.00 38.95 3.02
4150 4341 1.332997 GCATGGTACTCTGCATTCTGC 59.667 52.381 13.15 0.00 45.29 4.26
4186 6643 1.625818 GCTTCTTCAACCTGGAGGAGA 59.374 52.381 0.00 0.00 38.94 3.71
4296 6766 1.266175 CTTGACAGTGAAGCCAGCTTG 59.734 52.381 10.13 0.00 36.26 4.01
4298 6768 1.228367 ACAGTGAAGCCAGCTTGGG 60.228 57.895 10.13 0.00 38.19 4.12
4349 6819 3.823304 ACTCAGATTTTCAAAGGAGCACC 59.177 43.478 0.00 0.00 0.00 5.01
4364 6834 1.883732 CACCGTCGGTCTCAGTGAT 59.116 57.895 15.67 0.00 31.02 3.06
4370 6840 2.607038 CGTCGGTCTCAGTGATCAAACA 60.607 50.000 0.00 0.00 0.00 2.83
4539 7009 3.467803 GTTCGGGAGATGTATTTCCTGG 58.532 50.000 9.62 0.00 39.79 4.45
4542 7012 2.418669 GGGAGATGTATTTCCTGGGGA 58.581 52.381 0.00 0.00 33.85 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.897864 ACTAGCCATAATGGAGAGTAACATAC 58.102 38.462 0.00 0.00 40.96 2.39
1 2 7.950684 AGACTAGCCATAATGGAGAGTAACATA 59.049 37.037 0.00 0.00 40.96 2.29
2 3 6.784969 AGACTAGCCATAATGGAGAGTAACAT 59.215 38.462 0.00 0.00 40.96 2.71
3 4 6.136857 AGACTAGCCATAATGGAGAGTAACA 58.863 40.000 0.00 0.00 40.96 2.41
4 5 6.658188 AGACTAGCCATAATGGAGAGTAAC 57.342 41.667 0.00 0.00 40.96 2.50
5 6 7.039644 GCTTAGACTAGCCATAATGGAGAGTAA 60.040 40.741 0.00 0.00 40.96 2.24
6 7 6.434652 GCTTAGACTAGCCATAATGGAGAGTA 59.565 42.308 0.00 0.00 40.96 2.59
7 8 5.245075 GCTTAGACTAGCCATAATGGAGAGT 59.755 44.000 0.00 0.00 40.96 3.24
8 9 5.719173 GCTTAGACTAGCCATAATGGAGAG 58.281 45.833 0.00 0.00 40.96 3.20
9 10 5.730296 GCTTAGACTAGCCATAATGGAGA 57.270 43.478 0.00 0.00 40.96 3.71
20 21 3.628032 GGTTTGGAATGGCTTAGACTAGC 59.372 47.826 0.00 0.00 40.48 3.42
21 22 4.843728 TGGTTTGGAATGGCTTAGACTAG 58.156 43.478 0.00 0.00 0.00 2.57
22 23 4.919774 TGGTTTGGAATGGCTTAGACTA 57.080 40.909 0.00 0.00 0.00 2.59
23 24 3.806949 TGGTTTGGAATGGCTTAGACT 57.193 42.857 0.00 0.00 0.00 3.24
24 25 4.462483 TGATTGGTTTGGAATGGCTTAGAC 59.538 41.667 0.00 0.00 0.00 2.59
25 26 4.671831 TGATTGGTTTGGAATGGCTTAGA 58.328 39.130 0.00 0.00 0.00 2.10
26 27 5.170748 GTTGATTGGTTTGGAATGGCTTAG 58.829 41.667 0.00 0.00 0.00 2.18
75 79 0.987294 CACTGTCTGGGATCTGGGTT 59.013 55.000 0.00 0.00 0.00 4.11
77 81 1.222936 GCACTGTCTGGGATCTGGG 59.777 63.158 0.00 0.00 0.00 4.45
86 90 1.955778 TCCAATTGGTTGCACTGTCTG 59.044 47.619 23.76 0.00 36.34 3.51
119 123 1.545136 TGTCACGCCGTATTGGACTAA 59.455 47.619 6.93 0.00 42.00 2.24
156 160 1.457455 GGGGAGGAGCTGGAGAGAG 60.457 68.421 0.00 0.00 0.00 3.20
157 161 1.522917 AAGGGGAGGAGCTGGAGAGA 61.523 60.000 0.00 0.00 0.00 3.10
158 162 0.620121 AAAGGGGAGGAGCTGGAGAG 60.620 60.000 0.00 0.00 0.00 3.20
159 163 0.178861 AAAAGGGGAGGAGCTGGAGA 60.179 55.000 0.00 0.00 0.00 3.71
160 164 0.701147 AAAAAGGGGAGGAGCTGGAG 59.299 55.000 0.00 0.00 0.00 3.86
205 209 1.767681 AGAGAAGCATGGATGGAGGAC 59.232 52.381 0.00 0.00 0.00 3.85
260 306 5.544176 AGATTAGACAAGTCAAGGGTCAAGA 59.456 40.000 2.72 0.00 34.04 3.02
487 550 2.171003 TCAACGAGAGAATGGAGAGCA 58.829 47.619 0.00 0.00 0.00 4.26
499 562 8.651391 TTTAGAGTAACAACAAATCAACGAGA 57.349 30.769 0.00 0.00 0.00 4.04
622 685 6.710744 AGACCAAAGATTAGACGATTGTTTGT 59.289 34.615 0.00 0.00 0.00 2.83
623 686 7.118390 AGAGACCAAAGATTAGACGATTGTTTG 59.882 37.037 0.00 0.00 0.00 2.93
689 752 2.674754 GGTGGATTTGAGGGGCGA 59.325 61.111 0.00 0.00 0.00 5.54
849 912 0.986527 TCCTGCAGAGAATTGGAGCA 59.013 50.000 17.39 0.00 35.44 4.26
1092 1155 1.149782 ACAGGAGGGAGAGGAGGACA 61.150 60.000 0.00 0.00 0.00 4.02
1817 1880 4.893424 AAACATGCTAACAACGACTTGT 57.107 36.364 0.00 0.00 42.81 3.16
1841 1904 1.334243 CTAACAACGACCCCGCAAAAA 59.666 47.619 0.00 0.00 39.95 1.94
1842 1905 0.945813 CTAACAACGACCCCGCAAAA 59.054 50.000 0.00 0.00 39.95 2.44
1843 1906 1.508808 GCTAACAACGACCCCGCAAA 61.509 55.000 0.00 0.00 39.95 3.68
1844 1907 1.962306 GCTAACAACGACCCCGCAA 60.962 57.895 0.00 0.00 39.95 4.85
1845 1908 2.357760 GCTAACAACGACCCCGCA 60.358 61.111 0.00 0.00 39.95 5.69
1846 1909 1.743995 ATGCTAACAACGACCCCGC 60.744 57.895 0.00 0.00 39.95 6.13
1847 1910 1.977594 GCATGCTAACAACGACCCCG 61.978 60.000 11.37 0.00 42.50 5.73
1848 1911 0.676782 AGCATGCTAACAACGACCCC 60.677 55.000 21.21 0.00 0.00 4.95
1849 1912 1.165270 AAGCATGCTAACAACGACCC 58.835 50.000 23.00 0.00 0.00 4.46
1906 1969 4.680567 ACAAAAACCACACGTTACACAAAC 59.319 37.500 0.00 0.00 33.05 2.93
2071 2134 4.207891 TCAAGTTATCACTCAAGGAGGC 57.792 45.455 0.00 0.00 33.35 4.70
2088 2151 7.909267 TCATTTATCGAATACAGCAGTTCAAG 58.091 34.615 0.00 0.00 0.00 3.02
2248 2312 7.041576 TGCTGATCCAAGAATAATCTTCATTCG 60.042 37.037 0.00 0.00 44.11 3.34
2313 2377 9.903682 TGTAAGTATGAAGTAGCGGTAAATATC 57.096 33.333 0.00 0.00 0.00 1.63
2323 2387 7.752557 GGTAACTGTGTAAGTATGAAGTAGC 57.247 40.000 0.00 0.00 38.56 3.58
2488 2552 1.130186 GTCGTGACGTAACTCCTCTCC 59.870 57.143 4.40 0.00 0.00 3.71
2775 2840 6.715344 AATGCATTTCACAAGTGCTTAATG 57.285 33.333 5.99 13.35 39.52 1.90
2786 2851 8.999220 TGCAGAATTTATAAATGCATTTCACA 57.001 26.923 27.28 11.61 0.00 3.58
2858 2923 1.094073 CCTCTGAATTCCGGCTGCTG 61.094 60.000 2.27 0.26 0.00 4.41
2981 3046 5.885230 TGTGAATCACATGACCAATCTTC 57.115 39.130 12.63 0.00 39.62 2.87
3133 3199 5.126384 CGGCAACAGGAAAAATAAATAGGGA 59.874 40.000 0.00 0.00 0.00 4.20
3149 3215 1.244019 CCTTCTTTCCCCGGCAACAG 61.244 60.000 0.00 0.00 0.00 3.16
3160 3226 6.808008 TGTTCATCTTGATGTCCTTCTTTC 57.192 37.500 10.01 0.00 0.00 2.62
3161 3227 6.718454 ACATGTTCATCTTGATGTCCTTCTTT 59.282 34.615 10.01 0.00 0.00 2.52
3162 3228 6.243900 ACATGTTCATCTTGATGTCCTTCTT 58.756 36.000 10.01 0.00 0.00 2.52
3163 3229 5.813383 ACATGTTCATCTTGATGTCCTTCT 58.187 37.500 10.01 0.00 0.00 2.85
3164 3230 5.220548 CGACATGTTCATCTTGATGTCCTTC 60.221 44.000 0.00 1.82 32.93 3.46
3184 3250 6.593770 AGCAAAACAATGTATGATACTCGACA 59.406 34.615 4.03 0.00 0.00 4.35
3220 3289 8.515414 GCAAAAGAGAAAGTGTATGGTCTAATT 58.485 33.333 0.00 0.00 0.00 1.40
3221 3290 7.121315 GGCAAAAGAGAAAGTGTATGGTCTAAT 59.879 37.037 0.00 0.00 0.00 1.73
3225 3294 4.762251 AGGCAAAAGAGAAAGTGTATGGTC 59.238 41.667 0.00 0.00 0.00 4.02
3234 3303 7.148171 CCCTTCAGTAATAGGCAAAAGAGAAAG 60.148 40.741 0.00 0.00 0.00 2.62
3258 3327 0.252239 AATGACCAAAAGGGAGCCCC 60.252 55.000 0.91 2.16 45.90 5.80
3289 3358 6.605594 ACAAAGAAAAGAAGTATCAACCCACA 59.394 34.615 0.00 0.00 0.00 4.17
3291 3360 7.654022 AACAAAGAAAAGAAGTATCAACCCA 57.346 32.000 0.00 0.00 0.00 4.51
3339 3521 9.184523 TCTTAACAGATTCAAACTGGAAAGAAA 57.815 29.630 9.94 0.00 37.33 2.52
3362 3544 9.023962 TGGCTTCATTTACACATCTTAAATCTT 57.976 29.630 0.00 0.00 28.55 2.40
3398 3586 7.274686 GGGGACAAATTTGTTGTTCGTATATTG 59.725 37.037 24.02 0.00 42.43 1.90
3404 3592 3.028130 AGGGGACAAATTTGTTGTTCGT 58.972 40.909 24.02 12.52 42.43 3.85
3405 3593 3.067461 TGAGGGGACAAATTTGTTGTTCG 59.933 43.478 24.02 0.00 42.43 3.95
3409 3597 7.981225 CCTAATTATGAGGGGACAAATTTGTTG 59.019 37.037 24.02 0.00 42.43 3.33
3415 3603 6.590656 TGACCTAATTATGAGGGGACAAAT 57.409 37.500 0.00 0.00 38.52 2.32
3416 3604 6.395780 TTGACCTAATTATGAGGGGACAAA 57.604 37.500 0.00 0.00 38.52 2.83
3419 3607 7.898014 AAATTTGACCTAATTATGAGGGGAC 57.102 36.000 0.00 0.00 38.52 4.46
3573 3763 0.754217 TACTATCGCCTGGTTCGCCT 60.754 55.000 0.00 0.00 38.36 5.52
3576 3766 0.660595 CGCTACTATCGCCTGGTTCG 60.661 60.000 0.00 0.00 0.00 3.95
3582 3772 0.603569 CATTCCCGCTACTATCGCCT 59.396 55.000 0.00 0.00 0.00 5.52
3591 3781 0.687920 TTGGTGTGTCATTCCCGCTA 59.312 50.000 0.00 0.00 0.00 4.26
3600 3790 1.145156 CGTGTCCCTTGGTGTGTCA 59.855 57.895 0.00 0.00 0.00 3.58
3618 3808 2.549992 GGGTTTGGATTGACCTTTTGGC 60.550 50.000 0.00 0.00 45.59 4.52
3633 3823 2.288152 CCACCTTGAATTGTCGGGTTTG 60.288 50.000 0.00 0.00 32.35 2.93
3637 3827 1.003118 TCTCCACCTTGAATTGTCGGG 59.997 52.381 0.00 0.00 0.00 5.14
3639 3829 4.455533 TGATTTCTCCACCTTGAATTGTCG 59.544 41.667 0.00 0.00 0.00 4.35
3663 3853 5.486526 CATTTCCATCATAGCTAGGTCTCC 58.513 45.833 5.15 0.00 0.00 3.71
3685 3875 1.278127 GAAGGTCCGGAAGAATCACCA 59.722 52.381 5.23 0.00 0.00 4.17
3705 3895 3.126514 AGCTTCTTTCTTGATCATGCACG 59.873 43.478 0.00 0.00 0.00 5.34
3757 3947 2.676121 CCCATGGAGCCGCAAACA 60.676 61.111 15.22 0.00 0.00 2.83
3808 3998 4.158209 CAGATGCTATCACGATCTCTCCAT 59.842 45.833 0.00 0.00 0.00 3.41
3996 4186 2.548920 GGGACGAGGAATCATAAGCTGG 60.549 54.545 0.00 0.00 0.00 4.85
4012 4202 3.055819 TCTCATCAAGGAAGAAAGGGACG 60.056 47.826 0.00 0.00 0.00 4.79
4067 4258 8.567948 TGAAGAACTGAACCATCAAATTTCTAC 58.432 33.333 0.00 0.00 34.49 2.59
4145 4336 9.565090 AGAAGCAATTATATGATACTTGCAGAA 57.435 29.630 18.19 0.00 43.49 3.02
4146 4337 9.565090 AAGAAGCAATTATATGATACTTGCAGA 57.435 29.630 18.19 0.00 43.49 4.26
4147 4338 9.823098 GAAGAAGCAATTATATGATACTTGCAG 57.177 33.333 18.19 0.00 43.49 4.41
4148 4339 9.341078 TGAAGAAGCAATTATATGATACTTGCA 57.659 29.630 18.19 0.00 43.49 4.08
4169 4360 4.446311 CCTTTTTCTCCTCCAGGTTGAAGA 60.446 45.833 0.00 0.00 36.34 2.87
4186 6643 1.063266 TGCCACCAACCTCTCCTTTTT 60.063 47.619 0.00 0.00 0.00 1.94
4296 6766 3.278157 GTTGCCAGTTAGCAGCCC 58.722 61.111 0.00 0.00 45.13 5.19
4298 6768 1.878775 CTGGTTGCCAGTTAGCAGC 59.121 57.895 6.99 0.00 45.82 5.25
4316 6786 4.035558 TGAAAATCTGAGTGAGTGTGCAAC 59.964 41.667 0.00 0.00 37.35 4.17
4349 6819 1.986378 GTTTGATCACTGAGACCGACG 59.014 52.381 0.00 0.00 0.00 5.12
4364 6834 1.493772 CGCTACACGGTTCTGTTTGA 58.506 50.000 0.00 0.00 38.44 2.69
4370 6840 2.261671 CAGGCGCTACACGGTTCT 59.738 61.111 7.64 0.00 43.93 3.01
4393 6863 2.791655 CCACCTGAACCCTACCTTTTC 58.208 52.381 0.00 0.00 0.00 2.29
4522 6992 2.418669 TCCCCAGGAAATACATCTCCC 58.581 52.381 0.00 0.00 31.50 4.30


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

AutoCloner maintained by Alex Coulton.