Multiple sequence alignment - TraesCS3A01G232200

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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 TraesCS3A01G232200 chr3A 100.000 2369 0 0 1 2369 433885833 433888201 0.000000e+00 4375
1 TraesCS3A01G232200 chr3A 93.609 798 37 6 1573 2369 433963235 433964019 0.000000e+00 1179
2 TraesCS3A01G232200 chr3D 91.506 1966 105 27 134 2079 301578974 301577051 0.000000e+00 2649
3 TraesCS3A01G232200 chr3D 92.544 228 17 0 2142 2369 301577017 301576790 6.310000e-86 327
4 TraesCS3A01G232200 chr3B 92.078 1843 89 21 243 2079 419565473 419567264 0.000000e+00 2542
5 TraesCS3A01G232200 chr3B 96.930 228 6 1 2142 2369 419567298 419567524 4.780000e-102 381
6 TraesCS3A01G232200 chr7A 89.344 122 11 2 2249 2369 700142511 700142631 4.080000e-33 152
7 TraesCS3A01G232200 chr5B 88.430 121 13 1 2249 2369 90824764 90824883 6.820000e-31 145


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 TraesCS3A01G232200 chr3A 433885833 433888201 2368 False 4375.0 4375 100.000 1 2369 1 chr3A.!!$F1 2368
1 TraesCS3A01G232200 chr3A 433963235 433964019 784 False 1179.0 1179 93.609 1573 2369 1 chr3A.!!$F2 796
2 TraesCS3A01G232200 chr3D 301576790 301578974 2184 True 1488.0 2649 92.025 134 2369 2 chr3D.!!$R1 2235
3 TraesCS3A01G232200 chr3B 419565473 419567524 2051 False 1461.5 2542 94.504 243 2369 2 chr3B.!!$F1 2126

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
808 823 0.035056 CGAATCCCAAGCTCCCAACT 60.035 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 1780 0.184933 CCTTGTGGTGGGGTTCTTCA 59.815 55.0 0.0 0.0 0.0 3.02 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 3.391382 GGAGGACCTCCCGTGTGG 61.391 72.222 28.16 0.00 44.36 4.17
23 24 4.083862 GAGGACCTCCCGTGTGGC 62.084 72.222 10.74 0.00 40.87 5.01
28 29 4.722700 CCTCCCGTGTGGCCCAAG 62.723 72.222 0.00 0.00 0.00 3.61
50 51 1.664873 GGGGGCAAGATCGAGTAAAC 58.335 55.000 0.00 0.00 0.00 2.01
51 52 1.287425 GGGGCAAGATCGAGTAAACG 58.713 55.000 0.00 0.00 0.00 3.60
52 53 1.134907 GGGGCAAGATCGAGTAAACGA 60.135 52.381 0.00 0.00 46.04 3.85
71 72 3.692791 GATTAAGAATCGGGCAACACC 57.307 47.619 0.00 0.00 39.74 4.16
72 73 2.570415 TTAAGAATCGGGCAACACCA 57.430 45.000 0.00 0.00 42.05 4.17
73 74 2.570415 TAAGAATCGGGCAACACCAA 57.430 45.000 0.00 0.00 42.05 3.67
74 75 1.698506 AAGAATCGGGCAACACCAAA 58.301 45.000 0.00 0.00 42.05 3.28
75 76 0.958822 AGAATCGGGCAACACCAAAC 59.041 50.000 0.00 0.00 42.05 2.93
76 77 0.958822 GAATCGGGCAACACCAAACT 59.041 50.000 0.00 0.00 42.05 2.66
77 78 0.673437 AATCGGGCAACACCAAACTG 59.327 50.000 0.00 0.00 42.05 3.16
78 79 1.178534 ATCGGGCAACACCAAACTGG 61.179 55.000 0.00 0.00 45.02 4.00
87 88 4.196372 CCAAACTGGTGCCCACAT 57.804 55.556 0.40 0.00 31.35 3.21
88 89 2.439837 CCAAACTGGTGCCCACATT 58.560 52.632 0.40 0.00 31.35 2.71
89 90 0.758123 CCAAACTGGTGCCCACATTT 59.242 50.000 0.40 0.00 31.35 2.32
90 91 1.540797 CCAAACTGGTGCCCACATTTG 60.541 52.381 13.74 13.74 35.73 2.32
91 92 1.411977 CAAACTGGTGCCCACATTTGA 59.588 47.619 14.72 0.00 36.99 2.69
92 93 1.039856 AACTGGTGCCCACATTTGAC 58.960 50.000 0.40 0.00 0.00 3.18
93 94 0.106268 ACTGGTGCCCACATTTGACA 60.106 50.000 0.40 0.00 0.00 3.58
94 95 0.599558 CTGGTGCCCACATTTGACAG 59.400 55.000 0.40 0.00 0.00 3.51
95 96 0.184692 TGGTGCCCACATTTGACAGA 59.815 50.000 0.40 0.00 0.00 3.41
96 97 0.598065 GGTGCCCACATTTGACAGAC 59.402 55.000 0.40 0.00 0.00 3.51
97 98 0.598065 GTGCCCACATTTGACAGACC 59.402 55.000 0.00 0.00 0.00 3.85
98 99 0.478072 TGCCCACATTTGACAGACCT 59.522 50.000 0.00 0.00 0.00 3.85
99 100 1.168714 GCCCACATTTGACAGACCTC 58.831 55.000 0.00 0.00 0.00 3.85
100 101 1.271597 GCCCACATTTGACAGACCTCT 60.272 52.381 0.00 0.00 0.00 3.69
101 102 2.704572 CCCACATTTGACAGACCTCTC 58.295 52.381 0.00 0.00 0.00 3.20
102 103 2.616510 CCCACATTTGACAGACCTCTCC 60.617 54.545 0.00 0.00 0.00 3.71
103 104 2.616510 CCACATTTGACAGACCTCTCCC 60.617 54.545 0.00 0.00 0.00 4.30
104 105 2.304180 CACATTTGACAGACCTCTCCCT 59.696 50.000 0.00 0.00 0.00 4.20
105 106 2.982488 ACATTTGACAGACCTCTCCCTT 59.018 45.455 0.00 0.00 0.00 3.95
106 107 3.395941 ACATTTGACAGACCTCTCCCTTT 59.604 43.478 0.00 0.00 0.00 3.11
107 108 4.141158 ACATTTGACAGACCTCTCCCTTTT 60.141 41.667 0.00 0.00 0.00 2.27
108 109 3.771577 TTGACAGACCTCTCCCTTTTC 57.228 47.619 0.00 0.00 0.00 2.29
109 110 1.978580 TGACAGACCTCTCCCTTTTCC 59.021 52.381 0.00 0.00 0.00 3.13
110 111 1.978580 GACAGACCTCTCCCTTTTCCA 59.021 52.381 0.00 0.00 0.00 3.53
111 112 2.372172 GACAGACCTCTCCCTTTTCCAA 59.628 50.000 0.00 0.00 0.00 3.53
112 113 2.106684 ACAGACCTCTCCCTTTTCCAAC 59.893 50.000 0.00 0.00 0.00 3.77
113 114 1.705745 AGACCTCTCCCTTTTCCAACC 59.294 52.381 0.00 0.00 0.00 3.77
114 115 0.778083 ACCTCTCCCTTTTCCAACCC 59.222 55.000 0.00 0.00 0.00 4.11
115 116 0.777446 CCTCTCCCTTTTCCAACCCA 59.223 55.000 0.00 0.00 0.00 4.51
116 117 1.146982 CCTCTCCCTTTTCCAACCCAA 59.853 52.381 0.00 0.00 0.00 4.12
117 118 2.239400 CTCTCCCTTTTCCAACCCAAC 58.761 52.381 0.00 0.00 0.00 3.77
118 119 1.856920 TCTCCCTTTTCCAACCCAACT 59.143 47.619 0.00 0.00 0.00 3.16
119 120 3.057586 TCTCCCTTTTCCAACCCAACTA 58.942 45.455 0.00 0.00 0.00 2.24
120 121 3.154710 CTCCCTTTTCCAACCCAACTAC 58.845 50.000 0.00 0.00 0.00 2.73
121 122 2.787035 TCCCTTTTCCAACCCAACTACT 59.213 45.455 0.00 0.00 0.00 2.57
122 123 3.982052 TCCCTTTTCCAACCCAACTACTA 59.018 43.478 0.00 0.00 0.00 1.82
123 124 4.604490 TCCCTTTTCCAACCCAACTACTAT 59.396 41.667 0.00 0.00 0.00 2.12
124 125 5.075344 TCCCTTTTCCAACCCAACTACTATT 59.925 40.000 0.00 0.00 0.00 1.73
125 126 6.275144 TCCCTTTTCCAACCCAACTACTATTA 59.725 38.462 0.00 0.00 0.00 0.98
126 127 6.949463 CCCTTTTCCAACCCAACTACTATTAA 59.051 38.462 0.00 0.00 0.00 1.40
127 128 7.122204 CCCTTTTCCAACCCAACTACTATTAAG 59.878 40.741 0.00 0.00 0.00 1.85
128 129 7.362660 CCTTTTCCAACCCAACTACTATTAAGC 60.363 40.741 0.00 0.00 0.00 3.09
129 130 6.382919 TTCCAACCCAACTACTATTAAGCT 57.617 37.500 0.00 0.00 0.00 3.74
130 131 6.382919 TCCAACCCAACTACTATTAAGCTT 57.617 37.500 3.48 3.48 0.00 3.74
131 132 6.786122 TCCAACCCAACTACTATTAAGCTTT 58.214 36.000 3.20 0.00 0.00 3.51
132 133 6.657541 TCCAACCCAACTACTATTAAGCTTTG 59.342 38.462 3.20 0.00 0.00 2.77
133 134 6.322491 CAACCCAACTACTATTAAGCTTTGC 58.678 40.000 3.20 0.00 0.00 3.68
134 135 5.816682 ACCCAACTACTATTAAGCTTTGCT 58.183 37.500 3.20 0.00 42.56 3.91
143 144 3.042560 AGCTTTGCTTTCACCCGC 58.957 55.556 0.00 0.00 33.89 6.13
169 170 2.774439 AACAAAGTTTGCTTCGCGAT 57.226 40.000 10.88 0.00 33.01 4.58
179 180 5.753438 AGTTTGCTTCGCGATGAATATTCTA 59.247 36.000 24.47 3.85 35.63 2.10
180 181 5.576337 TTGCTTCGCGATGAATATTCTAC 57.424 39.130 24.47 9.13 35.63 2.59
181 182 4.871513 TGCTTCGCGATGAATATTCTACT 58.128 39.130 24.47 1.70 35.63 2.57
182 183 4.681483 TGCTTCGCGATGAATATTCTACTG 59.319 41.667 24.47 5.35 35.63 2.74
183 184 4.681942 GCTTCGCGATGAATATTCTACTGT 59.318 41.667 24.47 0.00 35.63 3.55
224 225 4.612259 GCAAGCATGTGTAGAGTGAGTTTG 60.612 45.833 0.00 0.00 0.00 2.93
225 226 4.607293 AGCATGTGTAGAGTGAGTTTGA 57.393 40.909 0.00 0.00 0.00 2.69
226 227 4.564041 AGCATGTGTAGAGTGAGTTTGAG 58.436 43.478 0.00 0.00 0.00 3.02
228 229 4.309933 CATGTGTAGAGTGAGTTTGAGCA 58.690 43.478 0.00 0.00 0.00 4.26
231 232 2.289072 TGTAGAGTGAGTTTGAGCAGCC 60.289 50.000 0.00 0.00 0.00 4.85
341 350 2.167487 GGACAGATCGGAAGCTTCTTCT 59.833 50.000 25.05 19.97 0.00 2.85
444 453 3.461982 CACACTCGCACGACGCTC 61.462 66.667 0.00 0.00 43.23 5.03
715 730 2.496817 CAGCTCAGGAGGTACCGC 59.503 66.667 7.18 7.18 44.74 5.68
724 739 1.328430 GGAGGTACCGCTGCTACCTT 61.328 60.000 18.34 6.08 43.51 3.50
725 740 0.535797 GAGGTACCGCTGCTACCTTT 59.464 55.000 18.34 1.79 43.51 3.11
738 753 2.680339 GCTACCTTTCTCCTTGATGCAC 59.320 50.000 0.00 0.00 0.00 4.57
742 757 1.471684 CTTTCTCCTTGATGCACCAGC 59.528 52.381 0.00 0.00 42.57 4.85
757 772 1.626654 CCAGCACAGTTACGCCTTCG 61.627 60.000 0.00 0.00 42.43 3.79
758 773 2.027625 AGCACAGTTACGCCTTCGC 61.028 57.895 0.00 0.00 39.84 4.70
775 790 1.206371 TCGCCTGCTTCTAAACCTACC 59.794 52.381 0.00 0.00 0.00 3.18
782 797 0.547229 TTCTAAACCTACCGCCCCCA 60.547 55.000 0.00 0.00 0.00 4.96
799 814 3.214328 CCCCATTCTAACGAATCCCAAG 58.786 50.000 0.00 0.00 37.77 3.61
800 815 2.618709 CCCATTCTAACGAATCCCAAGC 59.381 50.000 0.00 0.00 37.77 4.01
801 816 3.545703 CCATTCTAACGAATCCCAAGCT 58.454 45.455 0.00 0.00 37.77 3.74
802 817 3.561725 CCATTCTAACGAATCCCAAGCTC 59.438 47.826 0.00 0.00 37.77 4.09
803 818 2.981859 TCTAACGAATCCCAAGCTCC 57.018 50.000 0.00 0.00 0.00 4.70
804 819 1.485066 TCTAACGAATCCCAAGCTCCC 59.515 52.381 0.00 0.00 0.00 4.30
805 820 1.209504 CTAACGAATCCCAAGCTCCCA 59.790 52.381 0.00 0.00 0.00 4.37
806 821 0.404040 AACGAATCCCAAGCTCCCAA 59.596 50.000 0.00 0.00 0.00 4.12
807 822 0.322546 ACGAATCCCAAGCTCCCAAC 60.323 55.000 0.00 0.00 0.00 3.77
808 823 0.035056 CGAATCCCAAGCTCCCAACT 60.035 55.000 0.00 0.00 0.00 3.16
809 824 1.209504 CGAATCCCAAGCTCCCAACTA 59.790 52.381 0.00 0.00 0.00 2.24
810 825 2.355716 CGAATCCCAAGCTCCCAACTAA 60.356 50.000 0.00 0.00 0.00 2.24
811 826 2.808906 ATCCCAAGCTCCCAACTAAC 57.191 50.000 0.00 0.00 0.00 2.34
827 842 4.779993 ACTAACATTCCTCCTCCATTCC 57.220 45.455 0.00 0.00 0.00 3.01
942 957 1.166531 AGCCACACAACTTTCGCTCC 61.167 55.000 0.00 0.00 0.00 4.70
974 989 3.118454 CAACGCCCGAACGCTCAT 61.118 61.111 0.00 0.00 36.19 2.90
1016 1031 1.763256 CCATGGGAAGGGCAATGGG 60.763 63.158 2.85 0.00 36.68 4.00
1018 1033 3.025630 ATGGGAAGGGCAATGGGGG 62.026 63.158 0.00 0.00 0.00 5.40
1174 1195 2.754658 CACCTCCGGCGTCCTACT 60.755 66.667 6.01 0.00 0.00 2.57
1197 1218 4.947147 GTGTCCAACTGCCCGCCA 62.947 66.667 0.00 0.00 0.00 5.69
1372 1393 2.406616 CGGGCCTTTTGGTGATCGG 61.407 63.158 0.84 0.00 42.99 4.18
1382 1403 1.812922 GGTGATCGGTCTGCAGCAG 60.813 63.158 17.10 17.10 0.00 4.24
1425 1446 4.394078 TGTCGCGACGGAAGGACG 62.394 66.667 31.88 0.00 40.31 4.79
1524 1545 3.006537 AGTTCTTGCAATGCATCAAGCTT 59.993 39.130 18.71 0.00 45.94 3.74
1525 1546 3.226346 TCTTGCAATGCATCAAGCTTC 57.774 42.857 18.71 0.00 45.94 3.86
1526 1547 2.823747 TCTTGCAATGCATCAAGCTTCT 59.176 40.909 18.71 0.00 45.94 2.85
1527 1548 3.257375 TCTTGCAATGCATCAAGCTTCTT 59.743 39.130 18.71 0.00 45.94 2.52
1528 1549 3.226346 TGCAATGCATCAAGCTTCTTC 57.774 42.857 2.72 0.00 45.94 2.87
1529 1550 2.823747 TGCAATGCATCAAGCTTCTTCT 59.176 40.909 2.72 0.00 45.94 2.85
1530 1551 3.257375 TGCAATGCATCAAGCTTCTTCTT 59.743 39.130 2.72 0.00 45.94 2.52
1658 1680 4.450976 GTGGGTGATCTTTTTGGCTTTTT 58.549 39.130 0.00 0.00 0.00 1.94
1737 1760 4.036380 GGCTGTTTAAGTATTGGATTCCCG 59.964 45.833 0.00 0.00 34.29 5.14
1768 1791 4.862371 AGTTTACAACTTGAAGAACCCCA 58.138 39.130 0.00 0.00 39.04 4.96
1771 1794 1.286553 ACAACTTGAAGAACCCCACCA 59.713 47.619 0.00 0.00 0.00 4.17
1815 1838 8.729805 AATGGTTTATCAACAACAACAACAAT 57.270 26.923 0.00 0.00 34.15 2.71
1818 1841 9.823647 TGGTTTATCAACAACAACAACAATAAT 57.176 25.926 0.00 0.00 34.15 1.28
1856 1879 9.726438 AATAGGTAAAATGGCTAAGCTATACAG 57.274 33.333 0.00 0.00 32.91 2.74
1872 1895 7.308782 GCTATACAGCTGTTACTGACAATTT 57.691 36.000 27.06 0.00 44.93 1.82
1964 1988 6.319911 GCTCTAAGTAGCTTTTTGGGATCAAT 59.680 38.462 0.00 0.00 39.50 2.57
1997 2021 3.884037 ATTGGTGGATCTATGGGGAAC 57.116 47.619 0.00 0.00 0.00 3.62
2115 2196 4.122776 GACGCCAACTAGACAATGATCAT 58.877 43.478 1.18 1.18 0.00 2.45
2116 2197 4.517285 ACGCCAACTAGACAATGATCATT 58.483 39.130 15.36 15.36 0.00 2.57
2131 2212 7.260603 CAATGATCATTGTCTAGTTTTTCCCC 58.739 38.462 31.74 0.00 42.32 4.81
2132 2213 5.261216 TGATCATTGTCTAGTTTTTCCCCC 58.739 41.667 0.00 0.00 0.00 5.40
2147 2228 3.948735 CCCCCGCAAGAAAACTAGA 57.051 52.632 0.00 0.00 43.02 2.43
2148 2229 1.450025 CCCCCGCAAGAAAACTAGAC 58.550 55.000 0.00 0.00 43.02 2.59
2149 2230 1.271163 CCCCCGCAAGAAAACTAGACA 60.271 52.381 0.00 0.00 43.02 3.41
2150 2231 2.500229 CCCCGCAAGAAAACTAGACAA 58.500 47.619 0.00 0.00 43.02 3.18
2151 2232 3.081804 CCCCGCAAGAAAACTAGACAAT 58.918 45.455 0.00 0.00 43.02 2.71
2152 2233 3.119849 CCCCGCAAGAAAACTAGACAATG 60.120 47.826 0.00 0.00 43.02 2.82
2153 2234 3.751175 CCCGCAAGAAAACTAGACAATGA 59.249 43.478 0.00 0.00 43.02 2.57
2154 2235 4.396166 CCCGCAAGAAAACTAGACAATGAT 59.604 41.667 0.00 0.00 43.02 2.45
2155 2236 5.447818 CCCGCAAGAAAACTAGACAATGATC 60.448 44.000 0.00 0.00 43.02 2.92
2156 2237 5.122239 CCGCAAGAAAACTAGACAATGATCA 59.878 40.000 0.00 0.00 43.02 2.92
2173 2254 4.155709 TGATCAAATGTGTGCCCCTTTTA 58.844 39.130 0.00 0.00 0.00 1.52
2270 2351 2.751806 GGCTTGGAATGAAAGACCAGAG 59.248 50.000 0.00 0.00 35.08 3.35
2310 2391 3.423539 TGCTCTTCCACAAGCTTATGT 57.576 42.857 3.66 0.00 39.31 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.083862 GCCACACGGGAGGTCCTC 62.084 72.222 10.78 10.78 40.01 3.71
11 12 4.722700 CTTGGGCCACACGGGAGG 62.723 72.222 5.23 0.00 40.01 4.30
31 32 1.664873 GTTTACTCGATCTTGCCCCC 58.335 55.000 0.00 0.00 0.00 5.40
32 33 1.134907 TCGTTTACTCGATCTTGCCCC 60.135 52.381 0.00 0.00 34.85 5.80
33 34 2.288961 TCGTTTACTCGATCTTGCCC 57.711 50.000 0.00 0.00 34.85 5.36
51 52 3.013921 TGGTGTTGCCCGATTCTTAATC 58.986 45.455 0.00 0.00 36.04 1.75
52 53 3.080300 TGGTGTTGCCCGATTCTTAAT 57.920 42.857 0.00 0.00 36.04 1.40
53 54 2.570415 TGGTGTTGCCCGATTCTTAA 57.430 45.000 0.00 0.00 36.04 1.85
54 55 2.554893 GTTTGGTGTTGCCCGATTCTTA 59.445 45.455 0.00 0.00 36.04 2.10
55 56 1.339929 GTTTGGTGTTGCCCGATTCTT 59.660 47.619 0.00 0.00 36.04 2.52
56 57 0.958822 GTTTGGTGTTGCCCGATTCT 59.041 50.000 0.00 0.00 36.04 2.40
57 58 0.958822 AGTTTGGTGTTGCCCGATTC 59.041 50.000 0.00 0.00 36.04 2.52
58 59 0.673437 CAGTTTGGTGTTGCCCGATT 59.327 50.000 0.00 0.00 36.04 3.34
59 60 1.178534 CCAGTTTGGTGTTGCCCGAT 61.179 55.000 0.00 0.00 36.04 4.18
60 61 1.826054 CCAGTTTGGTGTTGCCCGA 60.826 57.895 0.00 0.00 36.04 5.14
61 62 2.727544 CCAGTTTGGTGTTGCCCG 59.272 61.111 0.00 0.00 36.04 6.13
78 79 0.598065 GGTCTGTCAAATGTGGGCAC 59.402 55.000 0.00 0.00 0.00 5.01
79 80 0.478072 AGGTCTGTCAAATGTGGGCA 59.522 50.000 0.00 0.00 0.00 5.36
80 81 1.168714 GAGGTCTGTCAAATGTGGGC 58.831 55.000 0.00 0.00 0.00 5.36
81 82 2.616510 GGAGAGGTCTGTCAAATGTGGG 60.617 54.545 0.00 0.00 0.00 4.61
82 83 2.616510 GGGAGAGGTCTGTCAAATGTGG 60.617 54.545 0.00 0.00 0.00 4.17
83 84 2.304180 AGGGAGAGGTCTGTCAAATGTG 59.696 50.000 0.00 0.00 0.00 3.21
84 85 2.625639 AGGGAGAGGTCTGTCAAATGT 58.374 47.619 0.00 0.00 0.00 2.71
85 86 3.710209 AAGGGAGAGGTCTGTCAAATG 57.290 47.619 0.00 0.00 0.00 2.32
86 87 4.507512 GGAAAAGGGAGAGGTCTGTCAAAT 60.508 45.833 0.00 0.00 0.00 2.32
87 88 3.181443 GGAAAAGGGAGAGGTCTGTCAAA 60.181 47.826 0.00 0.00 0.00 2.69
88 89 2.372172 GGAAAAGGGAGAGGTCTGTCAA 59.628 50.000 0.00 0.00 0.00 3.18
89 90 1.978580 GGAAAAGGGAGAGGTCTGTCA 59.021 52.381 0.00 0.00 0.00 3.58
90 91 1.978580 TGGAAAAGGGAGAGGTCTGTC 59.021 52.381 0.00 0.00 0.00 3.51
91 92 2.106684 GTTGGAAAAGGGAGAGGTCTGT 59.893 50.000 0.00 0.00 0.00 3.41
92 93 2.553247 GGTTGGAAAAGGGAGAGGTCTG 60.553 54.545 0.00 0.00 0.00 3.51
93 94 1.705745 GGTTGGAAAAGGGAGAGGTCT 59.294 52.381 0.00 0.00 0.00 3.85
94 95 1.271982 GGGTTGGAAAAGGGAGAGGTC 60.272 57.143 0.00 0.00 0.00 3.85
95 96 0.778083 GGGTTGGAAAAGGGAGAGGT 59.222 55.000 0.00 0.00 0.00 3.85
96 97 0.777446 TGGGTTGGAAAAGGGAGAGG 59.223 55.000 0.00 0.00 0.00 3.69
97 98 2.158460 AGTTGGGTTGGAAAAGGGAGAG 60.158 50.000 0.00 0.00 0.00 3.20
98 99 1.856920 AGTTGGGTTGGAAAAGGGAGA 59.143 47.619 0.00 0.00 0.00 3.71
99 100 2.381752 AGTTGGGTTGGAAAAGGGAG 57.618 50.000 0.00 0.00 0.00 4.30
100 101 2.787035 AGTAGTTGGGTTGGAAAAGGGA 59.213 45.455 0.00 0.00 0.00 4.20
101 102 3.238788 AGTAGTTGGGTTGGAAAAGGG 57.761 47.619 0.00 0.00 0.00 3.95
102 103 7.362660 GCTTAATAGTAGTTGGGTTGGAAAAGG 60.363 40.741 0.00 0.00 0.00 3.11
103 104 7.393515 AGCTTAATAGTAGTTGGGTTGGAAAAG 59.606 37.037 0.00 0.00 0.00 2.27
104 105 7.235804 AGCTTAATAGTAGTTGGGTTGGAAAA 58.764 34.615 0.00 0.00 0.00 2.29
105 106 6.786122 AGCTTAATAGTAGTTGGGTTGGAAA 58.214 36.000 0.00 0.00 0.00 3.13
106 107 6.382919 AGCTTAATAGTAGTTGGGTTGGAA 57.617 37.500 0.00 0.00 0.00 3.53
107 108 6.382919 AAGCTTAATAGTAGTTGGGTTGGA 57.617 37.500 0.00 0.00 0.00 3.53
108 109 6.625081 GCAAAGCTTAATAGTAGTTGGGTTGG 60.625 42.308 0.00 0.00 0.00 3.77
109 110 6.151144 AGCAAAGCTTAATAGTAGTTGGGTTG 59.849 38.462 0.00 0.00 33.89 3.77
110 111 6.246163 AGCAAAGCTTAATAGTAGTTGGGTT 58.754 36.000 0.00 0.00 33.89 4.11
111 112 5.816682 AGCAAAGCTTAATAGTAGTTGGGT 58.183 37.500 0.00 0.00 33.89 4.51
126 127 1.827789 TGCGGGTGAAAGCAAAGCT 60.828 52.632 0.00 0.00 42.56 3.74
127 128 2.727544 TGCGGGTGAAAGCAAAGC 59.272 55.556 0.00 0.00 40.78 3.51
163 164 5.391449 GCTACAGTAGAATATTCATCGCGA 58.609 41.667 13.09 13.09 0.00 5.87
169 170 5.515797 AGTGCGCTACAGTAGAATATTCA 57.484 39.130 17.56 1.25 0.00 2.57
179 180 1.273606 ACTCATCAAGTGCGCTACAGT 59.726 47.619 9.73 1.11 36.65 3.55
180 181 2.001812 ACTCATCAAGTGCGCTACAG 57.998 50.000 9.73 2.80 36.65 2.74
181 182 2.735444 GCTACTCATCAAGTGCGCTACA 60.735 50.000 9.73 0.00 39.11 2.74
182 183 1.855360 GCTACTCATCAAGTGCGCTAC 59.145 52.381 9.73 5.32 39.11 3.58
183 184 1.476488 TGCTACTCATCAAGTGCGCTA 59.524 47.619 9.73 0.00 39.11 4.26
224 225 1.355971 CATTTTGCATGTGGCTGCTC 58.644 50.000 0.00 0.00 45.15 4.26
225 226 0.672401 GCATTTTGCATGTGGCTGCT 60.672 50.000 0.00 0.00 44.26 4.24
226 227 1.791662 GCATTTTGCATGTGGCTGC 59.208 52.632 0.00 0.00 44.26 5.25
280 289 2.027837 TGTGACTGGTCTGGATGTCATG 60.028 50.000 0.00 0.00 40.78 3.07
289 298 1.303799 GCTGCCATGTGACTGGTCTG 61.304 60.000 2.38 0.00 38.63 3.51
341 350 3.680937 CCGTACCAAGTTTGATAAAGCGA 59.319 43.478 0.00 0.00 0.00 4.93
500 515 2.084101 CATGTGCATGTGCGTGTGC 61.084 57.895 4.13 0.62 45.83 4.57
501 516 4.140301 CATGTGCATGTGCGTGTG 57.860 55.556 4.13 0.00 45.83 3.82
593 608 0.594602 CATGAGCGTGCATTATGGGG 59.405 55.000 0.00 0.00 0.00 4.96
715 730 2.941720 GCATCAAGGAGAAAGGTAGCAG 59.058 50.000 0.00 0.00 0.00 4.24
724 739 0.401356 TGCTGGTGCATCAAGGAGAA 59.599 50.000 0.00 0.00 45.31 2.87
725 740 2.068915 TGCTGGTGCATCAAGGAGA 58.931 52.632 0.00 0.00 45.31 3.71
738 753 1.626654 CGAAGGCGTAACTGTGCTGG 61.627 60.000 0.00 0.00 0.00 4.85
757 772 1.653151 CGGTAGGTTTAGAAGCAGGC 58.347 55.000 0.00 0.00 0.00 4.85
758 773 1.653151 GCGGTAGGTTTAGAAGCAGG 58.347 55.000 0.00 0.00 0.00 4.85
775 790 1.226746 GATTCGTTAGAATGGGGGCG 58.773 55.000 0.00 0.00 46.30 6.13
799 814 2.239907 AGGAGGAATGTTAGTTGGGAGC 59.760 50.000 0.00 0.00 0.00 4.70
800 815 3.118223 GGAGGAGGAATGTTAGTTGGGAG 60.118 52.174 0.00 0.00 0.00 4.30
801 816 2.844348 GGAGGAGGAATGTTAGTTGGGA 59.156 50.000 0.00 0.00 0.00 4.37
802 817 2.576191 TGGAGGAGGAATGTTAGTTGGG 59.424 50.000 0.00 0.00 0.00 4.12
803 818 4.510167 ATGGAGGAGGAATGTTAGTTGG 57.490 45.455 0.00 0.00 0.00 3.77
804 819 4.884164 GGAATGGAGGAGGAATGTTAGTTG 59.116 45.833 0.00 0.00 0.00 3.16
805 820 4.540099 TGGAATGGAGGAGGAATGTTAGTT 59.460 41.667 0.00 0.00 0.00 2.24
806 821 4.080299 GTGGAATGGAGGAGGAATGTTAGT 60.080 45.833 0.00 0.00 0.00 2.24
807 822 4.164988 AGTGGAATGGAGGAGGAATGTTAG 59.835 45.833 0.00 0.00 0.00 2.34
808 823 4.111577 AGTGGAATGGAGGAGGAATGTTA 58.888 43.478 0.00 0.00 0.00 2.41
809 824 2.922283 AGTGGAATGGAGGAGGAATGTT 59.078 45.455 0.00 0.00 0.00 2.71
810 825 2.507471 GAGTGGAATGGAGGAGGAATGT 59.493 50.000 0.00 0.00 0.00 2.71
811 826 2.158696 GGAGTGGAATGGAGGAGGAATG 60.159 54.545 0.00 0.00 0.00 2.67
827 842 3.056821 TCACGATCCACAAAGTAGGAGTG 60.057 47.826 0.00 0.00 37.34 3.51
893 908 0.944386 CGCTATGGTGGTTATGGTGC 59.056 55.000 0.00 0.00 0.00 5.01
974 989 2.734591 GCCGCATCCTATCCACGA 59.265 61.111 0.00 0.00 0.00 4.35
1174 1195 2.110213 GCAGTTGGACACACCGGA 59.890 61.111 9.46 0.00 42.61 5.14
1197 1218 0.697854 GGATGTATCCCCCTGGTGGT 60.698 60.000 0.00 0.00 41.20 4.16
1200 1221 0.647738 TCTGGATGTATCCCCCTGGT 59.352 55.000 8.37 0.00 46.59 4.00
1209 1230 1.188219 AGCCGCCGATCTGGATGTAT 61.188 55.000 7.64 0.00 42.00 2.29
1239 1260 2.043980 CGGGTACATGCGCCCTTTT 61.044 57.895 19.28 0.00 42.67 2.27
1318 1339 1.392168 CGCAAACGAACATACCGTGAT 59.608 47.619 0.00 0.00 43.93 3.06
1348 1369 0.879090 CACCAAAAGGCCCGTAGAAC 59.121 55.000 0.00 0.00 0.00 3.01
1536 1557 9.567848 TTCTGTAACAACAAAAATGAGAGAAAC 57.432 29.630 0.00 0.00 0.00 2.78
1658 1680 9.981114 AGAAGAAAGTTGTTTCAAGAAAGAAAA 57.019 25.926 6.69 0.00 44.08 2.29
1757 1780 0.184933 CCTTGTGGTGGGGTTCTTCA 59.815 55.000 0.00 0.00 0.00 3.02
1771 1794 4.082245 CCATTTGAAATCGCTTACCCTTGT 60.082 41.667 0.00 0.00 0.00 3.16
1818 1841 9.262358 GCCATTTTACCTATTTGTTGTTTGTTA 57.738 29.630 0.00 0.00 0.00 2.41
1822 1845 9.705290 CTTAGCCATTTTACCTATTTGTTGTTT 57.295 29.630 0.00 0.00 0.00 2.83
1823 1846 7.817478 GCTTAGCCATTTTACCTATTTGTTGTT 59.183 33.333 0.00 0.00 0.00 2.83
1833 1856 5.998363 GCTGTATAGCTTAGCCATTTTACCT 59.002 40.000 3.91 0.00 46.57 3.08
1855 1878 5.507985 GGAAGCAAAATTGTCAGTAACAGCT 60.508 40.000 0.00 0.00 39.58 4.24
1856 1879 4.681483 GGAAGCAAAATTGTCAGTAACAGC 59.319 41.667 0.00 0.00 39.58 4.40
1872 1895 2.360801 CCTTCTCCAAAAACGGAAGCAA 59.639 45.455 0.00 0.00 35.30 3.91
1997 2021 2.370189 AGTCCTTGTGAGAAGAACTGGG 59.630 50.000 0.00 0.00 0.00 4.45
2043 2069 7.374228 GTGCATTGTAATGAAATATCACGACTG 59.626 37.037 8.70 0.00 38.69 3.51
2129 2210 1.271163 TGTCTAGTTTTCTTGCGGGGG 60.271 52.381 0.00 0.00 0.00 5.40
2130 2211 2.178912 TGTCTAGTTTTCTTGCGGGG 57.821 50.000 0.00 0.00 0.00 5.73
2131 2212 3.751175 TCATTGTCTAGTTTTCTTGCGGG 59.249 43.478 0.00 0.00 0.00 6.13
2132 2213 5.122239 TGATCATTGTCTAGTTTTCTTGCGG 59.878 40.000 0.00 0.00 0.00 5.69
2133 2214 6.169419 TGATCATTGTCTAGTTTTCTTGCG 57.831 37.500 0.00 0.00 0.00 4.85
2134 2215 8.857216 CATTTGATCATTGTCTAGTTTTCTTGC 58.143 33.333 0.00 0.00 0.00 4.01
2135 2216 9.903682 ACATTTGATCATTGTCTAGTTTTCTTG 57.096 29.630 0.00 0.00 0.00 3.02
2136 2217 9.903682 CACATTTGATCATTGTCTAGTTTTCTT 57.096 29.630 8.44 0.00 0.00 2.52
2137 2218 9.071276 ACACATTTGATCATTGTCTAGTTTTCT 57.929 29.630 8.44 0.00 0.00 2.52
2138 2219 9.121517 CACACATTTGATCATTGTCTAGTTTTC 57.878 33.333 8.44 0.00 0.00 2.29
2139 2220 7.596248 GCACACATTTGATCATTGTCTAGTTTT 59.404 33.333 8.44 0.00 0.00 2.43
2140 2221 7.086376 GCACACATTTGATCATTGTCTAGTTT 58.914 34.615 8.44 0.00 0.00 2.66
2141 2222 6.349611 GGCACACATTTGATCATTGTCTAGTT 60.350 38.462 8.44 0.00 0.00 2.24
2142 2223 5.124457 GGCACACATTTGATCATTGTCTAGT 59.876 40.000 8.44 3.05 0.00 2.57
2143 2224 5.449588 GGGCACACATTTGATCATTGTCTAG 60.450 44.000 8.44 2.54 0.00 2.43
2144 2225 4.398988 GGGCACACATTTGATCATTGTCTA 59.601 41.667 8.44 0.00 0.00 2.59
2145 2226 3.194116 GGGCACACATTTGATCATTGTCT 59.806 43.478 8.44 0.00 0.00 3.41
2146 2227 3.514645 GGGCACACATTTGATCATTGTC 58.485 45.455 8.44 0.29 0.00 3.18
2147 2228 2.234414 GGGGCACACATTTGATCATTGT 59.766 45.455 0.00 0.70 0.00 2.71
2148 2229 2.498481 AGGGGCACACATTTGATCATTG 59.502 45.455 0.00 0.00 0.00 2.82
2149 2230 2.823959 AGGGGCACACATTTGATCATT 58.176 42.857 0.00 0.00 0.00 2.57
2150 2231 2.537633 AGGGGCACACATTTGATCAT 57.462 45.000 0.00 0.00 0.00 2.45
2151 2232 2.307496 AAGGGGCACACATTTGATCA 57.693 45.000 0.00 0.00 0.00 2.92
2152 2233 3.683365 AAAAGGGGCACACATTTGATC 57.317 42.857 0.00 0.00 0.00 2.92
2153 2234 3.055891 GCTAAAAGGGGCACACATTTGAT 60.056 43.478 0.00 0.00 0.00 2.57
2154 2235 2.298729 GCTAAAAGGGGCACACATTTGA 59.701 45.455 0.00 0.00 0.00 2.69
2155 2236 2.299867 AGCTAAAAGGGGCACACATTTG 59.700 45.455 0.00 0.00 0.00 2.32
2156 2237 2.608623 AGCTAAAAGGGGCACACATTT 58.391 42.857 0.00 0.00 0.00 2.32
2200 2281 8.579850 AAATTGATGATAGTTAGGCTTGTTGA 57.420 30.769 0.00 0.00 0.00 3.18
2270 2351 0.968405 TTTGGCAAGGCTCCACATTC 59.032 50.000 0.00 0.00 32.45 2.67
2310 2391 2.158871 ACCGCAACCTTTGACTAGTTCA 60.159 45.455 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.