Multiple sequence alignment - TraesCS3D01G530300

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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 TraesCS3D01G530300 chr3D 100.000 3850 0 0 1 3850 607066690 607062841 0.000000e+00 7110
1 TraesCS3D01G530300 chr3D 86.471 170 18 4 1788 1952 132031134 132030965 8.500000e-42 182
2 TraesCS3D01G530300 chr3A 87.590 3183 218 92 19 3144 739520121 739517059 0.000000e+00 3526
3 TraesCS3D01G530300 chr3A 93.994 666 28 8 3192 3850 739517054 739516394 0.000000e+00 998
4 TraesCS3D01G530300 chr3B 91.512 1673 98 24 2193 3850 816519828 816518185 0.000000e+00 2263
5 TraesCS3D01G530300 chr3B 95.462 1190 45 3 16 1202 816521997 816520814 0.000000e+00 1890
6 TraesCS3D01G530300 chr3B 85.833 840 79 14 1229 2055 816520821 816520009 0.000000e+00 856
7 TraesCS3D01G530300 chr3B 75.436 574 75 27 16 581 820499544 820499029 6.480000e-53 219
8 TraesCS3D01G530300 chr7B 76.125 578 77 23 16 586 709219836 709220359 2.970000e-61 246
9 TraesCS3D01G530300 chr7B 78.882 322 32 17 1789 2103 652701239 652700947 6.570000e-43 185
10 TraesCS3D01G530300 chr7B 85.799 169 20 4 1788 1952 43126816 43126648 3.950000e-40 176
11 TraesCS3D01G530300 chr4D 79.567 323 30 19 1788 2103 505006119 505005826 8.440000e-47 198
12 TraesCS3D01G530300 chr1D 87.059 170 17 4 1788 1952 225721479 225721310 1.830000e-43 187
13 TraesCS3D01G530300 chr7D 86.471 170 17 4 1788 1952 185423346 185423514 8.500000e-42 182
14 TraesCS3D01G530300 chr2B 86.391 169 19 4 1788 1952 387368217 387368049 8.500000e-42 182
15 TraesCS3D01G530300 chr1A 92.771 83 6 0 3636 3718 12157669 12157751 1.880000e-23 121


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 TraesCS3D01G530300 chr3D 607062841 607066690 3849 True 7110.000000 7110 100.000000 1 3850 1 chr3D.!!$R2 3849
1 TraesCS3D01G530300 chr3A 739516394 739520121 3727 True 2262.000000 3526 90.792000 19 3850 2 chr3A.!!$R1 3831
2 TraesCS3D01G530300 chr3B 816518185 816521997 3812 True 1669.666667 2263 90.935667 16 3850 3 chr3B.!!$R2 3834
3 TraesCS3D01G530300 chr3B 820499029 820499544 515 True 219.000000 219 75.436000 16 581 1 chr3B.!!$R1 565
4 TraesCS3D01G530300 chr7B 709219836 709220359 523 False 246.000000 246 76.125000 16 586 1 chr7B.!!$F1 570

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
457 469 0.038166 TTGGAGAATGGTGACCAGGC 59.962 55.0 11.23 4.29 36.75 4.85 F
1027 1050 0.032952 TGTCAGTTACAGTGACCCGC 59.967 55.0 8.85 0.00 45.57 6.13 F
1372 1398 0.106149 AACTTGTTCTCGCCGGTTCT 59.894 50.0 1.90 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1676 0.578211 TCGCGACGTGGAAACTTTTC 59.422 50.0 3.71 0.0 36.46 2.29 R
2675 2826 0.191064 TTCCTCACCTCTGGACACCT 59.809 55.0 0.00 0.0 31.24 4.00 R
3371 3552 0.601558 TTGTCCACTAGGCTGTCGTC 59.398 55.0 0.00 0.0 33.74 4.20 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
41 42 2.158623 TGCCAGAGTGGTGAAAAGTGAT 60.159 45.455 0.00 0.00 40.46 3.06
58 59 6.575162 AAGTGATCCAATAAAGAACCACAC 57.425 37.500 0.00 0.00 0.00 3.82
457 469 0.038166 TTGGAGAATGGTGACCAGGC 59.962 55.000 11.23 4.29 36.75 4.85
477 489 1.208052 CTTTCCAGAAGGGCGAGATCA 59.792 52.381 0.00 0.00 36.21 2.92
487 499 1.220529 GGCGAGATCATGCGATTTGA 58.779 50.000 6.80 0.00 29.66 2.69
586 598 0.947244 GTGGGAGACAAGTGCAAGTG 59.053 55.000 0.00 0.00 0.00 3.16
618 630 5.421693 TGCAATAACTTGGGTATTGAGCAAT 59.578 36.000 16.49 0.97 34.17 3.56
623 635 3.056607 ACTTGGGTATTGAGCAATGCAAC 60.057 43.478 8.35 1.42 35.50 4.17
624 636 2.523245 TGGGTATTGAGCAATGCAACA 58.477 42.857 8.35 4.41 35.50 3.33
725 738 3.930336 TCCTCAACTCATACAGCAACAG 58.070 45.455 0.00 0.00 0.00 3.16
761 779 7.237982 TCTGAAACTCCTATTTCCCATTTTCA 58.762 34.615 0.00 0.00 37.72 2.69
845 864 4.184649 TCCTCCTTTTGCCTTCTTTTCT 57.815 40.909 0.00 0.00 0.00 2.52
876 895 4.434713 ACTTTTGAGTCACCAACAACAC 57.565 40.909 0.00 0.00 0.00 3.32
1027 1050 0.032952 TGTCAGTTACAGTGACCCGC 59.967 55.000 8.85 0.00 45.57 6.13
1029 1052 1.736645 CAGTTACAGTGACCCGCCG 60.737 63.158 0.00 0.00 0.00 6.46
1200 1223 1.597742 TGTTGTTCCTTGCTCTCTGC 58.402 50.000 0.00 0.00 43.25 4.26
1240 1263 6.624352 TTGGTTTCATTTCACTCTGAGAAG 57.376 37.500 12.44 3.66 0.00 2.85
1271 1294 0.643820 GTTTCGTTATGAGGCGACGG 59.356 55.000 0.00 0.00 36.82 4.79
1299 1322 3.062639 CGTTTGGTTTCTGATCTGATCCG 59.937 47.826 14.71 8.82 0.00 4.18
1372 1398 0.106149 AACTTGTTCTCGCCGGTTCT 59.894 50.000 1.90 0.00 0.00 3.01
1379 1405 1.961277 CTCGCCGGTTCTTGTTGCT 60.961 57.895 1.90 0.00 0.00 3.91
1395 1421 3.133901 TGTTGCTCTGTGACAGGTTCTTA 59.866 43.478 13.33 0.00 31.51 2.10
1402 1428 6.238759 GCTCTGTGACAGGTTCTTACATTTTT 60.239 38.462 13.33 0.00 31.51 1.94
1456 1482 2.930950 CTGTTGAACCTTTCCTGACCA 58.069 47.619 0.00 0.00 0.00 4.02
1508 1534 4.157649 GTTTTTGTGGTTGCTTGCAAAAG 58.842 39.130 9.75 0.00 40.42 2.27
1631 1660 7.836183 AGAATGATCTAAAGTTGGGTGCTTTAT 59.164 33.333 0.00 0.00 37.65 1.40
1647 1676 6.293845 GGTGCTTTATTCATTCTAGCTCATGG 60.294 42.308 0.00 0.00 33.15 3.66
1674 1703 1.136774 CCACGTCGCGAGATTGAGA 59.863 57.895 10.24 0.00 45.19 3.27
1696 1725 5.652452 AGAAAGTTGACTGCACCTTTTAACT 59.348 36.000 0.00 0.00 36.95 2.24
1699 1728 7.582667 AAGTTGACTGCACCTTTTAACTAAT 57.417 32.000 0.00 0.00 0.00 1.73
1727 1762 5.640147 AGACAGAAGGATCCGATTAGATCT 58.360 41.667 5.98 0.00 42.02 2.75
1888 1933 2.549332 GCAGGAGGAACACTGCTTC 58.451 57.895 9.22 0.00 46.85 3.86
1942 1988 3.282885 CTTTCCCTTGTGCCTTCTATCC 58.717 50.000 0.00 0.00 0.00 2.59
1943 1989 1.213296 TCCCTTGTGCCTTCTATCCC 58.787 55.000 0.00 0.00 0.00 3.85
1947 1993 2.648059 CTTGTGCCTTCTATCCCCAAG 58.352 52.381 0.00 0.00 0.00 3.61
1975 2021 4.096833 TGCTGGAATTACTGCTATGCAAAG 59.903 41.667 19.07 0.00 38.41 2.77
1982 2028 7.910683 GGAATTACTGCTATGCAAAGTAACTTC 59.089 37.037 13.55 15.23 38.41 3.01
1987 2033 5.868257 TGCTATGCAAAGTAACTTCGATTG 58.132 37.500 0.00 0.00 34.76 2.67
1993 2039 4.956184 GCAAAGTAACTTCGATTGCGTATC 59.044 41.667 2.25 0.00 37.27 2.24
2003 2049 6.688385 ACTTCGATTGCGTATCAATTTTGATG 59.312 34.615 14.54 2.03 44.95 3.07
2011 2057 7.951287 TGCGTATCAATTTTGATGAAAACATG 58.049 30.769 14.54 0.00 46.68 3.21
2015 2061 5.002516 TCAATTTTGATGAAAACATGGCCC 58.997 37.500 0.00 0.00 33.86 5.80
2020 2066 2.225091 TGATGAAAACATGGCCCTGAGT 60.225 45.455 15.66 0.00 0.00 3.41
2033 2079 4.764823 TGGCCCTGAGTTAATAAACTGTTG 59.235 41.667 0.00 0.00 46.09 3.33
2056 2102 5.105432 TGCTGCTGGAAATGCATTTACAATA 60.105 36.000 31.57 22.96 39.91 1.90
2057 2103 5.987347 GCTGCTGGAAATGCATTTACAATAT 59.013 36.000 31.57 7.84 39.91 1.28
2059 2105 7.517734 GCTGCTGGAAATGCATTTACAATATTG 60.518 37.037 31.57 22.26 39.91 1.90
2063 2109 9.976511 CTGGAAATGCATTTACAATATTGAGAT 57.023 29.630 31.57 4.48 39.91 2.75
2064 2110 9.970395 TGGAAATGCATTTACAATATTGAGATC 57.030 29.630 30.57 11.27 37.65 2.75
2083 2131 7.004086 TGAGATCTTTTTGTGAATAAGGGTGT 58.996 34.615 0.00 0.00 0.00 4.16
2084 2132 7.040478 TGAGATCTTTTTGTGAATAAGGGTGTG 60.040 37.037 0.00 0.00 0.00 3.82
2085 2133 7.004086 AGATCTTTTTGTGAATAAGGGTGTGA 58.996 34.615 0.00 0.00 0.00 3.58
2086 2134 6.633500 TCTTTTTGTGAATAAGGGTGTGAG 57.367 37.500 0.00 0.00 0.00 3.51
2098 2146 1.003580 GGGTGTGAGCAATCTGGAGAA 59.996 52.381 0.00 0.00 0.00 2.87
2099 2147 2.356535 GGGTGTGAGCAATCTGGAGAAT 60.357 50.000 0.00 0.00 0.00 2.40
2158 2271 4.823989 CAGAGTGATTTTGTTTGTCCCTCT 59.176 41.667 0.00 0.00 0.00 3.69
2162 2275 6.601332 AGTGATTTTGTTTGTCCCTCTCTTA 58.399 36.000 0.00 0.00 0.00 2.10
2165 2278 7.648112 GTGATTTTGTTTGTCCCTCTCTTAAAC 59.352 37.037 0.00 0.00 33.20 2.01
2166 2279 7.340743 TGATTTTGTTTGTCCCTCTCTTAAACA 59.659 33.333 0.00 0.00 38.88 2.83
2167 2280 7.469537 TTTTGTTTGTCCCTCTCTTAAACAA 57.530 32.000 8.87 8.87 44.60 2.83
2172 2285 5.367945 TGTCCCTCTCTTAAACAAAGTGT 57.632 39.130 0.00 0.00 36.51 3.55
2175 2288 5.467063 GTCCCTCTCTTAAACAAAGTGTCAG 59.533 44.000 0.00 0.00 36.51 3.51
2183 2296 4.574599 AAACAAAGTGTCAGATGGCTTC 57.425 40.909 0.00 0.00 0.00 3.86
2188 2301 2.719739 AGTGTCAGATGGCTTCATTGG 58.280 47.619 3.03 0.00 0.00 3.16
2260 2407 5.505780 TCACTAATGGGGTTTACTTGATGG 58.494 41.667 0.00 0.00 0.00 3.51
2353 2500 6.778069 CACTCCCATCTTCTCAAGGTACTATA 59.222 42.308 0.00 0.00 38.49 1.31
2354 2501 7.453126 CACTCCCATCTTCTCAAGGTACTATAT 59.547 40.741 0.00 0.00 38.49 0.86
2387 2534 9.893634 CTATATCTATATATCCCTCCTACGTGG 57.106 40.741 0.00 0.00 30.72 4.94
2395 2542 1.041447 CCTCCTACGTGGGAATCGGT 61.041 60.000 21.99 0.00 34.66 4.69
2396 2543 0.384669 CTCCTACGTGGGAATCGGTC 59.615 60.000 21.99 0.00 34.66 4.79
2426 2574 4.346129 GGCACGAAAAACTCATCATCATC 58.654 43.478 0.00 0.00 0.00 2.92
2427 2575 4.142622 GGCACGAAAAACTCATCATCATCA 60.143 41.667 0.00 0.00 0.00 3.07
2428 2576 4.790140 GCACGAAAAACTCATCATCATCAC 59.210 41.667 0.00 0.00 0.00 3.06
2443 2591 6.779860 TCATCATCACCATCATCTGATCATT 58.220 36.000 0.00 0.00 31.21 2.57
2513 2661 1.596603 CATCGCCACCTGCATATGAA 58.403 50.000 6.97 0.00 41.33 2.57
2567 2715 3.403558 GACCCTGAGCCTGACCCC 61.404 72.222 0.00 0.00 0.00 4.95
2713 2864 1.742761 AGATGATGGTCGCCTGTTTG 58.257 50.000 0.00 0.00 0.00 2.93
2774 2926 2.419990 GCCTTTTGTTTTCAGGCCTGTT 60.420 45.455 31.58 0.00 39.57 3.16
2810 2962 0.760189 AGGAGAGGCTGCAGAGGATC 60.760 60.000 20.43 9.32 0.00 3.36
2875 3027 9.704098 GTTAACTATAAGCTCTAATTGTGTTGC 57.296 33.333 0.00 0.00 0.00 4.17
2910 3062 1.082690 GAGCAGTTCTAAGCCTGTGC 58.917 55.000 0.00 0.00 37.95 4.57
2953 3107 9.203163 ACTATATAACCTTGGCTATCCATCTAC 57.797 37.037 0.00 0.00 43.05 2.59
2961 3120 5.745312 TGGCTATCCATCTACCAATACAG 57.255 43.478 0.00 0.00 37.47 2.74
3022 3201 7.865385 TCAAATTAATGTGCTTCTTTGGTGTAC 59.135 33.333 0.22 0.00 0.00 2.90
3023 3202 6.892658 ATTAATGTGCTTCTTTGGTGTACA 57.107 33.333 0.00 0.00 0.00 2.90
3047 3226 7.766278 ACATACTGAGAGGATTAACATGAACAC 59.234 37.037 0.00 0.00 0.00 3.32
3075 3254 4.523943 CAGTGTTCCATTGAGATTTTCCCA 59.476 41.667 0.00 0.00 0.00 4.37
3121 3300 7.614499 GCGACGTCAAATAATTTCAGTTCAAAC 60.614 37.037 17.16 0.00 0.00 2.93
3123 3302 9.233232 GACGTCAAATAATTTCAGTTCAAACTT 57.767 29.630 11.55 0.00 37.08 2.66
3177 3356 5.548056 AGAACTGGAGTAAAATGGGAGAAGA 59.452 40.000 0.00 0.00 0.00 2.87
3190 3369 5.282055 TGGGAGAAGAATATACACAGCAG 57.718 43.478 0.00 0.00 0.00 4.24
3364 3545 0.876342 GGAGGATTAACAGCGGCGAG 60.876 60.000 12.98 4.29 0.00 5.03
3369 3550 2.029649 GGATTAACAGCGGCGAGGTATA 60.030 50.000 12.98 0.00 0.00 1.47
3370 3551 2.497107 TTAACAGCGGCGAGGTATAC 57.503 50.000 12.98 0.00 0.00 1.47
3371 3552 0.308684 TAACAGCGGCGAGGTATACG 59.691 55.000 12.98 0.00 0.00 3.06
3377 3558 2.016961 GGCGAGGTATACGACGACA 58.983 57.895 19.30 0.00 33.43 4.35
3544 3725 1.172812 GCCTGTCCCTGCGAGTTTTT 61.173 55.000 0.00 0.00 0.00 1.94
3575 3756 4.395231 GGAATGAGTTTGGTAGTAAGTGCC 59.605 45.833 0.00 0.00 0.00 5.01
3705 3886 3.833265 GTCGACGACACCGATTTTCTCG 61.833 54.545 22.66 0.00 38.57 4.04
3717 3898 0.106708 TTTTCTCGTGAGCAGGCTGT 59.893 50.000 17.16 2.59 0.00 4.40
3737 3918 9.662947 AGGCTGTAAAGAGTAAATACGTTAATT 57.337 29.630 0.00 0.00 0.00 1.40
3739 3920 9.698617 GCTGTAAAGAGTAAATACGTTAATTGG 57.301 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.405831 CATGTCTTTGCTCTGTTCTCCA 58.594 45.455 0.00 0.00 0.00 3.86
1 2 2.161211 GCATGTCTTTGCTCTGTTCTCC 59.839 50.000 0.00 0.00 39.57 3.71
2 3 2.161211 GGCATGTCTTTGCTCTGTTCTC 59.839 50.000 0.00 0.00 42.38 2.87
3 4 2.157738 GGCATGTCTTTGCTCTGTTCT 58.842 47.619 0.00 0.00 42.38 3.01
4 5 1.881973 TGGCATGTCTTTGCTCTGTTC 59.118 47.619 0.00 0.00 42.38 3.18
5 6 1.884579 CTGGCATGTCTTTGCTCTGTT 59.115 47.619 0.00 0.00 42.38 3.16
6 7 1.072806 TCTGGCATGTCTTTGCTCTGT 59.927 47.619 0.00 0.00 42.38 3.41
7 8 1.738350 CTCTGGCATGTCTTTGCTCTG 59.262 52.381 0.00 0.00 42.38 3.35
8 9 1.350351 ACTCTGGCATGTCTTTGCTCT 59.650 47.619 0.00 0.00 42.38 4.09
9 10 1.467734 CACTCTGGCATGTCTTTGCTC 59.532 52.381 0.00 0.00 42.38 4.26
10 11 1.531423 CACTCTGGCATGTCTTTGCT 58.469 50.000 0.00 0.00 42.38 3.91
11 12 0.524862 CCACTCTGGCATGTCTTTGC 59.475 55.000 0.00 0.00 42.01 3.68
12 13 1.538512 CACCACTCTGGCATGTCTTTG 59.461 52.381 0.00 0.00 42.67 2.77
13 14 1.421268 TCACCACTCTGGCATGTCTTT 59.579 47.619 0.00 0.00 42.67 2.52
14 15 1.059098 TCACCACTCTGGCATGTCTT 58.941 50.000 0.00 0.00 42.67 3.01
41 42 5.505780 CCCTATGTGTGGTTCTTTATTGGA 58.494 41.667 0.00 0.00 0.00 3.53
457 469 1.208052 TGATCTCGCCCTTCTGGAAAG 59.792 52.381 0.00 0.00 35.39 2.62
477 489 2.012673 GTGGAAGCTCTCAAATCGCAT 58.987 47.619 0.00 0.00 0.00 4.73
607 619 3.220507 TGCTGTTGCATTGCTCAATAC 57.779 42.857 10.49 1.58 45.31 1.89
624 636 9.923143 GGTACCTTGAACTTAAATAAATTTGCT 57.077 29.630 4.06 0.00 0.00 3.91
761 779 1.396996 CGAGGAATTGTTTTCGCCGAT 59.603 47.619 0.00 0.00 0.00 4.18
799 817 6.855836 TGCATAAAGAGACAACATGGATTTC 58.144 36.000 0.00 0.00 0.00 2.17
845 864 3.006967 GTGACTCAAAAGTAGGAGCAGGA 59.993 47.826 0.00 0.00 35.28 3.86
1083 1106 2.903855 GCATCCACCTCCATGGCG 60.904 66.667 6.96 0.00 39.85 5.69
1173 1196 1.202348 GCAAGGAACAACATACCTGGC 59.798 52.381 0.00 0.00 42.38 4.85
1200 1223 6.540914 TGAAACCAAACAACAGTTAGTAGGAG 59.459 38.462 11.11 0.00 0.00 3.69
1251 1274 1.342555 CGTCGCCTCATAACGAAACA 58.657 50.000 0.00 0.00 40.47 2.83
1271 1294 0.741915 TCAGAAACCAAACGGCAACC 59.258 50.000 0.00 0.00 0.00 3.77
1299 1322 5.011635 ACCCAATAAACCATGAAGAAACCAC 59.988 40.000 0.00 0.00 0.00 4.16
1372 1398 2.092968 AGAACCTGTCACAGAGCAACAA 60.093 45.455 6.30 0.00 32.44 2.83
1379 1405 7.054124 AGAAAAATGTAAGAACCTGTCACAGA 58.946 34.615 6.30 0.00 32.44 3.41
1444 1470 5.990120 ATCTGAAAAATGGTCAGGAAAGG 57.010 39.130 1.85 0.00 42.37 3.11
1508 1534 4.790765 AAGCAAGGCTCCAAGTTAATTC 57.209 40.909 0.00 0.00 38.25 2.17
1631 1660 7.765695 AAACTTTTCCATGAGCTAGAATGAA 57.234 32.000 0.00 0.00 0.00 2.57
1647 1676 0.578211 TCGCGACGTGGAAACTTTTC 59.422 50.000 3.71 0.00 36.46 2.29
1696 1725 7.782897 ATCGGATCCTTCTGTCTTGATATTA 57.217 36.000 10.75 0.00 0.00 0.98
1699 1728 7.004691 TCTAATCGGATCCTTCTGTCTTGATA 58.995 38.462 10.75 0.00 0.00 2.15
1727 1762 5.782047 CTGTAAGCAAATCCAATCCAACAA 58.218 37.500 0.00 0.00 0.00 2.83
1771 1811 7.805071 CCATCTTCTGAGTAACATCAACAAAAC 59.195 37.037 0.00 0.00 0.00 2.43
1930 1976 1.282157 ACACTTGGGGATAGAAGGCAC 59.718 52.381 0.00 0.00 0.00 5.01
1942 1988 3.573967 AGTAATTCCAGCAAACACTTGGG 59.426 43.478 0.00 0.00 32.76 4.12
1943 1989 4.549458 CAGTAATTCCAGCAAACACTTGG 58.451 43.478 0.00 0.00 32.76 3.61
1947 1993 3.923017 AGCAGTAATTCCAGCAAACAC 57.077 42.857 0.00 0.00 0.00 3.32
1975 2021 7.690637 TCAAAATTGATACGCAATCGAAGTTAC 59.309 33.333 0.00 0.00 46.25 2.50
1982 2028 7.435203 TTTCATCAAAATTGATACGCAATCG 57.565 32.000 8.24 0.00 46.25 3.34
1987 2033 7.393327 CCATGTTTTCATCAAAATTGATACGC 58.607 34.615 8.24 0.19 45.62 4.42
1989 2035 7.201635 GGGCCATGTTTTCATCAAAATTGATAC 60.202 37.037 4.39 4.50 45.62 2.24
1993 2039 5.005094 AGGGCCATGTTTTCATCAAAATTG 58.995 37.500 6.18 0.00 38.64 2.32
2003 2049 6.524101 TTATTAACTCAGGGCCATGTTTTC 57.476 37.500 18.43 0.00 0.00 2.29
2011 2057 4.380550 GCAACAGTTTATTAACTCAGGGCC 60.381 45.833 0.00 0.00 42.67 5.80
2015 2061 6.082338 CAGCAGCAACAGTTTATTAACTCAG 58.918 40.000 0.00 0.00 42.67 3.35
2020 2066 6.398234 TTTCCAGCAGCAACAGTTTATTAA 57.602 33.333 0.00 0.00 0.00 1.40
2033 2079 3.235157 TGTAAATGCATTTCCAGCAGC 57.765 42.857 27.28 10.78 46.36 5.25
2056 2102 8.526147 CACCCTTATTCACAAAAAGATCTCAAT 58.474 33.333 0.00 0.00 0.00 2.57
2057 2103 7.505585 ACACCCTTATTCACAAAAAGATCTCAA 59.494 33.333 0.00 0.00 0.00 3.02
2059 2105 7.174946 TCACACCCTTATTCACAAAAAGATCTC 59.825 37.037 0.00 0.00 0.00 2.75
2063 2109 5.009610 GCTCACACCCTTATTCACAAAAAGA 59.990 40.000 0.00 0.00 0.00 2.52
2064 2110 5.221224 TGCTCACACCCTTATTCACAAAAAG 60.221 40.000 0.00 0.00 0.00 2.27
2068 2116 3.500448 TGCTCACACCCTTATTCACAA 57.500 42.857 0.00 0.00 0.00 3.33
2083 2131 2.199208 TGGGATTCTCCAGATTGCTCA 58.801 47.619 0.00 0.00 38.64 4.26
2084 2132 3.287867 TTGGGATTCTCCAGATTGCTC 57.712 47.619 0.00 0.00 38.64 4.26
2085 2133 3.744940 TTTGGGATTCTCCAGATTGCT 57.255 42.857 0.00 0.00 38.64 3.91
2086 2134 3.703052 ACATTTGGGATTCTCCAGATTGC 59.297 43.478 0.00 0.00 38.64 3.56
2098 2146 7.988937 TCAGGAGCTATATAAACATTTGGGAT 58.011 34.615 0.00 0.00 0.00 3.85
2099 2147 7.387265 TCAGGAGCTATATAAACATTTGGGA 57.613 36.000 0.00 0.00 0.00 4.37
2130 2220 6.255670 GGGACAAACAAAATCACTCTGTTTTC 59.744 38.462 0.00 0.00 40.40 2.29
2149 2262 5.751586 ACACTTTGTTTAAGAGAGGGACAA 58.248 37.500 0.00 0.00 37.30 3.18
2158 2271 5.376625 AGCCATCTGACACTTTGTTTAAGA 58.623 37.500 0.00 0.00 37.30 2.10
2162 2275 3.953612 TGAAGCCATCTGACACTTTGTTT 59.046 39.130 0.00 0.00 0.00 2.83
2165 2278 4.482386 CAATGAAGCCATCTGACACTTTG 58.518 43.478 0.00 0.00 31.40 2.77
2166 2279 3.508793 CCAATGAAGCCATCTGACACTTT 59.491 43.478 0.00 0.00 31.40 2.66
2167 2280 3.087031 CCAATGAAGCCATCTGACACTT 58.913 45.455 0.00 0.00 31.40 3.16
2172 2285 3.726557 AGAACCAATGAAGCCATCTGA 57.273 42.857 0.00 0.00 31.40 3.27
2175 2288 7.229306 TGTTATCATAGAACCAATGAAGCCATC 59.771 37.037 0.00 0.00 36.95 3.51
2227 2373 8.962679 GTAAACCCCATTAGTGATTCAACATTA 58.037 33.333 0.00 0.00 0.00 1.90
2228 2374 6.933514 AAACCCCATTAGTGATTCAACATT 57.066 33.333 0.00 0.00 0.00 2.71
2232 2378 7.235079 TCAAGTAAACCCCATTAGTGATTCAA 58.765 34.615 0.00 0.00 0.00 2.69
2395 2542 2.413211 TTTTTCGTGCCGGGATGGGA 62.413 55.000 15.88 2.66 38.63 4.37
2396 2543 1.974343 TTTTTCGTGCCGGGATGGG 60.974 57.895 15.88 0.00 38.63 4.00
2426 2574 4.134563 TCTGCAATGATCAGATGATGGTG 58.865 43.478 13.84 0.00 35.81 4.17
2427 2575 4.390264 CTCTGCAATGATCAGATGATGGT 58.610 43.478 13.84 0.00 39.56 3.55
2428 2576 3.753797 CCTCTGCAATGATCAGATGATGG 59.246 47.826 13.84 6.66 39.56 3.51
2443 2591 1.892819 CGAAGGCTTCCTCCTCTGCA 61.893 60.000 20.97 0.00 34.82 4.41
2498 2646 2.042686 TCACTTCATATGCAGGTGGC 57.957 50.000 7.30 0.00 45.13 5.01
2513 2661 2.171448 GCTCATCATGTAGGGGTTCACT 59.829 50.000 0.00 0.00 0.00 3.41
2567 2715 1.134461 CAGATGAACTGGGAGAGCAGG 60.134 57.143 0.00 0.00 42.39 4.85
2662 2813 2.821366 CACCTGCTGCCGGATGAC 60.821 66.667 17.38 0.00 0.00 3.06
2672 2823 1.152247 TCACCTCTGGACACCTGCT 60.152 57.895 0.00 0.00 0.00 4.24
2675 2826 0.191064 TTCCTCACCTCTGGACACCT 59.809 55.000 0.00 0.00 31.24 4.00
2713 2864 6.969473 GCTTAGCCATTGTAAATCTCTGAAAC 59.031 38.462 0.00 0.00 0.00 2.78
2875 3027 3.007398 ACTGCTCAAGAAACCCTAGACAG 59.993 47.826 0.00 0.00 0.00 3.51
2953 3107 6.578020 CAAAGTATGCAAATGCTGTATTGG 57.422 37.500 6.97 0.00 42.66 3.16
3022 3201 7.225538 GGTGTTCATGTTAATCCTCTCAGTATG 59.774 40.741 0.00 0.00 37.54 2.39
3023 3202 7.092891 TGGTGTTCATGTTAATCCTCTCAGTAT 60.093 37.037 0.00 0.00 0.00 2.12
3047 3226 5.909621 AATCTCAATGGAACACTGATTGG 57.090 39.130 0.00 0.00 45.92 3.16
3075 3254 5.049167 TCGCAAGCAAATGAAAATCAGTTT 58.951 33.333 0.00 0.00 31.77 2.66
3123 3302 9.280174 ACTTTACTATTCGTTTCCTTGAATTGA 57.720 29.630 3.99 0.00 36.32 2.57
3148 3327 7.664318 TCTCCCATTTTACTCCAGTTCTTTTAC 59.336 37.037 0.00 0.00 0.00 2.01
3152 3331 5.843019 TCTCCCATTTTACTCCAGTTCTT 57.157 39.130 0.00 0.00 0.00 2.52
3153 3332 5.548056 TCTTCTCCCATTTTACTCCAGTTCT 59.452 40.000 0.00 0.00 0.00 3.01
3155 3334 5.843019 TCTTCTCCCATTTTACTCCAGTT 57.157 39.130 0.00 0.00 0.00 3.16
3158 3337 8.998814 TGTATATTCTTCTCCCATTTTACTCCA 58.001 33.333 0.00 0.00 0.00 3.86
3177 3356 5.957771 TCTCCCTTTCTGCTGTGTATATT 57.042 39.130 0.00 0.00 0.00 1.28
3190 3369 2.421619 CTCTGTGTGCTTCTCCCTTTC 58.578 52.381 0.00 0.00 0.00 2.62
3364 3545 2.032204 CACTAGGCTGTCGTCGTATACC 60.032 54.545 0.00 0.00 0.00 2.73
3369 3550 1.303074 TCCACTAGGCTGTCGTCGT 60.303 57.895 0.00 0.00 33.74 4.34
3370 3551 1.136984 GTCCACTAGGCTGTCGTCG 59.863 63.158 0.00 0.00 33.74 5.12
3371 3552 0.601558 TTGTCCACTAGGCTGTCGTC 59.398 55.000 0.00 0.00 33.74 4.20
3377 3558 3.007614 ACGTAACATTTGTCCACTAGGCT 59.992 43.478 0.00 0.00 33.74 4.58
3544 3725 3.565307 ACCAAACTCATTCCTGCTTTCA 58.435 40.909 0.00 0.00 0.00 2.69
3575 3756 4.142315 CCCATCATAGAACAGCAAAACCTG 60.142 45.833 0.00 0.00 38.78 4.00
3705 3886 2.464157 ACTCTTTACAGCCTGCTCAC 57.536 50.000 0.00 0.00 0.00 3.51
3737 3918 3.885901 CGACCATCTTATCTCTGTCTCCA 59.114 47.826 0.00 0.00 0.00 3.86
3739 3920 5.060506 TCTCGACCATCTTATCTCTGTCTC 58.939 45.833 0.00 0.00 0.00 3.36
3820 4004 2.590575 AACCACACGCCCTTGTCG 60.591 61.111 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.