Multiple sequence alignment - TraesCS5D01G493600

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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 TraesCS5D01G493600 chr5D 100.000 3919 0 0 1 3919 526293289 526289371 0.000000e+00 7238
1 TraesCS5D01G493600 chr5A 92.961 3381 194 25 1 3357 653408440 653405080 0.000000e+00 4885
2 TraesCS5D01G493600 chr5A 83.430 863 83 23 3060 3916 653405083 653404275 0.000000e+00 747
3 TraesCS5D01G493600 chr5A 94.048 84 5 0 2295 2378 626021904 626021821 1.140000e-25 128
4 TraesCS5D01G493600 chr5B 91.919 2945 187 18 897 3830 661358679 661355775 0.000000e+00 4072
5 TraesCS5D01G493600 chr5B 88.152 633 44 18 17 628 661359863 661359241 0.000000e+00 725
6 TraesCS5D01G493600 chr5B 87.730 326 28 7 598 913 661359237 661358914 1.720000e-98 370
7 TraesCS5D01G493600 chr2A 85.592 701 73 12 2562 3246 706228685 706227997 0.000000e+00 710
8 TraesCS5D01G493600 chr2A 81.973 294 24 8 2295 2570 706244740 706244458 5.100000e-54 222
9 TraesCS5D01G493600 chr7A 95.238 84 4 0 2295 2378 419270333 419270250 2.460000e-27 134


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 TraesCS5D01G493600 chr5D 526289371 526293289 3918 True 7238.000000 7238 100.0000 1 3919 1 chr5D.!!$R1 3918
1 TraesCS5D01G493600 chr5A 653404275 653408440 4165 True 2816.000000 4885 88.1955 1 3916 2 chr5A.!!$R2 3915
2 TraesCS5D01G493600 chr5B 661355775 661359863 4088 True 1722.333333 4072 89.2670 17 3830 3 chr5B.!!$R1 3813
3 TraesCS5D01G493600 chr2A 706227997 706228685 688 True 710.000000 710 85.5920 2562 3246 1 chr2A.!!$R1 684

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
906 1226 0.111089 CTTCGCTTCAGAACGCACAC 60.111 55.0 5.72 0.0 0.0 3.82 F
1164 1486 0.036010 CATTCCTCCTCAAGCACGGT 60.036 55.0 0.00 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 2668 0.249955 TCCATCTCTGCGTCAATGCA 59.750 50.0 0.00 0.0 43.95 3.96 R
3119 3754 0.738975 TATGTTCTCTCGGCGGTCTG 59.261 55.0 7.21 0.0 0.00 3.51 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
49 52 5.072193 TCTCTGGAGGCATGCTATTTATTCA 59.928 40.000 18.92 4.55 0.00 2.57
112 115 0.733909 TGTTCACTCGATCTGCTGCG 60.734 55.000 0.00 0.00 0.00 5.18
139 142 9.793259 AGGAAACTCTTTACAAACATCAGATTA 57.207 29.630 0.00 0.00 32.90 1.75
215 236 2.225091 TGCAAGGAATGAACATGGAGGT 60.225 45.455 0.00 0.00 0.00 3.85
232 254 4.137543 GGAGGTTTGAGTGTTCATTCTGT 58.862 43.478 0.00 0.00 32.27 3.41
539 561 7.341445 TGAAACACAGCTACCAAATTAGTTT 57.659 32.000 0.00 0.00 0.00 2.66
759 826 2.747396 AGCAGCTTGTCTCTTCAGAG 57.253 50.000 0.00 0.00 43.36 3.35
795 863 9.902196 AAACTGTAACCTTATTTATCAAAACGG 57.098 29.630 0.00 0.00 0.00 4.44
796 864 8.625786 ACTGTAACCTTATTTATCAAAACGGT 57.374 30.769 0.00 0.00 0.00 4.83
816 884 3.440228 GTCAGAGAAGATTAGCGTGGTC 58.560 50.000 0.00 0.00 0.00 4.02
830 898 2.412847 GCGTGGTCTCTGTGCAAAATAC 60.413 50.000 0.00 0.00 0.00 1.89
906 1226 0.111089 CTTCGCTTCAGAACGCACAC 60.111 55.000 5.72 0.00 0.00 3.82
925 1245 1.226888 GTTCGCGCCGTAGAGGAAT 60.227 57.895 0.00 0.00 45.00 3.01
935 1256 2.166459 CCGTAGAGGAATCAGTTGAGCA 59.834 50.000 0.00 0.00 45.00 4.26
938 1259 0.723981 GAGGAATCAGTTGAGCACGC 59.276 55.000 0.00 0.00 0.00 5.34
940 1261 1.014044 GGAATCAGTTGAGCACGCGA 61.014 55.000 15.93 0.00 0.00 5.87
1160 1482 0.107993 CTCGCATTCCTCCTCAAGCA 60.108 55.000 0.00 0.00 0.00 3.91
1164 1486 0.036010 CATTCCTCCTCAAGCACGGT 60.036 55.000 0.00 0.00 0.00 4.83
1201 1523 0.907230 GGTCCTCACCAGGCTCTTCT 60.907 60.000 0.00 0.00 43.17 2.85
1659 1981 2.581354 GGGCTGTCGAGTGATGCT 59.419 61.111 0.00 0.00 0.00 3.79
1663 1985 0.389037 GCTGTCGAGTGATGCTGTCA 60.389 55.000 0.00 0.00 0.00 3.58
1713 2035 2.606213 TGGCCGGATGAGGTGACA 60.606 61.111 5.05 0.00 0.00 3.58
1752 2074 3.372730 GCCGCTGATTTGGGTGCA 61.373 61.111 0.00 0.00 0.00 4.57
1818 2140 1.816863 TTGGGAGGTCTGTGACGCTC 61.817 60.000 0.00 0.00 32.65 5.03
1968 2290 2.156098 TGGGAAAGAGGCTGTGGCT 61.156 57.895 0.00 0.00 42.48 4.75
1995 2317 2.669391 CGAAGAAATGAAGGCTGTTGGC 60.669 50.000 0.00 0.00 40.90 4.52
2151 2473 2.080693 TGTATGGTCGACATGTTTGGC 58.919 47.619 18.91 0.00 40.82 4.52
2172 2494 3.372730 GCCGGCATGGTTGAGCAA 61.373 61.111 24.80 0.00 41.21 3.91
2181 2503 0.467290 TGGTTGAGCAAGGGTTGGAC 60.467 55.000 0.00 0.00 0.00 4.02
2256 2578 2.249557 CTGCTTGTCGTGCTCATGGC 62.250 60.000 0.00 0.00 42.22 4.40
2280 2602 0.037326 TCGAGCTCGGTGAAAGCATT 60.037 50.000 33.98 0.00 42.35 3.56
2298 2620 4.018415 AGCATTAGCAGGGACCTTCTTAAA 60.018 41.667 0.00 0.00 45.49 1.52
2343 2665 0.885879 ACGTCATGCTCTCCAACGTA 59.114 50.000 4.86 0.00 43.97 3.57
2346 2668 2.930040 CGTCATGCTCTCCAACGTATTT 59.070 45.455 0.00 0.00 0.00 1.40
2349 2671 2.177394 TGCTCTCCAACGTATTTGCA 57.823 45.000 0.00 0.00 33.34 4.08
2385 2707 5.832221 TGGAAGGAGAAGTCAGAGATTAGA 58.168 41.667 0.00 0.00 0.00 2.10
2397 2719 6.488006 AGTCAGAGATTAGAAGAGAGATGAGC 59.512 42.308 0.00 0.00 0.00 4.26
2406 2728 3.386932 AGAGAGATGAGCAAGAGAGGT 57.613 47.619 0.00 0.00 0.00 3.85
2601 2934 3.540314 CTTGATGAGGAGGACAAGGAG 57.460 52.381 0.00 0.00 36.92 3.69
2602 2935 1.871418 TGATGAGGAGGACAAGGAGG 58.129 55.000 0.00 0.00 0.00 4.30
2790 3126 1.305930 GGAGCCGTTTCCATCGCTTT 61.306 55.000 0.00 0.00 37.20 3.51
2832 3168 3.703052 GCAAGGATTTCTGGTGATTGGAT 59.297 43.478 0.00 0.00 0.00 3.41
2855 3193 4.447138 TGTGTTTCACCAGGTTATCCTT 57.553 40.909 0.00 0.00 35.44 3.36
2917 3257 0.792640 GTGCAGGTGATCGTGAACTG 59.207 55.000 0.00 0.00 35.71 3.16
2957 3303 2.421619 CTTCTGCAAGTCCTTGAGGTC 58.578 52.381 11.12 0.00 42.93 3.85
3026 3372 7.334421 TGATGTTTACTGAAGATTACTGGAAGC 59.666 37.037 0.00 0.00 37.60 3.86
3033 3379 5.744171 TGAAGATTACTGGAAGCAGCATTA 58.256 37.500 0.00 0.00 37.60 1.90
3069 3704 6.413783 TTCAGATACTTCACCTTGTGTACA 57.586 37.500 0.00 0.00 34.79 2.90
3070 3705 6.413783 TCAGATACTTCACCTTGTGTACAA 57.586 37.500 0.00 0.00 34.79 2.41
3075 3710 4.932146 ACTTCACCTTGTGTACAAAATGC 58.068 39.130 0.00 0.00 35.15 3.56
3084 3719 4.397420 TGTGTACAAAATGCCTCATCAGT 58.603 39.130 0.00 0.00 0.00 3.41
3119 3754 8.405418 AGGACTAAGATTTCTTACAAAAACCC 57.595 34.615 0.00 0.00 37.40 4.11
3125 3760 4.904253 TTTCTTACAAAAACCCAGACCG 57.096 40.909 0.00 0.00 0.00 4.79
3126 3761 2.223745 TCTTACAAAAACCCAGACCGC 58.776 47.619 0.00 0.00 0.00 5.68
3129 3764 1.894756 CAAAAACCCAGACCGCCGA 60.895 57.895 0.00 0.00 0.00 5.54
3147 3782 4.560128 GCCGAGAGAACATATCTAATGCA 58.440 43.478 0.00 0.00 38.96 3.96
3177 3812 4.460382 AGTTTGCATCCTGTTCGAATCATT 59.540 37.500 0.00 0.00 0.00 2.57
3223 3858 9.851686 AAGATACCATTCTATGCATAGACAAAA 57.148 29.630 31.46 19.61 39.00 2.44
3228 3863 7.013655 ACCATTCTATGCATAGACAAAATCCAC 59.986 37.037 31.46 0.00 39.00 4.02
3238 3873 7.467267 GCATAGACAAAATCCACGACATGTATT 60.467 37.037 0.00 0.00 0.00 1.89
3239 3874 9.040939 CATAGACAAAATCCACGACATGTATTA 57.959 33.333 0.00 0.00 0.00 0.98
3240 3875 9.778741 ATAGACAAAATCCACGACATGTATTAT 57.221 29.630 0.00 0.00 0.00 1.28
3241 3876 7.919690 AGACAAAATCCACGACATGTATTATG 58.080 34.615 0.00 0.00 0.00 1.90
3242 3877 7.768582 AGACAAAATCCACGACATGTATTATGA 59.231 33.333 0.00 0.00 0.00 2.15
3243 3878 8.450578 ACAAAATCCACGACATGTATTATGAT 57.549 30.769 0.00 0.00 0.00 2.45
3244 3879 9.554395 ACAAAATCCACGACATGTATTATGATA 57.446 29.630 0.00 0.00 0.00 2.15
3307 3942 6.678878 CAGATAAATGCATCTCCCAATCTTG 58.321 40.000 0.00 0.00 32.83 3.02
3312 3947 1.404391 GCATCTCCCAATCTTGTGCTG 59.596 52.381 0.00 0.00 0.00 4.41
3325 3960 0.831711 TGTGCTGTCTCAGTGGCCTA 60.832 55.000 3.32 0.00 33.43 3.93
3336 3971 3.173151 TCAGTGGCCTATCTGAGTTTCA 58.827 45.455 17.30 0.81 36.04 2.69
3345 3980 4.334759 CCTATCTGAGTTTCATTGGCACTG 59.665 45.833 0.00 0.00 0.00 3.66
3364 4000 1.074889 TGTTCTAAGCCTTCCCCAACC 59.925 52.381 0.00 0.00 0.00 3.77
3377 4013 1.475751 CCCCAACCATCTCATTCTCCG 60.476 57.143 0.00 0.00 0.00 4.63
3411 4047 6.934083 TCATTCATGCAGTGAGTTTGTAACTA 59.066 34.615 0.00 0.00 43.03 2.24
3428 4064 8.437360 TTGTAACTAACCATGCATCTATGAAG 57.563 34.615 0.00 0.00 0.00 3.02
3442 4078 2.306341 ATGAAGTGTCTGCCATCTCG 57.694 50.000 0.00 0.00 0.00 4.04
3461 4097 1.469767 CGATGGTGTTGCTGATCTCGA 60.470 52.381 0.00 0.00 0.00 4.04
3474 4110 3.264947 TGATCTCGACCAATGCTTTGAG 58.735 45.455 13.58 6.59 34.60 3.02
3475 4111 3.055891 TGATCTCGACCAATGCTTTGAGA 60.056 43.478 13.58 8.55 36.95 3.27
3480 4116 3.882888 TCGACCAATGCTTTGAGACTTTT 59.117 39.130 13.58 0.00 34.60 2.27
3506 4142 1.302993 TTGTACGCCCTTGCCTTCC 60.303 57.895 0.00 0.00 0.00 3.46
3507 4143 1.774894 TTGTACGCCCTTGCCTTCCT 61.775 55.000 0.00 0.00 0.00 3.36
3508 4144 1.745489 GTACGCCCTTGCCTTCCTG 60.745 63.158 0.00 0.00 0.00 3.86
3511 4147 2.629656 CGCCCTTGCCTTCCTGTTG 61.630 63.158 0.00 0.00 0.00 3.33
3518 4154 0.106769 TGCCTTCCTGTTGTTGCAGA 60.107 50.000 0.00 0.00 38.70 4.26
3537 4173 4.934602 GCAGAGAGCTGTTAAGTCAATCTT 59.065 41.667 0.00 0.00 44.17 2.40
3549 4185 2.843113 AGTCAATCTTAGCCTCCTTGCT 59.157 45.455 0.00 0.00 45.38 3.91
3557 4193 0.036022 AGCCTCCTTGCTCAAGTGAC 59.964 55.000 8.60 0.00 36.75 3.67
3558 4194 0.036022 GCCTCCTTGCTCAAGTGACT 59.964 55.000 8.60 0.00 36.72 3.41
3570 4206 4.142447 GCTCAAGTGACTGCATCATCATTT 60.142 41.667 0.00 0.00 40.28 2.32
3580 4216 4.717877 TGCATCATCATTTACTACAGGGG 58.282 43.478 0.00 0.00 0.00 4.79
3586 4222 5.070446 TCATCATTTACTACAGGGGCTACAG 59.930 44.000 0.00 0.00 0.00 2.74
3603 4239 4.998033 GCTACAGGGGTAATATTTCTCTGC 59.002 45.833 14.57 2.55 0.00 4.26
3617 4253 4.431416 TTCTCTGCACTTCCCTTTGTAA 57.569 40.909 0.00 0.00 0.00 2.41
3624 4260 3.502595 GCACTTCCCTTTGTAAAGTCTCC 59.497 47.826 3.90 0.00 34.20 3.71
3631 4267 5.538433 TCCCTTTGTAAAGTCTCCCATTTTG 59.462 40.000 3.90 0.00 34.20 2.44
3645 4281 6.069673 TCTCCCATTTTGTAGGATTCTGCTTA 60.070 38.462 0.00 0.00 0.00 3.09
3653 4289 9.905713 TTTTGTAGGATTCTGCTTATCAATAGT 57.094 29.630 0.00 0.00 0.00 2.12
3656 4292 8.874156 TGTAGGATTCTGCTTATCAATAGTCAT 58.126 33.333 0.00 0.00 0.00 3.06
3674 4310 5.663456 AGTCATGAAATTTGTTTGCACTGT 58.337 33.333 0.00 0.00 0.00 3.55
3676 4312 7.264221 AGTCATGAAATTTGTTTGCACTGTAA 58.736 30.769 0.00 0.00 0.00 2.41
3682 4318 4.481930 TTTGTTTGCACTGTAAGGATCG 57.518 40.909 0.00 0.00 39.30 3.69
3691 4327 4.201724 GCACTGTAAGGATCGAACACATTC 60.202 45.833 0.00 0.00 39.30 2.67
3695 4331 5.547465 TGTAAGGATCGAACACATTCAAGT 58.453 37.500 0.00 0.00 34.14 3.16
3697 4333 3.600388 AGGATCGAACACATTCAAGTCC 58.400 45.455 0.00 0.00 34.14 3.85
3698 4334 2.678336 GGATCGAACACATTCAAGTCCC 59.322 50.000 0.00 0.00 34.14 4.46
3701 4337 1.197721 CGAACACATTCAAGTCCCTGC 59.802 52.381 0.00 0.00 34.14 4.85
3721 4357 3.316308 TGCTTTCTTGTTTGCCTCTTCTC 59.684 43.478 0.00 0.00 0.00 2.87
3723 4359 4.757149 GCTTTCTTGTTTGCCTCTTCTCTA 59.243 41.667 0.00 0.00 0.00 2.43
3724 4360 5.106752 GCTTTCTTGTTTGCCTCTTCTCTAG 60.107 44.000 0.00 0.00 0.00 2.43
3725 4361 5.552870 TTCTTGTTTGCCTCTTCTCTAGT 57.447 39.130 0.00 0.00 0.00 2.57
3726 4362 5.140747 TCTTGTTTGCCTCTTCTCTAGTC 57.859 43.478 0.00 0.00 0.00 2.59
3739 4377 3.239449 TCTCTAGTCCTCTGCCAAAACA 58.761 45.455 0.00 0.00 0.00 2.83
3746 4384 0.890683 CTCTGCCAAAACATCCCACC 59.109 55.000 0.00 0.00 0.00 4.61
3768 4406 3.117738 CCAGCCAATCTTATGAACCTCCT 60.118 47.826 0.00 0.00 0.00 3.69
3772 4410 4.706962 GCCAATCTTATGAACCTCCTTGTT 59.293 41.667 0.00 0.00 0.00 2.83
3787 4425 4.579869 TCCTTGTTTCTGCTGTTAGATCC 58.420 43.478 0.00 0.00 0.00 3.36
3788 4426 4.287067 TCCTTGTTTCTGCTGTTAGATCCT 59.713 41.667 0.00 0.00 0.00 3.24
3789 4427 4.633565 CCTTGTTTCTGCTGTTAGATCCTC 59.366 45.833 0.00 0.00 0.00 3.71
3790 4428 5.486526 CTTGTTTCTGCTGTTAGATCCTCT 58.513 41.667 0.00 0.00 0.00 3.69
3807 4445 5.593679 TCCTCTAACCTTTTCGATACTGG 57.406 43.478 0.00 0.00 0.00 4.00
3808 4446 5.266788 TCCTCTAACCTTTTCGATACTGGA 58.733 41.667 0.00 0.00 0.00 3.86
3818 4456 1.065551 TCGATACTGGAGTGATGTGCG 59.934 52.381 0.00 0.00 0.00 5.34
3832 4470 1.890876 TGTGCGTCTTATTTGCCTGT 58.109 45.000 0.00 0.00 0.00 4.00
3836 4474 3.621268 GTGCGTCTTATTTGCCTGTATGA 59.379 43.478 0.00 0.00 0.00 2.15
3842 4480 5.880332 GTCTTATTTGCCTGTATGAGTGGAA 59.120 40.000 0.00 0.00 0.00 3.53
3843 4481 6.374333 GTCTTATTTGCCTGTATGAGTGGAAA 59.626 38.462 0.00 0.00 0.00 3.13
3844 4482 6.374333 TCTTATTTGCCTGTATGAGTGGAAAC 59.626 38.462 0.00 0.00 0.00 2.78
3850 4488 4.651778 CCTGTATGAGTGGAAACCAGAAA 58.348 43.478 0.00 0.00 32.34 2.52
3880 4518 8.361139 ACATATGTTAATCTACAGGTCTAGTGC 58.639 37.037 1.41 0.00 0.00 4.40
3881 4519 8.580720 CATATGTTAATCTACAGGTCTAGTGCT 58.419 37.037 0.00 0.00 0.00 4.40
3882 4520 6.852420 TGTTAATCTACAGGTCTAGTGCTT 57.148 37.500 0.00 0.00 0.00 3.91
3883 4521 7.241042 TGTTAATCTACAGGTCTAGTGCTTT 57.759 36.000 0.00 0.00 0.00 3.51
3884 4522 8.357290 TGTTAATCTACAGGTCTAGTGCTTTA 57.643 34.615 0.00 0.00 0.00 1.85
3885 4523 8.467598 TGTTAATCTACAGGTCTAGTGCTTTAG 58.532 37.037 0.00 0.00 0.00 1.85
3886 4524 8.468399 GTTAATCTACAGGTCTAGTGCTTTAGT 58.532 37.037 0.00 0.00 0.00 2.24
3887 4525 5.899120 TCTACAGGTCTAGTGCTTTAGTG 57.101 43.478 0.00 0.00 0.00 2.74
3900 4538 2.038033 GCTTTAGTGTACTGTGGACCCA 59.962 50.000 0.00 0.00 0.00 4.51
3903 4541 1.729586 AGTGTACTGTGGACCCATGT 58.270 50.000 0.00 0.00 0.00 3.21
3916 4554 4.595781 TGGACCCATGTTCAGTAGTTACTT 59.404 41.667 0.00 0.00 33.46 2.24
3917 4555 4.935808 GGACCCATGTTCAGTAGTTACTTG 59.064 45.833 0.00 0.00 33.46 3.16
3918 4556 5.279809 GGACCCATGTTCAGTAGTTACTTGA 60.280 44.000 0.00 0.00 33.46 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.444421 AGCATGCCTCCAGAGAAAAAG 58.556 47.619 15.66 0.00 0.00 2.27
22 23 3.939740 ATAGCATGCCTCCAGAGAAAA 57.060 42.857 15.66 0.00 0.00 2.29
112 115 7.730364 TCTGATGTTTGTAAAGAGTTTCCTC 57.270 36.000 0.00 0.00 38.04 3.71
185 206 8.415553 CCATGTTCATTCCTTGCAAGATTATTA 58.584 33.333 28.05 6.61 0.00 0.98
204 225 3.882888 TGAACACTCAAACCTCCATGTTC 59.117 43.478 7.75 7.75 43.90 3.18
208 229 4.763793 CAGAATGAACACTCAAACCTCCAT 59.236 41.667 0.00 0.00 39.69 3.41
215 236 8.397906 CAAAGTAGAACAGAATGAACACTCAAA 58.602 33.333 0.00 0.00 39.69 2.69
232 254 3.181445 ACCTGGTCATGCACAAAGTAGAA 60.181 43.478 0.00 0.00 0.00 2.10
539 561 8.908903 TCTCAAAAAGTTTTACAATGCTCCTTA 58.091 29.630 0.24 0.00 0.00 2.69
710 774 5.641636 TCAGTTAAGAGAAACATGCGCAATA 59.358 36.000 17.11 0.00 0.00 1.90
716 780 7.114106 GCTTTTCTTCAGTTAAGAGAAACATGC 59.886 37.037 0.00 0.00 44.95 4.06
759 826 3.477530 AGGTTACAGTTTTGTCAGCCTC 58.522 45.455 0.00 0.00 38.76 4.70
762 829 9.556030 GATAAATAAGGTTACAGTTTTGTCAGC 57.444 33.333 0.00 0.00 38.76 4.26
772 839 8.723311 TGACCGTTTTGATAAATAAGGTTACAG 58.277 33.333 0.00 0.00 32.41 2.74
795 863 3.129638 AGACCACGCTAATCTTCTCTGAC 59.870 47.826 0.00 0.00 0.00 3.51
796 864 3.357203 AGACCACGCTAATCTTCTCTGA 58.643 45.455 0.00 0.00 0.00 3.27
835 903 4.592485 TTGGAAATTTAGCCAAGCGAAA 57.408 36.364 7.15 0.00 39.14 3.46
841 909 4.141620 TGGCAACTTTGGAAATTTAGCCAA 60.142 37.500 7.15 7.15 45.60 4.52
906 1226 2.931713 ATTCCTCTACGGCGCGAACG 62.932 60.000 12.10 16.89 44.07 3.95
910 1230 1.658717 CTGATTCCTCTACGGCGCG 60.659 63.158 6.90 0.00 0.00 6.86
925 1245 1.227118 TGTTCGCGTGCTCAACTGA 60.227 52.632 5.77 0.00 0.00 3.41
938 1259 1.341802 GATCTTCGCTGCGTGTTCG 59.658 57.895 22.48 7.13 40.37 3.95
940 1261 1.225855 TTTGATCTTCGCTGCGTGTT 58.774 45.000 22.48 10.92 0.00 3.32
954 1275 0.893727 GTGGGTCCTGCGGTTTTGAT 60.894 55.000 0.00 0.00 0.00 2.57
1160 1482 2.214920 GGGTTGGAGTGGAGACCGT 61.215 63.158 0.00 0.00 32.91 4.83
1164 1486 2.203788 AGCGGGTTGGAGTGGAGA 60.204 61.111 0.00 0.00 0.00 3.71
1488 1810 4.124351 TAGTGGTCGGCGGCGAAG 62.124 66.667 36.31 5.71 0.00 3.79
1602 1924 3.381983 ATCGCGCTCCAGGTGACA 61.382 61.111 5.56 0.00 0.00 3.58
1617 1939 1.660575 CACGTACCCGCCGATCATC 60.661 63.158 0.00 0.00 37.70 2.92
1659 1981 1.191489 TCTCCCGGAACAGCATGACA 61.191 55.000 0.73 0.00 39.69 3.58
1663 1985 1.153086 GCATCTCCCGGAACAGCAT 60.153 57.895 0.73 0.00 0.00 3.79
1696 2018 2.606213 TGTCACCTCATCCGGCCA 60.606 61.111 2.24 0.00 0.00 5.36
1713 2035 1.982938 CGAAAGGACCCCGAGGACT 60.983 63.158 0.00 0.00 36.73 3.85
1968 2290 3.250762 CAGCCTTCATTTCTTCGAACACA 59.749 43.478 0.00 0.00 0.00 3.72
1995 2317 1.423721 CGACATCATCAGGTGGCACG 61.424 60.000 12.17 0.00 0.00 5.34
2172 2494 1.164041 CGCGAACAAAGTCCAACCCT 61.164 55.000 0.00 0.00 0.00 4.34
2181 2503 2.574212 GGCATCGCGCGAACAAAG 60.574 61.111 38.07 23.20 43.84 2.77
2280 2602 4.426704 ACTCTTTAAGAAGGTCCCTGCTA 58.573 43.478 0.00 0.00 30.21 3.49
2298 2620 1.786937 CCTCATGAGCAGGGTACTCT 58.213 55.000 17.76 0.00 35.12 3.24
2343 2665 2.098607 CCATCTCTGCGTCAATGCAAAT 59.901 45.455 0.00 0.00 45.74 2.32
2346 2668 0.249955 TCCATCTCTGCGTCAATGCA 59.750 50.000 0.00 0.00 43.95 3.96
2349 2671 1.833630 TCCTTCCATCTCTGCGTCAAT 59.166 47.619 0.00 0.00 0.00 2.57
2385 2707 3.711863 ACCTCTCTTGCTCATCTCTCTT 58.288 45.455 0.00 0.00 0.00 2.85
2397 2719 4.636206 GGCACCTTTGTAATACCTCTCTTG 59.364 45.833 0.00 0.00 0.00 3.02
2406 2728 2.722094 CAGCCTGGCACCTTTGTAATA 58.278 47.619 22.65 0.00 0.00 0.98
2596 2929 2.348998 CTGAAGCGCACCCTCCTT 59.651 61.111 11.47 0.00 0.00 3.36
2602 2935 4.030452 GTGCCACTGAAGCGCACC 62.030 66.667 11.47 0.05 45.64 5.01
2697 3033 1.532868 GCATGACAATCGGAGCATACC 59.467 52.381 0.00 0.00 0.00 2.73
2739 3075 7.094463 CGTACTATGATCTCCCGGTTATAAACT 60.094 40.741 0.00 0.00 0.00 2.66
2808 3144 3.119245 CCAATCACCAGAAATCCTTGCAG 60.119 47.826 0.00 0.00 0.00 4.41
2832 3168 4.798882 AGGATAACCTGGTGAAACACAAA 58.201 39.130 0.00 0.00 45.92 2.83
2855 3193 3.118261 ACTCTTCACTGCACCTCAGAAAA 60.118 43.478 0.00 0.00 45.72 2.29
2917 3257 5.988561 AGAAGCTCCTCGAAAATACATCATC 59.011 40.000 0.00 0.00 0.00 2.92
2957 3303 7.975616 AGCTTTGTGTTACATATAAATTGGCAG 59.024 33.333 0.00 0.00 0.00 4.85
3069 3704 6.594788 AAATGTGTACTGATGAGGCATTTT 57.405 33.333 0.00 0.00 33.12 1.82
3070 3705 7.148018 CCTTAAATGTGTACTGATGAGGCATTT 60.148 37.037 0.00 0.00 38.25 2.32
3075 3710 6.644347 AGTCCTTAAATGTGTACTGATGAGG 58.356 40.000 0.00 0.00 0.00 3.86
3108 3743 1.320507 GGCGGTCTGGGTTTTTGTAA 58.679 50.000 0.00 0.00 0.00 2.41
3119 3754 0.738975 TATGTTCTCTCGGCGGTCTG 59.261 55.000 7.21 0.00 0.00 3.51
3125 3760 4.560128 TGCATTAGATATGTTCTCTCGGC 58.440 43.478 0.00 0.00 35.79 5.54
3126 3761 6.754209 GGTATGCATTAGATATGTTCTCTCGG 59.246 42.308 3.54 0.00 35.79 4.63
3129 3764 6.501805 TGGGGTATGCATTAGATATGTTCTCT 59.498 38.462 3.54 0.00 35.79 3.10
3147 3782 1.640670 ACAGGATGCAAACTGGGGTAT 59.359 47.619 20.74 1.76 42.53 2.73
3246 3881 9.899661 AACAAAAGGCAGTCATACTATTATGTA 57.100 29.630 0.54 0.00 37.06 2.29
3247 3882 8.807948 AACAAAAGGCAGTCATACTATTATGT 57.192 30.769 0.54 0.00 37.06 2.29
3248 3883 8.892723 TGAACAAAAGGCAGTCATACTATTATG 58.107 33.333 0.00 0.00 37.08 1.90
3296 3931 2.289882 TGAGACAGCACAAGATTGGGAG 60.290 50.000 0.00 0.00 31.80 4.30
3297 3932 1.699083 TGAGACAGCACAAGATTGGGA 59.301 47.619 0.00 0.00 31.80 4.37
3298 3933 2.082231 CTGAGACAGCACAAGATTGGG 58.918 52.381 0.00 0.00 33.81 4.12
3299 3934 2.483106 CACTGAGACAGCACAAGATTGG 59.517 50.000 0.00 0.00 34.37 3.16
3300 3935 2.483106 CCACTGAGACAGCACAAGATTG 59.517 50.000 0.00 0.00 34.37 2.67
3301 3936 2.775890 CCACTGAGACAGCACAAGATT 58.224 47.619 0.00 0.00 34.37 2.40
3302 3937 1.610102 GCCACTGAGACAGCACAAGAT 60.610 52.381 0.00 0.00 34.37 2.40
3307 3942 0.539051 ATAGGCCACTGAGACAGCAC 59.461 55.000 5.01 0.00 34.37 4.40
3325 3960 3.759581 ACAGTGCCAATGAAACTCAGAT 58.240 40.909 0.00 0.00 0.00 2.90
3345 3980 1.074889 TGGTTGGGGAAGGCTTAGAAC 59.925 52.381 0.00 0.81 0.00 3.01
3357 3992 1.475751 CGGAGAATGAGATGGTTGGGG 60.476 57.143 0.00 0.00 0.00 4.96
3364 4000 3.529533 AGAAGCAACGGAGAATGAGATG 58.470 45.455 0.00 0.00 0.00 2.90
3377 4013 3.918591 CACTGCATGAATGAAGAAGCAAC 59.081 43.478 5.24 0.00 36.90 4.17
3411 4047 4.880120 CAGACACTTCATAGATGCATGGTT 59.120 41.667 2.46 0.00 0.00 3.67
3442 4078 1.929836 GTCGAGATCAGCAACACCATC 59.070 52.381 0.00 0.00 0.00 3.51
3446 4082 1.795768 TTGGTCGAGATCAGCAACAC 58.204 50.000 0.00 0.00 0.00 3.32
3461 4097 4.038402 CAGGAAAAGTCTCAAAGCATTGGT 59.962 41.667 1.24 0.00 37.15 3.67
3474 4110 3.059120 GGCGTACAAGAACAGGAAAAGTC 60.059 47.826 0.00 0.00 0.00 3.01
3475 4111 2.876550 GGCGTACAAGAACAGGAAAAGT 59.123 45.455 0.00 0.00 0.00 2.66
3480 4116 1.053424 AAGGGCGTACAAGAACAGGA 58.947 50.000 0.00 0.00 0.00 3.86
3506 4142 1.590932 ACAGCTCTCTGCAACAACAG 58.409 50.000 0.00 0.00 44.10 3.16
3507 4143 2.042686 AACAGCTCTCTGCAACAACA 57.957 45.000 0.00 0.00 44.10 3.33
3508 4144 3.561725 ACTTAACAGCTCTCTGCAACAAC 59.438 43.478 0.00 0.00 44.10 3.32
3511 4147 3.393800 TGACTTAACAGCTCTCTGCAAC 58.606 45.455 0.00 0.00 44.10 4.17
3518 4154 5.188751 AGGCTAAGATTGACTTAACAGCTCT 59.811 40.000 0.00 0.00 40.07 4.09
3537 4173 1.276421 GTCACTTGAGCAAGGAGGCTA 59.724 52.381 14.14 0.00 45.99 3.93
3549 4185 6.175471 AGTAAATGATGATGCAGTCACTTGA 58.825 36.000 0.00 0.00 40.28 3.02
3557 4193 4.758674 CCCCTGTAGTAAATGATGATGCAG 59.241 45.833 0.00 0.00 0.00 4.41
3558 4194 4.717877 CCCCTGTAGTAAATGATGATGCA 58.282 43.478 0.00 0.00 0.00 3.96
3570 4206 0.263765 CCCCTGTAGCCCCTGTAGTA 59.736 60.000 0.00 0.00 0.00 1.82
3580 4216 4.998033 GCAGAGAAATATTACCCCTGTAGC 59.002 45.833 0.00 0.00 0.00 3.58
3586 4222 4.822350 GGAAGTGCAGAGAAATATTACCCC 59.178 45.833 0.00 0.00 0.00 4.95
3603 4239 4.072839 GGGAGACTTTACAAAGGGAAGTG 58.927 47.826 6.66 0.00 40.31 3.16
3617 4253 6.183347 CAGAATCCTACAAAATGGGAGACTT 58.817 40.000 0.00 0.00 42.15 3.01
3624 4260 7.572523 TGATAAGCAGAATCCTACAAAATGG 57.427 36.000 0.00 0.00 0.00 3.16
3631 4267 9.149225 CATGACTATTGATAAGCAGAATCCTAC 57.851 37.037 0.00 0.00 0.00 3.18
3645 4281 8.928733 GTGCAAACAAATTTCATGACTATTGAT 58.071 29.630 16.32 5.80 0.00 2.57
3653 4289 6.700960 CCTTACAGTGCAAACAAATTTCATGA 59.299 34.615 0.00 0.00 0.00 3.07
3656 4292 6.214191 TCCTTACAGTGCAAACAAATTTCA 57.786 33.333 0.00 0.00 0.00 2.69
3668 4304 2.683968 TGTGTTCGATCCTTACAGTGC 58.316 47.619 0.00 0.00 0.00 4.40
3674 4310 5.175859 GGACTTGAATGTGTTCGATCCTTA 58.824 41.667 0.00 0.00 37.15 2.69
3676 4312 3.600388 GGACTTGAATGTGTTCGATCCT 58.400 45.455 0.00 0.00 37.15 3.24
3682 4318 2.508526 AGCAGGGACTTGAATGTGTTC 58.491 47.619 0.00 0.00 34.60 3.18
3691 4327 3.709987 CAAACAAGAAAGCAGGGACTTG 58.290 45.455 0.00 0.00 43.30 3.16
3695 4331 1.039856 GGCAAACAAGAAAGCAGGGA 58.960 50.000 0.00 0.00 0.00 4.20
3697 4333 1.959282 AGAGGCAAACAAGAAAGCAGG 59.041 47.619 0.00 0.00 0.00 4.85
3698 4334 3.317430 AGAAGAGGCAAACAAGAAAGCAG 59.683 43.478 0.00 0.00 0.00 4.24
3701 4337 5.994668 ACTAGAGAAGAGGCAAACAAGAAAG 59.005 40.000 0.00 0.00 0.00 2.62
3721 4357 3.274288 GGATGTTTTGGCAGAGGACTAG 58.726 50.000 0.00 0.00 0.00 2.57
3723 4359 1.272147 GGGATGTTTTGGCAGAGGACT 60.272 52.381 0.00 0.00 0.00 3.85
3724 4360 1.177401 GGGATGTTTTGGCAGAGGAC 58.823 55.000 0.00 0.00 0.00 3.85
3725 4361 0.776810 TGGGATGTTTTGGCAGAGGA 59.223 50.000 0.00 0.00 0.00 3.71
3726 4362 0.890683 GTGGGATGTTTTGGCAGAGG 59.109 55.000 0.00 0.00 0.00 3.69
3739 4377 1.607225 TAAGATTGGCTGGGTGGGAT 58.393 50.000 0.00 0.00 0.00 3.85
3746 4384 3.117738 AGGAGGTTCATAAGATTGGCTGG 60.118 47.826 0.00 0.00 0.00 4.85
3787 4425 6.037098 CACTCCAGTATCGAAAAGGTTAGAG 58.963 44.000 0.00 0.00 0.00 2.43
3788 4426 5.713389 TCACTCCAGTATCGAAAAGGTTAGA 59.287 40.000 0.00 0.00 0.00 2.10
3789 4427 5.962433 TCACTCCAGTATCGAAAAGGTTAG 58.038 41.667 0.00 0.00 0.00 2.34
3790 4428 5.988310 TCACTCCAGTATCGAAAAGGTTA 57.012 39.130 0.00 0.00 0.00 2.85
3804 4442 2.654749 TAAGACGCACATCACTCCAG 57.345 50.000 0.00 0.00 0.00 3.86
3807 4445 3.485877 GGCAAATAAGACGCACATCACTC 60.486 47.826 0.00 0.00 0.00 3.51
3808 4446 2.420022 GGCAAATAAGACGCACATCACT 59.580 45.455 0.00 0.00 0.00 3.41
3818 4456 5.428253 TCCACTCATACAGGCAAATAAGAC 58.572 41.667 0.00 0.00 0.00 3.01
3832 4470 8.877864 ATGTTTATTTCTGGTTTCCACTCATA 57.122 30.769 0.00 0.00 0.00 2.15
3836 4474 8.650143 ACATATGTTTATTTCTGGTTTCCACT 57.350 30.769 1.41 0.00 0.00 4.00
3880 4518 4.253685 CATGGGTCCACAGTACACTAAAG 58.746 47.826 0.00 0.00 0.00 1.85
3881 4519 3.649023 ACATGGGTCCACAGTACACTAAA 59.351 43.478 0.00 0.00 0.00 1.85
3882 4520 3.244582 ACATGGGTCCACAGTACACTAA 58.755 45.455 0.00 0.00 0.00 2.24
3883 4521 2.897350 ACATGGGTCCACAGTACACTA 58.103 47.619 0.00 0.00 0.00 2.74
3884 4522 1.729586 ACATGGGTCCACAGTACACT 58.270 50.000 0.00 0.00 0.00 3.55
3885 4523 2.224426 TGAACATGGGTCCACAGTACAC 60.224 50.000 0.00 0.00 0.00 2.90
3886 4524 2.038426 CTGAACATGGGTCCACAGTACA 59.962 50.000 0.00 0.00 0.00 2.90
3887 4525 2.038557 ACTGAACATGGGTCCACAGTAC 59.961 50.000 8.61 0.00 35.59 2.73


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

AutoCloner maintained by Alex Coulton.