Multiple sequence alignment - TraesCS6D01G346900

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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 TraesCS6D01G346900 chr6D 100.000 3889 0 0 1 3889 445892465 445896353 0.000000e+00 7182.0
1 TraesCS6D01G346900 chr6D 85.714 2310 251 41 19 2284 445820859 445818585 0.000000e+00 2364.0
2 TraesCS6D01G346900 chr6D 87.586 1450 158 15 1376 2823 445839184 445840613 0.000000e+00 1661.0
3 TraesCS6D01G346900 chr6D 84.041 871 107 14 2172 3032 445911217 445912065 0.000000e+00 809.0
4 TraesCS6D01G346900 chr6D 81.159 207 25 6 3150 3344 445855193 445855397 1.870000e-33 154.0
5 TraesCS6D01G346900 chr6D 86.014 143 18 2 2864 3005 445840623 445840764 6.730000e-33 152.0
6 TraesCS6D01G346900 chr6D 79.283 251 19 15 3582 3825 445846664 445846888 1.130000e-30 145.0
7 TraesCS6D01G346900 chr6D 96.875 32 1 0 3855 3886 467207969 467208000 2.000000e-03 54.7
8 TraesCS6D01G346900 chr6A 95.334 3215 113 17 3 3207 592548351 592551538 0.000000e+00 5072.0
9 TraesCS6D01G346900 chr6A 86.595 1022 120 13 1352 2366 592477357 592476346 0.000000e+00 1112.0
10 TraesCS6D01G346900 chr6A 86.801 644 74 7 564 1200 592559252 592559891 0.000000e+00 708.0
11 TraesCS6D01G346900 chr6A 83.562 584 55 14 3199 3779 592551597 592552142 3.470000e-140 508.0
12 TraesCS6D01G346900 chr6A 79.167 240 38 8 3115 3344 592539547 592539784 5.200000e-34 156.0
13 TraesCS6D01G346900 chr6A 77.027 222 34 15 3287 3504 592490981 592490773 1.140000e-20 111.0
14 TraesCS6D01G346900 chr6A 100.000 32 0 0 3855 3886 613635999 613636030 4.200000e-05 60.2
15 TraesCS6D01G346900 chr6B 94.961 3215 116 14 1 3207 673610114 673606938 0.000000e+00 4998.0
16 TraesCS6D01G346900 chr6B 94.704 3210 139 16 1 3207 672893018 672896199 0.000000e+00 4957.0
17 TraesCS6D01G346900 chr6B 96.570 2391 67 3 1 2384 672943594 672945976 0.000000e+00 3947.0
18 TraesCS6D01G346900 chr6B 85.492 2316 248 43 19 2284 673688369 673690646 0.000000e+00 2335.0
19 TraesCS6D01G346900 chr6B 85.337 2312 245 46 19 2277 672628598 672626328 0.000000e+00 2305.0
20 TraesCS6D01G346900 chr6B 87.884 1692 172 17 1352 3032 673544481 673542812 0.000000e+00 1958.0
21 TraesCS6D01G346900 chr6B 87.246 1725 173 22 1352 3063 673026051 673027741 0.000000e+00 1923.0
22 TraesCS6D01G346900 chr6B 86.640 1527 160 26 1321 2825 672884364 672885868 0.000000e+00 1650.0
23 TraesCS6D01G346900 chr6B 86.464 1219 141 12 5 1202 673545899 673544684 0.000000e+00 1315.0
24 TraesCS6D01G346900 chr6B 86.622 1039 118 19 1339 2362 673757588 673758620 0.000000e+00 1129.0
25 TraesCS6D01G346900 chr6B 86.172 781 67 18 2418 3182 672945972 672946727 0.000000e+00 806.0
26 TraesCS6D01G346900 chr6B 90.643 513 48 0 2 514 673024633 673025145 0.000000e+00 682.0
27 TraesCS6D01G346900 chr6B 91.111 450 28 8 3403 3848 672947077 672947518 2.000000e-167 599.0
28 TraesCS6D01G346900 chr6B 89.154 461 31 10 3403 3852 673606728 673606276 1.220000e-154 556.0
29 TraesCS6D01G346900 chr6B 92.328 378 23 4 3403 3774 672896409 672896786 2.060000e-147 532.0
30 TraesCS6D01G346900 chr6B 77.638 872 112 39 2864 3707 672885876 672886692 1.650000e-123 453.0
31 TraesCS6D01G346900 chr6B 91.429 140 10 2 3196 3334 672896254 672896392 1.430000e-44 191.0
32 TraesCS6D01G346900 chr6B 91.429 140 10 2 3196 3334 672946922 672947060 1.430000e-44 191.0
33 TraesCS6D01G346900 chr6B 91.429 140 10 2 3196 3334 673606883 673606745 1.430000e-44 191.0
34 TraesCS6D01G346900 chr6B 78.135 311 47 12 3229 3536 673681527 673681819 1.110000e-40 178.0
35 TraesCS6D01G346900 chr6B 83.051 177 30 0 3617 3793 673358716 673358540 1.120000e-35 161.0
36 TraesCS6D01G346900 chr6B 77.528 267 37 13 3278 3536 672633384 672633133 5.240000e-29 139.0
37 TraesCS6D01G346900 chr4D 97.500 40 1 0 3848 3887 47986228 47986267 6.970000e-08 69.4
38 TraesCS6D01G346900 chr5A 100.000 36 0 0 3854 3889 205332003 205331968 2.510000e-07 67.6
39 TraesCS6D01G346900 chr5A 100.000 36 0 0 3854 3889 287630905 287630940 2.510000e-07 67.6
40 TraesCS6D01G346900 chr4B 100.000 36 0 0 3854 3889 359179716 359179751 2.510000e-07 67.6
41 TraesCS6D01G346900 chr2A 93.478 46 2 1 3845 3889 424168274 424168229 2.510000e-07 67.6
42 TraesCS6D01G346900 chr2D 100.000 31 0 0 3854 3884 547573960 547573990 1.510000e-04 58.4


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 TraesCS6D01G346900 chr6D 445892465 445896353 3888 False 7182.000000 7182 100.000000 1 3889 1 chr6D.!!$F3 3888
1 TraesCS6D01G346900 chr6D 445818585 445820859 2274 True 2364.000000 2364 85.714000 19 2284 1 chr6D.!!$R1 2265
2 TraesCS6D01G346900 chr6D 445839184 445840764 1580 False 906.500000 1661 86.800000 1376 3005 2 chr6D.!!$F6 1629
3 TraesCS6D01G346900 chr6D 445911217 445912065 848 False 809.000000 809 84.041000 2172 3032 1 chr6D.!!$F4 860
4 TraesCS6D01G346900 chr6A 592548351 592552142 3791 False 2790.000000 5072 89.448000 3 3779 2 chr6A.!!$F4 3776
5 TraesCS6D01G346900 chr6A 592476346 592477357 1011 True 1112.000000 1112 86.595000 1352 2366 1 chr6A.!!$R1 1014
6 TraesCS6D01G346900 chr6A 592559252 592559891 639 False 708.000000 708 86.801000 564 1200 1 chr6A.!!$F2 636
7 TraesCS6D01G346900 chr6B 673688369 673690646 2277 False 2335.000000 2335 85.492000 19 2284 1 chr6B.!!$F2 2265
8 TraesCS6D01G346900 chr6B 672626328 672628598 2270 True 2305.000000 2305 85.337000 19 2277 1 chr6B.!!$R1 2258
9 TraesCS6D01G346900 chr6B 673606276 673610114 3838 True 1915.000000 4998 91.848000 1 3852 3 chr6B.!!$R5 3851
10 TraesCS6D01G346900 chr6B 672893018 672896786 3768 False 1893.333333 4957 92.820333 1 3774 3 chr6B.!!$F5 3773
11 TraesCS6D01G346900 chr6B 673542812 673545899 3087 True 1636.500000 1958 87.174000 5 3032 2 chr6B.!!$R4 3027
12 TraesCS6D01G346900 chr6B 672943594 672947518 3924 False 1385.750000 3947 91.320500 1 3848 4 chr6B.!!$F6 3847
13 TraesCS6D01G346900 chr6B 673024633 673027741 3108 False 1302.500000 1923 88.944500 2 3063 2 chr6B.!!$F7 3061
14 TraesCS6D01G346900 chr6B 673757588 673758620 1032 False 1129.000000 1129 86.622000 1339 2362 1 chr6B.!!$F3 1023
15 TraesCS6D01G346900 chr6B 672884364 672886692 2328 False 1051.500000 1650 82.139000 1321 3707 2 chr6B.!!$F4 2386

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
318 319 2.764637 AATGGGTTGTCGTGCCCCTC 62.765 60.000 0.0 0.0 44.20 4.30 F
1529 1697 1.067516 CTTTGGCAGGACAACACCAAG 59.932 52.381 0.0 0.0 42.78 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 2015 1.675310 CTGATTTGCCTGGTCGCCA 60.675 57.895 0.00 0.0 0.0 5.69 R
3084 3328 0.465705 TCAGGAAGCATCACCGGATC 59.534 55.000 9.46 0.0 0.0 3.36 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
318 319 2.764637 AATGGGTTGTCGTGCCCCTC 62.765 60.000 0.00 0.00 44.20 4.30
567 601 3.681835 GACTCCGGTGCCACGACT 61.682 66.667 0.00 0.00 35.47 4.18
684 724 3.099170 ATGCCCGCTCCCAATCCT 61.099 61.111 0.00 0.00 0.00 3.24
1337 1485 5.057819 TGTGTTTCCTATGTTCGTAGCAAA 58.942 37.500 0.00 0.00 0.00 3.68
1529 1697 1.067516 CTTTGGCAGGACAACACCAAG 59.932 52.381 0.00 0.00 42.78 3.61
1533 1701 1.843421 CAGGACAACACCAAGGGGA 59.157 57.895 0.00 0.00 38.05 4.81
1667 1835 4.401519 CAGATGGAAATTCTGGTCAAGCAT 59.598 41.667 0.00 0.00 37.53 3.79
1844 2015 0.472471 ACCACGAGGACAAACACCAT 59.528 50.000 5.68 0.00 38.69 3.55
2314 2503 6.639632 AAACAATAGTGACAATTCAGCAGT 57.360 33.333 0.00 0.00 30.10 4.40
2341 2530 2.552809 CGCCATCCATATCCCATGAACA 60.553 50.000 0.00 0.00 0.00 3.18
2342 2531 3.087031 GCCATCCATATCCCATGAACAG 58.913 50.000 0.00 0.00 0.00 3.16
2343 2532 3.693807 CCATCCATATCCCATGAACAGG 58.306 50.000 0.00 0.00 0.00 4.00
2363 2558 4.530161 CAGGAGGAGGAAGAAGAAGAAAGA 59.470 45.833 0.00 0.00 0.00 2.52
2844 3066 1.493950 CTGCCATCGCCATCGTCTTC 61.494 60.000 0.00 0.00 36.96 2.87
2845 3067 2.589492 GCCATCGCCATCGTCTTCG 61.589 63.158 0.00 0.00 36.96 3.79
2846 3068 2.589492 CCATCGCCATCGTCTTCGC 61.589 63.158 0.00 0.00 36.96 4.70
2933 3167 0.757188 TGCTCTAGCTAGCTGTCCCC 60.757 60.000 27.68 11.67 43.19 4.81
2997 3239 2.163454 TCCCAGTTGGAACATGCCT 58.837 52.632 0.00 0.00 41.40 4.75
3027 3269 1.078848 CCACTCACTAGGCAGGTGC 60.079 63.158 0.00 0.00 41.14 5.01
3048 3292 6.414079 GTGCGTGTATCTTAATCAACTGATG 58.586 40.000 0.00 0.00 34.49 3.07
3070 3314 2.875296 TGCAAGGTAGGTGATGCTTTT 58.125 42.857 0.00 0.00 39.49 2.27
3071 3315 3.230134 TGCAAGGTAGGTGATGCTTTTT 58.770 40.909 0.00 0.00 39.49 1.94
3072 3316 4.402829 TGCAAGGTAGGTGATGCTTTTTA 58.597 39.130 0.00 0.00 39.49 1.52
3073 3317 5.016173 TGCAAGGTAGGTGATGCTTTTTAT 58.984 37.500 0.00 0.00 39.49 1.40
3074 3318 5.480073 TGCAAGGTAGGTGATGCTTTTTATT 59.520 36.000 0.00 0.00 39.49 1.40
3075 3319 6.014669 TGCAAGGTAGGTGATGCTTTTTATTT 60.015 34.615 0.00 0.00 39.49 1.40
3076 3320 6.873605 GCAAGGTAGGTGATGCTTTTTATTTT 59.126 34.615 0.00 0.00 35.93 1.82
3077 3321 7.387673 GCAAGGTAGGTGATGCTTTTTATTTTT 59.612 33.333 0.00 0.00 35.93 1.94
3096 3340 1.750193 TTTGGAAGATCCGGTGATGC 58.250 50.000 0.00 0.00 40.17 3.91
3097 3341 0.911769 TTGGAAGATCCGGTGATGCT 59.088 50.000 0.00 0.00 40.17 3.79
3098 3342 0.911769 TGGAAGATCCGGTGATGCTT 59.088 50.000 0.00 0.00 40.17 3.91
3099 3343 1.134401 TGGAAGATCCGGTGATGCTTC 60.134 52.381 0.00 8.45 40.17 3.86
3110 3354 3.616076 CGGTGATGCTTCCTGATCCTATC 60.616 52.174 0.00 0.00 0.00 2.08
3112 3356 4.041444 GGTGATGCTTCCTGATCCTATCTT 59.959 45.833 0.00 0.00 0.00 2.40
3113 3357 5.247110 GGTGATGCTTCCTGATCCTATCTTA 59.753 44.000 0.00 0.00 0.00 2.10
3142 3394 5.429957 AAGAACTTGAATGAGAAGTGCAC 57.570 39.130 9.40 9.40 32.02 4.57
3221 3659 5.570844 GCCTGAAGTAGTGTCCAATCCTAAA 60.571 44.000 0.00 0.00 0.00 1.85
3330 3777 1.691195 TTCACCGAACACCTGCAGGA 61.691 55.000 39.19 10.61 38.94 3.86
3334 3781 3.414700 GAACACCTGCAGGACGCG 61.415 66.667 39.19 23.92 46.97 6.01
3335 3782 4.235762 AACACCTGCAGGACGCGT 62.236 61.111 39.19 24.55 46.97 6.01
3368 3815 2.679059 GCAGATGAAGGCAACAGAGCTA 60.679 50.000 0.00 0.00 41.41 3.32
3399 3850 3.028130 CGTGCCGCCGATAGTAGA 58.972 61.111 0.00 0.00 0.00 2.59
3400 3851 1.579932 CGTGCCGCCGATAGTAGAT 59.420 57.895 0.00 0.00 0.00 1.98
3401 3852 0.800631 CGTGCCGCCGATAGTAGATA 59.199 55.000 0.00 0.00 0.00 1.98
3431 3892 0.875728 CGTACGCTAGGATCAGAGGG 59.124 60.000 0.52 8.17 0.00 4.30
3437 3898 1.457643 TAGGATCAGAGGGTGGCGG 60.458 63.158 0.00 0.00 0.00 6.13
3442 3903 1.344953 ATCAGAGGGTGGCGGCATTA 61.345 55.000 17.19 0.00 0.00 1.90
3445 3906 1.136828 AGAGGGTGGCGGCATTATAA 58.863 50.000 17.19 0.00 0.00 0.98
3555 4021 2.740714 GAACCAGCCGCGCTAAGTG 61.741 63.158 5.56 0.00 36.40 3.16
3584 4051 2.630592 GATCTTCCGCCGAGGGACAC 62.631 65.000 0.00 0.00 41.52 3.67
3592 4059 2.580601 CCGAGGGACACCGGAAAGT 61.581 63.158 9.46 2.96 46.68 2.66
3784 4268 1.210967 CCTGGGCGGGTAGTTCATTTA 59.789 52.381 0.00 0.00 0.00 1.40
3796 4280 9.326413 CGGGTAGTTCATTTATCACTTTAATCT 57.674 33.333 0.00 0.00 0.00 2.40
3814 4298 1.915141 CTCCAATGGAGCACAAACCT 58.085 50.000 17.25 0.00 43.29 3.50
3843 4327 4.918588 TCTTTTCGAAAAGGCCTAATCCT 58.081 39.130 37.27 0.00 44.22 3.24
3848 4332 7.797038 TTTCGAAAAGGCCTAATCCTTATAC 57.203 36.000 5.16 0.00 45.25 1.47
3852 4336 8.707449 TCGAAAAGGCCTAATCCTTATACTAAA 58.293 33.333 5.16 0.00 45.25 1.85
3853 4337 8.989980 CGAAAAGGCCTAATCCTTATACTAAAG 58.010 37.037 5.16 0.00 45.25 1.85
3854 4338 9.286170 GAAAAGGCCTAATCCTTATACTAAAGG 57.714 37.037 5.16 0.00 45.25 3.11
3855 4339 7.949468 AAGGCCTAATCCTTATACTAAAGGT 57.051 36.000 5.16 0.00 44.23 3.50
3856 4340 7.317722 AGGCCTAATCCTTATACTAAAGGTG 57.682 40.000 1.29 0.00 45.37 4.00
3857 4341 6.850231 AGGCCTAATCCTTATACTAAAGGTGT 59.150 38.462 1.29 0.00 45.37 4.16
3858 4342 6.935208 GGCCTAATCCTTATACTAAAGGTGTG 59.065 42.308 0.00 0.00 45.37 3.82
3859 4343 7.419865 GGCCTAATCCTTATACTAAAGGTGTGT 60.420 40.741 0.00 0.00 45.37 3.72
3860 4344 7.991460 GCCTAATCCTTATACTAAAGGTGTGTT 59.009 37.037 2.76 0.00 45.37 3.32
3861 4345 9.543783 CCTAATCCTTATACTAAAGGTGTGTTC 57.456 37.037 2.76 0.00 45.37 3.18
3862 4346 9.245962 CTAATCCTTATACTAAAGGTGTGTTCG 57.754 37.037 2.76 0.00 45.37 3.95
3863 4347 5.969423 TCCTTATACTAAAGGTGTGTTCGG 58.031 41.667 2.76 0.00 45.37 4.30
3864 4348 5.481473 TCCTTATACTAAAGGTGTGTTCGGT 59.519 40.000 2.76 0.00 45.37 4.69
3865 4349 6.014327 TCCTTATACTAAAGGTGTGTTCGGTT 60.014 38.462 2.76 0.00 45.37 4.44
3866 4350 6.652062 CCTTATACTAAAGGTGTGTTCGGTTT 59.348 38.462 0.00 0.00 41.06 3.27
3867 4351 7.148523 CCTTATACTAAAGGTGTGTTCGGTTTC 60.149 40.741 0.00 0.00 41.06 2.78
3868 4352 4.146745 ACTAAAGGTGTGTTCGGTTTCT 57.853 40.909 0.00 0.00 0.00 2.52
3869 4353 4.124970 ACTAAAGGTGTGTTCGGTTTCTC 58.875 43.478 0.00 0.00 0.00 2.87
3870 4354 3.277142 AAAGGTGTGTTCGGTTTCTCT 57.723 42.857 0.00 0.00 0.00 3.10
3871 4355 2.528041 AGGTGTGTTCGGTTTCTCTC 57.472 50.000 0.00 0.00 0.00 3.20
3872 4356 2.040178 AGGTGTGTTCGGTTTCTCTCT 58.960 47.619 0.00 0.00 0.00 3.10
3873 4357 2.135933 GGTGTGTTCGGTTTCTCTCTG 58.864 52.381 0.00 0.00 0.00 3.35
3874 4358 1.527311 GTGTGTTCGGTTTCTCTCTGC 59.473 52.381 0.00 0.00 0.00 4.26
3875 4359 1.412710 TGTGTTCGGTTTCTCTCTGCT 59.587 47.619 0.00 0.00 0.00 4.24
3876 4360 2.062519 GTGTTCGGTTTCTCTCTGCTC 58.937 52.381 0.00 0.00 0.00 4.26
3877 4361 1.000955 TGTTCGGTTTCTCTCTGCTCC 59.999 52.381 0.00 0.00 0.00 4.70
3878 4362 1.273886 GTTCGGTTTCTCTCTGCTCCT 59.726 52.381 0.00 0.00 0.00 3.69
3879 4363 1.178276 TCGGTTTCTCTCTGCTCCTC 58.822 55.000 0.00 0.00 0.00 3.71
3880 4364 0.891373 CGGTTTCTCTCTGCTCCTCA 59.109 55.000 0.00 0.00 0.00 3.86
3881 4365 1.273606 CGGTTTCTCTCTGCTCCTCAA 59.726 52.381 0.00 0.00 0.00 3.02
3882 4366 2.694213 GGTTTCTCTCTGCTCCTCAAC 58.306 52.381 0.00 0.00 0.00 3.18
3883 4367 2.301583 GGTTTCTCTCTGCTCCTCAACT 59.698 50.000 0.00 0.00 0.00 3.16
3884 4368 3.584834 GTTTCTCTCTGCTCCTCAACTC 58.415 50.000 0.00 0.00 0.00 3.01
3885 4369 1.846007 TCTCTCTGCTCCTCAACTCC 58.154 55.000 0.00 0.00 0.00 3.85
3886 4370 1.076187 TCTCTCTGCTCCTCAACTCCA 59.924 52.381 0.00 0.00 0.00 3.86
3887 4371 1.204467 CTCTCTGCTCCTCAACTCCAC 59.796 57.143 0.00 0.00 0.00 4.02
3888 4372 1.203112 TCTCTGCTCCTCAACTCCACT 60.203 52.381 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 4.767255 GCCTGCCAGACACCTCCG 62.767 72.222 0.00 0.00 0.00 4.63
228 229 3.685214 GATGACCACGAGCGACGCT 62.685 63.158 24.77 24.77 46.94 5.07
318 319 1.522355 CAGCACCATGACTAGCCGG 60.522 63.158 0.00 0.00 0.00 6.13
506 531 3.506096 CTACGGAGCTGGCGACGA 61.506 66.667 15.78 3.01 0.00 4.20
560 594 0.255890 ATTGGGAATGGGAGTCGTGG 59.744 55.000 0.00 0.00 0.00 4.94
567 601 1.846439 GAGTCAGGATTGGGAATGGGA 59.154 52.381 0.00 0.00 0.00 4.37
684 724 1.892209 TCGTGTCAGTGCTAGAGTCA 58.108 50.000 0.00 0.00 0.00 3.41
734 774 0.593263 GAACCGTTCGTCGACAGTGT 60.593 55.000 17.16 0.00 42.86 3.55
1337 1485 4.464008 TGCAGAGAATGGAAGAAACAGTT 58.536 39.130 0.00 0.00 0.00 3.16
1529 1697 4.041762 TCACCGGCCATGTTCCCC 62.042 66.667 0.00 0.00 0.00 4.81
1533 1701 4.360405 GGGGTCACCGGCCATGTT 62.360 66.667 0.00 0.00 37.78 2.71
1844 2015 1.675310 CTGATTTGCCTGGTCGCCA 60.675 57.895 0.00 0.00 0.00 5.69
2314 2503 1.965930 GATATGGATGGCGCGGCAA 60.966 57.895 39.24 23.92 0.00 4.52
2341 2530 4.757692 TCTTTCTTCTTCTTCCTCCTCCT 58.242 43.478 0.00 0.00 0.00 3.69
2342 2531 5.491323 TTCTTTCTTCTTCTTCCTCCTCC 57.509 43.478 0.00 0.00 0.00 4.30
2343 2532 6.292150 TGTTTCTTTCTTCTTCTTCCTCCTC 58.708 40.000 0.00 0.00 0.00 3.71
2363 2558 5.388599 TCTTCCTTTCTTCCTCCTTGTTT 57.611 39.130 0.00 0.00 0.00 2.83
2846 3068 2.581354 CCCTCAAGCCTCTCACGG 59.419 66.667 0.00 0.00 0.00 4.94
2933 3167 8.211116 TCAACTAGACTAGGAATCTAGAAACG 57.789 38.462 18.15 7.23 45.86 3.60
2990 3232 3.255642 GTGGACAAACAATGTAGGCATGT 59.744 43.478 0.00 0.00 44.12 3.21
2997 3239 5.547465 CCTAGTGAGTGGACAAACAATGTA 58.453 41.667 0.00 0.00 44.12 2.29
3027 3269 7.042523 TGCATCATCAGTTGATTAAGATACACG 60.043 37.037 0.00 0.00 42.62 4.49
3048 3292 2.338577 AGCATCACCTACCTTGCATC 57.661 50.000 0.00 0.00 37.56 3.91
3075 3319 2.491693 GCATCACCGGATCTTCCAAAAA 59.508 45.455 9.46 0.00 35.91 1.94
3076 3320 2.091541 GCATCACCGGATCTTCCAAAA 58.908 47.619 9.46 0.00 35.91 2.44
3077 3321 1.281867 AGCATCACCGGATCTTCCAAA 59.718 47.619 9.46 0.00 35.91 3.28
3078 3322 0.911769 AGCATCACCGGATCTTCCAA 59.088 50.000 9.46 0.00 35.91 3.53
3079 3323 0.911769 AAGCATCACCGGATCTTCCA 59.088 50.000 9.46 0.00 35.91 3.53
3080 3324 1.587547 GAAGCATCACCGGATCTTCC 58.412 55.000 9.46 0.00 34.78 3.46
3081 3325 1.139853 AGGAAGCATCACCGGATCTTC 59.860 52.381 9.46 12.24 37.18 2.87
3082 3326 1.134280 CAGGAAGCATCACCGGATCTT 60.134 52.381 9.46 3.14 0.00 2.40
3083 3327 0.467384 CAGGAAGCATCACCGGATCT 59.533 55.000 9.46 0.00 0.00 2.75
3084 3328 0.465705 TCAGGAAGCATCACCGGATC 59.534 55.000 9.46 0.00 0.00 3.36
3085 3329 1.071385 GATCAGGAAGCATCACCGGAT 59.929 52.381 9.46 0.00 42.00 4.18
3086 3330 0.465705 GATCAGGAAGCATCACCGGA 59.534 55.000 9.46 0.00 35.21 5.14
3087 3331 0.533755 GGATCAGGAAGCATCACCGG 60.534 60.000 0.00 0.00 0.00 5.28
3088 3332 0.467384 AGGATCAGGAAGCATCACCG 59.533 55.000 0.00 0.00 0.00 4.94
3089 3333 3.582208 AGATAGGATCAGGAAGCATCACC 59.418 47.826 0.00 0.00 0.00 4.02
3090 3334 4.888326 AGATAGGATCAGGAAGCATCAC 57.112 45.455 0.00 0.00 0.00 3.06
3091 3335 6.958778 AGATAAGATAGGATCAGGAAGCATCA 59.041 38.462 0.00 0.00 0.00 3.07
3092 3336 7.123997 TGAGATAAGATAGGATCAGGAAGCATC 59.876 40.741 0.00 0.00 0.00 3.91
3093 3337 6.958778 TGAGATAAGATAGGATCAGGAAGCAT 59.041 38.462 0.00 0.00 0.00 3.79
3094 3338 6.318112 TGAGATAAGATAGGATCAGGAAGCA 58.682 40.000 0.00 0.00 0.00 3.91
3095 3339 6.849085 TGAGATAAGATAGGATCAGGAAGC 57.151 41.667 0.00 0.00 0.00 3.86
3133 3385 5.376625 TCAGTTTCCTAAATGTGCACTTCT 58.623 37.500 19.41 0.26 31.55 2.85
3142 3394 8.299570 AGTACAAATGCTTCAGTTTCCTAAATG 58.700 33.333 0.00 0.00 0.00 2.32
3221 3659 6.051717 CCTCTCGGTCAGTGATTATCATTTT 58.948 40.000 0.00 0.00 0.00 1.82
3334 3781 1.202687 TCATCTGCATTCGGGGATCAC 60.203 52.381 0.00 0.00 0.00 3.06
3335 3782 1.130777 TCATCTGCATTCGGGGATCA 58.869 50.000 0.00 0.00 0.00 2.92
3344 3791 2.753452 CTCTGTTGCCTTCATCTGCATT 59.247 45.455 0.00 0.00 37.33 3.56
3391 3842 7.167968 CGTACGCATCTACTCCTATCTACTATC 59.832 44.444 0.52 0.00 0.00 2.08
3392 3843 6.979817 CGTACGCATCTACTCCTATCTACTAT 59.020 42.308 0.52 0.00 0.00 2.12
3393 3844 6.328714 CGTACGCATCTACTCCTATCTACTA 58.671 44.000 0.52 0.00 0.00 1.82
3394 3845 5.170021 CGTACGCATCTACTCCTATCTACT 58.830 45.833 0.52 0.00 0.00 2.57
3395 3846 4.201705 GCGTACGCATCTACTCCTATCTAC 60.202 50.000 33.90 0.00 41.49 2.59
3396 3847 3.931468 GCGTACGCATCTACTCCTATCTA 59.069 47.826 33.90 0.00 41.49 1.98
3397 3848 2.743126 GCGTACGCATCTACTCCTATCT 59.257 50.000 33.90 0.00 41.49 1.98
3398 3849 2.743126 AGCGTACGCATCTACTCCTATC 59.257 50.000 38.58 7.31 44.88 2.08
3399 3850 2.780714 AGCGTACGCATCTACTCCTAT 58.219 47.619 38.58 13.49 44.88 2.57
3400 3851 2.251409 AGCGTACGCATCTACTCCTA 57.749 50.000 38.58 0.00 44.88 2.94
3401 3852 2.144730 CTAGCGTACGCATCTACTCCT 58.855 52.381 38.58 19.15 44.88 3.69
3431 3892 3.146066 TCTCCAATTATAATGCCGCCAC 58.854 45.455 0.00 0.00 0.00 5.01
3437 3898 7.099764 TCGAGAATCCTCTCCAATTATAATGC 58.900 38.462 0.00 0.00 44.70 3.56
3442 3903 4.321601 CGCTCGAGAATCCTCTCCAATTAT 60.322 45.833 18.75 0.00 44.70 1.28
3445 3906 1.339610 CGCTCGAGAATCCTCTCCAAT 59.660 52.381 18.75 0.00 44.70 3.16
3555 4021 1.884926 CGGAAGATCGCAAGGAGCC 60.885 63.158 0.00 0.00 41.38 4.70
3584 4051 1.675641 CTGGCCTTCCACTTTCCGG 60.676 63.158 3.32 0.00 37.47 5.14
3664 4140 3.452786 CGCCGCTCCTTCTCTCCA 61.453 66.667 0.00 0.00 0.00 3.86
3713 4197 0.604780 CACTGTCCACTCAAGGCAGG 60.605 60.000 0.00 0.00 37.22 4.85
3717 4201 2.847327 ATGTCACTGTCCACTCAAGG 57.153 50.000 0.00 0.00 0.00 3.61
3796 4280 2.380064 AAGGTTTGTGCTCCATTGGA 57.620 45.000 5.05 5.05 0.00 3.53
3822 4306 5.644977 AAGGATTAGGCCTTTTCGAAAAG 57.355 39.130 33.84 33.84 45.85 2.27
3823 4307 8.050930 AGTATAAGGATTAGGCCTTTTCGAAAA 58.949 33.333 21.35 21.35 45.85 2.29
3834 4318 7.506971 ACACACCTTTAGTATAAGGATTAGGC 58.493 38.462 9.26 0.00 46.28 3.93
3843 4327 7.444299 AGAAACCGAACACACCTTTAGTATAA 58.556 34.615 0.00 0.00 0.00 0.98
3848 4332 4.377897 AGAGAAACCGAACACACCTTTAG 58.622 43.478 0.00 0.00 0.00 1.85
3852 4336 2.040178 AGAGAGAAACCGAACACACCT 58.960 47.619 0.00 0.00 0.00 4.00
3853 4337 2.135933 CAGAGAGAAACCGAACACACC 58.864 52.381 0.00 0.00 0.00 4.16
3854 4338 1.527311 GCAGAGAGAAACCGAACACAC 59.473 52.381 0.00 0.00 0.00 3.82
3855 4339 1.412710 AGCAGAGAGAAACCGAACACA 59.587 47.619 0.00 0.00 0.00 3.72
3856 4340 2.062519 GAGCAGAGAGAAACCGAACAC 58.937 52.381 0.00 0.00 0.00 3.32
3857 4341 1.000955 GGAGCAGAGAGAAACCGAACA 59.999 52.381 0.00 0.00 0.00 3.18
3858 4342 1.273886 AGGAGCAGAGAGAAACCGAAC 59.726 52.381 0.00 0.00 0.00 3.95
3859 4343 1.546476 GAGGAGCAGAGAGAAACCGAA 59.454 52.381 0.00 0.00 0.00 4.30
3860 4344 1.178276 GAGGAGCAGAGAGAAACCGA 58.822 55.000 0.00 0.00 0.00 4.69
3861 4345 0.891373 TGAGGAGCAGAGAGAAACCG 59.109 55.000 0.00 0.00 0.00 4.44
3862 4346 2.301583 AGTTGAGGAGCAGAGAGAAACC 59.698 50.000 0.00 0.00 0.00 3.27
3863 4347 3.584834 GAGTTGAGGAGCAGAGAGAAAC 58.415 50.000 0.00 0.00 0.00 2.78
3864 4348 2.564947 GGAGTTGAGGAGCAGAGAGAAA 59.435 50.000 0.00 0.00 0.00 2.52
3865 4349 2.175202 GGAGTTGAGGAGCAGAGAGAA 58.825 52.381 0.00 0.00 0.00 2.87
3866 4350 1.076187 TGGAGTTGAGGAGCAGAGAGA 59.924 52.381 0.00 0.00 0.00 3.10
3867 4351 1.204467 GTGGAGTTGAGGAGCAGAGAG 59.796 57.143 0.00 0.00 0.00 3.20
3868 4352 1.203112 AGTGGAGTTGAGGAGCAGAGA 60.203 52.381 0.00 0.00 0.00 3.10
3869 4353 1.265236 AGTGGAGTTGAGGAGCAGAG 58.735 55.000 0.00 0.00 0.00 3.35
3870 4354 3.464878 AGTGGAGTTGAGGAGCAGA 57.535 52.632 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.