Multiple sequence alignment - TraesCS3D01G268000

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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 TraesCS3D01G268000 chr3D 100.000 3127 0 0 1 3127 372313332 372316458 0.000000e+00 5775
1 TraesCS3D01G268000 chr3B 91.032 3044 161 51 1 3002 486376929 486379902 0.000000e+00 4006
2 TraesCS3D01G268000 chr3B 86.029 136 11 7 2991 3123 486379922 486380052 4.210000e-29 139
3 TraesCS3D01G268000 chr3A 90.667 2775 149 46 1 2726 493711101 493713814 0.000000e+00 3589
4 TraesCS3D01G268000 chr7B 82.971 276 41 6 966 1239 451656605 451656334 8.660000e-61 244
5 TraesCS3D01G268000 chr7B 80.952 252 37 10 1893 2140 451655876 451655632 4.120000e-44 189
6 TraesCS3D01G268000 chr7D 81.625 283 46 6 966 1245 434912262 434911983 2.430000e-56 230
7 TraesCS3D01G268000 chr7D 78.846 260 40 12 1893 2140 434911527 434911271 8.970000e-36 161
8 TraesCS3D01G268000 chr7D 89.764 127 10 3 1343 1468 75937422 75937546 3.230000e-35 159
9 TraesCS3D01G268000 chr7D 90.756 119 10 1 1346 1464 182605350 182605467 1.160000e-34 158
10 TraesCS3D01G268000 chr7A 81.362 279 42 8 966 1239 485200580 485200307 5.250000e-53 219
11 TraesCS3D01G268000 chr7A 80.408 245 39 7 1894 2131 485199801 485199559 8.910000e-41 178
12 TraesCS3D01G268000 chr5B 91.200 125 10 1 1345 1469 38365241 38365118 5.360000e-38 169
13 TraesCS3D01G268000 chr5B 92.174 115 8 1 1349 1463 691166914 691167027 8.970000e-36 161
14 TraesCS3D01G268000 chr2A 90.833 120 10 1 1344 1463 753527331 753527213 3.230000e-35 159
15 TraesCS3D01G268000 chr4B 90.756 119 10 1 1346 1464 254413365 254413248 1.160000e-34 158
16 TraesCS3D01G268000 chr6A 86.429 140 14 4 1346 1481 195645126 195645264 6.990000e-32 148
17 TraesCS3D01G268000 chr1D 92.632 95 7 0 1131 1225 463496711 463496617 1.510000e-28 137
18 TraesCS3D01G268000 chr1B 90.476 105 8 2 1123 1225 638930762 638930866 1.510000e-28 137


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 TraesCS3D01G268000 chr3D 372313332 372316458 3126 False 5775.0 5775 100.0000 1 3127 1 chr3D.!!$F1 3126
1 TraesCS3D01G268000 chr3B 486376929 486380052 3123 False 2072.5 4006 88.5305 1 3123 2 chr3B.!!$F1 3122
2 TraesCS3D01G268000 chr3A 493711101 493713814 2713 False 3589.0 3589 90.6670 1 2726 1 chr3A.!!$F1 2725
3 TraesCS3D01G268000 chr7B 451655632 451656605 973 True 216.5 244 81.9615 966 2140 2 chr7B.!!$R1 1174

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
412 431 0.170561 TCTCGGCAAGCTCTTACGAC 59.829 55.000 0.0 0.0 31.28 4.34 F
593 612 1.063912 TGAGTTGTGCTTCGTGCTTTG 59.936 47.619 5.0 0.0 43.37 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2177 0.039798 CAGTGCTGCAAAGACGCATT 60.040 50.000 2.77 0.0 42.06 3.56 R
2278 2407 1.002468 GGCATAACGCATAACAGGCAG 60.002 52.381 0.00 0.0 45.17 4.85 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
121 126 8.173542 TCTTTCCCGCTAAAAGAAAAACTAAT 57.826 30.769 3.43 0.00 39.22 1.73
163 168 1.895866 GCCCACTCTGTACTACCACCT 60.896 57.143 0.00 0.00 0.00 4.00
164 169 2.622452 GCCCACTCTGTACTACCACCTA 60.622 54.545 0.00 0.00 0.00 3.08
165 170 3.022406 CCCACTCTGTACTACCACCTAC 58.978 54.545 0.00 0.00 0.00 3.18
166 171 3.022406 CCACTCTGTACTACCACCTACC 58.978 54.545 0.00 0.00 0.00 3.18
167 172 3.308976 CCACTCTGTACTACCACCTACCT 60.309 52.174 0.00 0.00 0.00 3.08
168 173 3.695060 CACTCTGTACTACCACCTACCTG 59.305 52.174 0.00 0.00 0.00 4.00
169 174 3.288964 CTCTGTACTACCACCTACCTGG 58.711 54.545 0.00 0.00 42.93 4.45
170 175 2.921612 TCTGTACTACCACCTACCTGGA 59.078 50.000 0.00 0.00 39.71 3.86
171 176 3.053842 TCTGTACTACCACCTACCTGGAG 60.054 52.174 0.00 0.00 39.71 3.86
172 177 2.651334 TGTACTACCACCTACCTGGAGT 59.349 50.000 0.00 0.00 39.71 3.85
225 234 3.470709 CAGCCCACATGTAATAGTCCAG 58.529 50.000 0.00 0.00 0.00 3.86
408 427 1.899814 TCCTTTCTCGGCAAGCTCTTA 59.100 47.619 0.00 0.00 0.00 2.10
412 431 0.170561 TCTCGGCAAGCTCTTACGAC 59.829 55.000 0.00 0.00 31.28 4.34
496 515 4.391830 GTGTTTCTAGGTGCGAAATCATGA 59.608 41.667 0.00 0.00 33.45 3.07
498 517 5.647658 TGTTTCTAGGTGCGAAATCATGATT 59.352 36.000 15.36 15.36 33.45 2.57
501 520 5.427378 TCTAGGTGCGAAATCATGATTCAA 58.573 37.500 20.95 5.01 0.00 2.69
537 556 7.759886 TGTGTGTTACTAATATGTTGAGCTCTC 59.240 37.037 16.19 8.79 0.00 3.20
585 604 1.807142 GTTAGCCCTGAGTTGTGCTTC 59.193 52.381 0.00 0.00 35.34 3.86
593 612 1.063912 TGAGTTGTGCTTCGTGCTTTG 59.936 47.619 5.00 0.00 43.37 2.77
639 658 3.367932 TCGATGTGTTCTTCAATTCGCTC 59.632 43.478 0.00 0.00 34.70 5.03
749 768 5.839063 TGTGGCTAGTAAGGTAGAATAGCAT 59.161 40.000 4.73 0.00 42.67 3.79
802 821 4.500477 GTGGAGCATGCGATATTTTGTTTC 59.500 41.667 13.01 0.00 0.00 2.78
815 834 5.638596 ATTTTGTTTCGGGAAGGATACAC 57.361 39.130 0.00 0.00 41.41 2.90
831 850 6.925211 AGGATACACACTGGATGTAATATCG 58.075 40.000 0.00 0.00 40.64 2.92
886 905 4.759693 TCGTTGATGTTAAGCTTTCCACAT 59.240 37.500 3.20 11.12 32.41 3.21
1091 1111 6.909550 TTTGGCTCATTTACCTGTTTATGT 57.090 33.333 0.00 0.00 0.00 2.29
1365 1388 5.032846 TCATACTCCCTCAGTCTGGAATTT 58.967 41.667 0.00 0.00 36.43 1.82
1389 1412 9.868277 TTTCTTGTCGCATAAATGGATAAAAAT 57.132 25.926 0.00 0.00 0.00 1.82
1447 1470 7.335627 ACATCCATTTCTCCGACAAGTATTTA 58.664 34.615 0.00 0.00 0.00 1.40
1456 1479 5.853936 TCCGACAAGTATTTATGGATGGAG 58.146 41.667 0.00 0.00 0.00 3.86
1459 1482 5.454755 CGACAAGTATTTATGGATGGAGGGT 60.455 44.000 0.00 0.00 0.00 4.34
1516 1542 5.047306 TCGCTTTCTATGTTTTCTCTCTCCA 60.047 40.000 0.00 0.00 0.00 3.86
1554 1580 6.019479 GCTATGTCAGTCGTAAATTCCTCTTG 60.019 42.308 0.00 0.00 0.00 3.02
1707 1750 6.775939 ATCTTATTGTACATGCTGTCATCG 57.224 37.500 0.00 0.00 0.00 3.84
1770 1814 8.352942 CAGGAAAGGGAGTTGTATTTAATATGC 58.647 37.037 0.00 0.00 0.00 3.14
2046 2175 8.376889 TGTCATATCGCTTTATGCTAATTTCA 57.623 30.769 0.00 0.00 40.11 2.69
2048 2177 8.282592 GTCATATCGCTTTATGCTAATTTCACA 58.717 33.333 0.00 0.00 40.11 3.58
2052 2181 5.743398 TCGCTTTATGCTAATTTCACAATGC 59.257 36.000 0.00 0.00 40.11 3.56
2278 2407 4.833390 ACTTGAAAGTATGTCCCTACAGC 58.167 43.478 0.00 0.00 39.49 4.40
2308 2437 3.773860 TGCGTTATGCCAACCTATTTG 57.226 42.857 0.00 0.00 45.60 2.32
2344 2473 2.508300 GTCTCTCACTCTCTACCCCTCT 59.492 54.545 0.00 0.00 0.00 3.69
2345 2474 2.507886 TCTCTCACTCTCTACCCCTCTG 59.492 54.545 0.00 0.00 0.00 3.35
2362 2491 1.425066 TCTGCACCCCAAGTCAATCTT 59.575 47.619 0.00 0.00 36.75 2.40
2373 2502 8.386264 ACCCCAAGTCAATCTTATATGATAAGG 58.614 37.037 6.43 0.00 34.66 2.69
2433 2562 1.610522 GCATACTGACCCCATGAATGC 59.389 52.381 0.00 0.00 0.00 3.56
2434 2563 2.934887 CATACTGACCCCATGAATGCA 58.065 47.619 0.00 0.00 0.00 3.96
2444 2573 0.748450 CATGAATGCATGGACACCCC 59.252 55.000 5.67 0.00 46.45 4.95
2446 2575 1.294041 TGAATGCATGGACACCCCTA 58.706 50.000 0.00 0.00 35.38 3.53
2447 2576 1.064758 TGAATGCATGGACACCCCTAC 60.065 52.381 0.00 0.00 35.38 3.18
2448 2577 0.258774 AATGCATGGACACCCCTACC 59.741 55.000 0.00 0.00 35.38 3.18
2471 2606 5.186215 CCTCTATGAGCATCTGTCATCTGAT 59.814 44.000 0.00 0.00 36.11 2.90
2474 2609 7.773149 TCTATGAGCATCTGTCATCTGATATG 58.227 38.462 0.00 0.00 36.11 1.78
2512 2650 3.369052 CGGAGGAAAATGGTAGTAGTGCA 60.369 47.826 0.00 0.00 0.00 4.57
2542 2680 2.173569 GACTTATCCTGATGGGCTGGTT 59.826 50.000 0.00 0.00 36.96 3.67
2548 2686 1.380246 TGATGGGCTGGTTGCATCC 60.380 57.895 6.88 6.88 45.15 3.51
2603 2741 7.906527 CCAGTTGAGCAGAAAATTTTGAAAAAG 59.093 33.333 8.47 0.00 0.00 2.27
2628 2766 9.918630 AGTTGGAAATAAATTCAAGACATTCTG 57.081 29.630 0.00 0.00 39.98 3.02
2688 2839 5.754890 GCAAAGTTTCATTTGTGGATGTCTT 59.245 36.000 1.63 0.00 41.31 3.01
2727 2878 8.031864 TGATGTTCAAAAGTGCTTACAAAAAGA 58.968 29.630 0.00 0.00 0.00 2.52
2739 2890 7.653311 GTGCTTACAAAAAGAGGAAATGATTGT 59.347 33.333 0.00 0.00 34.31 2.71
2754 2913 2.869801 TGATTGTAATCAACCGATCGGC 59.130 45.455 33.62 15.88 42.11 5.54
2757 2916 1.593209 TAATCAACCGATCGGCCGC 60.593 57.895 33.62 6.46 39.32 6.53
2758 2917 2.023414 TAATCAACCGATCGGCCGCT 62.023 55.000 33.62 12.22 39.32 5.52
2765 2924 4.918201 GATCGGCCGCTCCCAAGG 62.918 72.222 23.51 0.00 0.00 3.61
2776 2935 2.046700 CCCAAGGTCGCCGCTTTA 60.047 61.111 0.00 0.00 0.00 1.85
2784 2943 1.209998 GTCGCCGCTTTATCTCTTCC 58.790 55.000 0.00 0.00 0.00 3.46
2785 2944 1.112113 TCGCCGCTTTATCTCTTCCT 58.888 50.000 0.00 0.00 0.00 3.36
2800 2959 7.738437 ATCTCTTCCTCTCTCAATCTTTCTT 57.262 36.000 0.00 0.00 0.00 2.52
2802 2961 6.047511 TCTTCCTCTCTCAATCTTTCTTGG 57.952 41.667 0.00 0.00 0.00 3.61
2836 2996 2.045045 CGGCTCCAGGATTTGCCA 60.045 61.111 16.59 0.00 45.13 4.92
2837 2997 1.454479 CGGCTCCAGGATTTGCCAT 60.454 57.895 16.59 0.00 45.13 4.40
2850 3010 3.058160 GCCATGAGCCGCAAGTGT 61.058 61.111 0.00 0.00 34.35 3.55
2851 3011 2.872557 CCATGAGCCGCAAGTGTG 59.127 61.111 0.00 0.00 0.00 3.82
2876 3039 1.039233 CCAAGCCACCCATCCATGTC 61.039 60.000 0.00 0.00 0.00 3.06
3002 3169 3.434319 GACGTCGGCGGTGGAGTA 61.434 66.667 16.39 0.00 43.45 2.59
3003 3170 2.981560 GACGTCGGCGGTGGAGTAA 61.982 63.158 16.39 0.00 43.45 2.24
3004 3171 2.259204 CGTCGGCGGTGGAGTAAA 59.741 61.111 7.21 0.00 0.00 2.01
3005 3172 1.373246 CGTCGGCGGTGGAGTAAAA 60.373 57.895 7.21 0.00 0.00 1.52
3006 3173 0.738412 CGTCGGCGGTGGAGTAAAAT 60.738 55.000 7.21 0.00 0.00 1.82
3007 3174 1.004595 GTCGGCGGTGGAGTAAAATC 58.995 55.000 7.21 0.00 0.00 2.17
3009 3176 0.725117 CGGCGGTGGAGTAAAATCAC 59.275 55.000 0.00 0.00 0.00 3.06
3010 3177 1.816074 GGCGGTGGAGTAAAATCACA 58.184 50.000 0.00 0.00 33.45 3.58
3011 3178 1.467342 GGCGGTGGAGTAAAATCACAC 59.533 52.381 0.00 0.00 33.45 3.82
3013 3180 2.812011 GCGGTGGAGTAAAATCACACTT 59.188 45.455 0.00 0.00 33.45 3.16
3014 3181 3.120304 GCGGTGGAGTAAAATCACACTTC 60.120 47.826 0.00 0.00 33.45 3.01
3016 3183 4.755123 CGGTGGAGTAAAATCACACTTCTT 59.245 41.667 0.00 0.00 33.45 2.52
3017 3184 5.238650 CGGTGGAGTAAAATCACACTTCTTT 59.761 40.000 0.00 0.00 33.45 2.52
3019 3186 7.570691 CGGTGGAGTAAAATCACACTTCTTTAC 60.571 40.741 0.00 0.00 35.44 2.01
3023 3219 6.849151 AGTAAAATCACACTTCTTTACCCCT 58.151 36.000 0.00 0.00 35.69 4.79
3024 3220 6.715264 AGTAAAATCACACTTCTTTACCCCTG 59.285 38.462 0.00 0.00 35.69 4.45
3026 3222 4.724279 ATCACACTTCTTTACCCCTGTT 57.276 40.909 0.00 0.00 0.00 3.16
3032 3228 2.507407 TCTTTACCCCTGTTCATGGC 57.493 50.000 0.00 0.00 0.00 4.40
3036 3232 3.727258 CCCCTGTTCATGGCCGGA 61.727 66.667 5.05 0.00 0.00 5.14
3049 3245 0.690762 GGCCGGATAATGCCTCCTTA 59.309 55.000 5.05 0.00 44.46 2.69
3054 3250 5.007682 GCCGGATAATGCCTCCTTATTTTA 58.992 41.667 5.05 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 44 0.178941 ATATTCGTACCCGAGCCCCT 60.179 55.000 0.00 0.00 45.24 4.79
43 45 0.037605 CATATTCGTACCCGAGCCCC 60.038 60.000 0.00 0.00 45.24 5.80
121 126 5.008316 GGCTTTCTTCACTCGGTTAGAAAAA 59.992 40.000 0.00 0.00 36.50 1.94
163 168 2.116238 GGGCTTATCACACTCCAGGTA 58.884 52.381 0.00 0.00 0.00 3.08
164 169 0.912486 GGGCTTATCACACTCCAGGT 59.088 55.000 0.00 0.00 0.00 4.00
165 170 0.911769 TGGGCTTATCACACTCCAGG 59.088 55.000 0.00 0.00 0.00 4.45
166 171 1.407437 GGTGGGCTTATCACACTCCAG 60.407 57.143 0.00 0.00 36.90 3.86
167 172 0.618458 GGTGGGCTTATCACACTCCA 59.382 55.000 0.00 0.00 36.90 3.86
168 173 0.912486 AGGTGGGCTTATCACACTCC 59.088 55.000 0.00 0.00 36.90 3.85
169 174 3.643792 AGATAGGTGGGCTTATCACACTC 59.356 47.826 0.00 0.00 36.49 3.51
170 175 3.658725 AGATAGGTGGGCTTATCACACT 58.341 45.455 0.00 0.00 36.49 3.55
171 176 5.337652 GGATAGATAGGTGGGCTTATCACAC 60.338 48.000 0.00 0.00 36.49 3.82
172 177 4.777896 GGATAGATAGGTGGGCTTATCACA 59.222 45.833 0.00 0.00 36.49 3.58
464 483 4.674623 CGCACCTAGAAACACTACGATCTT 60.675 45.833 0.00 0.00 0.00 2.40
537 556 1.032657 TCGAAAGGGAGGAGCTCGAG 61.033 60.000 8.45 8.45 33.87 4.04
585 604 2.979813 GGAAGTTTGCATACAAAGCACG 59.020 45.455 10.02 0.00 46.17 5.34
593 612 1.745653 GCCCAGAGGAAGTTTGCATAC 59.254 52.381 0.00 0.00 33.47 2.39
639 658 8.480133 AAGTATCCTAATACACCTAGGTTCTG 57.520 38.462 13.15 3.68 40.28 3.02
708 727 1.005867 CAAGCCCACAACACCATGC 60.006 57.895 0.00 0.00 0.00 4.06
749 768 2.342650 GCGCAGATGGCTTTTCCCA 61.343 57.895 0.30 0.00 41.67 4.37
802 821 1.191535 TCCAGTGTGTATCCTTCCCG 58.808 55.000 0.00 0.00 0.00 5.14
815 834 7.496529 AAATGTTCCGATATTACATCCAGTG 57.503 36.000 0.00 0.00 31.63 3.66
886 905 3.691575 TGGGCAATTGATTAACTTCGGA 58.308 40.909 10.34 0.00 0.00 4.55
1091 1111 0.469494 TTCAGGACACAGCAGAAGCA 59.531 50.000 0.00 0.00 45.49 3.91
1447 1470 7.397192 GCATTAATAAATACACCCTCCATCCAT 59.603 37.037 0.00 0.00 0.00 3.41
1456 1479 8.629158 TCACATCAAGCATTAATAAATACACCC 58.371 33.333 0.00 0.00 0.00 4.61
1469 1492 7.592533 GCGATACAAAATATCACATCAAGCATT 59.407 33.333 0.00 0.00 0.00 3.56
1493 1517 5.171476 TGGAGAGAGAAAACATAGAAAGCG 58.829 41.667 0.00 0.00 0.00 4.68
1516 1542 6.311445 CGACTGACATAGCAAAACTATCACTT 59.689 38.462 0.00 0.00 39.71 3.16
1554 1580 8.732746 ATTACAGGGTAATGACATAACAAGAC 57.267 34.615 1.09 0.00 0.00 3.01
1699 1742 0.379669 GCCTTTCATGGCGATGACAG 59.620 55.000 15.66 15.66 43.74 3.51
2046 2175 0.318107 GTGCTGCAAAGACGCATTGT 60.318 50.000 2.77 0.00 42.06 2.71
2048 2177 0.039798 CAGTGCTGCAAAGACGCATT 60.040 50.000 2.77 0.00 42.06 3.56
2278 2407 1.002468 GGCATAACGCATAACAGGCAG 60.002 52.381 0.00 0.00 45.17 4.85
2308 2437 5.667175 GTGAGAGACGTGTCACAAAAATAC 58.333 41.667 14.09 0.00 44.60 1.89
2344 2473 3.737559 ATAAGATTGACTTGGGGTGCA 57.262 42.857 0.00 0.00 39.38 4.57
2345 2474 5.376625 TCATATAAGATTGACTTGGGGTGC 58.623 41.667 0.00 0.00 39.38 5.01
2390 2519 5.518847 GCTCGTTTGCATCTATACTGTGTTA 59.481 40.000 0.00 0.00 0.00 2.41
2433 2562 2.471815 TAGAGGTAGGGGTGTCCATG 57.528 55.000 0.00 0.00 38.24 3.66
2434 2563 2.522705 TCATAGAGGTAGGGGTGTCCAT 59.477 50.000 0.00 0.00 38.24 3.41
2437 2566 1.964933 GCTCATAGAGGTAGGGGTGTC 59.035 57.143 0.00 0.00 0.00 3.67
2440 2569 2.452823 AGATGCTCATAGAGGTAGGGGT 59.547 50.000 0.00 0.00 0.00 4.95
2441 2570 2.830923 CAGATGCTCATAGAGGTAGGGG 59.169 54.545 0.00 0.00 0.00 4.79
2442 2571 3.505386 ACAGATGCTCATAGAGGTAGGG 58.495 50.000 0.00 0.00 0.00 3.53
2443 2572 4.148079 TGACAGATGCTCATAGAGGTAGG 58.852 47.826 0.00 0.00 0.00 3.18
2444 2573 5.711506 AGATGACAGATGCTCATAGAGGTAG 59.288 44.000 0.00 0.00 0.00 3.18
2446 2575 4.281435 CAGATGACAGATGCTCATAGAGGT 59.719 45.833 0.00 0.00 0.00 3.85
2447 2576 4.523558 TCAGATGACAGATGCTCATAGAGG 59.476 45.833 0.00 0.00 0.00 3.69
2448 2577 5.708877 TCAGATGACAGATGCTCATAGAG 57.291 43.478 0.00 0.00 0.00 2.43
2471 2606 3.118075 TCCGGCAATGTTCATTCTCCATA 60.118 43.478 0.00 0.72 0.00 2.74
2474 2609 1.672881 CTCCGGCAATGTTCATTCTCC 59.327 52.381 0.00 0.44 0.00 3.71
2542 2680 7.363705 CCATAAGTTCACAATTTTAGGGATGCA 60.364 37.037 0.00 0.00 30.64 3.96
2548 2686 8.034215 TGCATTCCATAAGTTCACAATTTTAGG 58.966 33.333 0.00 0.00 0.00 2.69
2727 2878 6.017934 CGATCGGTTGATTACAATCATTTCCT 60.018 38.462 7.38 0.00 44.27 3.36
2739 2890 1.593209 GCGGCCGATCGGTTGATTA 60.593 57.895 33.33 0.00 34.09 1.75
2748 2899 4.918201 CCTTGGGAGCGGCCGATC 62.918 72.222 34.47 34.47 37.63 3.69
2757 2916 2.515996 TAAAGCGGCGACCTTGGGAG 62.516 60.000 12.98 0.00 0.00 4.30
2758 2917 1.906105 ATAAAGCGGCGACCTTGGGA 61.906 55.000 12.98 0.00 0.00 4.37
2765 2924 1.202428 AGGAAGAGATAAAGCGGCGAC 60.202 52.381 12.98 1.23 0.00 5.19
2772 2931 9.533253 GAAAGATTGAGAGAGGAAGAGATAAAG 57.467 37.037 0.00 0.00 0.00 1.85
2776 2935 7.364939 CCAAGAAAGATTGAGAGAGGAAGAGAT 60.365 40.741 0.00 0.00 31.55 2.75
2784 2943 7.558604 AGAAGATCCAAGAAAGATTGAGAGAG 58.441 38.462 0.00 0.00 31.55 3.20
2785 2944 7.179872 TGAGAAGATCCAAGAAAGATTGAGAGA 59.820 37.037 0.00 0.00 31.55 3.10
2800 2959 2.105006 GCTGCAAGTGAGAAGATCCA 57.895 50.000 0.00 0.00 35.30 3.41
2852 3012 4.431131 ATGGGTGGCTTGGAGCGG 62.431 66.667 0.00 0.00 43.62 5.52
2854 3014 2.440980 GGATGGGTGGCTTGGAGC 60.441 66.667 0.00 0.00 41.46 4.70
2856 3016 1.307309 CATGGATGGGTGGCTTGGA 59.693 57.895 0.00 0.00 0.00 3.53
2857 3017 1.000739 ACATGGATGGGTGGCTTGG 59.999 57.895 0.00 0.00 0.00 3.61
2876 3039 2.420022 CGGCTAAACCTCTCAACAATGG 59.580 50.000 0.00 0.00 35.61 3.16
2915 3078 4.742201 CTGGCCACACCTCCGTCG 62.742 72.222 0.00 0.00 40.22 5.12
2941 3104 1.001181 GGTGGCCGACTTGTAACACTA 59.999 52.381 0.00 0.00 0.00 2.74
2942 3105 0.250166 GGTGGCCGACTTGTAACACT 60.250 55.000 0.00 0.00 0.00 3.55
2989 3156 0.609151 TGATTTTACTCCACCGCCGA 59.391 50.000 0.00 0.00 0.00 5.54
3002 3169 5.454966 ACAGGGGTAAAGAAGTGTGATTTT 58.545 37.500 0.00 0.00 0.00 1.82
3003 3170 5.061721 ACAGGGGTAAAGAAGTGTGATTT 57.938 39.130 0.00 0.00 0.00 2.17
3004 3171 4.724279 ACAGGGGTAAAGAAGTGTGATT 57.276 40.909 0.00 0.00 0.00 2.57
3005 3172 4.104102 TGAACAGGGGTAAAGAAGTGTGAT 59.896 41.667 0.00 0.00 0.00 3.06
3006 3173 3.456644 TGAACAGGGGTAAAGAAGTGTGA 59.543 43.478 0.00 0.00 0.00 3.58
3007 3174 3.815809 TGAACAGGGGTAAAGAAGTGTG 58.184 45.455 0.00 0.00 0.00 3.82
3009 3176 3.758554 CCATGAACAGGGGTAAAGAAGTG 59.241 47.826 0.00 0.00 0.00 3.16
3010 3177 3.814316 GCCATGAACAGGGGTAAAGAAGT 60.814 47.826 7.58 0.00 31.86 3.01
3011 3178 2.755103 GCCATGAACAGGGGTAAAGAAG 59.245 50.000 7.58 0.00 31.86 2.85
3013 3180 1.005450 GGCCATGAACAGGGGTAAAGA 59.995 52.381 0.00 0.00 31.86 2.52
3014 3181 1.474330 GGCCATGAACAGGGGTAAAG 58.526 55.000 0.00 0.00 31.86 1.85
3016 3183 1.301623 CGGCCATGAACAGGGGTAA 59.698 57.895 2.24 0.00 31.86 2.85
3017 3184 2.675242 CCGGCCATGAACAGGGGTA 61.675 63.158 2.24 0.00 31.86 3.69
3019 3186 1.705002 TATCCGGCCATGAACAGGGG 61.705 60.000 2.24 0.00 31.86 4.79
3023 3219 1.317613 GCATTATCCGGCCATGAACA 58.682 50.000 2.24 0.00 0.00 3.18
3032 3228 7.703058 AATAAAATAAGGAGGCATTATCCGG 57.297 36.000 0.00 0.00 42.02 5.14
3046 3242 9.444534 GGGTTGTTGTTGCAAAAATAAAATAAG 57.555 29.630 12.55 0.00 0.00 1.73
3049 3245 7.121907 ACAGGGTTGTTGTTGCAAAAATAAAAT 59.878 29.630 12.55 0.58 32.28 1.82
3054 3250 3.949132 ACAGGGTTGTTGTTGCAAAAAT 58.051 36.364 5.11 0.00 32.28 1.82


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

AutoCloner maintained by Alex Coulton.