Multiple sequence alignment - TraesCS3D01G117100

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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 TraesCS3D01G117100 chr3D 100.000 3984 0 0 1 3984 70715502 70711519 0.000000e+00 7358.0
1 TraesCS3D01G117100 chr3A 95.553 3216 87 14 1 3209 82395545 82392379 0.000000e+00 5096.0
2 TraesCS3D01G117100 chr3A 83.459 266 18 3 3639 3904 82351773 82351534 1.440000e-54 224.0
3 TraesCS3D01G117100 chr3A 90.278 72 5 1 2775 2844 82392751 82392680 4.240000e-15 93.5
4 TraesCS3D01G117100 chr3B 91.956 3369 199 29 24 3359 116149971 116146642 0.000000e+00 4654.0
5 TraesCS3D01G117100 chr3B 89.860 572 46 10 3415 3984 116146621 116146060 0.000000e+00 725.0
6 TraesCS3D01G117100 chr3B 86.353 447 26 12 24 469 116150562 116150150 4.690000e-124 455.0
7 TraesCS3D01G117100 chr3B 97.222 72 2 0 2813 2884 116147235 116147164 5.410000e-24 122.0
8 TraesCS3D01G117100 chr3B 92.593 81 5 1 3188 3267 116136309 116136229 9.050000e-22 115.0
9 TraesCS3D01G117100 chr3B 88.889 72 6 1 2775 2844 116147195 116147124 1.970000e-13 87.9


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 TraesCS3D01G117100 chr3D 70711519 70715502 3983 True 7358.00 7358 100.0000 1 3984 1 chr3D.!!$R1 3983
1 TraesCS3D01G117100 chr3A 82392379 82395545 3166 True 2594.75 5096 92.9155 1 3209 2 chr3A.!!$R2 3208
2 TraesCS3D01G117100 chr3B 116146060 116150562 4502 True 1208.78 4654 90.8560 24 3984 5 chr3B.!!$R2 3960

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
516 1124 1.047002 TTGGGTGTTTGCATGGGAAG 58.953 50.000 0.00 0.0 0.00 3.46 F
597 1205 2.618045 CCTAGTTGCAGTTAGTTGGGGG 60.618 54.545 6.01 0.0 0.00 5.40 F
1720 2345 0.315251 GCCAAGCCACAAAGGAAGTC 59.685 55.000 0.00 0.0 41.22 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 2036 0.034059 GCCCATCACCTAGGATGTCG 59.966 60.0 17.98 3.37 42.47 4.35 R
1789 2414 0.107993 CCATCTTCTTCTCGCTGCCA 60.108 55.0 0.00 0.00 0.00 4.92 R
3438 4073 0.693049 CACCAGGCTCTACCCAACTT 59.307 55.0 0.00 0.00 40.58 2.66 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
159 162 3.629142 ACTTGGTGGGTATTACAGAGC 57.371 47.619 0.00 0.00 0.00 4.09
192 195 4.351111 AGTTCTTTGGTGGTTCACTAGGAT 59.649 41.667 0.00 0.00 34.40 3.24
193 196 5.546499 AGTTCTTTGGTGGTTCACTAGGATA 59.454 40.000 0.00 0.00 34.40 2.59
194 197 5.677319 TCTTTGGTGGTTCACTAGGATAG 57.323 43.478 0.00 0.00 46.50 2.08
195 198 4.469945 TCTTTGGTGGTTCACTAGGATAGG 59.530 45.833 0.00 0.00 44.97 2.57
196 199 3.484953 TGGTGGTTCACTAGGATAGGT 57.515 47.619 0.00 0.00 44.97 3.08
253 257 4.696479 ACTGAACAGGAAATGACAGTCT 57.304 40.909 1.31 0.00 41.91 3.24
262 266 8.083828 ACAGGAAATGACAGTCTATCTATTGT 57.916 34.615 1.31 0.00 0.00 2.71
268 272 5.664457 TGACAGTCTATCTATTGTTGCCTG 58.336 41.667 1.31 0.00 0.00 4.85
273 277 8.924303 ACAGTCTATCTATTGTTGCCTGTATTA 58.076 33.333 0.00 0.00 0.00 0.98
327 331 4.921470 TGTAGCGATTTTCAGCAGTTAC 57.079 40.909 0.00 0.00 35.48 2.50
365 369 4.065088 TGTCATAAGAGTGCTCCAACAAC 58.935 43.478 0.00 0.00 0.00 3.32
382 386 3.078837 ACAACGTTGCCCTTAGGTAATG 58.921 45.455 27.61 0.00 46.92 1.90
516 1124 1.047002 TTGGGTGTTTGCATGGGAAG 58.953 50.000 0.00 0.00 0.00 3.46
530 1138 3.071874 TGGGAAGCGAATCAATCAACT 57.928 42.857 0.00 0.00 0.00 3.16
597 1205 2.618045 CCTAGTTGCAGTTAGTTGGGGG 60.618 54.545 6.01 0.00 0.00 5.40
1363 1988 2.620115 CACTGTCAACCACTGCTTCAAT 59.380 45.455 0.00 0.00 0.00 2.57
1411 2036 0.992802 GTGAGTTCGCCGAGATGTTC 59.007 55.000 0.00 0.00 0.00 3.18
1582 2207 1.470098 CTTGACCACATGGCTAAGCAC 59.530 52.381 0.00 0.00 39.32 4.40
1720 2345 0.315251 GCCAAGCCACAAAGGAAGTC 59.685 55.000 0.00 0.00 41.22 3.01
1783 2408 2.419324 GTGGAAGCTCTTGAGAATGCTG 59.581 50.000 1.30 0.00 35.79 4.41
1786 2411 3.946558 GGAAGCTCTTGAGAATGCTGAAT 59.053 43.478 1.30 0.00 35.79 2.57
1789 2414 4.333690 AGCTCTTGAGAATGCTGAATGTT 58.666 39.130 1.30 0.00 34.19 2.71
1948 2573 0.958876 CCAGCATGAGTGAGCAGCAA 60.959 55.000 0.00 0.00 39.69 3.91
2050 2675 4.520179 TCTTCTACATGATGTGCAAGCAT 58.480 39.130 8.61 0.00 0.00 3.79
2240 2865 1.406887 CCCAACCATCTGACTAACCCG 60.407 57.143 0.00 0.00 0.00 5.28
2256 2881 1.370778 CCGTGCTGTGCATGTGTTG 60.371 57.895 10.32 0.00 43.26 3.33
2305 2930 0.618968 AGAAGGAGGCCCTCAACGAT 60.619 55.000 13.90 0.00 43.48 3.73
2320 2945 1.115467 ACGATGATGTCCTCCCAGAC 58.885 55.000 0.00 0.00 37.28 3.51
2572 3197 7.467811 GCTTCCATCATATACAACTTCAAGGTG 60.468 40.741 0.00 0.00 39.30 4.00
2667 3292 1.274712 CTCAAGAGAAGGGAGCTGGT 58.725 55.000 0.00 0.00 0.00 4.00
2712 3337 8.957466 GCTATCTGTTTTCTTACTTGGGTTATT 58.043 33.333 0.00 0.00 0.00 1.40
2779 3404 9.899226 GGAATGGAATAACTAAACATAATCTGC 57.101 33.333 0.00 0.00 0.00 4.26
2802 3427 3.649073 TGTAGTGTTGAGATTGTCACCG 58.351 45.455 0.00 0.00 33.71 4.94
2860 3487 5.877012 CACCATGTAACAAGCTATCTGTTCT 59.123 40.000 5.55 0.00 0.00 3.01
2867 3494 7.813148 TGTAACAAGCTATCTGTTCTTAGTGTC 59.187 37.037 5.55 0.00 0.00 3.67
2914 3541 8.926710 GGAACAGAATATTATAGTGATTGGTCG 58.073 37.037 0.00 0.00 0.00 4.79
3016 3643 4.592942 TGCCTATCAAAAGTGCTTCTGAT 58.407 39.130 6.10 6.10 33.26 2.90
3049 3676 7.706179 CCTTGTGAAATTGAGTAAGAAAAGCAA 59.294 33.333 0.00 0.00 0.00 3.91
3075 3702 1.230324 GACCTGCACCTGTTGAGTTC 58.770 55.000 0.00 0.00 0.00 3.01
3106 3733 8.768955 CAGTTATTATGTGAGAATAGAACAGGC 58.231 37.037 0.00 0.00 0.00 4.85
3162 3789 7.697710 TCAAATGATCATATGTTTTGTTCGCTC 59.302 33.333 9.04 0.00 0.00 5.03
3235 3862 3.921021 GTCGTCAGAGTGGTTACTTGATG 59.079 47.826 0.00 0.00 37.25 3.07
3251 3878 4.581824 ACTTGATGCAGTTCACATTGAAGT 59.418 37.500 0.00 0.00 40.42 3.01
3303 3930 3.062234 GCCTGAGGAGTTTAATTTCGTCG 59.938 47.826 0.65 0.00 32.43 5.12
3310 3937 5.697633 AGGAGTTTAATTTCGTCGCTGTTAA 59.302 36.000 0.00 0.00 0.00 2.01
3311 3938 6.203338 AGGAGTTTAATTTCGTCGCTGTTAAA 59.797 34.615 0.00 0.00 0.00 1.52
3312 3939 7.019418 GGAGTTTAATTTCGTCGCTGTTAAAT 58.981 34.615 9.85 0.00 30.03 1.40
3359 3994 7.439157 TGATCCATTCAAAGTTCACAAGTAG 57.561 36.000 0.00 0.00 0.00 2.57
3360 3995 6.998074 TGATCCATTCAAAGTTCACAAGTAGT 59.002 34.615 0.00 0.00 0.00 2.73
3361 3996 8.154203 TGATCCATTCAAAGTTCACAAGTAGTA 58.846 33.333 0.00 0.00 0.00 1.82
3399 4034 9.780186 ACTAGTTAAGAACACTCTTTGCTTATT 57.220 29.630 0.00 0.00 42.17 1.40
3401 4036 7.797819 AGTTAAGAACACTCTTTGCTTATTCG 58.202 34.615 0.00 0.00 42.17 3.34
3402 4037 4.670227 AGAACACTCTTTGCTTATTCGC 57.330 40.909 0.00 0.00 0.00 4.70
3403 4038 4.065088 AGAACACTCTTTGCTTATTCGCA 58.935 39.130 0.00 0.00 38.31 5.10
3448 4083 9.832445 TGCTTAAGATTTCTATAAGTTGGGTAG 57.168 33.333 6.67 0.00 0.00 3.18
3452 4087 7.068686 AGATTTCTATAAGTTGGGTAGAGCC 57.931 40.000 0.00 0.00 0.00 4.70
3463 4098 1.689273 GGGTAGAGCCTGGTGATACTG 59.311 57.143 0.00 0.00 37.43 2.74
3475 4110 3.709141 TGGTGATACTGCAGCTATGGTAA 59.291 43.478 15.27 0.00 37.20 2.85
3476 4111 4.347876 TGGTGATACTGCAGCTATGGTAAT 59.652 41.667 15.27 0.00 37.20 1.89
3477 4112 5.542251 TGGTGATACTGCAGCTATGGTAATA 59.458 40.000 15.27 0.00 37.20 0.98
3478 4113 6.213397 TGGTGATACTGCAGCTATGGTAATAT 59.787 38.462 15.27 0.04 37.20 1.28
3488 4123 4.350816 AGCTATGGTAATATTGACAGGCCA 59.649 41.667 5.01 0.00 0.00 5.36
3512 4147 1.000060 GGCAAGCTTTCTGCATCACAA 60.000 47.619 10.85 0.00 45.94 3.33
3546 4181 0.824759 ACTGACAGGGCCGATAGTTC 59.175 55.000 7.51 0.00 0.00 3.01
3557 4192 3.802685 GGCCGATAGTTCCGCATATATTC 59.197 47.826 0.00 0.00 0.00 1.75
3558 4193 4.430007 GCCGATAGTTCCGCATATATTCA 58.570 43.478 0.00 0.00 0.00 2.57
3594 4229 4.425180 TGGGCACTTTTGACTTGTACTA 57.575 40.909 0.00 0.00 0.00 1.82
3628 4263 9.217278 CTGTAGATTGGAGAAATTAGGATGATG 57.783 37.037 0.00 0.00 0.00 3.07
3710 4345 3.777106 TTCAAACTCTCTGCATGAGGT 57.223 42.857 17.50 10.70 42.86 3.85
3723 4358 3.599730 CATGAGGTGCTCTCTGTACAA 57.400 47.619 0.00 0.00 42.86 2.41
3725 4360 3.667497 TGAGGTGCTCTCTGTACAAAG 57.333 47.619 0.00 0.00 42.86 2.77
3726 4361 2.289072 TGAGGTGCTCTCTGTACAAAGC 60.289 50.000 14.52 14.52 42.86 3.51
3728 4363 3.165875 AGGTGCTCTCTGTACAAAGCTA 58.834 45.455 19.46 8.42 35.76 3.32
3729 4364 3.578716 AGGTGCTCTCTGTACAAAGCTAA 59.421 43.478 19.46 4.21 35.76 3.09
3730 4365 3.680458 GGTGCTCTCTGTACAAAGCTAAC 59.320 47.826 19.46 12.85 35.76 2.34
3731 4366 4.307432 GTGCTCTCTGTACAAAGCTAACA 58.693 43.478 19.46 2.43 35.76 2.41
3732 4367 4.387256 GTGCTCTCTGTACAAAGCTAACAG 59.613 45.833 19.46 10.58 41.58 3.16
3733 4368 4.280929 TGCTCTCTGTACAAAGCTAACAGA 59.719 41.667 19.46 15.95 45.48 3.41
3734 4369 5.047021 TGCTCTCTGTACAAAGCTAACAGAT 60.047 40.000 19.46 0.00 46.20 2.90
3735 4370 5.872070 GCTCTCTGTACAAAGCTAACAGATT 59.128 40.000 16.74 0.00 46.20 2.40
3736 4371 6.035542 GCTCTCTGTACAAAGCTAACAGATTC 59.964 42.308 16.74 8.86 46.20 2.52
3760 4395 0.313043 AGTACAGTCCCGTCACGTTG 59.687 55.000 0.00 0.00 0.00 4.10
3761 4396 0.665369 GTACAGTCCCGTCACGTTGG 60.665 60.000 0.00 0.00 0.00 3.77
3762 4397 2.424705 TACAGTCCCGTCACGTTGGC 62.425 60.000 0.00 0.00 0.00 4.52
3797 4433 1.501582 GCCCATTACTCTCCTCCAGT 58.498 55.000 0.00 0.00 0.00 4.00
3819 4455 0.039035 TTTGGGCCGCATAAGGAGTT 59.961 50.000 0.00 0.00 0.00 3.01
3842 4478 4.814294 GTACTCACGGGCCGCCAG 62.814 72.222 28.71 23.67 0.00 4.85
3916 4552 0.108329 CGTTTAGTCCCACATCGCCT 60.108 55.000 0.00 0.00 0.00 5.52
3930 4566 3.758172 GCCTAGCGAGAGAGGGAG 58.242 66.667 0.00 0.00 33.04 4.30
3945 4581 3.773119 AGAGGGAGCGACCAGTTTATAAA 59.227 43.478 0.00 0.00 41.20 1.40
3953 4589 2.606272 GACCAGTTTATAAACCCGCTCG 59.394 50.000 21.92 8.09 39.71 5.03
3966 4602 2.512301 CGCTCGCTGCAGCTAACTC 61.512 63.158 34.22 17.73 43.06 3.01
3975 4611 0.246635 GCAGCTAACTCGTCCCTTCA 59.753 55.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.211485 CCTGAAACATAATGCTCAAGAAAAATT 57.789 29.630 0.00 0.00 0.00 1.82
12 13 7.820872 CCCTGAAACATAATGCTCAAGAAAAAT 59.179 33.333 0.00 0.00 0.00 1.82
34 35 0.976641 TGTGTTCTAGACAGGCCCTG 59.023 55.000 9.83 9.83 39.39 4.45
159 162 2.091541 ACCAAAGAACTGTGGTGTGTG 58.908 47.619 14.99 0.00 46.53 3.82
192 195 4.847512 TCTGTAACAAAGGGATGGAACCTA 59.152 41.667 0.00 0.00 37.35 3.08
193 196 3.655777 TCTGTAACAAAGGGATGGAACCT 59.344 43.478 0.00 0.00 40.96 3.50
194 197 3.756963 GTCTGTAACAAAGGGATGGAACC 59.243 47.826 0.00 0.00 0.00 3.62
195 198 3.756963 GGTCTGTAACAAAGGGATGGAAC 59.243 47.826 0.00 0.00 0.00 3.62
196 199 3.655777 AGGTCTGTAACAAAGGGATGGAA 59.344 43.478 0.00 0.00 0.00 3.53
253 257 9.860650 ACCAATTAATACAGGCAACAATAGATA 57.139 29.630 0.00 0.00 41.41 1.98
262 266 2.685897 GCGGACCAATTAATACAGGCAA 59.314 45.455 0.00 0.00 0.00 4.52
268 272 5.813080 AACTCTTGCGGACCAATTAATAC 57.187 39.130 0.00 0.00 31.91 1.89
273 277 3.950397 TCATAACTCTTGCGGACCAATT 58.050 40.909 0.00 0.00 31.91 2.32
314 318 2.543777 AGCCGAGTAACTGCTGAAAA 57.456 45.000 0.00 0.00 37.65 2.29
327 331 1.337167 TGACAGTGTTCATCAGCCGAG 60.337 52.381 0.00 0.00 0.00 4.63
365 369 3.118738 AGAGACATTACCTAAGGGCAACG 60.119 47.826 0.00 0.00 35.63 4.10
382 386 4.439016 CGTCTTAGCTTCCTAACCAGAGAC 60.439 50.000 0.00 0.00 30.63 3.36
516 1124 7.805071 CCAATCCTAATAAGTTGATTGATTCGC 59.195 37.037 12.22 0.00 44.24 4.70
530 1138 7.779798 CCTTGAAACTGATCCCAATCCTAATAA 59.220 37.037 0.00 0.00 0.00 1.40
597 1205 8.252624 AGACTGGTTATAATCCTCTTTAGACC 57.747 38.462 0.00 0.00 0.00 3.85
677 1286 3.007635 ACCCTTACAACTTTATGCGCTC 58.992 45.455 9.73 0.00 0.00 5.03
744 1357 5.121105 CAGATCAGATAAGCCATGTTGACA 58.879 41.667 0.00 0.00 0.00 3.58
1363 1988 4.774660 TGGGTAGTTGTTGAAGTTGGTA 57.225 40.909 0.00 0.00 0.00 3.25
1411 2036 0.034059 GCCCATCACCTAGGATGTCG 59.966 60.000 17.98 3.37 42.47 4.35
1720 2345 0.250234 TGAACAGCATTCCCTCCTCG 59.750 55.000 0.00 0.00 0.00 4.63
1783 2408 1.442769 TCTTCTCGCTGCCAACATTC 58.557 50.000 0.00 0.00 0.00 2.67
1786 2411 0.392706 TCTTCTTCTCGCTGCCAACA 59.607 50.000 0.00 0.00 0.00 3.33
1789 2414 0.107993 CCATCTTCTTCTCGCTGCCA 60.108 55.000 0.00 0.00 0.00 4.92
1948 2573 1.600916 GCGCAGGAACAGGGTCTTT 60.601 57.895 0.30 0.00 0.00 2.52
2240 2865 1.069022 CCTACAACACATGCACAGCAC 60.069 52.381 0.00 0.00 43.04 4.40
2256 2881 3.145551 TCGCCGGGAAGAGCCTAC 61.146 66.667 2.18 0.00 36.66 3.18
2305 2930 0.333652 TACCGTCTGGGAGGACATCA 59.666 55.000 0.00 0.00 40.75 3.07
2320 2945 0.744414 CCTTGCTCACCATGGTACCG 60.744 60.000 19.28 9.90 34.80 4.02
2572 3197 3.650950 TGGCCTTCCACCAGCTCC 61.651 66.667 3.32 0.00 37.47 4.70
2667 3292 4.478206 AGCAGTAAAGATCAAGCAGCTA 57.522 40.909 0.00 0.00 0.00 3.32
2712 3337 7.516155 GCATTTAGTTCTGTTCGATACGCATAA 60.516 37.037 0.00 0.00 0.00 1.90
2770 3395 7.783090 ATCTCAACACTACAAGCAGATTATG 57.217 36.000 0.00 0.00 0.00 1.90
2779 3404 4.150627 CGGTGACAATCTCAACACTACAAG 59.849 45.833 0.00 0.00 36.19 3.16
2802 3427 4.559251 CACTACGAACAGATAGCTTGTCAC 59.441 45.833 0.00 0.00 0.00 3.67
2860 3487 3.755112 TGGTGACAATTCCGACACTAA 57.245 42.857 0.00 0.00 37.44 2.24
2914 3541 9.897744 TGAAAATAACTCAAAAGATCATCACAC 57.102 29.630 0.00 0.00 0.00 3.82
2973 3600 5.406780 GGCAGATGCACATAAGATACAGTAC 59.593 44.000 7.19 0.00 44.36 2.73
3016 3643 1.146774 TCAATTTCACAAGGAGGGCCA 59.853 47.619 6.18 0.00 36.29 5.36
3049 3676 0.773644 ACAGGTGCAGGTCCAAGAAT 59.226 50.000 0.00 0.00 0.00 2.40
3106 3733 3.473367 CTCTGAAACAAAATGAGCGTCG 58.527 45.455 0.00 0.00 0.00 5.12
3280 3907 3.344515 ACGAAATTAAACTCCTCAGGCC 58.655 45.455 0.00 0.00 0.00 5.19
3282 3909 3.062234 GCGACGAAATTAAACTCCTCAGG 59.938 47.826 0.00 0.00 0.00 3.86
3310 3937 5.500234 TCCGAATGGAAATCTGTTCTGATT 58.500 37.500 0.00 0.30 42.85 2.57
3311 3938 5.102953 TCCGAATGGAAATCTGTTCTGAT 57.897 39.130 0.00 0.00 42.85 2.90
3312 3939 4.551702 TCCGAATGGAAATCTGTTCTGA 57.448 40.909 0.00 0.00 42.85 3.27
3330 3965 5.106197 TGTGAACTTTGAATGGATCATTCCG 60.106 40.000 15.38 8.38 46.65 4.30
3373 4008 9.780186 AATAAGCAAAGAGTGTTCTTAACTAGT 57.220 29.630 0.00 0.00 42.80 2.57
3376 4011 7.571428 GCGAATAAGCAAAGAGTGTTCTTAACT 60.571 37.037 0.00 0.00 42.80 2.24
3377 4012 6.520104 GCGAATAAGCAAAGAGTGTTCTTAAC 59.480 38.462 0.00 0.00 42.80 2.01
3379 4014 5.699001 TGCGAATAAGCAAAGAGTGTTCTTA 59.301 36.000 0.00 0.00 45.06 2.10
3380 4015 4.515191 TGCGAATAAGCAAAGAGTGTTCTT 59.485 37.500 0.00 0.00 45.06 2.52
3381 4016 4.065088 TGCGAATAAGCAAAGAGTGTTCT 58.935 39.130 0.00 0.00 45.06 3.01
3382 4017 4.404507 TGCGAATAAGCAAAGAGTGTTC 57.595 40.909 0.00 0.00 45.06 3.18
3437 4072 1.906574 CACCAGGCTCTACCCAACTTA 59.093 52.381 0.00 0.00 40.58 2.24
3438 4073 0.693049 CACCAGGCTCTACCCAACTT 59.307 55.000 0.00 0.00 40.58 2.66
3448 4083 0.813210 GCTGCAGTATCACCAGGCTC 60.813 60.000 16.64 0.00 0.00 4.70
3452 4087 2.103771 ACCATAGCTGCAGTATCACCAG 59.896 50.000 16.64 0.00 0.00 4.00
3463 4098 4.154918 GCCTGTCAATATTACCATAGCTGC 59.845 45.833 0.00 0.00 0.00 5.25
3488 4123 1.749634 GATGCAGAAAGCTTGCCTGAT 59.250 47.619 24.87 17.16 45.94 2.90
3512 4147 2.371841 TGTCAGTGTACCAAATGGAGCT 59.628 45.455 6.42 0.00 38.94 4.09
3557 4192 9.479549 AAAAGTGCCCAAATATATATCCCTATG 57.520 33.333 0.00 0.00 0.00 2.23
3558 4193 9.479549 CAAAAGTGCCCAAATATATATCCCTAT 57.520 33.333 0.00 0.00 0.00 2.57
3594 4229 4.338795 TCTCCAATCTACAGTCCCTTCT 57.661 45.455 0.00 0.00 0.00 2.85
3628 4263 1.337071 CAGATGCTGCCATTGATGTCC 59.663 52.381 0.00 0.00 0.00 4.02
3635 4270 1.337447 GCACAAACAGATGCTGCCATT 60.337 47.619 0.00 0.00 38.84 3.16
3637 4272 1.108132 TGCACAAACAGATGCTGCCA 61.108 50.000 0.00 0.00 42.55 4.92
3710 4345 4.280929 TCTGTTAGCTTTGTACAGAGAGCA 59.719 41.667 17.15 4.81 42.31 4.26
3716 4351 5.168569 TCCGAATCTGTTAGCTTTGTACAG 58.831 41.667 0.00 1.37 40.42 2.74
3718 4353 5.408356 TCTCCGAATCTGTTAGCTTTGTAC 58.592 41.667 0.00 0.00 0.00 2.90
3719 4354 5.185249 ACTCTCCGAATCTGTTAGCTTTGTA 59.815 40.000 0.00 0.00 0.00 2.41
3720 4355 4.021016 ACTCTCCGAATCTGTTAGCTTTGT 60.021 41.667 0.00 0.00 0.00 2.83
3721 4356 4.499183 ACTCTCCGAATCTGTTAGCTTTG 58.501 43.478 0.00 0.00 0.00 2.77
3722 4357 4.810191 ACTCTCCGAATCTGTTAGCTTT 57.190 40.909 0.00 0.00 0.00 3.51
3723 4358 4.705507 TGTACTCTCCGAATCTGTTAGCTT 59.294 41.667 0.00 0.00 0.00 3.74
3725 4360 4.096682 ACTGTACTCTCCGAATCTGTTAGC 59.903 45.833 0.00 0.00 0.00 3.09
3726 4361 5.220892 GGACTGTACTCTCCGAATCTGTTAG 60.221 48.000 0.00 0.00 0.00 2.34
3728 4363 3.444388 GGACTGTACTCTCCGAATCTGTT 59.556 47.826 0.00 0.00 0.00 3.16
3729 4364 3.018149 GGACTGTACTCTCCGAATCTGT 58.982 50.000 0.00 0.00 0.00 3.41
3730 4365 2.359531 GGGACTGTACTCTCCGAATCTG 59.640 54.545 0.00 0.00 0.00 2.90
3731 4366 2.657143 GGGACTGTACTCTCCGAATCT 58.343 52.381 0.00 0.00 0.00 2.40
3732 4367 1.334243 CGGGACTGTACTCTCCGAATC 59.666 57.143 10.42 0.00 42.94 2.52
3733 4368 1.340795 ACGGGACTGTACTCTCCGAAT 60.341 52.381 18.78 1.52 42.94 3.34
3734 4369 0.037303 ACGGGACTGTACTCTCCGAA 59.963 55.000 18.78 0.00 42.94 4.30
3735 4370 0.392193 GACGGGACTGTACTCTCCGA 60.392 60.000 18.78 0.00 42.94 4.55
3736 4371 0.675837 TGACGGGACTGTACTCTCCG 60.676 60.000 13.11 13.11 45.42 4.63
3760 4395 1.447314 CCGTCCTGTTAGTTCGGCC 60.447 63.158 0.00 0.00 35.01 6.13
3761 4396 4.180496 CCGTCCTGTTAGTTCGGC 57.820 61.111 0.00 0.00 35.01 5.54
3762 4397 1.447314 GGCCGTCCTGTTAGTTCGG 60.447 63.158 0.00 0.00 43.37 4.30
3764 4399 0.252197 ATGGGCCGTCCTGTTAGTTC 59.748 55.000 0.00 0.00 36.20 3.01
3797 4433 2.092103 ACTCCTTATGCGGCCCAAATTA 60.092 45.455 0.00 0.00 0.00 1.40
3835 4471 3.365265 CCACTTTGGACTGGCGGC 61.365 66.667 0.00 0.00 40.96 6.53
3842 4478 1.077716 CGGATCCCCCACTTTGGAC 60.078 63.158 6.06 0.00 40.96 4.02
3846 4482 2.677228 CAGCGGATCCCCCACTTT 59.323 61.111 6.06 0.00 34.14 2.66
3852 4488 4.570874 GGAAGCCAGCGGATCCCC 62.571 72.222 6.06 0.00 0.00 4.81
3877 4513 2.183555 CGTAGCGTTCTCCCCACC 59.816 66.667 0.00 0.00 0.00 4.61
3916 4552 1.524165 GTCGCTCCCTCTCTCGCTA 60.524 63.158 0.00 0.00 0.00 4.26
3922 4558 1.183549 TAAACTGGTCGCTCCCTCTC 58.816 55.000 0.00 0.00 34.77 3.20
3927 4563 2.941064 GGGTTTATAAACTGGTCGCTCC 59.059 50.000 23.89 12.56 38.89 4.70
3930 4566 1.063027 GCGGGTTTATAAACTGGTCGC 59.937 52.381 25.68 25.68 38.89 5.19
3953 4589 1.811679 GGGACGAGTTAGCTGCAGC 60.812 63.158 31.53 31.53 42.49 5.25


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

AutoCloner maintained by Alex Coulton.