Multiple sequence alignment - TraesCS2B01G316000

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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 TraesCS2B01G316000 chr2B 100.000 4412 0 0 1 4412 451449097 451453508 0.000000e+00 8148
1 TraesCS2B01G316000 chr2B 77.033 209 41 6 2501 2704 548611110 548611316 3.610000e-21 113
2 TraesCS2B01G316000 chr2D 94.626 4429 195 30 1 4405 380073171 380077580 0.000000e+00 6820
3 TraesCS2B01G316000 chr2D 72.536 903 206 28 2498 3367 599928019 599928912 5.660000e-64 255
4 TraesCS2B01G316000 chr2A 93.383 3793 209 26 1 3776 515297574 515301341 0.000000e+00 5576
5 TraesCS2B01G316000 chr2A 90.282 319 22 6 4094 4411 515301343 515301653 4.110000e-110 409
6 TraesCS2B01G316000 chr2A 72.119 911 206 33 2501 3375 611297959 611298857 9.540000e-57 231
7 TraesCS2B01G316000 chr1A 71.283 881 217 26 2504 3360 7189875 7189007 4.500000e-45 193
8 TraesCS2B01G316000 chr1B 72.698 619 144 18 2504 3102 548192090 548191477 2.710000e-42 183
9 TraesCS2B01G316000 chr1D 70.843 878 226 22 2504 3360 5522536 5521668 4.540000e-40 176
10 TraesCS2B01G316000 chr1D 72.375 619 146 18 2504 3102 407670949 407670336 5.870000e-39 172
11 TraesCS2B01G316000 chr3B 88.889 63 4 2 3931 3991 783294090 783294151 1.700000e-09 75


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 TraesCS2B01G316000 chr2B 451449097 451453508 4411 False 8148.0 8148 100.0000 1 4412 1 chr2B.!!$F1 4411
1 TraesCS2B01G316000 chr2D 380073171 380077580 4409 False 6820.0 6820 94.6260 1 4405 1 chr2D.!!$F1 4404
2 TraesCS2B01G316000 chr2D 599928019 599928912 893 False 255.0 255 72.5360 2498 3367 1 chr2D.!!$F2 869
3 TraesCS2B01G316000 chr2A 515297574 515301653 4079 False 2992.5 5576 91.8325 1 4411 2 chr2A.!!$F2 4410
4 TraesCS2B01G316000 chr2A 611297959 611298857 898 False 231.0 231 72.1190 2501 3375 1 chr2A.!!$F1 874

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
241 262 2.042686 ATTGTGTATGAGGTGCGCAT 57.957 45.0 15.91 0.0 32.91 4.73 F
1473 1513 0.673437 CCACGGACACATTTTTGCCT 59.327 50.0 0.00 0.0 0.00 4.75 F
2052 2092 0.507358 GAAGCACAAGTTCGACGGAC 59.493 55.0 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 2089 0.107165 GCATGGGGTAGAACCTGTCC 60.107 60.0 0.0 0.0 38.64 4.02 R
3378 3445 0.036732 AATGCGAACTTCCTCTGCCA 59.963 50.0 0.0 0.0 0.00 4.92 R
3738 3807 0.183731 CTAGGGCTTTGGGGATGGTC 59.816 60.0 0.0 0.0 0.00 4.02 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
65 66 8.726650 TCATTTTCACATACTTGAACATTTCG 57.273 30.769 0.00 0.00 35.18 3.46
132 134 9.377383 GTTTTATGTCCGTGGATATTTTTATCG 57.623 33.333 3.34 0.00 0.00 2.92
135 137 9.761504 TTATGTCCGTGGATATTTTTATCGTTA 57.238 29.630 3.34 0.00 0.00 3.18
143 145 7.637132 GTGGATATTTTTATCGTTACAACACGG 59.363 37.037 0.00 0.00 40.74 4.94
149 151 2.529780 TCGTTACAACACGGGAACAT 57.470 45.000 0.00 0.00 40.74 2.71
150 152 2.836262 TCGTTACAACACGGGAACATT 58.164 42.857 0.00 0.00 40.74 2.71
151 153 3.204526 TCGTTACAACACGGGAACATTT 58.795 40.909 0.00 0.00 40.74 2.32
152 154 3.626670 TCGTTACAACACGGGAACATTTT 59.373 39.130 0.00 0.00 40.74 1.82
241 262 2.042686 ATTGTGTATGAGGTGCGCAT 57.957 45.000 15.91 0.00 32.91 4.73
298 320 5.717119 TGACTTCGAGGAATAGTTGGTAAC 58.283 41.667 0.00 0.00 0.00 2.50
330 352 2.227388 CAGCAAGCCAGTCAAACCTAAG 59.773 50.000 0.00 0.00 0.00 2.18
412 434 5.220397 GCCAAAATTGCTTAATTTACGCCTC 60.220 40.000 2.82 0.00 32.51 4.70
623 663 3.226347 GTTGTGCACTTCATCGCTAAAC 58.774 45.455 19.41 6.02 0.00 2.01
642 682 7.200455 GCTAAACTAGACCTGAAGAAGATCTC 58.800 42.308 0.00 0.00 0.00 2.75
657 697 4.348863 AGATCTCCAATCACAGCATACC 57.651 45.455 0.00 0.00 0.00 2.73
737 777 6.105333 CCTTAGATCTGGTGAAGAAAGACTG 58.895 44.000 5.18 0.00 38.79 3.51
1206 1246 3.684908 CATATGGTTCAACACAGTCCCA 58.315 45.455 0.00 0.00 0.00 4.37
1227 1267 1.003718 GCTTACTCCAGCGTGGGTT 60.004 57.895 4.52 0.00 38.32 4.11
1290 1330 1.832608 CACGATCTCCGGGGATGGA 60.833 63.158 30.68 8.66 43.93 3.41
1332 1372 2.121948 TCCAGCAGCTCCATAATCTGT 58.878 47.619 0.00 0.00 0.00 3.41
1473 1513 0.673437 CCACGGACACATTTTTGCCT 59.327 50.000 0.00 0.00 0.00 4.75
1498 1538 2.972625 CGAAGCTTGGGTATGACAAGA 58.027 47.619 2.10 0.00 46.27 3.02
1543 1583 6.039717 CCTTGTTTCTTGGAAGAACTTGATCA 59.960 38.462 1.18 0.00 44.18 2.92
1548 1588 2.778299 TGGAAGAACTTGATCAACCCG 58.222 47.619 3.38 0.00 0.00 5.28
1766 1806 5.948758 TGTATACCTTGCATGATGAAACCAA 59.051 36.000 0.00 0.00 0.00 3.67
1845 1885 1.598701 GCTCACAGAATTGGGTGCCC 61.599 60.000 0.00 0.00 40.46 5.36
1917 1957 2.445427 TCCACCATTTGCGATGACAAT 58.555 42.857 1.75 0.00 0.00 2.71
1998 2038 3.632333 ACTAGATGATCGAACCAGTGGA 58.368 45.455 18.40 0.00 0.00 4.02
2032 2072 1.662629 CTCCATTAGACTGCAGCAACG 59.337 52.381 15.27 0.00 0.00 4.10
2042 2082 1.370900 GCAGCAACGGAAGCACAAG 60.371 57.895 0.00 0.00 0.00 3.16
2049 2089 1.213094 ACGGAAGCACAAGTTCGACG 61.213 55.000 0.00 0.00 0.00 5.12
2052 2092 0.507358 GAAGCACAAGTTCGACGGAC 59.493 55.000 0.00 0.00 0.00 4.79
2271 2311 4.516698 TCAAGCACAAATGGAGAAACTCTC 59.483 41.667 0.00 0.00 42.66 3.20
2574 2617 1.990614 GGGGTCTCTGGGTGACTCC 60.991 68.421 3.40 3.40 46.30 3.85
2575 2618 2.352032 GGGTCTCTGGGTGACTCCG 61.352 68.421 0.00 0.00 37.00 4.63
2739 2782 2.749076 TGTCTATGAGCACATGCCAAAC 59.251 45.455 6.91 0.00 43.38 2.93
3147 3214 3.194755 GTGACCATGGTGTTTATTTCCCC 59.805 47.826 25.52 3.21 0.00 4.81
3187 3254 3.329688 CTCGAAGGCAGCGACGTCT 62.330 63.158 14.70 0.00 33.71 4.18
3279 3346 0.737219 GCTGGTGCATCCAAGATGAC 59.263 55.000 8.74 4.24 46.59 3.06
3321 3388 2.027100 GGGAGAAGTGGTTCGGATTCTT 60.027 50.000 0.00 0.00 37.79 2.52
3331 3398 1.153086 CGGATTCTTGAGGGGCTGG 60.153 63.158 0.00 0.00 0.00 4.85
3378 3445 1.558756 AGGCTGCTTCAAGCTATGAGT 59.441 47.619 11.57 0.00 42.97 3.41
3384 3451 2.679059 GCTTCAAGCTATGAGTGGCAGA 60.679 50.000 0.71 0.00 39.77 4.26
3405 3472 1.732259 GGAAGTTCGCATTCGACATGT 59.268 47.619 0.00 0.00 45.43 3.21
3412 3479 2.927477 TCGCATTCGACATGTTCCTAAC 59.073 45.455 0.00 0.00 40.21 2.34
3451 3518 9.632638 TTTCAAGGGAATATTTCTATTCTGGAG 57.367 33.333 0.00 0.00 41.94 3.86
3452 3519 7.227156 TCAAGGGAATATTTCTATTCTGGAGC 58.773 38.462 0.00 0.00 41.94 4.70
3495 3562 6.713762 TTCCATGTGTCAGAAATGAAGTTT 57.286 33.333 0.00 0.00 0.00 2.66
3545 3612 3.793797 TGTATGATAGACCGTGTGTGG 57.206 47.619 0.00 0.00 0.00 4.17
3550 3617 0.895530 ATAGACCGTGTGTGGGAGTG 59.104 55.000 0.00 0.00 0.00 3.51
3563 3630 4.221262 GTGTGGGAGTGGTACAAGTGTATA 59.779 45.833 0.00 0.00 44.16 1.47
3564 3631 5.027460 TGTGGGAGTGGTACAAGTGTATAT 58.973 41.667 0.00 0.00 44.16 0.86
3570 3637 8.208903 GGGAGTGGTACAAGTGTATATATTTGT 58.791 37.037 13.47 13.47 44.16 2.83
3606 3674 2.133281 TGTGGCATTGGGAGAGAATG 57.867 50.000 0.00 0.00 34.47 2.67
3661 3730 7.148069 CGAGCTTAGGGAAACTTTAATCCATTT 60.148 37.037 0.00 0.00 37.46 2.32
3665 3734 9.860898 CTTAGGGAAACTTTAATCCATTTTCAG 57.139 33.333 0.00 0.00 37.46 3.02
3679 3748 9.442047 AATCCATTTTCAGAAGTTAGTGTCTAG 57.558 33.333 0.00 0.00 0.00 2.43
3712 3781 9.764363 ATCTCCAAAATTTAAGTTCCAAAAGTC 57.236 29.630 0.00 0.00 0.00 3.01
3735 3804 0.683179 GGGTATTGGGAAGGTGCCAC 60.683 60.000 0.00 0.00 37.69 5.01
3796 3865 4.060038 GGGTCGGCGTTTCGGAGA 62.060 66.667 6.85 0.00 0.00 3.71
3803 3872 1.802880 CGGCGTTTCGGAGAGATGAAT 60.803 52.381 0.00 0.00 38.43 2.57
3808 3877 4.238514 CGTTTCGGAGAGATGAATATCCC 58.761 47.826 0.00 0.00 38.43 3.85
3809 3878 4.238514 GTTTCGGAGAGATGAATATCCCG 58.761 47.826 0.00 0.00 38.43 5.14
3813 3882 3.449018 CGGAGAGATGAATATCCCGGATT 59.551 47.826 0.73 0.00 32.23 3.01
3820 3889 8.482128 AGAGATGAATATCCCGGATTAGATTTC 58.518 37.037 0.73 5.00 33.64 2.17
3825 3895 8.531982 TGAATATCCCGGATTAGATTTCAGTAG 58.468 37.037 0.73 0.00 0.00 2.57
3832 3902 7.272978 CCGGATTAGATTTCAGTAGAAAGGAA 58.727 38.462 0.00 0.00 46.13 3.36
3853 3923 7.880105 AGGAAATTCTCTTGAACACATCTTTC 58.120 34.615 0.00 0.00 34.71 2.62
3913 3984 1.686587 CCTCCAAAAACTTGTCACCCC 59.313 52.381 0.00 0.00 0.00 4.95
3924 3995 3.270877 CTTGTCACCCCTGTACATAAGC 58.729 50.000 0.00 0.00 0.00 3.09
3929 4000 1.120530 CCCCTGTACATAAGCCGTCT 58.879 55.000 0.00 0.00 0.00 4.18
3934 4005 5.011329 CCCCTGTACATAAGCCGTCTATTTA 59.989 44.000 0.00 0.00 0.00 1.40
3935 4006 6.295688 CCCCTGTACATAAGCCGTCTATTTAT 60.296 42.308 0.00 0.00 0.00 1.40
3936 4007 7.159372 CCCTGTACATAAGCCGTCTATTTATT 58.841 38.462 0.00 0.00 0.00 1.40
3981 4052 1.841302 ATGCTCCTGCCGGTTTCTCA 61.841 55.000 1.90 0.00 38.71 3.27
3985 4056 0.762418 TCCTGCCGGTTTCTCAAGAA 59.238 50.000 1.90 0.00 0.00 2.52
4009 4080 6.625873 AAAAACACAGAGACAAGATCTTCC 57.374 37.500 4.57 0.45 38.00 3.46
4010 4081 4.963318 AACACAGAGACAAGATCTTCCA 57.037 40.909 4.57 0.00 38.00 3.53
4011 4082 4.963318 ACACAGAGACAAGATCTTCCAA 57.037 40.909 4.57 0.00 38.00 3.53
4012 4083 4.892433 ACACAGAGACAAGATCTTCCAAG 58.108 43.478 4.57 0.00 38.00 3.61
4014 4085 5.163258 ACACAGAGACAAGATCTTCCAAGTT 60.163 40.000 4.57 0.00 38.00 2.66
4015 4086 5.407995 CACAGAGACAAGATCTTCCAAGTTC 59.592 44.000 4.57 2.31 38.00 3.01
4016 4087 4.624882 CAGAGACAAGATCTTCCAAGTTCG 59.375 45.833 4.57 0.00 38.00 3.95
4063 4134 3.195698 GATGGTCTTCGCCACGCC 61.196 66.667 0.00 0.00 41.94 5.68
4066 4137 1.966901 ATGGTCTTCGCCACGCCATA 61.967 55.000 0.00 0.00 41.94 2.74
4100 4171 1.341383 CCCATGGTTCTTCCCTTGAGG 60.341 57.143 11.73 0.00 32.74 3.86
4116 4187 6.161348 TCCCTTGAGGATATTTTTCCCACATA 59.839 38.462 0.00 0.00 40.93 2.29
4154 4225 7.110216 GTCTTATTATTGATGTACTTTTGCGCG 59.890 37.037 0.00 0.00 0.00 6.86
4156 4227 2.308347 TTGATGTACTTTTGCGCGTG 57.692 45.000 8.43 0.00 0.00 5.34
4176 4247 7.587757 GCGCGTGAGATAAATCTTGATAAATTT 59.412 33.333 8.43 0.00 37.25 1.82
4198 4269 7.925043 TTTAAGGCCTTAATACAAATCGACA 57.075 32.000 33.16 14.73 35.27 4.35
4199 4270 8.514330 TTTAAGGCCTTAATACAAATCGACAT 57.486 30.769 33.16 2.80 35.27 3.06
4200 4271 6.619801 AAGGCCTTAATACAAATCGACATC 57.380 37.500 18.87 0.00 0.00 3.06
4201 4272 4.750098 AGGCCTTAATACAAATCGACATCG 59.250 41.667 0.00 0.00 41.45 3.84
4203 4274 4.510340 GCCTTAATACAAATCGACATCGGT 59.490 41.667 0.73 0.00 40.29 4.69
4220 4292 5.768164 ACATCGGTTAAACCTCAAAGTCAAT 59.232 36.000 0.00 0.00 35.66 2.57
4222 4294 4.449743 TCGGTTAAACCTCAAAGTCAATCG 59.550 41.667 0.00 0.00 35.66 3.34
4236 4308 7.542477 TCAAAGTCAATCGTCTGATTAGAGAAC 59.458 37.037 0.00 0.00 42.94 3.01
4245 4317 6.653740 TCGTCTGATTAGAGAACTCTTGTACA 59.346 38.462 9.64 0.00 40.93 2.90
4246 4318 7.174426 TCGTCTGATTAGAGAACTCTTGTACAA 59.826 37.037 8.28 8.28 40.93 2.41
4259 4331 8.747538 AACTCTTGTACAAATAAACTTCCAGT 57.252 30.769 10.03 0.00 0.00 4.00
4341 4413 3.420893 TCCCTTAATTTCACTGCAGTGG 58.579 45.455 39.04 23.98 45.65 4.00
4342 4414 3.073798 TCCCTTAATTTCACTGCAGTGGA 59.926 43.478 39.04 32.66 45.65 4.02
4343 4415 4.019174 CCCTTAATTTCACTGCAGTGGAT 58.981 43.478 39.04 30.16 45.65 3.41
4344 4416 4.096984 CCCTTAATTTCACTGCAGTGGATC 59.903 45.833 39.04 0.00 45.65 3.36
4411 4483 6.173339 CAGGCTTTAGTTTCAAGATACTGGA 58.827 40.000 3.83 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 7.722795 TTCTTCGAAATGTTCAAGTATGTGA 57.277 32.000 0.00 0.00 0.00 3.58
131 133 3.612472 AAATGTTCCCGTGTTGTAACG 57.388 42.857 0.00 0.00 43.20 3.18
194 215 2.820178 TGGCTGTCCACATCTCTTAGA 58.180 47.619 0.00 0.00 37.47 2.10
197 218 1.211457 GGATGGCTGTCCACATCTCTT 59.789 52.381 0.00 0.00 46.92 2.85
241 262 1.001293 CGCTTGATATAGCCTGCAGGA 59.999 52.381 37.21 17.52 37.90 3.86
330 352 0.536006 AGTGTCCAACTGCTCTTGCC 60.536 55.000 0.00 0.00 37.88 4.52
412 434 0.737219 GGCCTGCTGATTGCTACAAG 59.263 55.000 0.00 0.00 43.37 3.16
623 663 6.323482 TGATTGGAGATCTTCTTCAGGTCTAG 59.677 42.308 1.86 0.00 43.81 2.43
642 682 2.022764 TGTCGGTATGCTGTGATTGG 57.977 50.000 0.00 0.00 0.00 3.16
676 716 2.742053 TGTCGCAGCTATTTTCCTTGAC 59.258 45.455 0.00 0.00 0.00 3.18
1206 1246 0.321653 CCCACGCTGGAGTAAGCTTT 60.322 55.000 3.20 0.00 40.96 3.51
1332 1372 4.406648 TGTGACTCTTGCTTGAGAAGAA 57.593 40.909 12.25 0.00 37.50 2.52
1473 1513 2.305607 ATACCCAAGCTTCGCCCCA 61.306 57.895 0.00 0.00 0.00 4.96
1498 1538 2.203070 GCGATTGAGGCCGGTGAT 60.203 61.111 1.90 0.00 0.00 3.06
1548 1588 0.820891 CATGGTATGCTCCAGTGGCC 60.821 60.000 3.51 0.00 41.05 5.36
1766 1806 7.016268 AGACATCCACATAATTACGGATAACCT 59.984 37.037 10.92 7.21 36.07 3.50
1820 1860 4.326826 CACCCAATTCTGTGAGCTTTCTA 58.673 43.478 0.00 0.00 34.37 2.10
1845 1885 0.320946 CTTTGGGCTGGGCAAACATG 60.321 55.000 0.00 0.00 0.00 3.21
1917 1957 0.321564 AGTTACAAGATGGCAGCGCA 60.322 50.000 11.47 0.00 0.00 6.09
1951 1991 1.033746 TCCTTCGGCGATCTAACGGT 61.034 55.000 11.76 0.00 0.00 4.83
1956 1996 1.107538 CCCAGTCCTTCGGCGATCTA 61.108 60.000 11.76 0.00 0.00 1.98
1998 2038 5.645497 GTCTAATGGAGTGTTTCTCAAGCAT 59.355 40.000 0.00 0.00 44.40 3.79
2032 2072 0.599204 TCCGTCGAACTTGTGCTTCC 60.599 55.000 0.00 0.00 0.00 3.46
2042 2082 1.402062 GGTAGAACCTGTCCGTCGAAC 60.402 57.143 0.00 0.00 34.73 3.95
2049 2089 0.107165 GCATGGGGTAGAACCTGTCC 60.107 60.000 0.00 0.00 38.64 4.02
2052 2092 0.552848 ATGGCATGGGGTAGAACCTG 59.447 55.000 0.00 0.00 38.64 4.00
2151 2191 2.787601 ATGCAGTGCAAGAACAGTTG 57.212 45.000 23.90 0.00 43.62 3.16
2271 2311 3.195698 GCGGCAAGGCGAAGGTAG 61.196 66.667 20.47 0.00 0.00 3.18
2790 2833 1.427819 GGCGATTTGGTACCTTGCG 59.572 57.895 14.36 12.33 0.00 4.85
2793 2836 0.107848 CGAGGGCGATTTGGTACCTT 60.108 55.000 14.36 0.00 40.82 3.50
3147 3214 0.110373 GCTTCTGGGCAACGTTAACG 60.110 55.000 25.68 25.68 46.33 3.18
3187 3254 0.994247 ATGTGATCCACCAAGCTCCA 59.006 50.000 0.00 0.00 32.73 3.86
3279 3346 1.693467 TTGTCGGTCGATCAAACTCG 58.307 50.000 0.00 0.00 39.99 4.18
3321 3388 2.041762 ATCTCAGCCAGCCCCTCA 59.958 61.111 0.00 0.00 0.00 3.86
3378 3445 0.036732 AATGCGAACTTCCTCTGCCA 59.963 50.000 0.00 0.00 0.00 4.92
3424 3491 9.989296 TCCAGAATAGAAATATTCCCTTGAAAA 57.011 29.630 4.74 0.00 37.20 2.29
3428 3495 6.432472 GGCTCCAGAATAGAAATATTCCCTTG 59.568 42.308 4.74 0.00 37.20 3.61
3435 3502 6.708885 TCATGGGCTCCAGAATAGAAATAT 57.291 37.500 0.00 0.00 36.75 1.28
3540 3607 1.140252 ACACTTGTACCACTCCCACAC 59.860 52.381 0.00 0.00 0.00 3.82
3545 3612 9.609346 AACAAATATATACACTTGTACCACTCC 57.391 33.333 1.84 0.00 31.90 3.85
3570 3637 6.502136 TGCCACATATTGTTGTTTATCGAA 57.498 33.333 0.00 0.00 0.00 3.71
3583 3651 4.524802 TTCTCTCCCAATGCCACATATT 57.475 40.909 0.00 0.00 0.00 1.28
3606 3674 4.595762 TCCAACTACGGGAATACTATGC 57.404 45.455 0.00 0.00 0.00 3.14
3613 3681 2.769663 TGTAGCATCCAACTACGGGAAT 59.230 45.455 0.00 0.00 42.41 3.01
3696 3765 4.219919 CCCAGGGACTTTTGGAACTTAAA 58.780 43.478 0.00 0.00 34.60 1.52
3712 3781 0.258774 CACCTTCCCAATACCCAGGG 59.741 60.000 2.85 2.85 46.90 4.45
3735 3804 1.380380 GGCTTTGGGGATGGTCAGG 60.380 63.158 0.00 0.00 0.00 3.86
3738 3807 0.183731 CTAGGGCTTTGGGGATGGTC 59.816 60.000 0.00 0.00 0.00 4.02
3796 3865 8.150827 TGAAATCTAATCCGGGATATTCATCT 57.849 34.615 10.54 0.00 0.00 2.90
3803 3872 8.486942 TTTCTACTGAAATCTAATCCGGGATA 57.513 34.615 10.54 0.00 37.27 2.59
3808 3877 8.718102 TTTCCTTTCTACTGAAATCTAATCCG 57.282 34.615 0.00 0.00 40.85 4.18
3820 3889 8.286097 GTGTTCAAGAGAATTTCCTTTCTACTG 58.714 37.037 0.00 0.00 36.10 2.74
3825 3895 7.880105 AGATGTGTTCAAGAGAATTTCCTTTC 58.120 34.615 0.00 0.00 35.92 2.62
3832 3902 8.455903 TCAAGAAAGATGTGTTCAAGAGAATT 57.544 30.769 0.00 0.00 35.92 2.17
3853 3923 4.668576 TTGTTAGAGCGCTTTCATCAAG 57.331 40.909 13.26 0.00 35.29 3.02
3864 3934 4.270084 TGTCTCTGTTTGTTTGTTAGAGCG 59.730 41.667 0.00 0.00 35.89 5.03
3949 4020 3.228453 CAGGAGCATTGCCCTTTCATAT 58.772 45.455 13.93 0.00 29.31 1.78
4009 4080 4.016706 ACCTCGCCCCCGAACTTG 62.017 66.667 0.00 0.00 43.87 3.16
4010 4081 4.016706 CACCTCGCCCCCGAACTT 62.017 66.667 0.00 0.00 43.87 2.66
4012 4083 2.814913 AAATCACCTCGCCCCCGAAC 62.815 60.000 0.00 0.00 43.87 3.95
4014 4085 3.006728 AAATCACCTCGCCCCCGA 61.007 61.111 0.00 0.00 42.01 5.14
4015 4086 2.824041 CAAATCACCTCGCCCCCG 60.824 66.667 0.00 0.00 0.00 5.73
4016 4087 3.140814 GCAAATCACCTCGCCCCC 61.141 66.667 0.00 0.00 0.00 5.40
4063 4134 1.394266 GGGTGGCTGGGTGCATTATG 61.394 60.000 0.00 0.00 45.15 1.90
4066 4137 3.242492 ATGGGTGGCTGGGTGCATT 62.242 57.895 0.00 0.00 45.15 3.56
4100 4171 9.665719 ACCAAATTTGTATGTGGGAAAAATATC 57.334 29.630 16.73 0.00 42.66 1.63
4127 4198 7.908082 GCGCAAAAGTACATCAATAATAAGACA 59.092 33.333 0.30 0.00 0.00 3.41
4142 4213 3.984018 TTATCTCACGCGCAAAAGTAC 57.016 42.857 5.73 0.00 0.00 2.73
4176 4247 6.422701 CGATGTCGATTTGTATTAAGGCCTTA 59.577 38.462 21.68 21.68 43.02 2.69
4188 4259 4.320870 AGGTTTAACCGATGTCGATTTGT 58.679 39.130 8.63 0.00 44.90 2.83
4193 4264 3.663995 TTGAGGTTTAACCGATGTCGA 57.336 42.857 8.63 0.00 44.90 4.20
4194 4265 3.744426 ACTTTGAGGTTTAACCGATGTCG 59.256 43.478 8.63 0.00 44.90 4.35
4195 4266 4.753107 TGACTTTGAGGTTTAACCGATGTC 59.247 41.667 8.63 14.79 44.90 3.06
4198 4269 5.121768 CGATTGACTTTGAGGTTTAACCGAT 59.878 40.000 8.63 0.00 44.90 4.18
4199 4270 4.449743 CGATTGACTTTGAGGTTTAACCGA 59.550 41.667 8.63 0.00 44.90 4.69
4200 4271 4.212636 ACGATTGACTTTGAGGTTTAACCG 59.787 41.667 8.63 0.00 44.90 4.44
4201 4272 5.469084 AGACGATTGACTTTGAGGTTTAACC 59.531 40.000 5.91 5.91 38.99 2.85
4203 4274 6.285224 TCAGACGATTGACTTTGAGGTTTAA 58.715 36.000 0.00 0.00 0.00 1.52
4220 4292 6.653740 TGTACAAGAGTTCTCTAATCAGACGA 59.346 38.462 2.63 0.00 0.00 4.20
4222 4294 9.646427 ATTTGTACAAGAGTTCTCTAATCAGAC 57.354 33.333 8.56 0.00 0.00 3.51
4259 4331 2.421619 TGAACGCTCACATGTGCATTA 58.578 42.857 21.38 2.72 34.50 1.90
4341 4413 0.454600 TTGCCTAGGTGACGTCGATC 59.545 55.000 11.31 3.92 0.00 3.69
4342 4414 0.456221 CTTGCCTAGGTGACGTCGAT 59.544 55.000 11.31 1.47 0.00 3.59
4343 4415 0.607217 TCTTGCCTAGGTGACGTCGA 60.607 55.000 11.31 0.00 0.00 4.20
4344 4416 0.242825 TTCTTGCCTAGGTGACGTCG 59.757 55.000 11.31 0.00 0.00 5.12
4371 4443 1.204704 GCCTGGGTTGATTAGTTTGGC 59.795 52.381 0.00 0.00 0.00 4.52
4383 4455 4.178956 TCTTGAAACTAAAGCCTGGGTT 57.821 40.909 5.07 5.07 0.00 4.11


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

AutoCloner maintained by Alex Coulton.