Multiple sequence alignment - TraesCS4D01G229100

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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 TraesCS4D01G229100 chr4D 100.000 5002 0 0 1 5002 388924386 388929387 0.000000e+00 9238.0
1 TraesCS4D01G229100 chr4B 92.435 3397 133 61 71 3420 477223072 477226391 0.000000e+00 4735.0
2 TraesCS4D01G229100 chr4B 92.714 796 39 11 3442 4228 477226379 477227164 0.000000e+00 1131.0
3 TraesCS4D01G229100 chr4B 94.583 720 33 4 4288 5002 477227279 477227997 0.000000e+00 1109.0
4 TraesCS4D01G229100 chr4A 94.184 3095 117 25 30 3076 70307828 70310907 0.000000e+00 4660.0
5 TraesCS4D01G229100 chr4A 92.761 1257 59 15 3756 5002 70311580 70312814 0.000000e+00 1788.0
6 TraesCS4D01G229100 chr4A 92.487 599 34 3 3135 3727 70310922 70311515 0.000000e+00 846.0
7 TraesCS4D01G229100 chr5D 92.045 88 5 2 2212 2298 404739808 404739722 6.800000e-24 122.0
8 TraesCS4D01G229100 chr5D 90.909 88 6 2 2212 2298 482310519 482310605 3.160000e-22 117.0
9 TraesCS4D01G229100 chr5D 87.500 88 9 2 2212 2298 482312948 482312862 3.190000e-17 100.0
10 TraesCS4D01G229100 chr5D 90.741 54 2 3 3250 3301 382488294 382488242 8.990000e-08 69.4
11 TraesCS4D01G229100 chr1D 90.909 88 6 2 2212 2298 52103908 52103822 3.160000e-22 117.0
12 TraesCS4D01G229100 chr2D 90.909 88 5 3 2212 2298 248754492 248754407 1.140000e-21 115.0
13 TraesCS4D01G229100 chr3D 88.636 88 8 2 2212 2298 424686061 424686147 6.850000e-19 106.0
14 TraesCS4D01G229100 chr5B 85.714 84 11 1 2212 2295 533893799 533893717 2.480000e-13 87.9
15 TraesCS4D01G229100 chr5B 90.741 54 2 3 3250 3301 458897049 458896997 8.990000e-08 69.4
16 TraesCS4D01G229100 chr5A 90.741 54 2 3 3250 3301 482902499 482902447 8.990000e-08 69.4
17 TraesCS4D01G229100 chr5A 100.000 29 0 0 2836 2864 617238311 617238283 3.000000e-03 54.7


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 TraesCS4D01G229100 chr4D 388924386 388929387 5001 False 9238.000000 9238 100.000 1 5002 1 chr4D.!!$F1 5001
1 TraesCS4D01G229100 chr4B 477223072 477227997 4925 False 2325.000000 4735 93.244 71 5002 3 chr4B.!!$F1 4931
2 TraesCS4D01G229100 chr4A 70307828 70312814 4986 False 2431.333333 4660 93.144 30 5002 3 chr4A.!!$F1 4972

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
28 29 0.621862 ACCCCTCCAATCTCCTCCAC 60.622 60.000 0.0 0.0 0.00 4.02 F
154 156 1.081376 CCACTTCGCTCTCGTTCGT 60.081 57.895 0.0 0.0 36.96 3.85 F
958 1003 1.302431 CCATGGCGGACAAGTGTGA 60.302 57.895 0.0 0.0 36.56 3.58 F
2388 2445 1.302511 CACCAACCACTTCTCCCCG 60.303 63.158 0.0 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1647 0.035152 TGGATCACGCCAAGATTGCT 60.035 50.0 0.00 0.0 34.31 3.91 R
1675 1728 0.179089 GAGCCACTGATCGAGCACAT 60.179 55.0 0.00 0.0 0.00 3.21 R
2653 2710 0.598942 TACAGCATTGTGTGTCGCGT 60.599 50.0 5.77 0.0 38.23 6.01 R
4110 4240 0.327480 TATCATGTCCCTGGGTGCCT 60.327 55.0 13.56 0.0 0.00 4.75 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
22 23 4.586306 TTTCCTTTACCCCTCCAATCTC 57.414 45.455 0.00 0.00 0.00 2.75
23 24 2.488836 TCCTTTACCCCTCCAATCTCC 58.511 52.381 0.00 0.00 0.00 3.71
24 25 2.047296 TCCTTTACCCCTCCAATCTCCT 59.953 50.000 0.00 0.00 0.00 3.69
25 26 2.439880 CCTTTACCCCTCCAATCTCCTC 59.560 54.545 0.00 0.00 0.00 3.71
26 27 2.191981 TTACCCCTCCAATCTCCTCC 57.808 55.000 0.00 0.00 0.00 4.30
27 28 1.023719 TACCCCTCCAATCTCCTCCA 58.976 55.000 0.00 0.00 0.00 3.86
28 29 0.621862 ACCCCTCCAATCTCCTCCAC 60.622 60.000 0.00 0.00 0.00 4.02
43 44 2.434359 CACCGCCTTTCTCCGTCC 60.434 66.667 0.00 0.00 0.00 4.79
60 61 2.893489 CGTCCCATCATCACAGATCCTA 59.107 50.000 0.00 0.00 0.00 2.94
61 62 3.305676 CGTCCCATCATCACAGATCCTAC 60.306 52.174 0.00 0.00 0.00 3.18
65 66 3.070590 CCATCATCACAGATCCTACTGCA 59.929 47.826 0.00 0.00 41.06 4.41
106 107 8.972662 TCTCCCAATTGACCATATCTATCTAA 57.027 34.615 7.12 0.00 0.00 2.10
107 108 9.566331 TCTCCCAATTGACCATATCTATCTAAT 57.434 33.333 7.12 0.00 0.00 1.73
109 110 9.566331 TCCCAATTGACCATATCTATCTAATCT 57.434 33.333 7.12 0.00 0.00 2.40
149 151 1.153939 CACCTCCACTTCGCTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
154 156 1.081376 CCACTTCGCTCTCGTTCGT 60.081 57.895 0.00 0.00 36.96 3.85
442 457 4.865761 GTCGCGGCGCCATGTAGA 62.866 66.667 28.98 13.82 0.00 2.59
660 675 2.667199 CCCGGTCCGTTGGTTCAC 60.667 66.667 11.06 0.00 0.00 3.18
958 1003 1.302431 CCATGGCGGACAAGTGTGA 60.302 57.895 0.00 0.00 36.56 3.58
1224 1270 4.380531 TCGATTCATGGTAGCATTTCCTC 58.619 43.478 4.25 0.00 0.00 3.71
1360 1409 1.728426 GCAAGCAAGCAAGCACGAG 60.728 57.895 3.19 0.00 36.85 4.18
1498 1547 2.431683 GTGCTGGTGAAGGAGGCA 59.568 61.111 0.00 0.00 0.00 4.75
1575 1628 1.376424 CAGTGCCGATGCTCACCTT 60.376 57.895 0.00 0.00 38.71 3.50
1593 1646 3.557903 TTCACCTCCCAGCAGCAGC 62.558 63.158 0.00 0.00 42.56 5.25
1594 1647 4.340246 CACCTCCCAGCAGCAGCA 62.340 66.667 3.17 0.00 45.49 4.41
1595 1648 4.031129 ACCTCCCAGCAGCAGCAG 62.031 66.667 3.17 0.00 45.49 4.24
1636 1689 5.493133 ACTGTTTGTTTTCTGCACGATTA 57.507 34.783 0.00 0.00 0.00 1.75
1675 1728 9.280174 ACCAAAAGTAATCGATTCTTTTACTGA 57.720 29.630 28.16 7.40 38.70 3.41
2080 2137 3.916392 AAGAAGCCCTGCGACGACG 62.916 63.158 2.12 2.12 42.93 5.12
2316 2373 4.803426 GACCTGAGGCGGACGCTG 62.803 72.222 16.72 4.88 41.60 5.18
2373 2430 2.102553 GAGCTCTACGACGCCACC 59.897 66.667 6.43 0.00 0.00 4.61
2388 2445 1.302511 CACCAACCACTTCTCCCCG 60.303 63.158 0.00 0.00 0.00 5.73
2475 2532 4.527157 GCGATCAAGCTGTGCCGC 62.527 66.667 7.80 7.80 40.13 6.53
2768 2840 0.324091 GTGGGAGAAGAGGTACCGGA 60.324 60.000 9.46 0.00 0.00 5.14
2889 2961 1.677637 GACTTCGAGCCCCAGGTAGG 61.678 65.000 0.00 0.00 37.03 3.18
2935 3009 4.683781 TGCAGTTTGTTTGTCTGTGTTTTC 59.316 37.500 0.00 0.00 0.00 2.29
3076 3157 1.790623 CGGGTACGTGTTCTTCTTGTG 59.209 52.381 0.00 0.00 34.81 3.33
3078 3159 2.542595 GGGTACGTGTTCTTCTTGTGTG 59.457 50.000 0.00 0.00 0.00 3.82
3082 3163 5.464389 GGTACGTGTTCTTCTTGTGTGTATT 59.536 40.000 0.00 0.00 0.00 1.89
3083 3164 6.642131 GGTACGTGTTCTTCTTGTGTGTATTA 59.358 38.462 0.00 0.00 0.00 0.98
3084 3165 6.764877 ACGTGTTCTTCTTGTGTGTATTAG 57.235 37.500 0.00 0.00 0.00 1.73
3087 3168 5.176958 GTGTTCTTCTTGTGTGTATTAGCGT 59.823 40.000 0.00 0.00 0.00 5.07
3088 3169 5.176774 TGTTCTTCTTGTGTGTATTAGCGTG 59.823 40.000 0.00 0.00 0.00 5.34
3089 3170 4.242475 TCTTCTTGTGTGTATTAGCGTGG 58.758 43.478 0.00 0.00 0.00 4.94
3091 3172 2.563620 TCTTGTGTGTATTAGCGTGGGA 59.436 45.455 0.00 0.00 0.00 4.37
3092 3173 2.373540 TGTGTGTATTAGCGTGGGAC 57.626 50.000 0.00 0.00 0.00 4.46
3094 3175 1.135315 GTGTGTATTAGCGTGGGACGA 60.135 52.381 0.00 0.00 46.05 4.20
3097 3178 1.194495 GTATTAGCGTGGGACGAACG 58.806 55.000 0.00 0.00 46.05 3.95
3098 3179 0.101040 TATTAGCGTGGGACGAACGG 59.899 55.000 0.00 0.00 46.05 4.44
3107 3188 3.550656 GACGAACGGTCAGGCTTG 58.449 61.111 0.00 0.00 45.36 4.01
3108 3189 1.300697 GACGAACGGTCAGGCTTGT 60.301 57.895 0.00 0.00 45.36 3.16
3109 3190 0.038892 GACGAACGGTCAGGCTTGTA 60.039 55.000 0.00 0.00 45.36 2.41
3110 3191 0.038526 ACGAACGGTCAGGCTTGTAG 60.039 55.000 0.00 0.00 0.00 2.74
3111 3192 0.038526 CGAACGGTCAGGCTTGTAGT 60.039 55.000 0.00 0.00 0.00 2.73
3112 3193 1.200716 CGAACGGTCAGGCTTGTAGTA 59.799 52.381 0.00 0.00 0.00 1.82
3113 3194 2.159282 CGAACGGTCAGGCTTGTAGTAT 60.159 50.000 0.00 0.00 0.00 2.12
3114 3195 3.675228 CGAACGGTCAGGCTTGTAGTATT 60.675 47.826 0.00 0.00 0.00 1.89
3115 3196 3.975168 ACGGTCAGGCTTGTAGTATTT 57.025 42.857 0.00 0.00 0.00 1.40
3116 3197 3.596214 ACGGTCAGGCTTGTAGTATTTG 58.404 45.455 0.00 0.00 0.00 2.32
3117 3198 2.351726 CGGTCAGGCTTGTAGTATTTGC 59.648 50.000 0.00 0.00 0.00 3.68
3118 3199 3.343617 GGTCAGGCTTGTAGTATTTGCA 58.656 45.455 0.00 0.00 0.00 4.08
3119 3200 3.375299 GGTCAGGCTTGTAGTATTTGCAG 59.625 47.826 0.00 0.00 0.00 4.41
3120 3201 4.253685 GTCAGGCTTGTAGTATTTGCAGA 58.746 43.478 0.00 0.00 0.00 4.26
3121 3202 4.331168 GTCAGGCTTGTAGTATTTGCAGAG 59.669 45.833 0.00 0.00 0.00 3.35
3122 3203 4.020218 TCAGGCTTGTAGTATTTGCAGAGT 60.020 41.667 0.00 0.00 0.00 3.24
3123 3204 5.186992 TCAGGCTTGTAGTATTTGCAGAGTA 59.813 40.000 0.00 0.00 0.00 2.59
3124 3205 5.292101 CAGGCTTGTAGTATTTGCAGAGTAC 59.708 44.000 0.00 0.00 0.00 2.73
3125 3206 5.046591 AGGCTTGTAGTATTTGCAGAGTACA 60.047 40.000 8.26 8.26 31.20 2.90
3126 3207 5.292101 GGCTTGTAGTATTTGCAGAGTACAG 59.708 44.000 10.90 8.18 33.98 2.74
3127 3208 5.292101 GCTTGTAGTATTTGCAGAGTACAGG 59.708 44.000 13.58 13.58 33.98 4.00
3128 3209 6.599356 TTGTAGTATTTGCAGAGTACAGGA 57.401 37.500 10.90 0.00 33.98 3.86
3129 3210 6.599356 TGTAGTATTTGCAGAGTACAGGAA 57.401 37.500 8.26 0.00 29.98 3.36
3130 3211 6.395629 TGTAGTATTTGCAGAGTACAGGAAC 58.604 40.000 8.26 3.04 29.98 3.62
3131 3212 5.483685 AGTATTTGCAGAGTACAGGAACA 57.516 39.130 0.00 0.00 0.00 3.18
3132 3213 5.238583 AGTATTTGCAGAGTACAGGAACAC 58.761 41.667 0.00 0.00 0.00 3.32
3133 3214 2.148916 TTGCAGAGTACAGGAACACG 57.851 50.000 0.00 0.00 0.00 4.49
3156 3241 5.618195 CGGAGTCTCTTTCAGTCTGAAGTAC 60.618 48.000 14.75 11.42 37.70 2.73
3166 3251 1.068333 GTCTGAAGTACCGCCGTGTTA 60.068 52.381 0.00 0.00 0.00 2.41
3338 3423 2.601367 CCAAAGGGCCACCACCAG 60.601 66.667 6.18 0.00 40.13 4.00
3372 3457 1.887707 GTAAGCCCTCGCAATCCCG 60.888 63.158 0.00 0.00 37.52 5.14
3386 3471 2.032680 ATCCCGATTAAACCCACACG 57.967 50.000 0.00 0.00 0.00 4.49
3430 3515 6.903883 ACGTTGTTACCATATCATTGTCTC 57.096 37.500 0.00 0.00 0.00 3.36
3431 3516 6.403049 ACGTTGTTACCATATCATTGTCTCA 58.597 36.000 0.00 0.00 0.00 3.27
3433 3518 7.389330 ACGTTGTTACCATATCATTGTCTCAAA 59.611 33.333 0.00 0.00 0.00 2.69
3486 3573 2.621055 CGTGTAGAGAGAGGGAGATTGG 59.379 54.545 0.00 0.00 0.00 3.16
3495 3582 2.268920 GGAGATTGGGCTGACGCA 59.731 61.111 0.00 0.00 38.10 5.24
3514 3601 2.806244 GCAGTTGGTCTGTTTGACGTAT 59.194 45.455 0.00 0.00 46.24 3.06
3579 3666 4.316823 TGGACCCGAGCCTGGACT 62.317 66.667 0.00 0.00 0.00 3.85
3696 3789 2.679639 CGTCTCTCTCTCAGTAGCAGGT 60.680 54.545 0.00 0.00 0.00 4.00
3699 3792 3.009584 TCTCTCTCTCAGTAGCAGGTTCA 59.990 47.826 0.00 0.00 0.00 3.18
3744 3837 2.097466 CGTCCTGCAGTTTTTGAAGTGT 59.903 45.455 13.81 0.00 29.39 3.55
3785 3914 3.388308 GTGGCAGATACTGAGCATACTG 58.612 50.000 2.81 0.00 32.44 2.74
3810 3939 4.117661 AAGAGGACGCGACGAGCC 62.118 66.667 15.93 5.83 44.76 4.70
4007 4136 3.077359 CTCCAGCTTCGATTGACCTTTT 58.923 45.455 0.00 0.00 0.00 2.27
4008 4137 2.813754 TCCAGCTTCGATTGACCTTTTG 59.186 45.455 0.00 0.00 0.00 2.44
4011 4140 4.222114 CAGCTTCGATTGACCTTTTGTTC 58.778 43.478 0.00 0.00 0.00 3.18
4017 4146 7.434013 GCTTCGATTGACCTTTTGTTCTTTTTA 59.566 33.333 0.00 0.00 0.00 1.52
4019 4148 7.763356 TCGATTGACCTTTTGTTCTTTTTACA 58.237 30.769 0.00 0.00 0.00 2.41
4060 4190 5.748630 GGATGAGTTTGGTTGTCTTTTGTTC 59.251 40.000 0.00 0.00 0.00 3.18
4110 4240 1.068895 CAAAGCAGGTGCCACATTTCA 59.931 47.619 0.00 0.00 43.38 2.69
4135 4265 0.034059 CCAGGGACATGATAGCCGAC 59.966 60.000 0.00 0.00 0.00 4.79
4139 4269 1.269831 GGGACATGATAGCCGACAGAC 60.270 57.143 0.00 0.00 0.00 3.51
4221 4351 4.517075 TGATGCTGTAATTCGGACACAAAA 59.483 37.500 0.00 0.00 0.00 2.44
4237 4367 2.416547 ACAAAAGCCACGATTCATCTCG 59.583 45.455 0.00 0.00 44.14 4.04
4238 4368 2.672874 CAAAAGCCACGATTCATCTCGA 59.327 45.455 0.00 0.00 41.12 4.04
4252 4421 8.712363 CGATTCATCTCGATTTATTTACATGGT 58.288 33.333 0.00 0.00 41.12 3.55
4253 4422 9.817365 GATTCATCTCGATTTATTTACATGGTG 57.183 33.333 0.00 0.00 0.00 4.17
4254 4423 8.731275 TTCATCTCGATTTATTTACATGGTGT 57.269 30.769 0.00 0.00 0.00 4.16
4255 4424 8.141835 TCATCTCGATTTATTTACATGGTGTG 57.858 34.615 0.00 0.00 0.00 3.82
4256 4425 6.358118 TCTCGATTTATTTACATGGTGTGC 57.642 37.500 0.00 0.00 0.00 4.57
4348 4549 5.993441 AGATCAATTGCTTGGAAACCAAAAG 59.007 36.000 0.00 0.00 43.44 2.27
4349 4550 5.096443 TCAATTGCTTGGAAACCAAAAGT 57.904 34.783 0.00 0.00 43.44 2.66
4350 4551 6.227298 TCAATTGCTTGGAAACCAAAAGTA 57.773 33.333 0.00 0.00 43.44 2.24
4351 4552 6.644347 TCAATTGCTTGGAAACCAAAAGTAA 58.356 32.000 0.00 1.01 43.44 2.24
4352 4553 6.760770 TCAATTGCTTGGAAACCAAAAGTAAG 59.239 34.615 0.00 0.00 43.44 2.34
4353 4554 5.669164 TTGCTTGGAAACCAAAAGTAAGT 57.331 34.783 4.78 0.00 43.44 2.24
4354 4555 5.257082 TGCTTGGAAACCAAAAGTAAGTC 57.743 39.130 4.78 0.00 43.44 3.01
4355 4556 4.707448 TGCTTGGAAACCAAAAGTAAGTCA 59.293 37.500 4.78 0.00 43.44 3.41
4356 4557 5.186021 TGCTTGGAAACCAAAAGTAAGTCAA 59.814 36.000 4.78 0.00 43.44 3.18
4555 4756 5.009010 GGGAACAACATATGGCAACTGATAG 59.991 44.000 7.80 0.00 37.61 2.08
4557 4758 6.238484 GGAACAACATATGGCAACTGATAGAC 60.238 42.308 7.80 0.00 37.61 2.59
4560 4761 6.484643 ACAACATATGGCAACTGATAGACATC 59.515 38.462 7.80 0.00 37.61 3.06
4623 4824 2.676121 CTCCATGGGCGCCAAACA 60.676 61.111 30.85 18.18 36.95 2.83
4649 4850 2.853290 GCCTTGCAGCTGCTGTTGT 61.853 57.895 36.61 0.00 42.66 3.32
4650 4851 1.518056 GCCTTGCAGCTGCTGTTGTA 61.518 55.000 36.61 15.23 42.66 2.41
4651 4852 0.953727 CCTTGCAGCTGCTGTTGTAA 59.046 50.000 36.61 21.37 42.66 2.41
4675 4876 1.454847 AGGTTTCTTTGCACCGCCA 60.455 52.632 0.00 0.00 38.21 5.69
4704 4905 2.721167 CCTGGTCGCCGAGATTCCA 61.721 63.158 0.00 0.00 0.00 3.53
4771 4972 5.511363 AGATCTCGGAACTTCCTCTCTTTA 58.489 41.667 6.25 0.00 33.30 1.85
4839 5040 3.507411 ACTGCTTAACCTCTGGTACTGA 58.493 45.455 0.00 0.00 33.12 3.41
4884 5085 1.807142 GGAACAAGGCTCTTCTTTCGG 59.193 52.381 0.00 0.00 0.00 4.30
4951 5155 2.094286 CACCTTTGGTTTGTGCAGAACA 60.094 45.455 13.21 0.00 32.24 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.264217 GGAGATTGGAGGGGTAAAGGAAAA 60.264 45.833 0.00 0.00 0.00 2.29
1 2 3.268595 GGAGATTGGAGGGGTAAAGGAAA 59.731 47.826 0.00 0.00 0.00 3.13
2 3 2.850568 GGAGATTGGAGGGGTAAAGGAA 59.149 50.000 0.00 0.00 0.00 3.36
3 4 2.047296 AGGAGATTGGAGGGGTAAAGGA 59.953 50.000 0.00 0.00 0.00 3.36
4 5 2.439880 GAGGAGATTGGAGGGGTAAAGG 59.560 54.545 0.00 0.00 0.00 3.11
5 6 2.439880 GGAGGAGATTGGAGGGGTAAAG 59.560 54.545 0.00 0.00 0.00 1.85
6 7 2.226039 TGGAGGAGATTGGAGGGGTAAA 60.226 50.000 0.00 0.00 0.00 2.01
7 8 1.368203 TGGAGGAGATTGGAGGGGTAA 59.632 52.381 0.00 0.00 0.00 2.85
8 9 1.023719 TGGAGGAGATTGGAGGGGTA 58.976 55.000 0.00 0.00 0.00 3.69
9 10 0.621862 GTGGAGGAGATTGGAGGGGT 60.622 60.000 0.00 0.00 0.00 4.95
10 11 1.348775 GGTGGAGGAGATTGGAGGGG 61.349 65.000 0.00 0.00 0.00 4.79
11 12 1.690219 CGGTGGAGGAGATTGGAGGG 61.690 65.000 0.00 0.00 0.00 4.30
12 13 1.826024 CGGTGGAGGAGATTGGAGG 59.174 63.158 0.00 0.00 0.00 4.30
13 14 1.144936 GCGGTGGAGGAGATTGGAG 59.855 63.158 0.00 0.00 0.00 3.86
14 15 2.367202 GGCGGTGGAGGAGATTGGA 61.367 63.158 0.00 0.00 0.00 3.53
15 16 1.915078 AAGGCGGTGGAGGAGATTGG 61.915 60.000 0.00 0.00 0.00 3.16
16 17 0.035056 AAAGGCGGTGGAGGAGATTG 60.035 55.000 0.00 0.00 0.00 2.67
17 18 0.253327 GAAAGGCGGTGGAGGAGATT 59.747 55.000 0.00 0.00 0.00 2.40
18 19 0.618968 AGAAAGGCGGTGGAGGAGAT 60.619 55.000 0.00 0.00 0.00 2.75
19 20 1.229209 AGAAAGGCGGTGGAGGAGA 60.229 57.895 0.00 0.00 0.00 3.71
20 21 1.219393 GAGAAAGGCGGTGGAGGAG 59.781 63.158 0.00 0.00 0.00 3.69
21 22 2.291043 GGAGAAAGGCGGTGGAGGA 61.291 63.158 0.00 0.00 0.00 3.71
22 23 2.269241 GGAGAAAGGCGGTGGAGG 59.731 66.667 0.00 0.00 0.00 4.30
23 24 2.125512 CGGAGAAAGGCGGTGGAG 60.126 66.667 0.00 0.00 0.00 3.86
24 25 2.920912 ACGGAGAAAGGCGGTGGA 60.921 61.111 0.00 0.00 0.00 4.02
25 26 2.434359 GACGGAGAAAGGCGGTGG 60.434 66.667 0.00 0.00 0.00 4.61
26 27 2.434359 GGACGGAGAAAGGCGGTG 60.434 66.667 0.00 0.00 0.00 4.94
27 28 3.703127 GGGACGGAGAAAGGCGGT 61.703 66.667 0.00 0.00 0.00 5.68
28 29 2.925162 GATGGGACGGAGAAAGGCGG 62.925 65.000 0.00 0.00 0.00 6.13
43 44 3.070590 TGCAGTAGGATCTGTGATGATGG 59.929 47.826 0.00 0.00 37.70 3.51
60 61 6.149474 GGAGAAAAGTATTGTATGTGTGCAGT 59.851 38.462 0.00 0.00 0.00 4.40
61 62 6.403636 GGGAGAAAAGTATTGTATGTGTGCAG 60.404 42.308 0.00 0.00 0.00 4.41
65 66 8.522830 CAATTGGGAGAAAAGTATTGTATGTGT 58.477 33.333 0.00 0.00 0.00 3.72
106 107 4.228895 TGCAATGCTATGGGATGGATAGAT 59.771 41.667 6.82 0.00 0.00 1.98
107 108 3.588396 TGCAATGCTATGGGATGGATAGA 59.412 43.478 6.82 0.00 0.00 1.98
109 110 4.018233 TGATGCAATGCTATGGGATGGATA 60.018 41.667 6.82 0.00 0.00 2.59
149 151 0.232303 CAGACGCAGGTGAAACGAAC 59.768 55.000 0.00 0.00 38.12 3.95
154 156 2.108157 ACGCAGACGCAGGTGAAA 59.892 55.556 0.00 0.00 45.53 2.69
224 226 1.808945 CTAGGCTGCTGTCTTTTGTGG 59.191 52.381 2.05 0.00 0.00 4.17
442 457 9.273016 CGTGGAGATGGTATATAAAATTTCACT 57.727 33.333 0.00 0.00 0.00 3.41
854 899 0.810031 CCCTGTTGGCCGATACGAAG 60.810 60.000 0.00 0.00 0.00 3.79
958 1003 2.102252 GCTCGAGAGAATCACCAGGAAT 59.898 50.000 18.75 0.00 41.32 3.01
1158 1203 4.397919 TGACGGATAGGAGATGGGATAA 57.602 45.455 0.00 0.00 0.00 1.75
1224 1270 3.493129 TCCTTCGATTCAAGACAAACACG 59.507 43.478 0.00 0.00 0.00 4.49
1395 1444 3.966979 ACCATCAATACCAGCACATGAA 58.033 40.909 0.00 0.00 0.00 2.57
1575 1628 2.752358 CTGCTGCTGGGAGGTGAA 59.248 61.111 0.00 0.00 0.00 3.18
1593 1646 0.379669 GGATCACGCCAAGATTGCTG 59.620 55.000 0.00 0.00 0.00 4.41
1594 1647 0.035152 TGGATCACGCCAAGATTGCT 60.035 50.000 0.00 0.00 34.31 3.91
1595 1648 0.810648 TTGGATCACGCCAAGATTGC 59.189 50.000 0.00 0.00 42.75 3.56
1636 1689 1.102222 TTTTGGTGCGGGCGTTAACT 61.102 50.000 3.71 0.00 0.00 2.24
1675 1728 0.179089 GAGCCACTGATCGAGCACAT 60.179 55.000 0.00 0.00 0.00 3.21
2182 2239 2.358737 CTCGTGGTCACCCTTGGC 60.359 66.667 0.00 0.00 0.00 4.52
2361 2418 2.025418 GTGGTTGGTGGCGTCGTAG 61.025 63.158 0.00 0.00 0.00 3.51
2373 2430 2.351276 CCCGGGGAGAAGTGGTTG 59.649 66.667 14.71 0.00 0.00 3.77
2388 2445 4.932105 TTGCCCACCAGGTTGCCC 62.932 66.667 8.16 0.00 38.26 5.36
2649 2706 1.722163 CATTGTGTGTCGCGTGTGC 60.722 57.895 5.77 0.00 37.91 4.57
2651 2708 1.887242 AGCATTGTGTGTCGCGTGT 60.887 52.632 5.77 0.00 0.00 4.49
2653 2710 0.598942 TACAGCATTGTGTGTCGCGT 60.599 50.000 5.77 0.00 38.23 6.01
2654 2711 0.721154 ATACAGCATTGTGTGTCGCG 59.279 50.000 0.00 0.00 38.23 5.87
2657 2714 4.150451 GCCAAAAATACAGCATTGTGTGTC 59.850 41.667 0.00 0.00 38.23 3.67
2658 2715 4.057432 GCCAAAAATACAGCATTGTGTGT 58.943 39.130 0.00 1.86 38.23 3.72
2659 2716 4.150980 CAGCCAAAAATACAGCATTGTGTG 59.849 41.667 0.00 0.00 38.23 3.82
2791 2863 1.883732 GGAGTGCACGTAGCTCAGA 59.116 57.895 12.01 0.00 45.94 3.27
2869 2941 1.677637 CTACCTGGGGCTCGAAGTCC 61.678 65.000 0.00 0.00 39.92 3.85
2889 2961 6.258947 GCATCCCTGAATTTAAGAGTACAGTC 59.741 42.308 0.00 0.00 0.00 3.51
2935 3009 5.635417 TCAGAGTTCATGTCTGTCAGTAG 57.365 43.478 10.60 0.00 41.92 2.57
3065 3146 5.389516 CCACGCTAATACACACAAGAAGAAC 60.390 44.000 0.00 0.00 0.00 3.01
3076 3157 1.922545 GTTCGTCCCACGCTAATACAC 59.077 52.381 0.00 0.00 42.21 2.90
3078 3159 1.194495 CGTTCGTCCCACGCTAATAC 58.806 55.000 0.00 0.00 42.21 1.89
3082 3163 2.981560 GACCGTTCGTCCCACGCTA 61.982 63.158 0.00 0.00 42.21 4.26
3083 3164 4.353437 GACCGTTCGTCCCACGCT 62.353 66.667 0.00 0.00 42.21 5.07
3084 3165 4.651008 TGACCGTTCGTCCCACGC 62.651 66.667 0.00 0.00 42.21 5.34
3087 3168 3.998672 GCCTGACCGTTCGTCCCA 61.999 66.667 0.00 0.00 41.18 4.37
3088 3169 3.236003 AAGCCTGACCGTTCGTCCC 62.236 63.158 0.00 0.00 41.18 4.46
3089 3170 2.027625 CAAGCCTGACCGTTCGTCC 61.028 63.158 0.00 0.00 41.18 4.79
3091 3172 0.038526 CTACAAGCCTGACCGTTCGT 60.039 55.000 0.00 0.00 0.00 3.85
3092 3173 0.038526 ACTACAAGCCTGACCGTTCG 60.039 55.000 0.00 0.00 0.00 3.95
3094 3175 3.975168 AATACTACAAGCCTGACCGTT 57.025 42.857 0.00 0.00 0.00 4.44
3097 3178 3.343617 TGCAAATACTACAAGCCTGACC 58.656 45.455 0.00 0.00 0.00 4.02
3098 3179 4.253685 TCTGCAAATACTACAAGCCTGAC 58.746 43.478 0.00 0.00 0.00 3.51
3099 3180 4.020218 ACTCTGCAAATACTACAAGCCTGA 60.020 41.667 0.00 0.00 0.00 3.86
3100 3181 4.256920 ACTCTGCAAATACTACAAGCCTG 58.743 43.478 0.00 0.00 0.00 4.85
3102 3183 5.175859 TGTACTCTGCAAATACTACAAGCC 58.824 41.667 0.00 0.00 0.00 4.35
3103 3184 5.292101 CCTGTACTCTGCAAATACTACAAGC 59.708 44.000 0.00 0.00 0.00 4.01
3105 3186 6.599356 TCCTGTACTCTGCAAATACTACAA 57.401 37.500 0.00 0.00 0.00 2.41
3106 3187 6.014925 TGTTCCTGTACTCTGCAAATACTACA 60.015 38.462 0.00 0.00 0.00 2.74
3107 3188 6.310711 GTGTTCCTGTACTCTGCAAATACTAC 59.689 42.308 0.00 0.00 0.00 2.73
3108 3189 6.395629 GTGTTCCTGTACTCTGCAAATACTA 58.604 40.000 0.00 0.00 0.00 1.82
3109 3190 5.238583 GTGTTCCTGTACTCTGCAAATACT 58.761 41.667 0.00 0.00 0.00 2.12
3110 3191 4.091509 CGTGTTCCTGTACTCTGCAAATAC 59.908 45.833 0.00 0.00 0.00 1.89
3111 3192 4.242475 CGTGTTCCTGTACTCTGCAAATA 58.758 43.478 0.00 0.00 0.00 1.40
3112 3193 3.067106 CGTGTTCCTGTACTCTGCAAAT 58.933 45.455 0.00 0.00 0.00 2.32
3113 3194 2.479837 CGTGTTCCTGTACTCTGCAAA 58.520 47.619 0.00 0.00 0.00 3.68
3114 3195 1.270094 CCGTGTTCCTGTACTCTGCAA 60.270 52.381 0.00 0.00 0.00 4.08
3115 3196 0.317160 CCGTGTTCCTGTACTCTGCA 59.683 55.000 0.00 0.00 0.00 4.41
3116 3197 0.601558 TCCGTGTTCCTGTACTCTGC 59.398 55.000 0.00 0.00 0.00 4.26
3117 3198 1.887198 ACTCCGTGTTCCTGTACTCTG 59.113 52.381 0.00 0.00 0.00 3.35
3118 3199 2.161030 GACTCCGTGTTCCTGTACTCT 58.839 52.381 0.00 0.00 0.00 3.24
3119 3200 2.161030 AGACTCCGTGTTCCTGTACTC 58.839 52.381 0.00 0.00 0.00 2.59
3120 3201 2.161030 GAGACTCCGTGTTCCTGTACT 58.839 52.381 0.00 0.00 0.00 2.73
3121 3202 2.161030 AGAGACTCCGTGTTCCTGTAC 58.839 52.381 0.00 0.00 0.00 2.90
3122 3203 2.581216 AGAGACTCCGTGTTCCTGTA 57.419 50.000 0.00 0.00 0.00 2.74
3123 3204 1.705873 AAGAGACTCCGTGTTCCTGT 58.294 50.000 0.00 0.00 0.00 4.00
3124 3205 2.035961 TGAAAGAGACTCCGTGTTCCTG 59.964 50.000 0.00 0.00 0.00 3.86
3125 3206 2.297597 CTGAAAGAGACTCCGTGTTCCT 59.702 50.000 0.00 0.00 34.07 3.36
3126 3207 2.036089 ACTGAAAGAGACTCCGTGTTCC 59.964 50.000 0.00 0.00 37.43 3.62
3127 3208 3.004944 AGACTGAAAGAGACTCCGTGTTC 59.995 47.826 0.00 0.00 37.43 3.18
3128 3209 2.959707 AGACTGAAAGAGACTCCGTGTT 59.040 45.455 0.00 0.00 37.43 3.32
3129 3210 2.294791 CAGACTGAAAGAGACTCCGTGT 59.705 50.000 0.00 0.00 37.43 4.49
3130 3211 2.554462 TCAGACTGAAAGAGACTCCGTG 59.446 50.000 1.64 0.00 37.43 4.94
3131 3212 2.865079 TCAGACTGAAAGAGACTCCGT 58.135 47.619 1.64 0.00 37.43 4.69
3132 3213 3.254657 ACTTCAGACTGAAAGAGACTCCG 59.745 47.826 18.26 6.56 35.73 4.63
3133 3214 4.864704 ACTTCAGACTGAAAGAGACTCC 57.135 45.455 18.26 0.00 35.73 3.85
3156 3241 2.433664 GTCACCCTAACACGGCGG 60.434 66.667 13.24 2.35 0.00 6.13
3166 3251 3.264450 AGGATTTTGATCTTCGTCACCCT 59.736 43.478 0.00 0.00 0.00 4.34
3338 3423 2.735762 GCTTACCCACATGACGAGACTC 60.736 54.545 0.00 0.00 0.00 3.36
3372 3457 3.440872 TGGTTATGCGTGTGGGTTTAATC 59.559 43.478 0.00 0.00 0.00 1.75
3386 3471 2.185004 ACACAGTGAGGTGGTTATGC 57.815 50.000 7.81 0.00 43.08 3.14
3438 3523 8.285394 AGCATGATGATATGATAACAACGTTTC 58.715 33.333 0.00 0.00 0.00 2.78
3478 3563 1.817099 CTGCGTCAGCCCAATCTCC 60.817 63.158 0.00 0.00 44.33 3.71
3486 3573 2.031163 AGACCAACTGCGTCAGCC 59.969 61.111 6.74 0.00 44.33 4.85
3495 3582 3.807622 CACATACGTCAAACAGACCAACT 59.192 43.478 0.00 0.00 44.66 3.16
3514 3601 1.934220 GATCGGAGTCGCCTGTCACA 61.934 60.000 0.00 0.00 36.13 3.58
3579 3666 1.300620 CCACCTCGTCGTGCTTCAA 60.301 57.895 0.00 0.00 32.10 2.69
3785 3914 4.516195 GCGTCCTCTTCTCCCCGC 62.516 72.222 0.00 0.00 0.00 6.13
3836 3965 0.957395 GGTAGGTCTCGTCGTCCACA 60.957 60.000 0.00 0.00 0.00 4.17
3969 4098 3.869272 GGATCGGCTGCAGCGTTG 61.869 66.667 31.19 22.78 43.26 4.10
4011 4140 9.468532 CCAGAAAGGAGAAGAAAATGTAAAAAG 57.531 33.333 0.00 0.00 41.22 2.27
4034 4163 5.163519 ACAAAAGACAACCAAACTCATCCAG 60.164 40.000 0.00 0.00 0.00 3.86
4110 4240 0.327480 TATCATGTCCCTGGGTGCCT 60.327 55.000 13.56 0.00 0.00 4.75
4135 4265 0.675837 CTCTGTGGGTGGCATGTCTG 60.676 60.000 0.00 0.00 0.00 3.51
4139 4269 1.619654 TTTTCTCTGTGGGTGGCATG 58.380 50.000 0.00 0.00 0.00 4.06
4221 4351 2.898729 AATCGAGATGAATCGTGGCT 57.101 45.000 0.00 0.00 43.20 4.75
4237 4367 9.056005 TCAGATAGCACACCATGTAAATAAATC 57.944 33.333 0.00 0.00 0.00 2.17
4238 4368 8.978874 TCAGATAGCACACCATGTAAATAAAT 57.021 30.769 0.00 0.00 0.00 1.40
4310 4501 3.328382 TTGATCTACGGACAACCTTGG 57.672 47.619 0.00 0.00 0.00 3.61
4555 4756 3.084039 TCATTTGCCTGACCTTGATGTC 58.916 45.455 0.00 0.00 35.77 3.06
4557 4758 4.730949 ATTCATTTGCCTGACCTTGATG 57.269 40.909 0.00 0.00 0.00 3.07
4560 4761 3.181483 GGCTATTCATTTGCCTGACCTTG 60.181 47.826 0.00 0.00 43.05 3.61
4623 4824 0.601558 CAGCTGCAAGGCAAGTGATT 59.398 50.000 0.00 0.00 38.41 2.57
4649 4850 3.255642 GGTGCAAAGAAACCTGATGCTTA 59.744 43.478 0.00 0.00 37.86 3.09
4650 4851 2.036346 GGTGCAAAGAAACCTGATGCTT 59.964 45.455 0.00 0.00 37.86 3.91
4651 4852 1.615392 GGTGCAAAGAAACCTGATGCT 59.385 47.619 0.00 0.00 37.86 3.79
4704 4905 2.045047 TCCTTGGAGATTGAGGAGACCT 59.955 50.000 0.00 0.00 34.74 3.85
4771 4972 3.621958 GCAAGGCTGAGAAGGAAGAGAAT 60.622 47.826 0.00 0.00 0.00 2.40
4884 5085 1.285023 CAGCAGTCAAGCACCTTGC 59.715 57.895 0.22 0.00 45.46 4.01


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

AutoCloner maintained by Alex Coulton.