Multiple sequence alignment - TraesCS3B01G354300

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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 TraesCS3B01G354300 chr3B 100.000 4665 0 0 1 4665 564768718 564773382 0.000000e+00 8615
1 TraesCS3B01G354300 chr3B 85.946 185 21 4 4482 4665 813887777 813887597 4.760000e-45 193
2 TraesCS3B01G354300 chr3D 92.322 3308 144 39 1412 4665 432540647 432543898 0.000000e+00 4601
3 TraesCS3B01G354300 chr3D 90.766 509 36 7 931 1433 432540123 432540626 0.000000e+00 669
4 TraesCS3B01G354300 chr3A 90.278 2664 127 43 1412 4016 570670957 570673547 0.000000e+00 3363
5 TraesCS3B01G354300 chr3A 88.699 761 66 12 1 743 570668745 570669503 0.000000e+00 911
6 TraesCS3B01G354300 chr3A 88.043 644 46 15 4027 4665 570674007 570674624 0.000000e+00 734
7 TraesCS3B01G354300 chr3A 90.556 540 45 2 884 1417 570670385 570670924 0.000000e+00 710
8 TraesCS3B01G354300 chr3A 92.157 153 10 2 737 887 570669927 570670079 1.020000e-51 215
9 TraesCS3B01G354300 chr6A 76.373 601 116 15 3892 4481 508286233 508285648 2.730000e-77 300
10 TraesCS3B01G354300 chr6D 77.691 511 97 12 3892 4390 367856985 367856480 3.530000e-76 296
11 TraesCS3B01G354300 chr7D 87.634 186 17 4 4482 4665 246517988 246517807 1.320000e-50 211
12 TraesCS3B01G354300 chr7D 83.243 185 24 4 4482 4665 32213733 32213911 3.730000e-36 163
13 TraesCS3B01G354300 chr6B 86.170 188 20 3 4482 4665 632189681 632189866 1.020000e-46 198
14 TraesCS3B01G354300 chr2D 86.559 186 18 5 4482 4665 108315992 108316172 1.020000e-46 198
15 TraesCS3B01G354300 chr1A 85.027 187 23 3 4482 4665 476987188 476987372 7.970000e-43 185
16 TraesCS3B01G354300 chr1B 80.749 187 28 5 4482 4665 606323035 606322854 6.290000e-29 139
17 TraesCS3B01G354300 chr5B 85.849 106 6 7 4558 4663 2805198 2805294 2.300000e-18 104


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 TraesCS3B01G354300 chr3B 564768718 564773382 4664 False 8615.0 8615 100.0000 1 4665 1 chr3B.!!$F1 4664
1 TraesCS3B01G354300 chr3D 432540123 432543898 3775 False 2635.0 4601 91.5440 931 4665 2 chr3D.!!$F1 3734
2 TraesCS3B01G354300 chr3A 570668745 570674624 5879 False 1186.6 3363 89.9466 1 4665 5 chr3A.!!$F1 4664
3 TraesCS3B01G354300 chr6A 508285648 508286233 585 True 300.0 300 76.3730 3892 4481 1 chr6A.!!$R1 589
4 TraesCS3B01G354300 chr6D 367856480 367856985 505 True 296.0 296 77.6910 3892 4390 1 chr6D.!!$R1 498

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
174 175 0.478507 AGGTGGGTCTTTTCCTGTGG 59.521 55.0 0.00 0.00 0.00 4.17 F
835 1285 0.670162 GGCATTGAACAGTGCACAGT 59.330 50.0 21.04 15.24 44.58 3.55 F
2428 3253 0.102481 ATGAAGCTACCGGTGCTACG 59.898 55.0 25.20 8.24 40.22 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1879 0.250513 AGCGAACTTTGCTAGGGGAG 59.749 55.0 1.22 0.0 41.87 4.30 R
2430 3255 0.462047 AACTGTATGGCGCACCTAGC 60.462 55.0 10.83 0.0 40.87 3.42 R
3719 4580 0.323087 ACCACCCGAGGTTTTATGCC 60.323 55.0 0.00 0.0 39.34 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
22 23 2.543861 CCTAGGTCGTTGGATCGTGATG 60.544 54.545 0.00 0.00 0.00 3.07
35 36 1.068541 TCGTGATGGACAACTCAGACG 60.069 52.381 0.00 0.00 0.00 4.18
137 138 1.110518 TGTTGGACGGGCCCTTTTTC 61.111 55.000 22.43 10.57 34.97 2.29
138 139 0.826256 GTTGGACGGGCCCTTTTTCT 60.826 55.000 22.43 0.00 34.97 2.52
141 142 1.241990 GGACGGGCCCTTTTTCTCAC 61.242 60.000 22.43 0.00 0.00 3.51
160 161 2.225491 CACGGTTAACATGTTGAGGTGG 59.775 50.000 21.42 7.80 0.00 4.61
161 162 1.810151 CGGTTAACATGTTGAGGTGGG 59.190 52.381 21.42 0.44 0.00 4.61
171 172 2.230660 GTTGAGGTGGGTCTTTTCCTG 58.769 52.381 0.00 0.00 0.00 3.86
174 175 0.478507 AGGTGGGTCTTTTCCTGTGG 59.521 55.000 0.00 0.00 0.00 4.17
186 200 1.583556 TCCTGTGGATAGGTGCATGT 58.416 50.000 0.00 0.00 38.99 3.21
224 238 7.549141 AGGATCACCTATTTAGTATTCCCTCT 58.451 38.462 0.00 0.00 45.83 3.69
225 239 7.456269 AGGATCACCTATTTAGTATTCCCTCTG 59.544 40.741 0.00 0.00 45.83 3.35
254 270 7.751793 CCAAAATACTTCGCGGTTTTAGTTTAT 59.248 33.333 6.13 0.00 0.00 1.40
292 308 7.936847 TGTGAACTAGAACCATGACAAGTATTT 59.063 33.333 0.00 0.00 0.00 1.40
296 312 7.458397 ACTAGAACCATGACAAGTATTTTGGA 58.542 34.615 0.00 0.00 0.00 3.53
363 380 7.701924 ACGTGAATTGGTTGCAATATAATTCAG 59.298 33.333 29.08 25.36 43.97 3.02
505 522 7.056844 AGTAGCATAATAGGAAGGAAGTCAC 57.943 40.000 0.00 0.00 0.00 3.67
507 524 6.567602 AGCATAATAGGAAGGAAGTCACTT 57.432 37.500 0.00 0.00 0.00 3.16
509 526 7.406104 AGCATAATAGGAAGGAAGTCACTTTT 58.594 34.615 0.00 0.00 0.00 2.27
518 535 7.394641 AGGAAGGAAGTCACTTTTCCATTTATC 59.605 37.037 19.16 1.95 45.28 1.75
533 550 1.378531 TTATCGTGGCATGTTGAGGC 58.621 50.000 6.60 0.00 0.00 4.70
537 554 2.747460 TGGCATGTTGAGGCGAGC 60.747 61.111 0.00 0.00 0.00 5.03
539 556 2.482374 GCATGTTGAGGCGAGCAC 59.518 61.111 0.00 0.00 0.00 4.40
565 582 3.378742 AGCGTGTGGTTGTGATTTTGTAA 59.621 39.130 0.00 0.00 0.00 2.41
593 610 6.749216 ATAAGTGCATACGTTATTCTGACG 57.251 37.500 0.00 0.00 45.46 4.35
617 634 6.199393 GTGTTGTGAACTCAAGTGGTATTTC 58.801 40.000 0.00 0.00 0.00 2.17
624 641 6.040278 TGAACTCAAGTGGTATTTCATGCAAA 59.960 34.615 0.00 0.00 0.00 3.68
629 646 5.726980 AGTGGTATTTCATGCAAACACAT 57.273 34.783 4.91 0.00 0.00 3.21
633 650 4.864247 GGTATTTCATGCAAACACATGGAC 59.136 41.667 0.00 0.00 46.08 4.02
648 665 3.378112 ACATGGACGATATGTTGCAAAGG 59.622 43.478 0.00 0.00 35.32 3.11
708 726 2.111756 GTGTTTTTCTGTTGCTGCGAG 58.888 47.619 0.00 0.00 0.00 5.03
711 729 1.436195 TTTTCTGTTGCTGCGAGCGT 61.436 50.000 0.00 0.00 46.26 5.07
739 1188 4.818005 TCTTATGCTGCATACAGGTGAATG 59.182 41.667 21.19 3.50 44.63 2.67
761 1210 5.181748 TGTTTGTGGGGAAAATGAACTTTG 58.818 37.500 0.00 0.00 0.00 2.77
829 1279 0.958091 TTTCCGGGCATTGAACAGTG 59.042 50.000 0.00 0.00 0.00 3.66
830 1280 1.523154 TTCCGGGCATTGAACAGTGC 61.523 55.000 12.61 12.61 42.43 4.40
831 1281 2.267351 CCGGGCATTGAACAGTGCA 61.267 57.895 20.17 0.00 44.58 4.57
832 1282 1.081242 CGGGCATTGAACAGTGCAC 60.081 57.895 20.17 9.40 44.58 4.57
833 1283 1.794151 CGGGCATTGAACAGTGCACA 61.794 55.000 21.04 0.00 46.25 4.57
835 1285 0.670162 GGCATTGAACAGTGCACAGT 59.330 50.000 21.04 15.24 44.58 3.55
836 1286 1.601162 GGCATTGAACAGTGCACAGTG 60.601 52.381 21.04 12.23 44.58 3.66
852 1303 3.057548 TGAACCATGCGCTGCAGG 61.058 61.111 17.12 6.85 43.65 4.85
897 1657 3.064820 CGCACAAACTAAACCACACTTCT 59.935 43.478 0.00 0.00 0.00 2.85
917 1677 1.748493 TGGCTGAAAAGCGAGTTTTGT 59.252 42.857 1.07 0.00 38.54 2.83
941 1701 2.736719 CGAGTACATCCCACAGCTCTTG 60.737 54.545 0.00 0.00 0.00 3.02
1020 1780 5.363292 TCGCCTATATAACCCACTAACACAA 59.637 40.000 0.00 0.00 0.00 3.33
1065 1825 7.739498 AGTTCTAATCGGTTACACAACAATT 57.261 32.000 0.00 0.00 36.29 2.32
1104 1864 0.686112 AGCCCCTTCTCTCTTCTCCG 60.686 60.000 0.00 0.00 0.00 4.63
1105 1865 0.973496 GCCCCTTCTCTCTTCTCCGT 60.973 60.000 0.00 0.00 0.00 4.69
1119 1879 2.210116 TCTCCGTCACAAAGAAACTGC 58.790 47.619 0.00 0.00 0.00 4.40
1125 1885 1.494721 TCACAAAGAAACTGCTCCCCT 59.505 47.619 0.00 0.00 0.00 4.79
1142 1902 0.804989 CCTAGCAAAGTTCGCTTGGG 59.195 55.000 8.27 1.37 45.22 4.12
1151 1911 4.980805 TCGCTTGGGCACACCGAC 62.981 66.667 6.79 0.00 44.64 4.79
1161 1921 1.218316 CACACCGACCTTCCTAGCC 59.782 63.158 0.00 0.00 0.00 3.93
1194 1954 2.457743 TTTGCTTCGCCGCCTTCCTA 62.458 55.000 0.00 0.00 0.00 2.94
1202 1962 1.614241 GCCGCCTTCCTACTCCTCAA 61.614 60.000 0.00 0.00 0.00 3.02
1203 1963 1.123928 CCGCCTTCCTACTCCTCAAT 58.876 55.000 0.00 0.00 0.00 2.57
1211 1977 1.415659 CCTACTCCTCAATCCTGCCAG 59.584 57.143 0.00 0.00 0.00 4.85
1216 1982 1.751927 CTCAATCCTGCCAGGGTGC 60.752 63.158 11.68 0.00 35.59 5.01
1487 2291 4.771356 GTACGTGGCTCAGCGCGA 62.771 66.667 12.10 1.16 40.44 5.87
1647 2451 3.872728 CGACGACATCGCTCGGGA 61.873 66.667 14.34 0.00 45.52 5.14
1648 2452 2.278013 GACGACATCGCTCGGGAC 60.278 66.667 0.14 0.00 44.43 4.46
2113 2923 8.448615 GCACCTTTAGTATGTTCGATAAACTTT 58.551 33.333 0.00 0.00 38.76 2.66
2172 2990 1.543802 CCGCATCAAAGCCTTAAACCA 59.456 47.619 0.00 0.00 0.00 3.67
2231 3049 5.401079 GCTAGTGCAATAGAGACGATCTTTC 59.599 44.000 24.52 0.00 38.09 2.62
2322 3140 3.744942 CAGTGAAGAGTGGTCAGTGAATG 59.255 47.826 0.00 0.00 45.47 2.67
2362 3187 9.675464 CCATAAACCAGTCACCTAAATTTAGTA 57.325 33.333 20.99 6.33 0.00 1.82
2386 3211 4.036380 GGACAAGTTTGGTACCTGTTCTTG 59.964 45.833 23.91 23.91 31.57 3.02
2427 3252 2.159085 AGAATGAAGCTACCGGTGCTAC 60.159 50.000 25.20 16.15 40.22 3.58
2428 3253 0.102481 ATGAAGCTACCGGTGCTACG 59.898 55.000 25.20 8.24 40.22 3.51
2429 3254 1.246056 TGAAGCTACCGGTGCTACGT 61.246 55.000 25.20 14.18 40.22 3.57
2430 3255 0.801067 GAAGCTACCGGTGCTACGTG 60.801 60.000 25.20 6.65 40.22 4.49
2431 3256 2.830704 AAGCTACCGGTGCTACGTGC 62.831 60.000 25.20 14.39 40.22 5.34
2432 3257 2.882876 CTACCGGTGCTACGTGCT 59.117 61.111 19.93 0.00 43.37 4.40
2433 3258 1.996786 GCTACCGGTGCTACGTGCTA 61.997 60.000 19.93 0.00 43.37 3.49
2709 3545 2.428888 ACTGAAAGGTCGTTACGGAC 57.571 50.000 4.53 1.92 39.30 4.79
2710 3546 1.335324 ACTGAAAGGTCGTTACGGACG 60.335 52.381 4.53 7.20 46.77 4.79
2744 3580 3.248266 GTTGAAAGCAAGCATGTGATCC 58.752 45.455 0.00 0.00 34.01 3.36
2780 3630 1.608055 CCATGGATGGCTCGCATTTA 58.392 50.000 5.56 0.00 41.75 1.40
2781 3631 2.165167 CCATGGATGGCTCGCATTTAT 58.835 47.619 5.56 0.00 41.75 1.40
2795 3645 6.043327 TCGCATTTATACAACAGTATGCAC 57.957 37.500 0.00 0.00 42.53 4.57
2917 3767 2.489985 CCTACAGGACCTCAGGATCGAT 60.490 54.545 11.91 0.00 37.39 3.59
3125 3975 0.320683 CCAGAACTGCGTGATCACCA 60.321 55.000 20.03 16.55 0.00 4.17
3384 4234 2.383527 GGGACTTCGCGCTCAACAG 61.384 63.158 5.56 0.00 0.00 3.16
3543 4393 4.329545 GCTCAAGGGCACGGGTGA 62.330 66.667 2.38 0.00 0.00 4.02
3605 4455 6.238648 CCCTTCGTTTGATGTTTGTTTACTCT 60.239 38.462 0.00 0.00 0.00 3.24
3671 4525 5.010933 TCACCACGGCATCCTAAATAAAAA 58.989 37.500 0.00 0.00 0.00 1.94
3712 4566 6.154021 ACTCGTGTTACCTATAATCTTGTGGT 59.846 38.462 0.00 0.00 35.05 4.16
3719 4580 5.918608 ACCTATAATCTTGTGGTAGCACAG 58.081 41.667 25.27 19.20 36.35 3.66
3787 4649 8.867112 CATTTCATGCTTGATATTTTGTAGCT 57.133 30.769 2.75 0.00 33.15 3.32
3792 4654 6.573664 TGCTTGATATTTTGTAGCTGTTGT 57.426 33.333 0.00 0.00 33.15 3.32
3796 4658 8.427774 GCTTGATATTTTGTAGCTGTTGTTTTC 58.572 33.333 0.00 0.00 0.00 2.29
3823 4708 3.281727 TGCTCCTGGATGAACAATACC 57.718 47.619 0.00 0.00 0.00 2.73
3824 4709 2.213499 GCTCCTGGATGAACAATACCG 58.787 52.381 0.00 0.00 0.00 4.02
3825 4710 2.213499 CTCCTGGATGAACAATACCGC 58.787 52.381 0.00 0.00 0.00 5.68
3890 4776 4.082625 TGTGGATATTCGTGTTAGTGTCGT 60.083 41.667 0.00 0.00 0.00 4.34
4084 5423 4.235372 CTGGGACCTAAACATAGAGGGAT 58.765 47.826 0.00 0.00 37.14 3.85
4171 5510 0.467474 CATCATGGGATGCTGGCACT 60.467 55.000 0.00 0.00 44.03 4.40
4175 5514 2.091720 TCATGGGATGCTGGCACTTATT 60.092 45.455 0.00 0.00 0.00 1.40
4233 5576 3.382278 TCCATCTGAGCTTCTTGGAGAT 58.618 45.455 4.95 0.00 32.80 2.75
4279 5622 1.467734 GCTCCAGCACAGAATCAACAG 59.532 52.381 0.00 0.00 41.59 3.16
4305 5648 2.450609 TCAAGACCAGCTTCGTAACC 57.549 50.000 0.00 0.00 33.60 2.85
4395 5742 7.629027 GCTTTTGCCATGTAAATAGATTAGC 57.371 36.000 0.00 0.00 40.15 3.09
4421 5768 6.450845 TTTTTGCTTTCTTTCGCATGTATG 57.549 33.333 0.00 0.00 35.85 2.39
4510 5858 3.281341 TGACAATGTTCATGCGAAACC 57.719 42.857 0.00 0.00 31.43 3.27
4511 5859 2.620585 TGACAATGTTCATGCGAAACCA 59.379 40.909 0.00 0.00 31.43 3.67
4514 5862 3.068024 ACAATGTTCATGCGAAACCAAGT 59.932 39.130 0.00 0.00 31.43 3.16
4519 5867 4.688879 TGTTCATGCGAAACCAAGTAGTAG 59.311 41.667 0.00 0.00 31.43 2.57
4532 5880 4.083324 CCAAGTAGTAGTGTTTCGTCGGTA 60.083 45.833 0.00 0.00 0.00 4.02
4576 5925 5.465056 GTGACATTTTGGGTAACATTTGGTG 59.535 40.000 0.00 0.00 39.74 4.17
4601 5952 9.499585 TGTTCAAATTTGTTAATTTTGCACATG 57.500 25.926 17.47 0.00 40.97 3.21
4609 5960 9.661187 TTTGTTAATTTTGCACATGCTAAAATG 57.339 25.926 15.54 0.00 45.54 2.32
4617 5968 6.095432 TGCACATGCTAAAATGTTTAACCT 57.905 33.333 5.31 0.00 38.75 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.329379 CACTTAGCGTCTGAGTTGTCC 58.671 52.381 2.38 0.00 27.61 4.02
35 36 0.253044 TGAGGCACATCCCACTTAGC 59.747 55.000 0.00 0.00 34.51 3.09
111 112 2.560119 GCCCGTCCAACATGCAACA 61.560 57.895 0.00 0.00 0.00 3.33
137 138 3.186409 CACCTCAACATGTTAACCGTGAG 59.814 47.826 11.53 12.84 34.01 3.51
138 139 3.135225 CACCTCAACATGTTAACCGTGA 58.865 45.455 11.53 3.00 34.01 4.35
141 142 1.810151 CCCACCTCAACATGTTAACCG 59.190 52.381 11.53 0.00 0.00 4.44
160 161 3.610911 CACCTATCCACAGGAAAAGACC 58.389 50.000 0.00 0.00 39.18 3.85
161 162 3.010420 GCACCTATCCACAGGAAAAGAC 58.990 50.000 0.00 0.00 39.18 3.01
171 172 3.118629 TCTCTCAACATGCACCTATCCAC 60.119 47.826 0.00 0.00 0.00 4.02
174 175 6.317140 TCAATTTCTCTCAACATGCACCTATC 59.683 38.462 0.00 0.00 0.00 2.08
186 200 5.768980 AGGTGATCCTCAATTTCTCTCAA 57.231 39.130 0.00 0.00 40.58 3.02
206 220 7.374975 TGGAACAGAGGGAATACTAAATAGG 57.625 40.000 0.00 0.00 0.00 2.57
216 230 5.648092 CGAAGTATTTTGGAACAGAGGGAAT 59.352 40.000 0.00 0.00 42.39 3.01
217 231 5.001232 CGAAGTATTTTGGAACAGAGGGAA 58.999 41.667 0.00 0.00 42.39 3.97
224 238 2.496111 ACCGCGAAGTATTTTGGAACA 58.504 42.857 8.23 0.00 0.00 3.18
225 239 3.547649 AACCGCGAAGTATTTTGGAAC 57.452 42.857 8.23 0.00 0.00 3.62
267 283 7.907214 AATACTTGTCATGGTTCTAGTTCAC 57.093 36.000 0.00 0.00 0.00 3.18
275 291 5.856455 CGTTCCAAAATACTTGTCATGGTTC 59.144 40.000 0.00 0.00 0.00 3.62
292 308 7.520798 TCTAGTATATTACTCCCTCGTTCCAA 58.479 38.462 0.00 0.00 40.14 3.53
494 511 7.094762 ACGATAAATGGAAAAGTGACTTCCTTC 60.095 37.037 0.00 0.00 42.52 3.46
501 518 4.083003 TGCCACGATAAATGGAAAAGTGAC 60.083 41.667 0.00 0.00 39.87 3.67
503 520 4.433186 TGCCACGATAAATGGAAAAGTG 57.567 40.909 0.00 0.00 39.87 3.16
505 522 4.997565 ACATGCCACGATAAATGGAAAAG 58.002 39.130 0.00 0.00 39.87 2.27
507 524 4.460731 TCAACATGCCACGATAAATGGAAA 59.539 37.500 0.00 0.00 39.87 3.13
509 526 3.615155 TCAACATGCCACGATAAATGGA 58.385 40.909 0.00 0.00 39.87 3.41
518 535 2.741985 TCGCCTCAACATGCCACG 60.742 61.111 0.00 0.00 0.00 4.94
539 556 1.221466 ATCACAACCACACGCTGTCG 61.221 55.000 0.00 0.00 42.43 4.35
543 560 1.748493 ACAAAATCACAACCACACGCT 59.252 42.857 0.00 0.00 0.00 5.07
569 586 7.161829 CGTCAGAATAACGTATGCACTTATT 57.838 36.000 0.00 0.00 35.47 1.40
582 599 5.233476 TGAGTTCACAACACGTCAGAATAAC 59.767 40.000 0.00 0.00 0.00 1.89
588 605 2.930040 ACTTGAGTTCACAACACGTCAG 59.070 45.455 0.00 0.00 0.00 3.51
593 610 5.751243 AATACCACTTGAGTTCACAACAC 57.249 39.130 0.00 0.00 0.00 3.32
594 611 5.883115 TGAAATACCACTTGAGTTCACAACA 59.117 36.000 0.00 0.00 0.00 3.33
617 634 2.925578 ATCGTCCATGTGTTTGCATG 57.074 45.000 0.00 0.00 44.18 4.06
624 641 2.984562 TGCAACATATCGTCCATGTGT 58.015 42.857 0.00 0.00 38.43 3.72
629 646 1.742831 GCCTTTGCAACATATCGTCCA 59.257 47.619 0.00 0.00 37.47 4.02
673 690 5.295787 AGAAAAACACTTGCACTATGAACGA 59.704 36.000 0.00 0.00 0.00 3.85
681 698 3.056607 AGCAACAGAAAAACACTTGCACT 60.057 39.130 0.00 0.00 36.51 4.40
682 699 3.061161 CAGCAACAGAAAAACACTTGCAC 59.939 43.478 0.00 0.00 36.51 4.57
708 726 1.063166 GCAGCATAAGAGCCAACGC 59.937 57.895 0.00 0.00 34.23 4.84
711 729 3.208594 CTGTATGCAGCATAAGAGCCAA 58.791 45.455 16.99 0.00 35.77 4.52
739 1188 4.035091 GCAAAGTTCATTTTCCCCACAAAC 59.965 41.667 0.00 0.00 0.00 2.93
789 1239 1.619432 GGGCCAGATTCCAACCATGAA 60.619 52.381 4.39 0.00 0.00 2.57
790 1240 0.033208 GGGCCAGATTCCAACCATGA 60.033 55.000 4.39 0.00 0.00 3.07
829 1279 2.126734 GCGCATGGTTCACTGTGC 60.127 61.111 0.30 0.00 41.13 4.57
830 1280 1.208358 CAGCGCATGGTTCACTGTG 59.792 57.895 11.47 0.17 0.00 3.66
831 1281 2.620112 GCAGCGCATGGTTCACTGT 61.620 57.895 11.47 0.00 0.00 3.55
832 1282 2.177531 GCAGCGCATGGTTCACTG 59.822 61.111 11.47 0.00 0.00 3.66
833 1283 2.281692 TGCAGCGCATGGTTCACT 60.282 55.556 11.47 0.00 31.71 3.41
835 1285 3.057548 CCTGCAGCGCATGGTTCA 61.058 61.111 11.47 0.00 38.13 3.18
836 1286 4.487412 GCCTGCAGCGCATGGTTC 62.487 66.667 18.68 0.00 38.13 3.62
852 1303 2.105930 CCCTCTACGCTCAGCAGC 59.894 66.667 0.00 0.00 42.96 5.25
897 1657 1.748493 ACAAAACTCGCTTTTCAGCCA 59.252 42.857 0.00 0.00 44.06 4.75
917 1677 1.108776 GCTGTGGGATGTACTCGGTA 58.891 55.000 0.00 0.00 0.00 4.02
941 1701 2.267188 TTCATGAATTTGCTCTGCGC 57.733 45.000 3.38 0.00 39.77 6.09
1020 1780 2.571212 TGGAAATGCACTTGTCGAGTT 58.429 42.857 0.00 0.00 36.10 3.01
1065 1825 0.532640 CGTTGATCGGATCCATGGCA 60.533 55.000 13.41 0.83 35.71 4.92
1104 1864 1.609072 GGGGAGCAGTTTCTTTGTGAC 59.391 52.381 0.00 0.00 0.00 3.67
1105 1865 1.494721 AGGGGAGCAGTTTCTTTGTGA 59.505 47.619 0.00 0.00 0.00 3.58
1119 1879 0.250513 AGCGAACTTTGCTAGGGGAG 59.749 55.000 1.22 0.00 41.87 4.30
1125 1885 0.536233 TGCCCAAGCGAACTTTGCTA 60.536 50.000 3.81 0.00 43.14 3.49
1136 1896 4.643387 AGGTCGGTGTGCCCAAGC 62.643 66.667 0.00 0.00 40.48 4.01
1142 1902 1.448013 GCTAGGAAGGTCGGTGTGC 60.448 63.158 0.00 0.00 0.00 4.57
1151 1911 0.908198 AAGCAGAGTGGCTAGGAAGG 59.092 55.000 0.00 0.00 45.07 3.46
1161 1921 2.503920 AGCAAAAGCAAAGCAGAGTG 57.496 45.000 0.00 0.00 0.00 3.51
1194 1954 1.277580 CCCTGGCAGGATTGAGGAGT 61.278 60.000 34.84 0.00 37.67 3.85
1202 1962 4.052518 GGTGCACCCTGGCAGGAT 62.053 66.667 34.84 17.02 45.96 3.24
1216 1982 0.890996 GGGGAGTTTGTGCAGAGGTG 60.891 60.000 0.00 0.00 0.00 4.00
1334 2100 3.721706 GCTGGTGGAGGGACCTGG 61.722 72.222 0.00 0.00 39.86 4.45
1471 2275 3.822192 ATCGCGCTGAGCCACGTA 61.822 61.111 13.17 2.71 44.76 3.57
1487 2291 2.048222 CACGTGGTCGGTGAGCAT 60.048 61.111 7.95 0.00 42.05 3.79
1665 2469 1.144565 CGATGGAAGCTCGTCTGCTG 61.145 60.000 0.00 0.00 43.24 4.41
1666 2470 1.140589 CGATGGAAGCTCGTCTGCT 59.859 57.895 0.00 0.00 46.40 4.24
1667 2471 1.153745 ACGATGGAAGCTCGTCTGC 60.154 57.895 0.00 0.00 45.63 4.26
1668 2472 0.803768 CCACGATGGAAGCTCGTCTG 60.804 60.000 0.00 0.00 45.63 3.51
1831 2641 1.831736 ACCCCCTTCTTCACGTAGATG 59.168 52.381 0.00 0.00 0.00 2.90
2231 3049 3.287312 ACAGATTGGTTTTGTGATGCG 57.713 42.857 0.00 0.00 0.00 4.73
2322 3140 3.491447 GGTTTATGGCCATCAATCAGTGC 60.491 47.826 24.80 4.30 0.00 4.40
2332 3153 1.640670 AGGTGACTGGTTTATGGCCAT 59.359 47.619 24.45 24.45 41.13 4.40
2362 3187 3.458487 AGAACAGGTACCAAACTTGTCCT 59.542 43.478 15.94 0.00 46.84 3.85
2386 3211 9.464714 TCATTCTTTATTGTTACTCTATCTCGC 57.535 33.333 0.00 0.00 0.00 5.03
2427 3252 2.106131 TATGGCGCACCTAGCACG 59.894 61.111 10.83 0.00 46.13 5.34
2428 3253 1.153449 TGTATGGCGCACCTAGCAC 60.153 57.895 10.83 0.00 46.13 4.40
2429 3254 1.143838 CTGTATGGCGCACCTAGCA 59.856 57.895 10.83 0.00 46.13 3.49
2430 3255 0.462047 AACTGTATGGCGCACCTAGC 60.462 55.000 10.83 0.00 40.87 3.42
2431 3256 1.290203 CAACTGTATGGCGCACCTAG 58.710 55.000 10.83 2.85 36.63 3.02
2432 3257 0.742990 GCAACTGTATGGCGCACCTA 60.743 55.000 10.83 0.00 36.63 3.08
2433 3258 2.040544 GCAACTGTATGGCGCACCT 61.041 57.895 10.83 0.00 36.63 4.00
2565 3399 2.357952 GGTGGCGGAAATAAAAGCTAGG 59.642 50.000 0.00 0.00 0.00 3.02
2611 3445 2.512286 CCTGCGATGCATCACCGT 60.512 61.111 25.70 0.00 38.13 4.83
2668 3502 8.968242 TCAGTACGTATACTTGTAGTACATACG 58.032 37.037 23.09 23.09 43.44 3.06
2780 3630 1.663695 GGCCGTGCATACTGTTGTAT 58.336 50.000 0.00 0.00 39.76 2.29
2781 3631 0.738063 CGGCCGTGCATACTGTTGTA 60.738 55.000 19.50 0.00 0.00 2.41
3292 4142 2.148365 GTACACCGTGCGCGAGTAC 61.148 63.158 27.06 27.06 43.70 2.73
3358 4208 2.031465 GCGAAGTCCCCGTTCCAA 59.969 61.111 0.00 0.00 0.00 3.53
3384 4234 1.031235 GTACTCCCCGTAGAAGAGCC 58.969 60.000 0.00 0.00 31.13 4.70
3543 4393 4.203076 GCCCATCGTCGTACGCCT 62.203 66.667 11.24 0.00 42.21 5.52
3605 4455 8.030692 CAGAACTGCCATTAAAGATTTGATGAA 58.969 33.333 10.64 0.50 36.57 2.57
3671 4525 5.724328 ACACGAGTGACACTGATAAATCAT 58.276 37.500 14.14 0.00 36.02 2.45
3712 4566 2.627945 CGAGGTTTTATGCCTGTGCTA 58.372 47.619 0.00 0.00 36.29 3.49
3719 4580 0.323087 ACCACCCGAGGTTTTATGCC 60.323 55.000 0.00 0.00 39.34 4.40
3809 4694 4.855715 TTTTTGCGGTATTGTTCATCCA 57.144 36.364 0.00 0.00 0.00 3.41
3890 4776 7.451255 TCATGAAGGAGCCAAAAGAAAATCTTA 59.549 33.333 0.00 0.00 35.27 2.10
3899 4785 3.415212 TCTGTCATGAAGGAGCCAAAAG 58.585 45.455 0.00 0.00 0.00 2.27
3922 4812 6.741992 TGTGCAGAATATTTCTTGTACTGG 57.258 37.500 13.58 0.00 38.11 4.00
3960 4850 7.812191 GCACAACTCACATTTGAATAATGGTAA 59.188 33.333 0.00 0.00 32.14 2.85
4036 5375 3.067320 GGAATCCCAGCAATTAAGAGCAC 59.933 47.826 4.93 0.00 0.00 4.40
4123 5462 2.696707 CAAGAGCAATTGGGCCATACAT 59.303 45.455 7.26 0.00 0.00 2.29
4126 5465 2.241941 TCTCAAGAGCAATTGGGCCATA 59.758 45.455 7.26 0.00 30.29 2.74
4171 5510 8.994429 ATTTTACCATTTCGTTGCATCAATAA 57.006 26.923 0.00 0.00 0.00 1.40
4175 5514 6.266168 AGATTTTACCATTTCGTTGCATCA 57.734 33.333 0.00 0.00 0.00 3.07
4233 5576 3.701664 TCAGATCAGCCTTGAGTAGACA 58.298 45.455 0.00 0.00 36.61 3.41
4277 5620 1.952296 AGCTGGTCTTGAAACTTGCTG 59.048 47.619 0.00 0.00 0.00 4.41
4279 5622 2.603173 CGAAGCTGGTCTTGAAACTTGC 60.603 50.000 0.00 0.00 34.56 4.01
4305 5648 4.260784 GCTTTATAGATGCTGGTCAAACCG 60.261 45.833 0.00 0.00 42.58 4.44
4494 5842 4.518970 ACTACTTGGTTTCGCATGAACATT 59.481 37.500 0.00 0.00 32.71 2.71
4495 5843 4.072131 ACTACTTGGTTTCGCATGAACAT 58.928 39.130 0.00 0.00 32.71 2.71
4496 5844 3.472652 ACTACTTGGTTTCGCATGAACA 58.527 40.909 0.00 0.00 32.71 3.18
4497 5845 4.689345 ACTACTACTTGGTTTCGCATGAAC 59.311 41.667 0.00 0.00 32.71 3.18
4498 5846 4.688879 CACTACTACTTGGTTTCGCATGAA 59.311 41.667 0.00 0.00 0.00 2.57
4510 5858 3.893720 ACCGACGAAACACTACTACTTG 58.106 45.455 0.00 0.00 0.00 3.16
4511 5859 5.689383 TTACCGACGAAACACTACTACTT 57.311 39.130 0.00 0.00 0.00 2.24
4576 5925 8.470679 GCATGTGCAAAATTAACAAATTTGAAC 58.529 29.630 24.64 0.00 41.14 3.18
4583 5932 9.661187 CATTTTAGCATGTGCAAAATTAACAAA 57.339 25.926 17.42 2.48 45.16 2.83
4586 5935 9.662545 AAACATTTTAGCATGTGCAAAATTAAC 57.337 25.926 17.42 0.00 45.16 2.01
4589 5938 9.662545 GTTAAACATTTTAGCATGTGCAAAATT 57.337 25.926 17.42 11.41 45.16 1.82
4590 5939 8.288913 GGTTAAACATTTTAGCATGTGCAAAAT 58.711 29.630 7.83 12.92 45.16 1.82
4609 5960 8.745837 GCGAAGTTTTAGGTAAAAAGGTTAAAC 58.254 33.333 0.00 0.00 37.74 2.01
4617 5968 6.293571 GCTACCTGCGAAGTTTTAGGTAAAAA 60.294 38.462 12.23 0.00 43.19 1.94


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

AutoCloner maintained by Alex Coulton.