Multiple sequence alignment - TraesCS3A01G103700

Loading Multiple Alignment...

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 TraesCS3A01G103700 chr3A 100.000 5413 0 0 1 5413 67151166 67156578 0.000000e+00 9997
1 TraesCS3A01G103700 chr3D 95.075 5178 180 37 271 5413 58113470 58118607 0.000000e+00 8080
2 TraesCS3A01G103700 chr3D 96.154 104 4 0 1 104 58113198 58113301 2.590000e-38 171
3 TraesCS3A01G103700 chr3B 94.864 2687 92 12 2737 5413 91431932 91434582 0.000000e+00 4156
4 TraesCS3A01G103700 chr3B 92.801 1903 90 22 190 2071 91429008 91430884 0.000000e+00 2712
5 TraesCS3A01G103700 chr3B 96.469 623 20 2 2055 2677 91431064 91431684 0.000000e+00 1027
6 TraesCS3A01G103700 chr3B 89.634 164 9 5 1 156 91428756 91428919 9.190000e-48 202


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 TraesCS3A01G103700 chr3A 67151166 67156578 5412 False 9997.00 9997 100.0000 1 5413 1 chr3A.!!$F1 5412
1 TraesCS3A01G103700 chr3D 58113198 58118607 5409 False 4125.50 8080 95.6145 1 5413 2 chr3D.!!$F1 5412
2 TraesCS3A01G103700 chr3B 91428756 91434582 5826 False 2024.25 4156 93.4420 1 5413 4 chr3B.!!$F1 5412

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
623 705 0.179029 CCTCCCGCCGTGGATAATTT 60.179 55.000 0.00 0.0 42.00 1.82 F
811 898 0.603975 GGAGCTCGCCTGTTGAACTT 60.604 55.000 7.83 0.0 0.00 2.66 F
1082 1181 1.517832 CTCCGCTCCACACCCTAAG 59.482 63.158 0.00 0.0 0.00 2.18 F
2237 2539 1.000938 GCCTCTGTTTCCACTTGCTTG 60.001 52.381 0.00 0.0 0.00 4.01 F
3426 3917 1.502231 CACAGTTCGTTGTGCTAGCT 58.498 50.000 17.23 0.0 41.65 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 2177 0.668535 AGGAAAACAAAGGCAGACGC 59.331 50.000 0.00 0.0 37.44 5.19 R
2221 2523 1.035139 AGGCAAGCAAGTGGAAACAG 58.965 50.000 0.00 0.0 44.46 3.16 R
3028 3518 2.039879 TGTGGTAGGAAAAGGAAGAGGC 59.960 50.000 0.00 0.0 0.00 4.70 R
3636 4127 2.235155 TGGTTCAGTATTAAGGCGCTGA 59.765 45.455 7.64 0.0 36.35 4.26 R
5001 5503 0.392461 TCCTATGTCGGGCAAACAGC 60.392 55.000 0.00 0.0 44.65 4.40 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
38 39 3.333680 ACCACTTCTCAAACCCCATGTAT 59.666 43.478 0.00 0.00 0.00 2.29
62 63 5.348724 TGTGCTCTTCTTTGCTAATACGAAG 59.651 40.000 0.00 3.16 34.03 3.79
132 140 4.085733 TGTAGTAACTACACGGCCCTAAA 58.914 43.478 0.00 0.00 41.33 1.85
157 166 1.227645 GCAGGCACAGCGATATGGA 60.228 57.895 0.00 0.00 0.00 3.41
159 168 0.940126 CAGGCACAGCGATATGGAAC 59.060 55.000 0.00 0.00 0.00 3.62
165 174 3.871594 GCACAGCGATATGGAACTAGTTT 59.128 43.478 10.02 0.00 0.00 2.66
168 177 4.804139 ACAGCGATATGGAACTAGTTTTCG 59.196 41.667 10.02 13.59 0.00 3.46
170 179 5.041940 AGCGATATGGAACTAGTTTTCGTC 58.958 41.667 10.02 9.61 0.00 4.20
175 184 7.063074 CGATATGGAACTAGTTTTCGTCAAGTT 59.937 37.037 10.02 0.00 33.26 2.66
176 185 5.978934 TGGAACTAGTTTTCGTCAAGTTC 57.021 39.130 10.02 5.22 43.32 3.01
177 186 5.667466 TGGAACTAGTTTTCGTCAAGTTCT 58.333 37.500 10.02 0.00 43.48 3.01
178 187 5.751990 TGGAACTAGTTTTCGTCAAGTTCTC 59.248 40.000 10.02 4.92 43.48 2.87
179 188 5.107951 GGAACTAGTTTTCGTCAAGTTCTCG 60.108 44.000 10.02 0.00 43.48 4.04
181 190 5.770417 ACTAGTTTTCGTCAAGTTCTCGAT 58.230 37.500 0.00 0.00 33.72 3.59
182 191 4.974103 AGTTTTCGTCAAGTTCTCGATG 57.026 40.909 0.00 0.00 33.72 3.84
184 193 4.444720 AGTTTTCGTCAAGTTCTCGATGAC 59.555 41.667 6.11 6.11 39.98 3.06
185 194 2.631418 TCGTCAAGTTCTCGATGACC 57.369 50.000 9.82 0.00 40.20 4.02
186 195 1.883926 TCGTCAAGTTCTCGATGACCA 59.116 47.619 9.82 0.00 40.20 4.02
187 196 2.095212 TCGTCAAGTTCTCGATGACCAG 60.095 50.000 9.82 0.00 40.20 4.00
192 264 3.584406 AGTTCTCGATGACCAGTTCTG 57.416 47.619 0.00 0.00 0.00 3.02
206 278 4.943705 ACCAGTTCTGTATGTAATTGCCTG 59.056 41.667 0.00 0.00 0.00 4.85
207 279 5.185454 CCAGTTCTGTATGTAATTGCCTGA 58.815 41.667 0.00 0.00 0.00 3.86
262 334 2.203983 TGCCAGAGCTTCAGGGGA 60.204 61.111 0.00 0.00 40.80 4.81
263 335 1.617536 TGCCAGAGCTTCAGGGGAT 60.618 57.895 0.00 0.00 40.80 3.85
302 374 2.509916 GGGATGGCAGAGCTGAGG 59.490 66.667 0.85 0.00 0.00 3.86
308 380 2.730524 GGCAGAGCTGAGGGAGGAC 61.731 68.421 0.85 0.00 0.00 3.85
312 384 0.324275 AGAGCTGAGGGAGGACAGAC 60.324 60.000 0.00 0.00 36.38 3.51
324 400 1.834263 AGGACAGACAGATACCTTGGC 59.166 52.381 0.00 0.00 0.00 4.52
597 679 5.479306 CCGTCGAGGATACAAATGGATAAT 58.521 41.667 6.70 0.00 45.00 1.28
598 680 6.627243 CCGTCGAGGATACAAATGGATAATA 58.373 40.000 6.70 0.00 45.00 0.98
599 681 7.094631 CCGTCGAGGATACAAATGGATAATAA 58.905 38.462 6.70 0.00 45.00 1.40
620 702 3.857038 GCCTCCCGCCGTGGATAA 61.857 66.667 0.00 0.00 42.00 1.75
623 705 0.179029 CCTCCCGCCGTGGATAATTT 60.179 55.000 0.00 0.00 42.00 1.82
627 709 1.170290 CCGCCGTGGATAATTTCCCC 61.170 60.000 0.00 0.00 44.77 4.81
629 711 1.605753 GCCGTGGATAATTTCCCCTC 58.394 55.000 0.00 0.00 44.77 4.30
677 764 0.607489 ACCTGGCAGTGCAGTCATTC 60.607 55.000 18.61 0.00 0.00 2.67
681 768 0.682209 GGCAGTGCAGTCATTCCCAT 60.682 55.000 18.61 0.00 0.00 4.00
717 804 4.021102 AGACATGGGAAGACGTTTCATT 57.979 40.909 0.00 0.00 0.00 2.57
752 839 3.420300 TTTGTGGGAAATACGCCTACA 57.580 42.857 0.00 0.00 43.90 2.74
758 845 2.285977 GGAAATACGCCTACAAGGGTG 58.714 52.381 0.00 0.00 42.11 4.61
772 859 1.561643 AGGGTGAAATCTCTCGAGCA 58.438 50.000 7.81 0.00 0.00 4.26
811 898 0.603975 GGAGCTCGCCTGTTGAACTT 60.604 55.000 7.83 0.00 0.00 2.66
920 1019 4.951963 GCCGAATCGAGCCCTCCG 62.952 72.222 3.36 0.00 0.00 4.63
1074 1173 3.766691 TAACCCGCTCCGCTCCAC 61.767 66.667 0.00 0.00 0.00 4.02
1082 1181 1.517832 CTCCGCTCCACACCCTAAG 59.482 63.158 0.00 0.00 0.00 2.18
1089 1188 1.906574 CTCCACACCCTAAGCCTAACA 59.093 52.381 0.00 0.00 0.00 2.41
1091 1190 1.679032 CCACACCCTAAGCCTAACAGC 60.679 57.143 0.00 0.00 0.00 4.40
1442 1546 4.069232 CTTCTCTCCCCGTGCGCA 62.069 66.667 5.66 5.66 0.00 6.09
1466 1570 2.426738 TGTTGTGTTTCAGGCTTTCAGG 59.573 45.455 0.00 0.00 0.00 3.86
1475 1579 1.661509 GGCTTTCAGGCGCACAAAC 60.662 57.895 10.83 0.00 0.00 2.93
1530 1634 5.120674 TCTCGTTAGCATCTGTGTTGAATTG 59.879 40.000 0.00 0.00 0.00 2.32
1554 1658 6.148150 TGCTTAAAATCGAATAACAGGAACGT 59.852 34.615 0.00 0.00 0.00 3.99
1563 1667 6.015504 CGAATAACAGGAACGTCTTCATTTG 58.984 40.000 0.00 0.00 0.00 2.32
1710 1814 2.143876 TAGCTGATTGGGAAAAGGCC 57.856 50.000 0.00 0.00 0.00 5.19
1812 1916 8.890472 AGTAATCAACAATAGGATATTAGGGCA 58.110 33.333 0.00 0.00 0.00 5.36
1913 2019 7.255491 TGCTTTGAAGATACTTGATGCATAG 57.745 36.000 0.00 0.00 0.00 2.23
1914 2020 6.825213 TGCTTTGAAGATACTTGATGCATAGT 59.175 34.615 0.00 2.81 0.00 2.12
1915 2021 7.986889 TGCTTTGAAGATACTTGATGCATAGTA 59.013 33.333 10.93 10.93 0.00 1.82
2071 2177 6.248433 AGCACCATATTATGATACCCTTTGG 58.752 40.000 5.21 0.00 37.80 3.28
2076 2378 4.706842 ATTATGATACCCTTTGGCGTCT 57.293 40.909 0.00 0.00 33.59 4.18
2148 2450 9.724839 GTATAAAACTGTGCTGTTTGTTTAAGA 57.275 29.630 7.72 0.00 39.71 2.10
2221 2523 4.070630 AGCTTTATCATCTCACAGCCTC 57.929 45.455 0.00 0.00 0.00 4.70
2233 2535 1.605710 CACAGCCTCTGTTTCCACTTG 59.394 52.381 0.00 0.00 42.59 3.16
2237 2539 1.000938 GCCTCTGTTTCCACTTGCTTG 60.001 52.381 0.00 0.00 0.00 4.01
2788 3278 9.220767 AGGATTTTCTGTTTGTCTATACTCAAC 57.779 33.333 0.00 0.00 0.00 3.18
2915 3405 6.312426 CGCCAGGAAGACTAATTGATATGATC 59.688 42.308 0.00 0.00 0.00 2.92
3017 3507 9.748708 TTTGAACCTCAGATTAAGAAAATTGTG 57.251 29.630 0.00 0.00 0.00 3.33
3027 3517 9.793259 AGATTAAGAAAATTGTGTCTCAGGTAA 57.207 29.630 0.00 0.00 0.00 2.85
3046 3536 3.722908 AAGCCTCTTCCTTTTCCTACC 57.277 47.619 0.00 0.00 0.00 3.18
3064 3554 5.650266 TCCTACCACACGATTTATTGCATTT 59.350 36.000 0.00 0.00 0.00 2.32
3065 3555 6.824196 TCCTACCACACGATTTATTGCATTTA 59.176 34.615 0.00 0.00 0.00 1.40
3071 3561 7.415765 CCACACGATTTATTGCATTTAAGGGTA 60.416 37.037 0.00 0.00 0.00 3.69
3072 3562 7.971168 CACACGATTTATTGCATTTAAGGGTAA 59.029 33.333 0.00 0.00 0.00 2.85
3426 3917 1.502231 CACAGTTCGTTGTGCTAGCT 58.498 50.000 17.23 0.00 41.65 3.32
3542 4033 8.619546 AGAACTGAAAGCTAATCATGCTATTTC 58.380 33.333 2.87 0.00 40.22 2.17
3848 4339 4.515191 TGGGTTCTTTCTGAATTCAAGTCG 59.485 41.667 9.88 0.00 36.99 4.18
3878 4369 4.282195 AGCCCTATTATGACAGCTACTGAC 59.718 45.833 0.78 0.00 35.18 3.51
3916 4407 5.927115 GCTTAGGTATACAGAAATTCCCTCG 59.073 44.000 5.01 0.00 0.00 4.63
4159 4650 5.643379 TTAGCATTTTAGTTGAAGCTGGG 57.357 39.130 0.00 0.00 33.83 4.45
4237 4728 5.782893 TGGGTAAGTTTTCTGTTGGATTG 57.217 39.130 0.00 0.00 0.00 2.67
4243 4734 7.279981 GGTAAGTTTTCTGTTGGATTGCTTTTT 59.720 33.333 0.00 0.00 0.00 1.94
4309 4800 6.212589 ACCCATTATTTTGTTTACCCCAAGAG 59.787 38.462 0.00 0.00 0.00 2.85
4358 4849 8.416329 AGTTGGGTCTGATTATTATTGCATTTC 58.584 33.333 0.00 0.00 0.00 2.17
4382 4873 4.617067 GCAGGTCATCGTGATAGATACAGG 60.617 50.000 0.00 0.00 0.00 4.00
4487 4979 6.484364 TGATCATGTATTTCTGGCTCACTA 57.516 37.500 0.00 0.00 0.00 2.74
4513 5005 3.488778 TTTGGCTAGTGTCCGGTAAAA 57.511 42.857 0.00 0.00 0.00 1.52
4541 5033 9.707957 TGGATTTATTTACTTTGGATACCATGT 57.292 29.630 0.00 0.00 31.53 3.21
4557 5049 3.130340 ACCATGTTGTGTTGACTGAAACC 59.870 43.478 0.00 0.00 0.00 3.27
4559 5051 4.353737 CATGTTGTGTTGACTGAAACCTG 58.646 43.478 0.00 0.00 0.00 4.00
4688 5181 4.279169 GGTCCCATCAATGTCAATACATGG 59.721 45.833 0.00 0.00 45.79 3.66
4714 5207 7.269724 GCGTAATTTATTTCCATAATACCGCAC 59.730 37.037 0.00 0.00 33.17 5.34
4784 5277 3.206150 TGTGCAGTTCCTCTTCTGTTTC 58.794 45.455 0.00 0.00 34.57 2.78
4798 5291 5.590259 TCTTCTGTTTCTTTTCCTCTTGTGG 59.410 40.000 0.00 0.00 0.00 4.17
4802 5295 5.751586 TGTTTCTTTTCCTCTTGTGGTACT 58.248 37.500 0.00 0.00 0.00 2.73
4829 5322 6.538742 GCACCACTAATGAGAAATAGCTGTTA 59.461 38.462 0.00 0.00 0.00 2.41
4886 5379 3.267483 CGATCGGTACAGTGGGATTTTT 58.733 45.455 7.38 0.00 0.00 1.94
4980 5482 3.535561 AGCATTGTTCGAACTAGATGGG 58.464 45.455 27.32 11.75 0.00 4.00
4981 5483 3.197766 AGCATTGTTCGAACTAGATGGGA 59.802 43.478 27.32 3.22 0.00 4.37
4990 5492 5.394738 TCGAACTAGATGGGAATGATAGGT 58.605 41.667 0.00 0.00 0.00 3.08
4991 5493 5.243954 TCGAACTAGATGGGAATGATAGGTG 59.756 44.000 0.00 0.00 0.00 4.00
4992 5494 5.011125 CGAACTAGATGGGAATGATAGGTGT 59.989 44.000 0.00 0.00 0.00 4.16
4993 5495 6.208797 CGAACTAGATGGGAATGATAGGTGTA 59.791 42.308 0.00 0.00 0.00 2.90
4994 5496 6.919775 ACTAGATGGGAATGATAGGTGTAC 57.080 41.667 0.00 0.00 0.00 2.90
4995 5497 6.625267 ACTAGATGGGAATGATAGGTGTACT 58.375 40.000 0.00 0.00 0.00 2.73
4996 5498 5.815233 AGATGGGAATGATAGGTGTACTG 57.185 43.478 0.00 0.00 0.00 2.74
4997 5499 5.467738 AGATGGGAATGATAGGTGTACTGA 58.532 41.667 0.00 0.00 0.00 3.41
4998 5500 6.087456 AGATGGGAATGATAGGTGTACTGAT 58.913 40.000 0.00 0.00 0.00 2.90
4999 5501 6.560304 AGATGGGAATGATAGGTGTACTGATT 59.440 38.462 0.00 0.00 0.00 2.57
5000 5502 6.575244 TGGGAATGATAGGTGTACTGATTT 57.425 37.500 0.00 0.00 0.00 2.17
5001 5503 6.356556 TGGGAATGATAGGTGTACTGATTTG 58.643 40.000 0.00 0.00 0.00 2.32
5002 5504 5.239525 GGGAATGATAGGTGTACTGATTTGC 59.760 44.000 0.00 0.00 0.00 3.68
5124 5639 6.343716 TCTTTTGCTTAGATTTTGCATGGA 57.656 33.333 0.00 0.00 36.55 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 4.816392 TCGTATTAGCAAAGAAGAGCACA 58.184 39.130 0.00 0.00 0.00 4.57
62 63 4.619973 TCTGTCAATTGATTGTTGGTTGC 58.380 39.130 12.12 0.00 38.84 4.17
126 127 2.027192 TGTGCCTGCTCTAGTTTTAGGG 60.027 50.000 0.00 0.00 0.00 3.53
132 140 1.079543 CGCTGTGCCTGCTCTAGTT 60.080 57.895 0.00 0.00 0.00 2.24
150 159 7.829378 ACTTGACGAAAACTAGTTCCATATC 57.171 36.000 8.95 4.49 0.00 1.63
157 166 5.585390 TCGAGAACTTGACGAAAACTAGTT 58.415 37.500 1.12 1.12 36.44 2.24
159 168 5.856986 TCATCGAGAACTTGACGAAAACTAG 59.143 40.000 0.00 0.00 39.38 2.57
165 174 2.295070 TGGTCATCGAGAACTTGACGAA 59.705 45.455 9.37 0.00 40.49 3.85
168 177 3.305398 ACTGGTCATCGAGAACTTGAC 57.695 47.619 7.43 7.43 39.19 3.18
170 179 3.677121 CAGAACTGGTCATCGAGAACTTG 59.323 47.826 0.00 0.00 34.06 3.16
175 184 4.017126 ACATACAGAACTGGTCATCGAGA 58.983 43.478 6.76 0.00 34.19 4.04
176 185 4.377839 ACATACAGAACTGGTCATCGAG 57.622 45.455 6.76 0.00 34.19 4.04
177 186 5.907866 TTACATACAGAACTGGTCATCGA 57.092 39.130 6.76 0.00 34.19 3.59
178 187 6.510157 GCAATTACATACAGAACTGGTCATCG 60.510 42.308 6.76 0.00 34.19 3.84
179 188 6.238484 GGCAATTACATACAGAACTGGTCATC 60.238 42.308 6.76 0.00 34.19 2.92
181 190 4.941263 GGCAATTACATACAGAACTGGTCA 59.059 41.667 6.76 0.00 34.19 4.02
182 191 5.065218 CAGGCAATTACATACAGAACTGGTC 59.935 44.000 6.76 0.00 34.19 4.02
184 193 5.185454 TCAGGCAATTACATACAGAACTGG 58.815 41.667 6.76 0.00 34.19 4.00
185 194 6.932356 ATCAGGCAATTACATACAGAACTG 57.068 37.500 0.00 0.00 0.00 3.16
186 195 6.992715 GGTATCAGGCAATTACATACAGAACT 59.007 38.462 0.00 0.00 0.00 3.01
187 196 6.765989 TGGTATCAGGCAATTACATACAGAAC 59.234 38.462 0.00 0.00 0.00 3.01
192 264 6.513393 GCAGTTGGTATCAGGCAATTACATAC 60.513 42.308 0.00 0.00 0.00 2.39
206 278 2.789409 AACTGGAGGCAGTTGGTATC 57.211 50.000 0.00 0.00 43.08 2.24
250 322 2.168728 ACGTTCTAATCCCCTGAAGCTC 59.831 50.000 0.00 0.00 0.00 4.09
262 334 2.423538 GCCATTTGCTCCACGTTCTAAT 59.576 45.455 0.00 0.00 36.87 1.73
263 335 1.810151 GCCATTTGCTCCACGTTCTAA 59.190 47.619 0.00 0.00 36.87 2.10
302 374 2.432510 CCAAGGTATCTGTCTGTCCTCC 59.567 54.545 0.00 0.00 0.00 4.30
308 380 1.139853 GAGGGCCAAGGTATCTGTCTG 59.860 57.143 6.18 0.00 0.00 3.51
312 384 1.227674 GCGAGGGCCAAGGTATCTG 60.228 63.158 6.18 0.00 0.00 2.90
467 543 2.124151 GCCGCCTGGGACATGAAT 60.124 61.111 0.00 0.00 38.20 2.57
620 702 2.237392 CGAACAGAGGAAGAGGGGAAAT 59.763 50.000 0.00 0.00 0.00 2.17
623 705 1.258445 GCGAACAGAGGAAGAGGGGA 61.258 60.000 0.00 0.00 0.00 4.81
627 709 1.807573 GCCGCGAACAGAGGAAGAG 60.808 63.158 8.23 0.00 43.02 2.85
629 711 2.815647 GGCCGCGAACAGAGGAAG 60.816 66.667 8.23 0.00 43.02 3.46
677 764 3.063045 GTCTAACGGAAGCGTAAAATGGG 59.937 47.826 0.00 0.00 0.00 4.00
681 768 3.680937 CCATGTCTAACGGAAGCGTAAAA 59.319 43.478 0.00 0.00 0.00 1.52
717 804 2.339418 CACAAATACGCAACCCGACTA 58.661 47.619 0.00 0.00 41.02 2.59
752 839 1.902508 TGCTCGAGAGATTTCACCCTT 59.097 47.619 18.75 0.00 40.84 3.95
758 845 2.541999 CGGGTAGTGCTCGAGAGATTTC 60.542 54.545 18.75 0.00 45.67 2.17
772 859 2.125269 GTGCGGCATTCGGGTAGT 60.125 61.111 5.72 0.00 39.69 2.73
1074 1173 2.014068 GCTGCTGTTAGGCTTAGGGTG 61.014 57.143 0.00 0.00 0.00 4.61
1082 1181 1.120530 TACTAGGGCTGCTGTTAGGC 58.879 55.000 0.00 0.00 42.08 3.93
1089 1188 1.344496 ACCAGGATTACTAGGGCTGCT 60.344 52.381 0.00 0.00 0.00 4.24
1091 1190 3.041946 AGAACCAGGATTACTAGGGCTG 58.958 50.000 0.00 0.00 0.00 4.85
1442 1546 3.509575 TGAAAGCCTGAAACACAACAGTT 59.490 39.130 0.00 0.00 32.93 3.16
1466 1570 4.337763 CTGATTCTATCAAGTTTGTGCGC 58.662 43.478 0.00 0.00 39.11 6.09
1475 1579 4.686191 ACTCCCTGCTGATTCTATCAAG 57.314 45.455 0.00 0.00 39.11 3.02
1530 1634 6.540205 ACGTTCCTGTTATTCGATTTTAAGC 58.460 36.000 0.00 0.00 0.00 3.09
1812 1916 5.545723 AGAGCAGGATAACCAGTGCTATTAT 59.454 40.000 5.85 0.00 44.21 1.28
1913 2019 9.944663 TTTGTTTTCAGTTCATAGAACACATAC 57.055 29.630 11.92 4.62 35.24 2.39
1915 2021 8.686334 ACTTTGTTTTCAGTTCATAGAACACAT 58.314 29.630 11.92 0.00 35.24 3.21
1991 2097 1.825090 TGTGATGCAATGTGAGGACC 58.175 50.000 0.00 0.00 0.00 4.46
2071 2177 0.668535 AGGAAAACAAAGGCAGACGC 59.331 50.000 0.00 0.00 37.44 5.19
2076 2378 1.063266 AGGTGGAGGAAAACAAAGGCA 60.063 47.619 0.00 0.00 0.00 4.75
2148 2450 9.935682 CATGTATCTACGAATAGCAACATTTTT 57.064 29.630 0.00 0.00 34.13 1.94
2221 2523 1.035139 AGGCAAGCAAGTGGAAACAG 58.965 50.000 0.00 0.00 44.46 3.16
2233 2535 2.426842 ATGAAGGACCTTAGGCAAGC 57.573 50.000 6.75 0.00 0.00 4.01
2237 2539 5.984695 AAAAGAAATGAAGGACCTTAGGC 57.015 39.130 6.75 0.00 0.00 3.93
2267 2569 4.466567 TGTGATTTCTTGCAACACGTAG 57.533 40.909 11.21 0.00 34.72 3.51
2915 3405 4.201419 CGCAAATTTGTGTGATGTGATTCG 60.201 41.667 21.08 7.43 34.14 3.34
3027 3517 2.306219 GTGGTAGGAAAAGGAAGAGGCT 59.694 50.000 0.00 0.00 0.00 4.58
3028 3518 2.039879 TGTGGTAGGAAAAGGAAGAGGC 59.960 50.000 0.00 0.00 0.00 4.70
3046 3536 6.329496 ACCCTTAAATGCAATAAATCGTGTG 58.671 36.000 0.00 0.00 0.00 3.82
3064 3554 7.334921 CACGTACATTCAGGATTTTTACCCTTA 59.665 37.037 0.00 0.00 0.00 2.69
3065 3555 6.150474 CACGTACATTCAGGATTTTTACCCTT 59.850 38.462 0.00 0.00 0.00 3.95
3071 3561 5.446143 TTGCACGTACATTCAGGATTTTT 57.554 34.783 0.00 0.00 0.00 1.94
3072 3562 5.446143 TTTGCACGTACATTCAGGATTTT 57.554 34.783 0.00 0.00 0.00 1.82
3291 3782 2.662006 TCTGGACGAATCTGAAGCAG 57.338 50.000 0.00 0.00 0.00 4.24
3450 3941 5.681337 TGAAATGCAACACATAAAGTCGA 57.319 34.783 0.00 0.00 38.34 4.20
3451 3942 4.321745 GCTGAAATGCAACACATAAAGTCG 59.678 41.667 0.00 0.00 38.34 4.18
3542 4033 8.305317 TCTCAGATAATATCTCAACATGCTGAG 58.695 37.037 18.25 18.25 44.09 3.35
3636 4127 2.235155 TGGTTCAGTATTAAGGCGCTGA 59.765 45.455 7.64 0.00 36.35 4.26
3957 4448 9.764870 CTGTTTTCAAGATATACAGAACACATG 57.235 33.333 0.00 0.00 38.74 3.21
4265 4756 2.578495 GTGCAGAACAAAGAATCAGCG 58.422 47.619 0.00 0.00 31.45 5.18
4309 4800 5.531634 TCAACAAGATGGCTTTCAACAATC 58.468 37.500 0.00 0.00 30.14 2.67
4358 4849 2.713895 ATCTATCACGATGACCTGCG 57.286 50.000 0.00 0.00 0.00 5.18
4382 4873 4.489771 CGACCACCTCCATGCCCC 62.490 72.222 0.00 0.00 0.00 5.80
4442 4934 6.913170 TCATCCACAAAGAAAGCTCAAATAC 58.087 36.000 0.00 0.00 0.00 1.89
4450 4942 5.320549 ACATGATCATCCACAAAGAAAGC 57.679 39.130 4.86 0.00 0.00 3.51
4487 4979 2.093447 CCGGACACTAGCCAAAAGATCT 60.093 50.000 0.00 0.00 0.00 2.75
4513 5005 9.936329 ATGGTATCCAAAGTAAATAAATCCACT 57.064 29.630 0.00 0.00 36.95 4.00
4541 5033 4.075682 TGAACAGGTTTCAGTCAACACAA 58.924 39.130 0.00 0.00 0.00 3.33
4557 5049 5.525378 GCTATTAGACAGAATGGGTGAACAG 59.475 44.000 0.00 0.00 43.62 3.16
4559 5051 5.675538 AGCTATTAGACAGAATGGGTGAAC 58.324 41.667 0.00 0.00 43.62 3.18
4651 5143 7.552050 TTGATGGGACCAAAATATGAGTTTT 57.448 32.000 0.00 0.00 0.00 2.43
4688 5181 7.269724 GTGCGGTATTATGGAAATAAATTACGC 59.730 37.037 0.00 0.00 0.00 4.42
4714 5207 1.214589 CGGACCCAACGTAGGTGAG 59.785 63.158 14.51 5.05 37.88 3.51
4784 5277 4.691216 GTGCTAGTACCACAAGAGGAAAAG 59.309 45.833 0.00 0.00 33.50 2.27
4798 5291 7.382759 GCTATTTCTCATTAGTGGTGCTAGTAC 59.617 40.741 1.77 1.77 0.00 2.73
4802 5295 6.127054 ACAGCTATTTCTCATTAGTGGTGCTA 60.127 38.462 0.00 0.00 0.00 3.49
4829 5322 0.773644 AGGTTCCAGCTGACAACCAT 59.226 50.000 32.59 21.66 41.91 3.55
4886 5379 1.351017 GTGACATGGTGAGAGGGGAAA 59.649 52.381 0.00 0.00 0.00 3.13
4887 5380 0.984230 GTGACATGGTGAGAGGGGAA 59.016 55.000 0.00 0.00 0.00 3.97
4888 5381 1.257750 CGTGACATGGTGAGAGGGGA 61.258 60.000 0.00 0.00 0.00 4.81
4980 5482 6.540189 ACAGCAAATCAGTACACCTATCATTC 59.460 38.462 0.00 0.00 0.00 2.67
4981 5483 6.418101 ACAGCAAATCAGTACACCTATCATT 58.582 36.000 0.00 0.00 0.00 2.57
5001 5503 0.392461 TCCTATGTCGGGCAAACAGC 60.392 55.000 0.00 0.00 44.65 4.40
5002 5504 2.332063 ATCCTATGTCGGGCAAACAG 57.668 50.000 0.00 0.00 0.00 3.16
5124 5639 1.542915 GCATTGACTTGTCATGGCACT 59.457 47.619 0.00 0.00 0.00 4.40
5128 5643 0.819582 GGGGCATTGACTTGTCATGG 59.180 55.000 4.18 1.72 0.00 3.66
5194 5709 1.517832 CGGCAACCACTAGAGGGAG 59.482 63.158 11.20 3.70 0.00 4.30
5234 5749 1.414550 GGGAAGCTGAGGATGGTACTC 59.585 57.143 0.00 0.00 35.55 2.59


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

AutoCloner maintained by Alex Coulton.