Multiple sequence alignment - TraesCS6B01G170000

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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 TraesCS6B01G170000 chr6B 100.000 2462 0 0 1 2462 182574760 182577221 0.000000e+00 4547.0
1 TraesCS6B01G170000 chr6B 93.886 687 37 4 98 781 182483701 182484385 0.000000e+00 1031.0
2 TraesCS6B01G170000 chr6B 94.118 255 11 1 835 1089 182353954 182354204 3.840000e-103 385.0
3 TraesCS6B01G170000 chr6B 85.849 212 19 7 1088 1297 182355650 182355852 5.330000e-52 215.0
4 TraesCS6B01G170000 chr6B 85.586 111 14 1 1981 2091 60859 60967 5.560000e-22 115.0
5 TraesCS6B01G170000 chr6D 91.017 2026 113 32 98 2093 97866679 97868665 0.000000e+00 2669.0
6 TraesCS6B01G170000 chr6D 88.592 824 42 29 831 1616 97808252 97809061 0.000000e+00 953.0
7 TraesCS6B01G170000 chr6D 81.072 597 88 11 136 722 97784207 97784788 1.040000e-123 453.0
8 TraesCS6B01G170000 chr6D 90.541 148 9 3 2319 2462 97869056 97869202 8.990000e-45 191.0
9 TraesCS6B01G170000 chr6D 75.000 492 65 41 1009 1459 97585768 97586242 9.050000e-40 174.0
10 TraesCS6B01G170000 chr6D 82.857 105 18 0 2352 2456 19541244 19541140 7.250000e-16 95.3
11 TraesCS6B01G170000 chr1D 90.367 2014 113 32 98 2093 212426929 212424979 0.000000e+00 2569.0
12 TraesCS6B01G170000 chr1D 82.833 233 18 15 2238 2462 212424662 212424444 3.230000e-44 189.0
13 TraesCS6B01G170000 chr1D 83.810 105 17 0 2358 2462 182032570 182032674 1.560000e-17 100.0
14 TraesCS6B01G170000 chr6A 86.509 719 52 32 1109 1815 116859841 116860526 0.000000e+00 749.0
15 TraesCS6B01G170000 chr6A 90.244 205 18 2 2259 2462 116861031 116861234 1.450000e-67 267.0
16 TraesCS6B01G170000 chrUn 86.861 411 24 11 1601 2000 479309630 479310021 1.350000e-117 433.0
17 TraesCS6B01G170000 chrUn 78.107 169 31 5 1983 2148 362714123 362713958 4.330000e-18 102.0
18 TraesCS6B01G170000 chrUn 78.107 169 31 5 1983 2148 405290064 405290229 4.330000e-18 102.0
19 TraesCS6B01G170000 chr7A 87.850 107 11 1 1983 2089 85260256 85260360 9.240000e-25 124.0
20 TraesCS6B01G170000 chr7A 79.195 149 25 4 1983 2128 596325262 596325117 5.600000e-17 99.0
21 TraesCS6B01G170000 chr2B 86.486 111 13 1 1981 2091 634082806 634082914 1.200000e-23 121.0
22 TraesCS6B01G170000 chr5B 89.362 94 10 0 2363 2456 707437616 707437709 4.300000e-23 119.0
23 TraesCS6B01G170000 chr3B 85.586 111 14 1 1981 2091 790644771 790644663 5.560000e-22 115.0
24 TraesCS6B01G170000 chr3B 94.444 36 0 1 106 139 132401473 132401438 1.000000e-03 54.7
25 TraesCS6B01G170000 chr1B 84.762 105 16 0 2358 2462 252971720 252971824 3.350000e-19 106.0
26 TraesCS6B01G170000 chr7D 87.356 87 11 0 2358 2444 634043530 634043444 1.560000e-17 100.0
27 TraesCS6B01G170000 chr4A 84.314 102 15 1 2362 2462 607264885 607264784 5.600000e-17 99.0
28 TraesCS6B01G170000 chr2D 97.222 36 0 1 102 136 27975590 27975625 2.640000e-05 60.2
29 TraesCS6B01G170000 chr7B 97.059 34 1 0 103 136 665384551 665384584 9.510000e-05 58.4
30 TraesCS6B01G170000 chr4B 100.000 31 0 0 106 136 35504572 35504542 9.510000e-05 58.4
31 TraesCS6B01G170000 chr5D 100.000 28 0 0 109 136 36489251 36489224 4.000000e-03 52.8


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 TraesCS6B01G170000 chr6B 182574760 182577221 2461 False 4547 4547 100.0000 1 2462 1 chr6B.!!$F3 2461
1 TraesCS6B01G170000 chr6B 182483701 182484385 684 False 1031 1031 93.8860 98 781 1 chr6B.!!$F2 683
2 TraesCS6B01G170000 chr6B 182353954 182355852 1898 False 300 385 89.9835 835 1297 2 chr6B.!!$F4 462
3 TraesCS6B01G170000 chr6D 97866679 97869202 2523 False 1430 2669 90.7790 98 2462 2 chr6D.!!$F4 2364
4 TraesCS6B01G170000 chr6D 97808252 97809061 809 False 953 953 88.5920 831 1616 1 chr6D.!!$F3 785
5 TraesCS6B01G170000 chr6D 97784207 97784788 581 False 453 453 81.0720 136 722 1 chr6D.!!$F2 586
6 TraesCS6B01G170000 chr1D 212424444 212426929 2485 True 1379 2569 86.6000 98 2462 2 chr1D.!!$R1 2364
7 TraesCS6B01G170000 chr6A 116859841 116861234 1393 False 508 749 88.3765 1109 2462 2 chr6A.!!$F1 1353

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
30 31 0.174389 TTTGCGTTTGTGCCATGTGT 59.826 45.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 3089 0.236711 CCGTTGAAACAGCAGCAGAG 59.763 55.0 0.0 0.0 0.0 3.35 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
21 22 4.468095 GTCTATGTCAGTTTGCGTTTGT 57.532 40.909 0.00 0.00 0.00 2.83
22 23 4.211389 GTCTATGTCAGTTTGCGTTTGTG 58.789 43.478 0.00 0.00 0.00 3.33
23 24 1.838913 ATGTCAGTTTGCGTTTGTGC 58.161 45.000 0.00 0.00 0.00 4.57
24 25 0.179150 TGTCAGTTTGCGTTTGTGCC 60.179 50.000 0.00 0.00 0.00 5.01
25 26 0.179150 GTCAGTTTGCGTTTGTGCCA 60.179 50.000 0.00 0.00 0.00 4.92
26 27 0.743688 TCAGTTTGCGTTTGTGCCAT 59.256 45.000 0.00 0.00 0.00 4.40
27 28 0.854062 CAGTTTGCGTTTGTGCCATG 59.146 50.000 0.00 0.00 0.00 3.66
28 29 0.459489 AGTTTGCGTTTGTGCCATGT 59.541 45.000 0.00 0.00 0.00 3.21
29 30 0.576328 GTTTGCGTTTGTGCCATGTG 59.424 50.000 0.00 0.00 0.00 3.21
30 31 0.174389 TTTGCGTTTGTGCCATGTGT 59.826 45.000 0.00 0.00 0.00 3.72
31 32 0.174389 TTGCGTTTGTGCCATGTGTT 59.826 45.000 0.00 0.00 0.00 3.32
32 33 0.527169 TGCGTTTGTGCCATGTGTTG 60.527 50.000 0.00 0.00 0.00 3.33
33 34 0.527385 GCGTTTGTGCCATGTGTTGT 60.527 50.000 0.00 0.00 0.00 3.32
34 35 1.268794 GCGTTTGTGCCATGTGTTGTA 60.269 47.619 0.00 0.00 0.00 2.41
35 36 2.380660 CGTTTGTGCCATGTGTTGTAC 58.619 47.619 0.00 0.00 0.00 2.90
36 37 2.738135 GTTTGTGCCATGTGTTGTACC 58.262 47.619 0.00 0.00 0.00 3.34
37 38 2.356665 TTGTGCCATGTGTTGTACCT 57.643 45.000 0.00 0.00 0.00 3.08
38 39 2.356665 TGTGCCATGTGTTGTACCTT 57.643 45.000 0.00 0.00 0.00 3.50
39 40 2.660572 TGTGCCATGTGTTGTACCTTT 58.339 42.857 0.00 0.00 0.00 3.11
40 41 3.027412 TGTGCCATGTGTTGTACCTTTT 58.973 40.909 0.00 0.00 0.00 2.27
41 42 3.449018 TGTGCCATGTGTTGTACCTTTTT 59.551 39.130 0.00 0.00 0.00 1.94
72 73 9.910267 TTCATTTCTCTTCCATCTATCAATGAA 57.090 29.630 0.00 0.00 36.33 2.57
73 74 9.910267 TCATTTCTCTTCCATCTATCAATGAAA 57.090 29.630 0.00 0.00 0.00 2.69
76 77 9.964354 TTTCTCTTCCATCTATCAATGAAAAGA 57.036 29.630 1.89 1.89 32.33 2.52
81 82 8.627208 TTCCATCTATCAATGAAAAGATAGGC 57.373 34.615 10.03 0.00 42.42 3.93
82 83 7.748677 TCCATCTATCAATGAAAAGATAGGCA 58.251 34.615 10.03 0.00 42.42 4.75
83 84 8.219868 TCCATCTATCAATGAAAAGATAGGCAA 58.780 33.333 10.03 1.03 42.42 4.52
84 85 8.295288 CCATCTATCAATGAAAAGATAGGCAAC 58.705 37.037 10.03 0.00 42.42 4.17
85 86 7.807977 TCTATCAATGAAAAGATAGGCAACC 57.192 36.000 8.96 0.00 42.42 3.77
86 87 5.859205 ATCAATGAAAAGATAGGCAACCC 57.141 39.130 0.00 0.00 37.17 4.11
87 88 4.023291 TCAATGAAAAGATAGGCAACCCC 58.977 43.478 0.00 0.00 37.17 4.95
88 89 2.122783 TGAAAAGATAGGCAACCCCG 57.877 50.000 0.00 0.00 39.21 5.73
89 90 0.738975 GAAAAGATAGGCAACCCCGC 59.261 55.000 0.00 0.00 39.21 6.13
177 178 1.170442 GGCGCAAAAGGGCTTAACTA 58.830 50.000 10.83 0.00 0.00 2.24
362 370 6.909909 ACTTGTAAGAAAAATTAGGCCGAAG 58.090 36.000 4.14 0.00 0.00 3.79
490 498 0.537371 ACTCTGGGCCAAAAAGACCG 60.537 55.000 8.04 0.00 0.00 4.79
688 698 3.027412 AGAGACGAGATAGCCATGTGTT 58.973 45.455 0.00 0.00 0.00 3.32
774 784 2.244510 TGGACCATGGATTAGGTTGCAT 59.755 45.455 21.47 0.00 38.50 3.96
793 803 1.519455 GTCCACGAAGCCGATCCAG 60.519 63.158 0.00 0.00 39.50 3.86
877 887 3.044235 TCTCTTTCGCAAAGATGAGCA 57.956 42.857 10.45 0.00 45.75 4.26
882 892 2.796651 GCAAAGATGAGCAGCCGG 59.203 61.111 0.00 0.00 0.00 6.13
883 893 1.746615 GCAAAGATGAGCAGCCGGA 60.747 57.895 5.05 0.00 0.00 5.14
884 894 1.712977 GCAAAGATGAGCAGCCGGAG 61.713 60.000 5.05 0.00 0.00 4.63
930 966 3.642755 CGACTGAACCGCTTGCTT 58.357 55.556 0.00 0.00 0.00 3.91
1080 1116 4.140543 TCTCCTATAAATACCAGCCCTCCA 60.141 45.833 0.00 0.00 0.00 3.86
1141 2624 2.095161 GTCTCACTCTCACCACGTAAGG 60.095 54.545 0.00 0.00 46.39 2.69
1180 2665 1.171308 TCTCGAGGGTTAACCAGTCG 58.829 55.000 29.54 29.54 43.89 4.18
1522 3042 2.031333 GCACCTTTGCTTCTCTCTGTTG 60.031 50.000 0.00 0.00 46.17 3.33
1565 3088 3.164268 TGTAGTACGGGGTTACATGTGT 58.836 45.455 9.11 0.00 0.00 3.72
1566 3089 3.193267 TGTAGTACGGGGTTACATGTGTC 59.807 47.826 9.11 0.87 0.00 3.67
1567 3090 2.532843 AGTACGGGGTTACATGTGTCT 58.467 47.619 9.11 0.00 0.00 3.41
1599 3143 1.536766 TCAACGGTAGTAGTGGTCGTG 59.463 52.381 0.00 0.00 34.18 4.35
1628 3173 1.071605 GTCATCGTCAGTGGTTCTGC 58.928 55.000 0.00 0.00 43.32 4.26
1629 3174 0.037326 TCATCGTCAGTGGTTCTGCC 60.037 55.000 0.00 0.00 43.32 4.85
1636 3181 1.078759 CAGTGGTTCTGCCGACGATC 61.079 60.000 0.00 0.00 41.21 3.69
1647 3192 2.734606 TGCCGACGATCTTTACAGTTTG 59.265 45.455 0.00 0.00 0.00 2.93
1648 3193 2.991190 GCCGACGATCTTTACAGTTTGA 59.009 45.455 0.00 0.00 0.00 2.69
1649 3194 3.617263 GCCGACGATCTTTACAGTTTGAT 59.383 43.478 0.00 0.00 0.00 2.57
1650 3195 4.092968 GCCGACGATCTTTACAGTTTGATT 59.907 41.667 0.00 0.00 0.00 2.57
1716 3261 3.019564 GTCTGGTCTATTGCTTGCCATT 58.980 45.455 0.00 0.00 0.00 3.16
1718 3263 4.640201 GTCTGGTCTATTGCTTGCCATTTA 59.360 41.667 0.00 0.00 0.00 1.40
1719 3264 5.300286 GTCTGGTCTATTGCTTGCCATTTAT 59.700 40.000 0.00 0.00 0.00 1.40
1720 3265 5.300034 TCTGGTCTATTGCTTGCCATTTATG 59.700 40.000 0.00 0.00 0.00 1.90
1721 3266 4.955450 TGGTCTATTGCTTGCCATTTATGT 59.045 37.500 0.00 0.00 0.00 2.29
1722 3267 5.163530 TGGTCTATTGCTTGCCATTTATGTG 60.164 40.000 0.00 0.00 0.00 3.21
1723 3268 5.067674 GGTCTATTGCTTGCCATTTATGTGA 59.932 40.000 0.00 0.00 0.00 3.58
1724 3269 6.204359 GTCTATTGCTTGCCATTTATGTGAG 58.796 40.000 0.00 0.00 0.00 3.51
1725 3270 2.945447 TGCTTGCCATTTATGTGAGC 57.055 45.000 0.00 0.00 0.00 4.26
1792 3347 3.090210 TCCAGTGGGAGTATTGTACGA 57.910 47.619 9.92 0.00 38.64 3.43
1830 3385 3.625897 TGACGTGACCCCAGGCTG 61.626 66.667 7.75 7.75 0.00 4.85
1953 3509 3.551259 CCAAGGTGGCGTCTACAAT 57.449 52.632 0.00 0.00 0.00 2.71
1957 3513 1.191535 AGGTGGCGTCTACAATAGCA 58.808 50.000 0.00 0.00 0.00 3.49
1960 3516 2.224066 GGTGGCGTCTACAATAGCAGAT 60.224 50.000 0.00 0.00 0.00 2.90
1966 3522 5.294552 GGCGTCTACAATAGCAGATCTTTTT 59.705 40.000 0.00 0.00 0.00 1.94
1991 3547 3.367498 CCTTTTGACAAACAAACGGTGGA 60.367 43.478 0.00 0.00 46.22 4.02
2000 3556 6.574350 ACAAACAAACGGTGGAATTTATTGA 58.426 32.000 0.00 0.00 0.00 2.57
2006 3562 8.093927 ACAAACGGTGGAATTTATTGATTCAAT 58.906 29.630 15.78 15.78 37.69 2.57
2033 3589 4.910195 AGCATCAAGAGGATACAAACACA 58.090 39.130 0.00 0.00 41.41 3.72
2043 3599 7.170965 AGAGGATACAAACACAATGAGAACAT 58.829 34.615 0.00 0.00 37.42 2.71
2045 3601 9.113838 GAGGATACAAACACAATGAGAACATAT 57.886 33.333 0.00 0.00 35.42 1.78
2046 3602 9.113838 AGGATACAAACACAATGAGAACATATC 57.886 33.333 0.00 0.00 35.42 1.63
2055 3611 5.604231 ACAATGAGAACATATCTGGCCTCTA 59.396 40.000 3.32 0.00 38.96 2.43
2056 3612 5.736951 ATGAGAACATATCTGGCCTCTAC 57.263 43.478 3.32 0.00 38.96 2.59
2057 3613 4.546674 TGAGAACATATCTGGCCTCTACA 58.453 43.478 3.32 0.00 38.96 2.74
2060 3616 4.904251 AGAACATATCTGGCCTCTACACAT 59.096 41.667 3.32 0.00 36.88 3.21
2072 3628 4.932200 GCCTCTACACATAGTTATGATGCC 59.068 45.833 6.16 0.00 37.15 4.40
2078 3634 6.439636 ACACATAGTTATGATGCCCATAGT 57.560 37.500 6.16 0.00 38.82 2.12
2084 3640 5.126067 AGTTATGATGCCCATAGTCAACAC 58.874 41.667 0.00 0.00 38.82 3.32
2093 3649 2.143122 CATAGTCAACACCAACACGCT 58.857 47.619 0.00 0.00 0.00 5.07
2094 3650 1.577468 TAGTCAACACCAACACGCTG 58.423 50.000 0.00 0.00 0.00 5.18
2095 3651 1.095228 AGTCAACACCAACACGCTGG 61.095 55.000 0.00 0.00 42.68 4.85
2102 3670 0.884704 ACCAACACGCTGGCAACTAG 60.885 55.000 0.00 0.00 40.45 2.57
2103 3811 0.884704 CCAACACGCTGGCAACTAGT 60.885 55.000 0.00 0.00 37.61 2.57
2137 3845 6.909550 AAGACAAAAGTTATACATGGGCAA 57.090 33.333 0.00 0.00 0.00 4.52
2167 3875 0.110056 CCGCTTGACAACATGTGCTC 60.110 55.000 0.00 0.00 32.67 4.26
2170 3878 1.398960 GCTTGACAACATGTGCTCGAC 60.399 52.381 0.00 0.00 0.00 4.20
2185 3893 0.039437 TCGACGACTCAACTTCTGCC 60.039 55.000 0.00 0.00 0.00 4.85
2193 3901 1.000283 CTCAACTTCTGCCTGACGACT 60.000 52.381 0.00 0.00 0.00 4.18
2202 3910 2.354510 CTGCCTGACGACTGTTCAAAAA 59.645 45.455 0.00 0.00 0.00 1.94
2233 4127 3.786368 TGACTTGATGTGTGGATTCCA 57.214 42.857 0.00 0.00 0.00 3.53
2255 4183 3.010584 ACTTCTAAACTGGATGCATGGGT 59.989 43.478 2.46 0.00 0.00 4.51
2282 4217 1.945394 GATGGCATGTGATCAGTGACC 59.055 52.381 3.81 11.02 0.00 4.02
2301 4236 0.184451 CATGGCATGCTTCCCTAGGT 59.816 55.000 18.92 0.00 0.00 3.08
2305 4240 0.469917 GCATGCTTCCCTAGGTGCTA 59.530 55.000 11.37 1.48 0.00 3.49
2309 4244 1.555075 TGCTTCCCTAGGTGCTACTTG 59.445 52.381 8.29 0.00 0.00 3.16
2340 4275 3.070878 TGTTGTGTGAGCATGGTTCTAGA 59.929 43.478 0.00 0.00 0.00 2.43
2402 4340 2.884012 TGGCAGTACAAAGAACATGTGG 59.116 45.455 0.00 0.00 32.27 4.17
2444 4382 0.398522 TCCATAGACCACCTGGCGAT 60.399 55.000 0.00 0.00 39.32 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.211389 CACAAACGCAAACTGACATAGAC 58.789 43.478 0.00 0.00 0.00 2.59
1 2 3.303725 GCACAAACGCAAACTGACATAGA 60.304 43.478 0.00 0.00 0.00 1.98
2 3 2.973224 GCACAAACGCAAACTGACATAG 59.027 45.455 0.00 0.00 0.00 2.23
3 4 2.287308 GGCACAAACGCAAACTGACATA 60.287 45.455 0.00 0.00 0.00 2.29
4 5 1.535860 GGCACAAACGCAAACTGACAT 60.536 47.619 0.00 0.00 0.00 3.06
5 6 0.179150 GGCACAAACGCAAACTGACA 60.179 50.000 0.00 0.00 0.00 3.58
6 7 0.179150 TGGCACAAACGCAAACTGAC 60.179 50.000 0.00 0.00 31.92 3.51
7 8 2.184323 TGGCACAAACGCAAACTGA 58.816 47.368 0.00 0.00 31.92 3.41
8 9 4.802424 TGGCACAAACGCAAACTG 57.198 50.000 0.00 0.00 31.92 3.16
20 21 3.726291 AAAAGGTACAACACATGGCAC 57.274 42.857 0.00 0.00 0.00 5.01
46 47 9.910267 TTCATTGATAGATGGAAGAGAAATGAA 57.090 29.630 0.00 0.00 38.49 2.57
47 48 9.910267 TTTCATTGATAGATGGAAGAGAAATGA 57.090 29.630 0.00 0.00 31.58 2.57
50 51 9.964354 TCTTTTCATTGATAGATGGAAGAGAAA 57.036 29.630 0.00 0.00 31.85 2.52
55 56 8.728833 GCCTATCTTTTCATTGATAGATGGAAG 58.271 37.037 17.11 10.03 42.67 3.46
56 57 8.219868 TGCCTATCTTTTCATTGATAGATGGAA 58.780 33.333 17.11 10.99 42.67 3.53
57 58 7.748677 TGCCTATCTTTTCATTGATAGATGGA 58.251 34.615 17.11 5.91 42.67 3.41
58 59 7.991084 TGCCTATCTTTTCATTGATAGATGG 57.009 36.000 16.31 14.18 42.67 3.51
59 60 8.295288 GGTTGCCTATCTTTTCATTGATAGATG 58.705 37.037 16.31 9.68 42.67 2.90
60 61 7.449704 GGGTTGCCTATCTTTTCATTGATAGAT 59.550 37.037 13.28 13.28 42.67 1.98
61 62 6.772716 GGGTTGCCTATCTTTTCATTGATAGA 59.227 38.462 10.48 2.59 42.67 1.98
62 63 6.015940 GGGGTTGCCTATCTTTTCATTGATAG 60.016 42.308 0.00 0.00 40.84 2.08
63 64 5.833131 GGGGTTGCCTATCTTTTCATTGATA 59.167 40.000 0.00 0.00 0.00 2.15
64 65 4.651045 GGGGTTGCCTATCTTTTCATTGAT 59.349 41.667 0.00 0.00 0.00 2.57
65 66 4.023291 GGGGTTGCCTATCTTTTCATTGA 58.977 43.478 0.00 0.00 0.00 2.57
66 67 3.181487 CGGGGTTGCCTATCTTTTCATTG 60.181 47.826 0.00 0.00 0.00 2.82
67 68 3.023832 CGGGGTTGCCTATCTTTTCATT 58.976 45.455 0.00 0.00 0.00 2.57
68 69 2.654863 CGGGGTTGCCTATCTTTTCAT 58.345 47.619 0.00 0.00 0.00 2.57
69 70 1.953311 GCGGGGTTGCCTATCTTTTCA 60.953 52.381 0.00 0.00 0.00 2.69
70 71 0.738975 GCGGGGTTGCCTATCTTTTC 59.261 55.000 0.00 0.00 0.00 2.29
71 72 2.882170 GCGGGGTTGCCTATCTTTT 58.118 52.632 0.00 0.00 0.00 2.27
72 73 4.657952 GCGGGGTTGCCTATCTTT 57.342 55.556 0.00 0.00 0.00 2.52
94 95 4.855531 AGCTTGCGTATCTTTTCGTTTTT 58.144 34.783 0.00 0.00 0.00 1.94
95 96 4.483476 AGCTTGCGTATCTTTTCGTTTT 57.517 36.364 0.00 0.00 0.00 2.43
96 97 4.483476 AAGCTTGCGTATCTTTTCGTTT 57.517 36.364 0.00 0.00 0.00 3.60
159 160 1.810755 AGTAGTTAAGCCCTTTTGCGC 59.189 47.619 0.00 0.00 36.02 6.09
177 178 6.058553 TGGATTGATGAGATGAGACAAAGT 57.941 37.500 0.00 0.00 0.00 2.66
274 282 4.338400 CACTGTCTATGATGAGGTTCCGTA 59.662 45.833 0.00 0.00 0.00 4.02
289 297 5.011635 TGAAATTGTAGGAGCACACTGTCTA 59.988 40.000 0.00 0.00 0.00 2.59
347 355 3.254903 GTGTGACCTTCGGCCTAATTTTT 59.745 43.478 0.00 0.00 0.00 1.94
362 370 8.892723 TCTAATTGATCATGTAATTGTGTGACC 58.107 33.333 0.00 0.00 0.00 4.02
406 414 3.127376 GGTGTTTGTGTTTGTCGTTAGGT 59.873 43.478 0.00 0.00 0.00 3.08
474 482 2.275380 CCCGGTCTTTTTGGCCCAG 61.275 63.158 0.00 0.00 37.05 4.45
490 498 2.371259 GCCTCTTCTCCCTGTCCCC 61.371 68.421 0.00 0.00 0.00 4.81
688 698 1.065491 AGCATTCGTTCAGGGCATACA 60.065 47.619 0.00 0.00 0.00 2.29
774 784 2.225791 CTGGATCGGCTTCGTGGACA 62.226 60.000 0.00 0.00 35.06 4.02
793 803 5.241728 AGAGTTTGGAAACATGCTAAAGGAC 59.758 40.000 5.11 0.00 42.32 3.85
827 837 5.471456 AGCTCATCTTTTCTTCAATTGTCGT 59.529 36.000 5.13 0.00 0.00 4.34
877 887 4.532126 TCATGGATATATTCAACTCCGGCT 59.468 41.667 0.00 0.00 0.00 5.52
1042 1078 1.120795 GGAGAGGAGATGGCTGGAGG 61.121 65.000 0.00 0.00 0.00 4.30
1080 1116 1.270907 CTGGTGCTGTAAGGAGGAGT 58.729 55.000 0.00 0.00 31.73 3.85
1141 2624 5.738225 CGAGAAATACGAAGGAGTAGAACAC 59.262 44.000 0.00 0.00 0.00 3.32
1180 2665 6.708054 CACTGATGGTATGAAAAGATAGGACC 59.292 42.308 0.00 0.00 0.00 4.46
1184 2682 6.422100 CCGTCACTGATGGTATGAAAAGATAG 59.578 42.308 8.96 0.00 34.27 2.08
1480 2996 1.800315 GCTTGCAGCGCATGTCTTG 60.800 57.895 11.47 0.00 38.76 3.02
1481 2997 2.564975 GCTTGCAGCGCATGTCTT 59.435 55.556 11.47 0.00 38.76 3.01
1514 3030 6.053005 ACGTTATTCAAACCTTCAACAGAGA 58.947 36.000 0.00 0.00 0.00 3.10
1522 3042 6.894828 ACATGTGTACGTTATTCAAACCTTC 58.105 36.000 0.00 0.00 0.00 3.46
1553 3076 2.350522 CAGCAGAGACACATGTAACCC 58.649 52.381 0.00 0.00 0.00 4.11
1565 3088 1.220529 CGTTGAAACAGCAGCAGAGA 58.779 50.000 0.00 0.00 0.00 3.10
1566 3089 0.236711 CCGTTGAAACAGCAGCAGAG 59.763 55.000 0.00 0.00 0.00 3.35
1567 3090 0.463654 ACCGTTGAAACAGCAGCAGA 60.464 50.000 0.00 0.00 0.00 4.26
1599 3143 0.386352 TGACGATGACAACGACGACC 60.386 55.000 12.41 0.00 34.70 4.79
1628 3173 5.779806 AATCAAACTGTAAAGATCGTCGG 57.220 39.130 0.00 0.00 0.00 4.79
1629 3174 7.950236 AGTAAATCAAACTGTAAAGATCGTCG 58.050 34.615 0.00 0.00 0.00 5.12
1674 3219 5.121454 AGACAGATGAAGAAGCATTTTCGTC 59.879 40.000 6.37 6.37 38.84 4.20
1716 3261 5.109210 CAACGACATAGGAAGCTCACATAA 58.891 41.667 0.00 0.00 0.00 1.90
1718 3263 3.525537 CAACGACATAGGAAGCTCACAT 58.474 45.455 0.00 0.00 0.00 3.21
1719 3264 2.930887 GCAACGACATAGGAAGCTCACA 60.931 50.000 0.00 0.00 0.00 3.58
1720 3265 1.661112 GCAACGACATAGGAAGCTCAC 59.339 52.381 0.00 0.00 0.00 3.51
1721 3266 1.405526 GGCAACGACATAGGAAGCTCA 60.406 52.381 0.00 0.00 0.00 4.26
1722 3267 1.134670 AGGCAACGACATAGGAAGCTC 60.135 52.381 0.00 0.00 46.39 4.09
1723 3268 0.905357 AGGCAACGACATAGGAAGCT 59.095 50.000 0.00 0.00 46.39 3.74
1724 3269 1.291132 GAGGCAACGACATAGGAAGC 58.709 55.000 0.00 0.00 46.39 3.86
1725 3270 1.473434 GGGAGGCAACGACATAGGAAG 60.473 57.143 0.00 0.00 46.39 3.46
1792 3347 3.498397 CACCGAGAGCAAAGTAACATGTT 59.502 43.478 16.68 16.68 0.00 2.71
1970 3526 3.839293 TCCACCGTTTGTTTGTCAAAAG 58.161 40.909 0.00 0.00 45.84 2.27
1973 3529 4.457834 AATTCCACCGTTTGTTTGTCAA 57.542 36.364 0.00 0.00 0.00 3.18
1979 3535 7.437748 TGAATCAATAAATTCCACCGTTTGTT 58.562 30.769 0.00 0.00 35.23 2.83
2000 3556 9.228949 GTATCCTCTTGATGCTTCATATTGAAT 57.771 33.333 2.75 0.00 33.79 2.57
2006 3562 7.280876 GTGTTTGTATCCTCTTGATGCTTCATA 59.719 37.037 2.75 0.00 37.04 2.15
2016 3572 7.041167 TGTTCTCATTGTGTTTGTATCCTCTTG 60.041 37.037 0.00 0.00 0.00 3.02
2021 3577 9.113838 AGATATGTTCTCATTGTGTTTGTATCC 57.886 33.333 0.00 0.00 35.70 2.59
2033 3589 5.604231 TGTAGAGGCCAGATATGTTCTCATT 59.396 40.000 5.01 0.00 35.70 2.57
2043 3599 7.238710 TCATAACTATGTGTAGAGGCCAGATA 58.761 38.462 5.01 0.00 35.26 1.98
2045 3601 5.454966 TCATAACTATGTGTAGAGGCCAGA 58.545 41.667 5.01 0.00 35.26 3.86
2046 3602 5.791336 TCATAACTATGTGTAGAGGCCAG 57.209 43.478 5.01 0.00 35.26 4.85
2055 3611 6.043127 TGACTATGGGCATCATAACTATGTGT 59.957 38.462 0.00 0.00 37.83 3.72
2056 3612 6.466812 TGACTATGGGCATCATAACTATGTG 58.533 40.000 0.00 0.00 37.83 3.21
2057 3613 6.686484 TGACTATGGGCATCATAACTATGT 57.314 37.500 0.00 0.00 37.83 2.29
2060 3616 6.288294 GTGTTGACTATGGGCATCATAACTA 58.712 40.000 0.00 0.00 37.83 2.24
2072 3628 1.196808 GCGTGTTGGTGTTGACTATGG 59.803 52.381 0.00 0.00 0.00 2.74
2078 3634 2.477176 GCCAGCGTGTTGGTGTTGA 61.477 57.895 4.63 0.00 44.68 3.18
2084 3640 0.884704 ACTAGTTGCCAGCGTGTTGG 60.885 55.000 0.00 0.00 41.35 3.77
2149 3857 0.451628 CGAGCACATGTTGTCAAGCG 60.452 55.000 0.00 0.00 0.00 4.68
2167 3875 0.039074 AGGCAGAAGTTGAGTCGTCG 60.039 55.000 0.00 0.00 0.00 5.12
2170 3878 1.423395 GTCAGGCAGAAGTTGAGTCG 58.577 55.000 0.00 0.00 0.00 4.18
2207 3915 6.037610 GGAATCCACACATCAAGTCATTAGAC 59.962 42.308 0.00 0.00 45.31 2.59
2208 3916 6.115446 GGAATCCACACATCAAGTCATTAGA 58.885 40.000 0.00 0.00 0.00 2.10
2209 3917 5.882000 TGGAATCCACACATCAAGTCATTAG 59.118 40.000 0.00 0.00 0.00 1.73
2210 3918 5.814481 TGGAATCCACACATCAAGTCATTA 58.186 37.500 0.00 0.00 0.00 1.90
2233 4127 3.010584 ACCCATGCATCCAGTTTAGAAGT 59.989 43.478 0.00 0.00 0.00 3.01
2242 4170 0.750546 CAGACCACCCATGCATCCAG 60.751 60.000 0.00 0.00 0.00 3.86
2255 4183 0.921166 ATCACATGCCATCCAGACCA 59.079 50.000 0.00 0.00 0.00 4.02
2282 4217 0.184451 ACCTAGGGAAGCATGCCATG 59.816 55.000 15.66 0.00 32.29 3.66
2359 4297 6.622245 GCCATGATGTTTGATGAATAGATCGG 60.622 42.308 0.00 0.00 0.00 4.18
2360 4298 6.072893 TGCCATGATGTTTGATGAATAGATCG 60.073 38.462 0.00 0.00 0.00 3.69
2402 4340 8.999431 TGGACATGAATCTAACTTTTGTTACTC 58.001 33.333 0.00 0.00 43.32 2.59


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

AutoCloner maintained by Alex Coulton.