Multiple sequence alignment - TraesCS3D01G276600

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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 TraesCS3D01G276600 chr3D 100.000 4043 0 0 1 4043 383548886 383544844 0.000000e+00 7467.0
1 TraesCS3D01G276600 chr3A 97.178 1949 41 6 2097 4043 506442747 506440811 0.000000e+00 3282.0
2 TraesCS3D01G276600 chr3A 92.048 1660 82 23 359 1980 506444514 506442867 0.000000e+00 2289.0
3 TraesCS3D01G276600 chr3A 93.048 374 15 4 1 365 506444946 506444575 1.650000e-148 536.0
4 TraesCS3D01G276600 chr3B 90.031 1625 74 37 422 1980 499176456 499174854 0.000000e+00 2023.0
5 TraesCS3D01G276600 chr3B 92.876 1137 41 18 2931 4035 499173784 499172656 0.000000e+00 1615.0
6 TraesCS3D01G276600 chr3B 97.971 838 16 1 2097 2933 499174719 499173882 0.000000e+00 1452.0
7 TraesCS3D01G276600 chr3B 91.781 292 10 7 1 286 499177161 499176878 1.050000e-105 394.0
8 TraesCS3D01G276600 chr4D 96.491 57 0 2 1723 1778 341693321 341693266 4.300000e-15 93.5
9 TraesCS3D01G276600 chr1D 88.750 80 4 4 1723 1800 246650052 246649976 4.300000e-15 93.5
10 TraesCS3D01G276600 chr1B 89.474 76 4 3 1723 1797 507851819 507851747 4.300000e-15 93.5
11 TraesCS3D01G276600 chr1A 89.474 76 4 3 1723 1797 479836158 479836086 4.300000e-15 93.5
12 TraesCS3D01G276600 chr6A 94.737 57 3 0 1725 1781 540838701 540838757 5.570000e-14 89.8
13 TraesCS3D01G276600 chr2D 87.838 74 7 2 1723 1796 241661975 241662046 7.200000e-13 86.1
14 TraesCS3D01G276600 chr2A 88.000 75 5 3 1725 1798 612845894 612845965 7.200000e-13 86.1


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 TraesCS3D01G276600 chr3D 383544844 383548886 4042 True 7467.000000 7467 100.000000 1 4043 1 chr3D.!!$R1 4042
1 TraesCS3D01G276600 chr3A 506440811 506444946 4135 True 2035.666667 3282 94.091333 1 4043 3 chr3A.!!$R1 4042
2 TraesCS3D01G276600 chr3B 499172656 499177161 4505 True 1371.000000 2023 93.164750 1 4035 4 chr3B.!!$R1 4034

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
814 1154 0.177604 CCTTGCTCTCTCTTCCGCAT 59.822 55.000 0.00 0.0 31.77 4.73 F
861 1216 0.234884 CCGTTGGTCTCGCACTTTTC 59.765 55.000 0.00 0.0 0.00 2.29 F
1093 1448 0.906756 CCTGAGAGGAGGAGCACCAA 60.907 60.000 2.07 0.0 37.67 3.67 F
1335 1708 1.068954 GCACAAGGTAACAAGCAGCTC 60.069 52.381 0.00 0.0 41.41 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2522 0.321021 TACGGCGAAGGGCTAAACAA 59.679 50.000 16.62 0.00 42.94 2.83 R
2834 3279 0.322546 CCCTCAGCCTTTTAGCGGTT 60.323 55.000 0.00 0.00 38.01 4.44 R
2915 3360 3.133901 ACATGTACCTGATATCGGCACAA 59.866 43.478 17.73 7.26 0.00 3.33 R
3099 3644 2.192263 CCCCTGCTTCTTAGGAGTTCT 58.808 52.381 0.00 0.00 38.10 3.01 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
88 93 6.625960 CGGAATCTCTCTCTAAATGTGTCACA 60.626 42.308 8.40 8.40 0.00 3.58
121 126 2.112815 GGCCACACACCTAATCGGC 61.113 63.158 0.00 0.00 38.85 5.54
162 167 2.640302 GCACTCACGCTCTCCTCCA 61.640 63.158 0.00 0.00 0.00 3.86
191 201 0.458669 GGTCCAGATAAACGGAGCGA 59.541 55.000 0.00 0.00 39.78 4.93
357 434 0.804989 CAAGGTGCCATTTCTCGACC 59.195 55.000 0.00 0.00 0.00 4.79
361 438 0.744771 GTGCCATTTCTCGACCTCCC 60.745 60.000 0.00 0.00 0.00 4.30
367 678 2.167398 TTTCTCGACCTCCCGCTTGG 62.167 60.000 0.00 0.00 0.00 3.61
371 682 2.943978 CGACCTCCCGCTTGGTTCT 61.944 63.158 0.00 0.00 36.59 3.01
394 705 0.673022 GCTCATCATCATCGCCCCTC 60.673 60.000 0.00 0.00 0.00 4.30
396 707 1.375140 CATCATCATCGCCCCTCGG 60.375 63.158 0.00 0.00 39.05 4.63
406 717 3.551407 CCCCTCGGCCTCCTAAGC 61.551 72.222 0.00 0.00 0.00 3.09
420 731 1.338200 CCTAAGCCTCGCTTCAACTGT 60.338 52.381 1.42 0.00 46.77 3.55
428 739 1.066914 CGCTTCAACTGTCTGCTCTC 58.933 55.000 0.00 0.00 0.00 3.20
437 748 0.884514 TGTCTGCTCTCCTCAGTTCG 59.115 55.000 0.00 0.00 33.48 3.95
460 771 3.134458 CTCCTGGTGAGTTTCTGTGTTC 58.866 50.000 0.00 0.00 36.27 3.18
504 822 5.689383 TTGCTTTGCTAAGAGTAAAGTGG 57.311 39.130 12.29 0.00 45.67 4.00
507 838 4.515567 GCTTTGCTAAGAGTAAAGTGGTGT 59.484 41.667 12.29 0.00 45.67 4.16
569 900 3.033185 CAAACGGTTTTAACACGAGCTG 58.967 45.455 2.79 0.00 0.00 4.24
610 941 3.589495 TGATCTCTGACTTGACTGCTG 57.411 47.619 0.00 0.00 0.00 4.41
616 947 0.598419 TGACTTGACTGCTGCGAGTG 60.598 55.000 9.00 0.00 30.26 3.51
661 992 3.316588 CGCTAGCCATTCTTCTGTCTCTA 59.683 47.826 9.66 0.00 0.00 2.43
662 993 4.556501 CGCTAGCCATTCTTCTGTCTCTAG 60.557 50.000 9.66 0.00 0.00 2.43
663 994 3.817709 AGCCATTCTTCTGTCTCTAGC 57.182 47.619 0.00 0.00 0.00 3.42
664 995 2.100584 AGCCATTCTTCTGTCTCTAGCG 59.899 50.000 0.00 0.00 0.00 4.26
665 996 2.099921 GCCATTCTTCTGTCTCTAGCGA 59.900 50.000 0.00 0.00 0.00 4.93
666 997 3.243704 GCCATTCTTCTGTCTCTAGCGAT 60.244 47.826 0.00 0.00 0.00 4.58
667 998 4.545610 CCATTCTTCTGTCTCTAGCGATC 58.454 47.826 0.00 0.00 0.00 3.69
668 999 4.545610 CATTCTTCTGTCTCTAGCGATCC 58.454 47.826 0.00 0.00 0.00 3.36
710 1050 7.224167 CCGTATCCTTCATGTTTACTTCCTTAC 59.776 40.741 0.00 0.00 0.00 2.34
726 1066 3.887110 TCCTTACTGTCTTGTCTTGTCGA 59.113 43.478 0.00 0.00 0.00 4.20
808 1148 0.988063 GGTTCCCCTTGCTCTCTCTT 59.012 55.000 0.00 0.00 0.00 2.85
811 1151 0.972983 TCCCCTTGCTCTCTCTTCCG 60.973 60.000 0.00 0.00 0.00 4.30
813 1153 1.593787 CCTTGCTCTCTCTTCCGCA 59.406 57.895 0.00 0.00 0.00 5.69
814 1154 0.177604 CCTTGCTCTCTCTTCCGCAT 59.822 55.000 0.00 0.00 31.77 4.73
861 1216 0.234884 CCGTTGGTCTCGCACTTTTC 59.765 55.000 0.00 0.00 0.00 2.29
897 1252 6.459670 TGAGTGTACAACTGAACTTGTCTA 57.540 37.500 0.00 0.00 40.07 2.59
1093 1448 0.906756 CCTGAGAGGAGGAGCACCAA 60.907 60.000 2.07 0.00 37.67 3.67
1119 1474 1.200020 GGCAGATCGAAAAACACAGGG 59.800 52.381 0.00 0.00 0.00 4.45
1167 1522 1.303970 GCTGAAGCTTGGCCTTCCT 60.304 57.895 2.10 0.00 40.34 3.36
1182 1537 1.275291 CTTCCTGGCCTCGTACAAGAA 59.725 52.381 3.32 0.00 0.00 2.52
1335 1708 1.068954 GCACAAGGTAACAAGCAGCTC 60.069 52.381 0.00 0.00 41.41 4.09
1640 2035 3.181492 GCCTTTGCTATCTTTTCTGCTCC 60.181 47.826 0.00 0.00 33.53 4.70
1662 2057 1.080093 CAAGGAACTACGCCTGCGA 60.080 57.895 19.52 1.09 38.49 5.10
1746 2141 8.355169 GGACTAAAACGTGTCTATATACATCCA 58.645 37.037 4.05 0.00 34.01 3.41
1866 2266 4.652822 TCTAAGGCTCAAAGGTTTCCTTC 58.347 43.478 1.36 0.00 43.92 3.46
1953 2353 5.452777 GTCTGAAGACACTGTTATTTTGCC 58.547 41.667 5.58 0.00 44.18 4.52
1955 2355 4.211125 TGAAGACACTGTTATTTTGCCCA 58.789 39.130 0.00 0.00 0.00 5.36
1956 2356 4.832266 TGAAGACACTGTTATTTTGCCCAT 59.168 37.500 0.00 0.00 0.00 4.00
1957 2357 5.048083 TGAAGACACTGTTATTTTGCCCATC 60.048 40.000 0.00 0.00 0.00 3.51
1980 2381 5.588648 TCTTTTACAGTTTCTGTCTTGTGGG 59.411 40.000 5.66 0.00 41.21 4.61
1981 2382 4.764050 TTACAGTTTCTGTCTTGTGGGA 57.236 40.909 5.66 0.00 41.21 4.37
1982 2383 3.864789 ACAGTTTCTGTCTTGTGGGAT 57.135 42.857 0.00 0.00 41.21 3.85
1988 2398 7.942341 ACAGTTTCTGTCTTGTGGGATTATTAA 59.058 33.333 0.00 0.00 41.21 1.40
2017 2427 9.917887 ACATTCTAGTACAGTGGTAGTATAGTT 57.082 33.333 0.00 0.00 35.43 2.24
2071 2515 9.793259 AGAAAAAGTGAATACTAGAATGAACCA 57.207 29.630 0.00 0.00 35.69 3.67
2074 2518 9.739276 AAAAGTGAATACTAGAATGAACCATGA 57.261 29.630 0.00 0.00 35.69 3.07
2075 2519 9.739276 AAAGTGAATACTAGAATGAACCATGAA 57.261 29.630 0.00 0.00 35.69 2.57
2076 2520 8.723942 AGTGAATACTAGAATGAACCATGAAC 57.276 34.615 0.00 0.00 34.74 3.18
2077 2521 7.492669 AGTGAATACTAGAATGAACCATGAACG 59.507 37.037 0.00 0.00 34.74 3.95
2078 2522 7.277981 GTGAATACTAGAATGAACCATGAACGT 59.722 37.037 0.00 0.00 0.00 3.99
2079 2523 7.822334 TGAATACTAGAATGAACCATGAACGTT 59.178 33.333 0.00 0.00 0.00 3.99
2080 2524 5.862924 ACTAGAATGAACCATGAACGTTG 57.137 39.130 5.00 0.00 0.00 4.10
2081 2525 5.305585 ACTAGAATGAACCATGAACGTTGT 58.694 37.500 5.00 0.00 0.00 3.32
2082 2526 5.763204 ACTAGAATGAACCATGAACGTTGTT 59.237 36.000 5.00 3.00 0.00 2.83
2083 2527 5.514274 AGAATGAACCATGAACGTTGTTT 57.486 34.783 5.00 0.00 0.00 2.83
2084 2528 6.627395 AGAATGAACCATGAACGTTGTTTA 57.373 33.333 5.00 0.37 0.00 2.01
2085 2529 6.668323 AGAATGAACCATGAACGTTGTTTAG 58.332 36.000 5.00 0.00 0.00 1.85
2086 2530 4.217754 TGAACCATGAACGTTGTTTAGC 57.782 40.909 5.00 0.00 0.00 3.09
2087 2531 3.003897 TGAACCATGAACGTTGTTTAGCC 59.996 43.478 5.00 0.00 0.00 3.93
2088 2532 1.883926 ACCATGAACGTTGTTTAGCCC 59.116 47.619 5.00 0.00 0.00 5.19
2089 2533 2.159382 CCATGAACGTTGTTTAGCCCT 58.841 47.619 5.00 0.00 0.00 5.19
2090 2534 2.556622 CCATGAACGTTGTTTAGCCCTT 59.443 45.455 5.00 0.00 0.00 3.95
2091 2535 3.365969 CCATGAACGTTGTTTAGCCCTTC 60.366 47.826 5.00 0.00 0.00 3.46
2092 2536 1.868498 TGAACGTTGTTTAGCCCTTCG 59.132 47.619 5.00 0.00 0.00 3.79
2095 2539 1.500396 GTTGTTTAGCCCTTCGCCG 59.500 57.895 0.00 0.00 38.78 6.46
2684 3129 9.367717 GTGAATATACTCTAGTTTACGAAGACG 57.632 37.037 0.00 0.00 45.75 4.18
2759 3204 7.639113 TTGTTCCATCATATACAGTTTTCCC 57.361 36.000 0.00 0.00 0.00 3.97
2805 3250 4.870426 CGACACCATCTAAACTGCTTGTAT 59.130 41.667 0.00 0.00 0.00 2.29
2834 3279 2.401583 ACTGCAGTGTGTTTGTCTCA 57.598 45.000 20.97 0.00 0.00 3.27
2915 3360 4.301628 GCAGCTGCACTTTTCTGTTAATT 58.698 39.130 33.36 0.00 41.59 1.40
2929 3474 6.603237 TCTGTTAATTTGTGCCGATATCAG 57.397 37.500 3.12 0.00 0.00 2.90
2940 3485 5.163395 TGTGCCGATATCAGGTACATGTTTA 60.163 40.000 23.14 1.77 46.69 2.01
2974 3519 2.157421 GCCACAGCTGACTCTTTCG 58.843 57.895 23.35 0.00 35.50 3.46
3090 3635 1.580845 ATGTTGCTCACTGAAGCCGC 61.581 55.000 4.78 0.00 41.77 6.53
3099 3644 2.946329 TCACTGAAGCCGCAAACTAAAA 59.054 40.909 0.00 0.00 0.00 1.52
3185 3756 6.088541 TGAGGATTAGTAGTTCAGTACCCT 57.911 41.667 0.00 0.00 0.00 4.34
3186 3757 6.500336 TGAGGATTAGTAGTTCAGTACCCTT 58.500 40.000 0.00 0.00 0.00 3.95
3549 4125 6.142817 CCTTTCTAAATTTGTGGTCACGAAG 58.857 40.000 0.00 0.00 38.04 3.79
3659 4235 1.571955 TGCTCCTCTGTGCCAATAGA 58.428 50.000 0.00 0.00 0.00 1.98
3929 4507 0.309922 CTGCACACTGGCTTCAACTG 59.690 55.000 0.00 0.00 34.04 3.16
4013 4591 5.463061 CCAAACTGACGAAAGCAAATTGAAT 59.537 36.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.354773 GGACGATCGCGATGACCC 60.355 66.667 29.09 19.10 41.64 4.46
88 93 2.123726 GCCGGGGAGATTTGCCAT 60.124 61.111 2.18 0.00 36.32 4.40
228 238 4.936802 TCTTTTGTCCCTAGACTAGAGCT 58.063 43.478 11.27 0.00 43.91 4.09
231 241 7.728981 TCTTCTTTCTTTTGTCCCTAGACTAGA 59.271 37.037 11.27 0.00 43.91 2.43
232 242 7.897864 TCTTCTTTCTTTTGTCCCTAGACTAG 58.102 38.462 2.18 2.18 43.91 2.57
233 243 7.850935 TCTTCTTTCTTTTGTCCCTAGACTA 57.149 36.000 0.00 0.00 43.91 2.59
234 244 6.749036 TCTTCTTTCTTTTGTCCCTAGACT 57.251 37.500 0.00 0.00 43.91 3.24
235 245 7.520776 GCTTTCTTCTTTCTTTTGTCCCTAGAC 60.521 40.741 0.00 0.00 43.83 2.59
272 282 3.797546 GAGCTCCTTGCACGCTGC 61.798 66.667 0.87 3.44 45.94 5.25
357 434 1.078848 CTCCAGAACCAAGCGGGAG 60.079 63.158 4.35 0.00 40.43 4.30
361 438 0.392193 ATGAGCTCCAGAACCAAGCG 60.392 55.000 12.15 0.00 40.95 4.68
367 678 3.058450 CGATGATGATGAGCTCCAGAAC 58.942 50.000 12.15 0.86 0.00 3.01
371 682 0.034476 GGCGATGATGATGAGCTCCA 59.966 55.000 12.15 2.80 0.00 3.86
406 717 0.320247 AGCAGACAGTTGAAGCGAGG 60.320 55.000 0.00 0.00 0.00 4.63
420 731 1.169577 GACGAACTGAGGAGAGCAGA 58.830 55.000 0.00 0.00 36.86 4.26
428 739 0.244994 CACCAGGAGACGAACTGAGG 59.755 60.000 0.00 0.00 36.86 3.86
460 771 1.067516 CCAAAACCAGAAGCCACAGTG 59.932 52.381 0.00 0.00 0.00 3.66
504 822 4.211164 GCAACCTCTTTAATTGGCAAACAC 59.789 41.667 3.01 0.00 0.00 3.32
507 838 4.630111 CTGCAACCTCTTTAATTGGCAAA 58.370 39.130 3.01 0.00 0.00 3.68
569 900 6.381481 TCATGTCAAACAATCATATCAGCC 57.619 37.500 0.00 0.00 0.00 4.85
610 941 2.383527 CGCTGGAGGAAACACTCGC 61.384 63.158 0.00 0.00 38.39 5.03
616 947 0.169009 GTGCATTCGCTGGAGGAAAC 59.831 55.000 0.00 0.00 39.64 2.78
661 992 4.521062 GCTCGTGGCTGGATCGCT 62.521 66.667 0.00 0.00 38.06 4.93
726 1066 1.947456 GGAAGACAGAAGGTTTTGCGT 59.053 47.619 0.00 0.00 0.00 5.24
808 1148 1.573829 GGTCAAAGCGAACATGCGGA 61.574 55.000 0.00 0.00 40.67 5.54
811 1151 0.874390 TGAGGTCAAAGCGAACATGC 59.126 50.000 0.00 0.00 31.63 4.06
813 1153 2.571212 TGTTGAGGTCAAAGCGAACAT 58.429 42.857 0.00 0.00 37.63 2.71
814 1154 2.031258 TGTTGAGGTCAAAGCGAACA 57.969 45.000 0.00 0.00 37.63 3.18
861 1216 2.656560 ACACTCAACTTAGCCTAGCG 57.343 50.000 0.00 0.00 0.00 4.26
897 1252 9.848710 AAGAATTGATGTCAATGATATGAGAGT 57.151 29.630 8.86 0.00 45.06 3.24
1093 1448 0.038166 TTTTTCGATCTGCCCTGCCT 59.962 50.000 0.00 0.00 0.00 4.75
1119 1474 3.437795 TCCTCGTCGCTCCCGAAC 61.438 66.667 0.00 0.00 46.34 3.95
1167 1522 0.246635 GCTCTTCTTGTACGAGGCCA 59.753 55.000 5.01 0.00 0.00 5.36
1256 1614 3.484806 TGGTGGCCGTGGAGTGTT 61.485 61.111 0.00 0.00 0.00 3.32
1335 1708 2.861935 CCAAGCACAAAAGCACAAGAAG 59.138 45.455 0.00 0.00 36.85 2.85
1453 1845 0.890996 CTGCCAGTTCCTTCCCACAC 60.891 60.000 0.00 0.00 0.00 3.82
1640 2035 0.673644 CAGGCGTAGTTCCTTGGTGG 60.674 60.000 0.00 0.00 37.10 4.61
1662 2057 6.115446 TCCTCGAATGAACTATCAAAGCAAT 58.885 36.000 0.00 0.00 39.49 3.56
1778 2175 5.895534 TGTAAACTACTCCCTCGGTTCATAT 59.104 40.000 0.00 0.00 0.00 1.78
1786 2183 2.416972 GCCACTGTAAACTACTCCCTCG 60.417 54.545 0.00 0.00 0.00 4.63
1935 2335 5.079643 AGATGGGCAAAATAACAGTGTCTT 58.920 37.500 0.00 0.00 0.00 3.01
1938 2338 5.806654 AAAGATGGGCAAAATAACAGTGT 57.193 34.783 0.00 0.00 0.00 3.55
1945 2345 8.087750 CAGAAACTGTAAAAGATGGGCAAAATA 58.912 33.333 0.00 0.00 0.00 1.40
1946 2346 6.930722 CAGAAACTGTAAAAGATGGGCAAAAT 59.069 34.615 0.00 0.00 0.00 1.82
1948 2348 5.362430 ACAGAAACTGTAAAAGATGGGCAAA 59.638 36.000 2.43 0.00 43.46 3.68
1951 2351 4.762251 AGACAGAAACTGTAAAAGATGGGC 59.238 41.667 4.36 0.00 45.44 5.36
1952 2352 6.263168 ACAAGACAGAAACTGTAAAAGATGGG 59.737 38.462 4.36 0.00 45.44 4.00
1953 2353 7.134815 CACAAGACAGAAACTGTAAAAGATGG 58.865 38.462 4.36 0.00 45.44 3.51
1955 2355 6.263168 CCCACAAGACAGAAACTGTAAAAGAT 59.737 38.462 4.36 0.00 45.44 2.40
1956 2356 5.588648 CCCACAAGACAGAAACTGTAAAAGA 59.411 40.000 4.36 0.00 45.44 2.52
1957 2357 5.588648 TCCCACAAGACAGAAACTGTAAAAG 59.411 40.000 4.36 0.00 45.44 2.27
2019 2429 8.723942 ATTTGTACTGCAATTGTTACCAAAAA 57.276 26.923 7.40 4.53 36.89 1.94
2051 2495 7.492669 CGTTCATGGTTCATTCTAGTATTCACT 59.507 37.037 0.00 0.00 38.91 3.41
2064 2508 4.320935 GGCTAAACAACGTTCATGGTTCAT 60.321 41.667 0.00 0.00 0.00 2.57
2068 2512 1.883926 GGGCTAAACAACGTTCATGGT 59.116 47.619 0.00 0.00 0.00 3.55
2069 2513 2.159382 AGGGCTAAACAACGTTCATGG 58.841 47.619 0.00 0.00 0.00 3.66
2070 2514 3.666902 CGAAGGGCTAAACAACGTTCATG 60.667 47.826 0.00 0.00 0.00 3.07
2071 2515 2.482721 CGAAGGGCTAAACAACGTTCAT 59.517 45.455 0.00 0.00 0.00 2.57
2072 2516 1.868498 CGAAGGGCTAAACAACGTTCA 59.132 47.619 0.00 0.00 0.00 3.18
2073 2517 1.399343 GCGAAGGGCTAAACAACGTTC 60.399 52.381 0.00 0.00 39.11 3.95
2074 2518 0.589708 GCGAAGGGCTAAACAACGTT 59.410 50.000 0.00 0.00 39.11 3.99
2075 2519 1.232621 GGCGAAGGGCTAAACAACGT 61.233 55.000 0.00 0.00 42.94 3.99
2076 2520 1.500396 GGCGAAGGGCTAAACAACG 59.500 57.895 0.00 0.00 42.94 4.10
2077 2521 1.232621 ACGGCGAAGGGCTAAACAAC 61.233 55.000 16.62 0.00 42.94 3.32
2078 2522 0.321021 TACGGCGAAGGGCTAAACAA 59.679 50.000 16.62 0.00 42.94 2.83
2079 2523 0.321021 TTACGGCGAAGGGCTAAACA 59.679 50.000 16.62 0.00 42.94 2.83
2080 2524 1.441738 TTTACGGCGAAGGGCTAAAC 58.558 50.000 16.62 0.00 42.94 2.01
2081 2525 2.406596 ATTTACGGCGAAGGGCTAAA 57.593 45.000 16.62 7.28 42.94 1.85
2082 2526 3.555586 GGATATTTACGGCGAAGGGCTAA 60.556 47.826 16.62 0.00 42.94 3.09
2083 2527 2.028748 GGATATTTACGGCGAAGGGCTA 60.029 50.000 16.62 0.00 42.94 3.93
2084 2528 1.270678 GGATATTTACGGCGAAGGGCT 60.271 52.381 16.62 0.00 42.94 5.19
2085 2529 1.154197 GGATATTTACGGCGAAGGGC 58.846 55.000 16.62 0.00 42.51 5.19
2086 2530 2.413837 CTGGATATTTACGGCGAAGGG 58.586 52.381 16.62 0.00 0.00 3.95
2087 2531 1.798813 GCTGGATATTTACGGCGAAGG 59.201 52.381 16.62 0.00 0.00 3.46
2088 2532 2.755650 AGCTGGATATTTACGGCGAAG 58.244 47.619 16.62 0.00 43.59 3.79
2089 2533 2.902705 AGCTGGATATTTACGGCGAA 57.097 45.000 16.62 0.00 43.59 4.70
2090 2534 4.530710 AATAGCTGGATATTTACGGCGA 57.469 40.909 16.62 0.00 43.59 5.54
2091 2535 5.867716 ACTAAATAGCTGGATATTTACGGCG 59.132 40.000 4.80 4.80 43.59 6.46
2092 2536 6.313164 GGACTAAATAGCTGGATATTTACGGC 59.687 42.308 0.00 0.00 36.83 5.68
2684 3129 0.908198 AGCATCCTGTCTCCTTCACC 59.092 55.000 0.00 0.00 0.00 4.02
2759 3204 7.481798 GTCGAGGAGCTTAACACAAATAATTTG 59.518 37.037 0.00 0.00 45.95 2.32
2805 3250 9.146984 GACAAACACACTGCAGTAGTTATTATA 57.853 33.333 27.25 0.00 37.60 0.98
2834 3279 0.322546 CCCTCAGCCTTTTAGCGGTT 60.323 55.000 0.00 0.00 38.01 4.44
2915 3360 3.133901 ACATGTACCTGATATCGGCACAA 59.866 43.478 17.73 7.26 0.00 3.33
2929 3474 5.185056 AGTTTGGGCAATCTAAACATGTACC 59.815 40.000 0.00 0.00 45.57 3.34
2991 3536 5.829924 AGCTCCAATCTGAAACAAAAGAAGA 59.170 36.000 0.00 0.00 0.00 2.87
2992 3537 6.081872 AGCTCCAATCTGAAACAAAAGAAG 57.918 37.500 0.00 0.00 0.00 2.85
2993 3538 6.772716 AGTAGCTCCAATCTGAAACAAAAGAA 59.227 34.615 0.00 0.00 0.00 2.52
2994 3539 6.299141 AGTAGCTCCAATCTGAAACAAAAGA 58.701 36.000 0.00 0.00 0.00 2.52
3058 3603 4.211794 GTGAGCAACATTCCAAATGGTTTG 59.788 41.667 0.00 1.64 40.32 2.93
3059 3604 4.101430 AGTGAGCAACATTCCAAATGGTTT 59.899 37.500 0.00 0.00 36.34 3.27
3090 3635 8.154649 TGCTTCTTAGGAGTTCTTTTAGTTTG 57.845 34.615 0.00 0.00 0.00 2.93
3099 3644 2.192263 CCCCTGCTTCTTAGGAGTTCT 58.808 52.381 0.00 0.00 38.10 3.01
3549 4125 3.486383 TGGTCAAACCTTTCTCATGGTC 58.514 45.455 0.00 0.00 39.58 4.02
3659 4235 0.317479 GTGTAGTCACGGTCTTGCCT 59.683 55.000 0.00 0.00 34.79 4.75
3667 4243 0.243907 CCTCCTGTGTGTAGTCACGG 59.756 60.000 0.00 0.00 46.49 4.94
3929 4507 5.128919 AGAAGTGATATGATCAAGTTGGCC 58.871 41.667 0.00 0.00 41.69 5.36


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

AutoCloner maintained by Alex Coulton.