Multiple sequence alignment - TraesCS5D01G394600

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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 TraesCS5D01G394600 chr5D 100.000 2300 0 0 1 2300 462668762 462671061 0.000000e+00 4248
1 TraesCS5D01G394600 chr5D 95.591 1134 36 9 114 1243 462745542 462746665 0.000000e+00 1805
2 TraesCS5D01G394600 chr5D 82.556 665 33 40 1229 1877 462746745 462747342 2.040000e-140 508
3 TraesCS5D01G394600 chr5D 81.967 122 20 1 2175 2294 449078812 449078933 4.040000e-18 102
4 TraesCS5D01G394600 chr5A 91.854 1154 50 20 114 1243 582652092 582653225 0.000000e+00 1570
5 TraesCS5D01G394600 chr5A 85.011 934 81 19 1399 2300 582654403 582655309 0.000000e+00 894
6 TraesCS5D01G394600 chr5A 82.847 274 33 9 1733 1997 582889686 582889954 1.370000e-57 233
7 TraesCS5D01G394600 chr5A 86.792 159 5 9 1250 1407 582653329 582653472 1.830000e-36 163
8 TraesCS5D01G394600 chr5B 87.607 1170 75 36 114 1243 569223590 569224729 0.000000e+00 1293
9 TraesCS5D01G394600 chr5B 86.819 1138 83 38 142 1243 569102984 569104090 0.000000e+00 1208
10 TraesCS5D01G394600 chr5B 90.821 719 30 14 1248 1958 569249808 569250498 0.000000e+00 929
11 TraesCS5D01G394600 chr5B 90.682 719 31 14 1248 1958 569148594 569149284 0.000000e+00 924
12 TraesCS5D01G394600 chr5B 85.096 208 28 3 2087 2294 569250602 569250806 2.320000e-50 209
13 TraesCS5D01G394600 chr5B 88.024 167 20 0 2087 2253 569149388 569149554 5.010000e-47 198
14 TraesCS5D01G394600 chr5B 80.208 192 25 7 1760 1949 568849056 568849236 5.160000e-27 132
15 TraesCS5D01G394600 chrUn 86.889 1167 84 39 114 1243 343623809 343624943 0.000000e+00 1243
16 TraesCS5D01G394600 chrUn 86.804 1167 86 39 114 1243 343569896 343571031 0.000000e+00 1240
17 TraesCS5D01G394600 chrUn 86.819 1138 83 38 142 1243 199466821 199465715 0.000000e+00 1208
18 TraesCS5D01G394600 chrUn 94.030 536 20 4 716 1243 67088228 67087697 0.000000e+00 802
19 TraesCS5D01G394600 chrUn 94.030 536 20 4 716 1243 307431406 307431937 0.000000e+00 802
20 TraesCS5D01G394600 chrUn 85.901 766 40 41 1248 1997 67087594 67086881 0.000000e+00 754
21 TraesCS5D01G394600 chrUn 85.976 763 39 41 1248 1994 307432040 307432750 0.000000e+00 754
22 TraesCS5D01G394600 chrUn 90.017 591 30 18 114 686 67088805 67088226 0.000000e+00 737
23 TraesCS5D01G394600 chrUn 90.017 591 30 18 114 686 307430829 307431408 0.000000e+00 737
24 TraesCS5D01G394600 chr1A 85.239 752 52 27 1248 1986 559978938 559978233 0.000000e+00 719
25 TraesCS5D01G394600 chr1A 83.990 762 48 29 1248 1997 559886528 559885829 0.000000e+00 664
26 TraesCS5D01G394600 chr1A 87.065 603 42 18 643 1243 559979609 559979041 0.000000e+00 649
27 TraesCS5D01G394600 chr1A 93.317 404 19 6 844 1243 559887030 559886631 7.080000e-165 590
28 TraesCS5D01G394600 chr1A 92.901 324 12 4 1251 1569 559941491 559941174 5.790000e-126 460
29 TraesCS5D01G394600 chr1A 86.585 328 32 5 1666 1986 559941158 559940836 3.640000e-93 351
30 TraesCS5D01G394600 chr1D 97.368 114 3 0 1 114 14576848 14576961 6.480000e-46 195
31 TraesCS5D01G394600 chr1D 96.491 114 4 0 1 114 14623261 14623148 3.020000e-44 189
32 TraesCS5D01G394600 chr1D 83.333 132 22 0 2169 2300 467781708 467781577 3.100000e-24 122
33 TraesCS5D01G394600 chr7D 96.491 114 4 0 1 114 109859170 109859057 3.020000e-44 189
34 TraesCS5D01G394600 chr7D 94.958 119 5 1 1 119 589032947 589033064 3.900000e-43 185
35 TraesCS5D01G394600 chr6D 96.460 113 4 0 1 113 16204050 16203938 1.080000e-43 187
36 TraesCS5D01G394600 chr6D 93.443 122 6 2 4 123 54228893 54229014 1.820000e-41 180
37 TraesCS5D01G394600 chr4D 95.690 116 5 0 1 116 31019620 31019505 1.080000e-43 187
38 TraesCS5D01G394600 chr3D 96.460 113 4 0 1 113 578371347 578371235 1.080000e-43 187
39 TraesCS5D01G394600 chr2D 96.460 113 4 0 1 113 644581980 644582092 1.080000e-43 187


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 TraesCS5D01G394600 chr5D 462668762 462671061 2299 False 4248.000000 4248 100.000000 1 2300 1 chr5D.!!$F2 2299
1 TraesCS5D01G394600 chr5D 462745542 462747342 1800 False 1156.500000 1805 89.073500 114 1877 2 chr5D.!!$F3 1763
2 TraesCS5D01G394600 chr5A 582652092 582655309 3217 False 875.666667 1570 87.885667 114 2300 3 chr5A.!!$F2 2186
3 TraesCS5D01G394600 chr5B 569223590 569224729 1139 False 1293.000000 1293 87.607000 114 1243 1 chr5B.!!$F3 1129
4 TraesCS5D01G394600 chr5B 569102984 569104090 1106 False 1208.000000 1208 86.819000 142 1243 1 chr5B.!!$F2 1101
5 TraesCS5D01G394600 chr5B 569249808 569250806 998 False 569.000000 929 87.958500 1248 2294 2 chr5B.!!$F5 1046
6 TraesCS5D01G394600 chr5B 569148594 569149554 960 False 561.000000 924 89.353000 1248 2253 2 chr5B.!!$F4 1005
7 TraesCS5D01G394600 chrUn 343623809 343624943 1134 False 1243.000000 1243 86.889000 114 1243 1 chrUn.!!$F2 1129
8 TraesCS5D01G394600 chrUn 343569896 343571031 1135 False 1240.000000 1240 86.804000 114 1243 1 chrUn.!!$F1 1129
9 TraesCS5D01G394600 chrUn 199465715 199466821 1106 True 1208.000000 1208 86.819000 142 1243 1 chrUn.!!$R1 1101
10 TraesCS5D01G394600 chrUn 67086881 67088805 1924 True 764.333333 802 89.982667 114 1997 3 chrUn.!!$R2 1883
11 TraesCS5D01G394600 chrUn 307430829 307432750 1921 False 764.333333 802 90.007667 114 1994 3 chrUn.!!$F3 1880
12 TraesCS5D01G394600 chr1A 559978233 559979609 1376 True 684.000000 719 86.152000 643 1986 2 chr1A.!!$R3 1343
13 TraesCS5D01G394600 chr1A 559885829 559887030 1201 True 627.000000 664 88.653500 844 1997 2 chr1A.!!$R1 1153
14 TraesCS5D01G394600 chr1A 559940836 559941491 655 True 405.500000 460 89.743000 1251 1986 2 chr1A.!!$R2 735

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
72 73 0.03759 TCAGGAACCGGGACAAATGG 59.962 55.0 6.32 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 2893 0.387929 AGAAACAGACGACGAAGGCA 59.612 50.0 0.0 0.0 0.0 4.75 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 3.969287 AAGAACCGGGACTAAAGGTAC 57.031 47.619 6.32 0.00 37.26 3.34
23 24 2.830321 AGAACCGGGACTAAAGGTACTG 59.170 50.000 6.32 0.00 40.86 2.74
26 27 0.177373 CGGGACTAAAGGTACTGGGC 59.823 60.000 0.00 0.00 40.86 5.36
27 28 1.581223 GGGACTAAAGGTACTGGGCT 58.419 55.000 0.00 0.00 40.86 5.19
28 29 1.914108 GGGACTAAAGGTACTGGGCTT 59.086 52.381 0.00 0.00 40.86 4.35
29 30 2.307980 GGGACTAAAGGTACTGGGCTTT 59.692 50.000 0.00 0.00 40.86 3.51
30 31 3.520721 GGGACTAAAGGTACTGGGCTTTA 59.479 47.826 0.00 0.00 40.86 1.85
31 32 4.383880 GGGACTAAAGGTACTGGGCTTTAG 60.384 50.000 19.51 19.51 40.86 1.85
33 34 5.423290 GGACTAAAGGTACTGGGCTTTAGTA 59.577 44.000 23.54 0.69 46.28 1.82
34 35 6.291648 ACTAAAGGTACTGGGCTTTAGTAC 57.708 41.667 22.80 14.49 45.23 2.73
38 39 3.156511 GTACTGGGCTTTAGTACCGAC 57.843 52.381 12.84 0.00 42.85 4.79
39 40 0.900421 ACTGGGCTTTAGTACCGACC 59.100 55.000 0.00 0.00 0.00 4.79
40 41 0.177373 CTGGGCTTTAGTACCGACCC 59.823 60.000 0.00 0.00 37.88 4.46
41 42 0.252375 TGGGCTTTAGTACCGACCCT 60.252 55.000 8.11 0.00 38.23 4.34
42 43 0.907486 GGGCTTTAGTACCGACCCTT 59.093 55.000 0.00 0.00 34.34 3.95
43 44 1.280133 GGGCTTTAGTACCGACCCTTT 59.720 52.381 0.00 0.00 34.34 3.11
44 45 2.501316 GGGCTTTAGTACCGACCCTTTA 59.499 50.000 0.00 0.00 34.34 1.85
45 46 3.431346 GGGCTTTAGTACCGACCCTTTAG 60.431 52.174 0.00 0.00 34.34 1.85
46 47 3.196469 GGCTTTAGTACCGACCCTTTAGT 59.804 47.826 0.00 0.00 0.00 2.24
47 48 4.428209 GCTTTAGTACCGACCCTTTAGTC 58.572 47.826 0.00 0.00 0.00 2.59
48 49 4.679106 GCTTTAGTACCGACCCTTTAGTCC 60.679 50.000 0.00 0.00 32.91 3.85
49 50 1.857965 AGTACCGACCCTTTAGTCCC 58.142 55.000 0.00 0.00 32.91 4.46
50 51 0.457443 GTACCGACCCTTTAGTCCCG 59.543 60.000 0.00 0.00 32.91 5.14
51 52 0.684153 TACCGACCCTTTAGTCCCGG 60.684 60.000 0.00 0.00 42.30 5.73
52 53 1.986210 CCGACCCTTTAGTCCCGGT 60.986 63.158 0.00 0.00 32.91 5.28
53 54 1.547472 CCGACCCTTTAGTCCCGGTT 61.547 60.000 0.00 0.00 32.91 4.44
54 55 0.108472 CGACCCTTTAGTCCCGGTTC 60.108 60.000 0.00 0.00 32.91 3.62
55 56 0.978907 GACCCTTTAGTCCCGGTTCA 59.021 55.000 0.00 0.00 0.00 3.18
56 57 0.981943 ACCCTTTAGTCCCGGTTCAG 59.018 55.000 0.00 0.00 0.00 3.02
57 58 0.252197 CCCTTTAGTCCCGGTTCAGG 59.748 60.000 0.00 0.00 0.00 3.86
58 59 1.272807 CCTTTAGTCCCGGTTCAGGA 58.727 55.000 0.00 0.00 0.00 3.86
59 60 1.626825 CCTTTAGTCCCGGTTCAGGAA 59.373 52.381 0.00 0.00 34.43 3.36
60 61 2.614734 CCTTTAGTCCCGGTTCAGGAAC 60.615 54.545 0.00 3.58 40.45 3.62
69 70 3.407443 GTTCAGGAACCGGGACAAA 57.593 52.632 6.32 0.00 35.36 2.83
70 71 1.905637 GTTCAGGAACCGGGACAAAT 58.094 50.000 6.32 0.00 35.36 2.32
71 72 1.539827 GTTCAGGAACCGGGACAAATG 59.460 52.381 6.32 0.00 35.36 2.32
72 73 0.037590 TCAGGAACCGGGACAAATGG 59.962 55.000 6.32 0.00 0.00 3.16
73 74 0.965363 CAGGAACCGGGACAAATGGG 60.965 60.000 6.32 0.00 0.00 4.00
74 75 2.348104 GGAACCGGGACAAATGGGC 61.348 63.158 6.32 0.00 0.00 5.36
75 76 2.283604 AACCGGGACAAATGGGCC 60.284 61.111 6.32 0.00 0.00 5.80
76 77 2.781431 GAACCGGGACAAATGGGCCT 62.781 60.000 6.32 0.00 0.00 5.19
77 78 2.037208 CCGGGACAAATGGGCCTT 59.963 61.111 4.53 0.00 0.00 4.35
78 79 1.304952 CCGGGACAAATGGGCCTTA 59.695 57.895 4.53 0.00 0.00 2.69
79 80 0.106217 CCGGGACAAATGGGCCTTAT 60.106 55.000 4.53 0.00 0.00 1.73
80 81 1.032014 CGGGACAAATGGGCCTTATG 58.968 55.000 4.53 3.10 0.00 1.90
81 82 1.409521 CGGGACAAATGGGCCTTATGA 60.410 52.381 4.53 0.00 0.00 2.15
82 83 2.745968 GGGACAAATGGGCCTTATGAA 58.254 47.619 4.53 0.00 0.00 2.57
83 84 2.430694 GGGACAAATGGGCCTTATGAAC 59.569 50.000 4.53 1.58 0.00 3.18
84 85 2.430694 GGACAAATGGGCCTTATGAACC 59.569 50.000 4.53 6.66 0.00 3.62
85 86 3.365472 GACAAATGGGCCTTATGAACCT 58.635 45.455 4.53 0.00 0.00 3.50
86 87 3.099141 ACAAATGGGCCTTATGAACCTG 58.901 45.455 4.53 0.00 0.00 4.00
87 88 2.431782 CAAATGGGCCTTATGAACCTGG 59.568 50.000 4.53 0.00 0.00 4.45
88 89 1.607225 ATGGGCCTTATGAACCTGGA 58.393 50.000 4.53 0.00 0.00 3.86
89 90 0.623723 TGGGCCTTATGAACCTGGAC 59.376 55.000 4.53 0.00 0.00 4.02
90 91 0.623723 GGGCCTTATGAACCTGGACA 59.376 55.000 0.84 0.25 0.00 4.02
91 92 1.005450 GGGCCTTATGAACCTGGACAA 59.995 52.381 0.84 0.00 0.00 3.18
92 93 2.556559 GGGCCTTATGAACCTGGACAAA 60.557 50.000 0.84 0.00 0.00 2.83
93 94 3.365472 GGCCTTATGAACCTGGACAAAT 58.635 45.455 0.00 0.00 0.00 2.32
94 95 3.131046 GGCCTTATGAACCTGGACAAATG 59.869 47.826 0.00 0.00 0.00 2.32
95 96 3.131046 GCCTTATGAACCTGGACAAATGG 59.869 47.826 0.00 5.51 0.00 3.16
96 97 3.701040 CCTTATGAACCTGGACAAATGGG 59.299 47.826 0.00 0.00 0.00 4.00
97 98 1.560505 ATGAACCTGGACAAATGGGC 58.439 50.000 0.00 0.00 0.00 5.36
98 99 0.541764 TGAACCTGGACAAATGGGCC 60.542 55.000 0.00 0.00 0.00 5.80
99 100 0.251787 GAACCTGGACAAATGGGCCT 60.252 55.000 4.53 0.00 0.00 5.19
100 101 0.190815 AACCTGGACAAATGGGCCTT 59.809 50.000 4.53 0.00 0.00 4.35
101 102 0.190815 ACCTGGACAAATGGGCCTTT 59.809 50.000 4.53 0.76 0.00 3.11
102 103 1.351076 CCTGGACAAATGGGCCTTTT 58.649 50.000 11.35 11.35 0.00 2.27
103 104 1.699083 CCTGGACAAATGGGCCTTTTT 59.301 47.619 14.22 6.91 0.00 1.94
104 105 2.289631 CCTGGACAAATGGGCCTTTTTC 60.290 50.000 14.22 13.86 0.00 2.29
105 106 2.634453 CTGGACAAATGGGCCTTTTTCT 59.366 45.455 14.22 3.47 0.00 2.52
106 107 3.831911 CTGGACAAATGGGCCTTTTTCTA 59.168 43.478 14.22 11.75 0.00 2.10
107 108 3.576550 TGGACAAATGGGCCTTTTTCTAC 59.423 43.478 14.22 4.94 0.00 2.59
108 109 3.056107 GGACAAATGGGCCTTTTTCTACC 60.056 47.826 14.22 11.12 0.00 3.18
109 110 3.576550 GACAAATGGGCCTTTTTCTACCA 59.423 43.478 14.22 0.00 35.39 3.25
110 111 3.578282 ACAAATGGGCCTTTTTCTACCAG 59.422 43.478 14.22 4.93 34.23 4.00
111 112 3.542969 AATGGGCCTTTTTCTACCAGT 57.457 42.857 4.53 0.00 34.23 4.00
112 113 2.286365 TGGGCCTTTTTCTACCAGTG 57.714 50.000 4.53 0.00 0.00 3.66
286 302 2.665165 TGGCAGAAGCAAGGAAAAGAA 58.335 42.857 0.00 0.00 44.61 2.52
287 303 2.362077 TGGCAGAAGCAAGGAAAAGAAC 59.638 45.455 0.00 0.00 44.61 3.01
307 323 1.676916 CGGCCAGCATAGTGGGATATG 60.677 57.143 2.24 0.00 38.14 1.78
429 451 4.011698 TCAAGGTCAATCCACACATGATG 58.988 43.478 0.00 0.00 39.02 3.07
1066 1133 2.607750 TGGAGGAGGAGTGCACCC 60.608 66.667 14.63 14.56 0.00 4.61
1634 2778 0.390340 GGTTCCCCGTCCGTTAGAAC 60.390 60.000 0.00 0.00 36.85 3.01
1757 2910 0.935196 GTTGCCTTCGTCGTCTGTTT 59.065 50.000 0.00 0.00 0.00 2.83
1929 3088 3.733337 CTGCAAGTTTGTCTGGTAGACT 58.267 45.455 10.03 0.00 45.27 3.24
1964 3125 0.841961 AGCTCTGGCATGCATCCTAA 59.158 50.000 21.36 0.00 41.70 2.69
1971 3132 1.678101 GGCATGCATCCTAACTTGACC 59.322 52.381 21.36 0.00 0.00 4.02
1999 3160 3.455990 GCTACCAAGCTAACTACTCCC 57.544 52.381 0.00 0.00 45.85 4.30
2001 3162 4.213513 GCTACCAAGCTAACTACTCCCTA 58.786 47.826 0.00 0.00 45.85 3.53
2007 3168 3.847081 AGCTAACTACTCCCTATGTCCC 58.153 50.000 0.00 0.00 0.00 4.46
2018 3182 2.698797 CCCTATGTCCCATGTAAGACGT 59.301 50.000 0.00 0.00 35.71 4.34
2053 3235 3.640029 GACTTACATTATGGGACGGAGGA 59.360 47.826 0.00 0.00 0.00 3.71
2054 3236 3.641906 ACTTACATTATGGGACGGAGGAG 59.358 47.826 0.00 0.00 0.00 3.69
2063 3245 2.225343 TGGGACGGAGGAGGTACTTTTA 60.225 50.000 0.00 0.00 41.55 1.52
2067 3249 4.202131 GGACGGAGGAGGTACTTTTATGAG 60.202 50.000 0.00 0.00 41.55 2.90
2075 3257 4.047883 AGGTACTTTTATGAGGGATGCCT 58.952 43.478 4.97 4.97 27.25 4.75
2076 3258 4.478686 AGGTACTTTTATGAGGGATGCCTT 59.521 41.667 7.42 0.00 27.25 4.35
2077 3259 5.044105 AGGTACTTTTATGAGGGATGCCTTT 60.044 40.000 7.42 0.58 27.25 3.11
2078 3260 5.656859 GGTACTTTTATGAGGGATGCCTTTT 59.343 40.000 7.42 0.18 0.00 2.27
2079 3261 6.154534 GGTACTTTTATGAGGGATGCCTTTTT 59.845 38.462 7.42 0.00 0.00 1.94
2155 3337 0.108585 TGTCCCAGAGAAAGTGCACC 59.891 55.000 14.63 0.00 0.00 5.01
2156 3338 0.606673 GTCCCAGAGAAAGTGCACCC 60.607 60.000 14.63 3.08 0.00 4.61
2205 3387 0.462047 GGTGATTGGGGCAGTACTCG 60.462 60.000 0.00 0.00 0.00 4.18
2210 3392 0.040058 TTGGGGCAGTACTCGGAGTA 59.960 55.000 13.70 13.70 0.00 2.59
2221 3403 4.967036 GTACTCGGAGTACTACCCAGTAT 58.033 47.826 31.37 1.74 45.70 2.12
2232 3414 0.397254 ACCCAGTATCGACCCCTCTG 60.397 60.000 0.00 0.00 0.00 3.35
2253 3435 3.372822 TGATTTTTGTTAGCCGTCCGATC 59.627 43.478 0.00 0.00 0.00 3.69
2257 3439 0.892755 TGTTAGCCGTCCGATCTGTT 59.107 50.000 0.00 0.00 0.00 3.16
2260 3442 1.672854 TAGCCGTCCGATCTGTTGGG 61.673 60.000 0.00 0.00 0.00 4.12
2261 3443 2.978824 CCGTCCGATCTGTTGGGT 59.021 61.111 0.00 0.00 0.00 4.51
2267 3449 3.458189 GTCCGATCTGTTGGGTGATTAG 58.542 50.000 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.463891 CAGTACCTTTAGTCCCGGTTCTTA 59.536 45.833 0.00 0.00 32.36 2.10
1 2 3.260128 CAGTACCTTTAGTCCCGGTTCTT 59.740 47.826 0.00 0.00 32.36 2.52
2 3 2.830321 CAGTACCTTTAGTCCCGGTTCT 59.170 50.000 0.00 0.15 32.36 3.01
3 4 2.093816 CCAGTACCTTTAGTCCCGGTTC 60.094 54.545 0.00 0.00 32.36 3.62
4 5 1.904537 CCAGTACCTTTAGTCCCGGTT 59.095 52.381 0.00 0.00 32.36 4.44
5 6 1.565067 CCAGTACCTTTAGTCCCGGT 58.435 55.000 0.00 0.00 34.86 5.28
6 7 0.828677 CCCAGTACCTTTAGTCCCGG 59.171 60.000 0.00 0.00 0.00 5.73
7 8 0.177373 GCCCAGTACCTTTAGTCCCG 59.823 60.000 0.00 0.00 0.00 5.14
8 9 1.581223 AGCCCAGTACCTTTAGTCCC 58.419 55.000 0.00 0.00 0.00 4.46
9 10 3.715638 AAAGCCCAGTACCTTTAGTCC 57.284 47.619 0.00 0.00 30.03 3.85
18 19 2.159184 GGTCGGTACTAAAGCCCAGTAC 60.159 54.545 10.25 10.25 45.01 2.73
19 20 2.102578 GGTCGGTACTAAAGCCCAGTA 58.897 52.381 0.00 0.00 0.00 2.74
20 21 0.900421 GGTCGGTACTAAAGCCCAGT 59.100 55.000 0.00 0.00 0.00 4.00
21 22 0.177373 GGGTCGGTACTAAAGCCCAG 59.823 60.000 0.00 0.00 36.25 4.45
22 23 0.252375 AGGGTCGGTACTAAAGCCCA 60.252 55.000 11.78 0.00 38.56 5.36
23 24 0.907486 AAGGGTCGGTACTAAAGCCC 59.093 55.000 0.00 0.00 36.46 5.19
24 25 2.775911 AAAGGGTCGGTACTAAAGCC 57.224 50.000 0.00 0.00 0.00 4.35
25 26 4.428209 GACTAAAGGGTCGGTACTAAAGC 58.572 47.826 0.00 0.00 0.00 3.51
26 27 4.142071 GGGACTAAAGGGTCGGTACTAAAG 60.142 50.000 0.00 0.00 37.12 1.85
27 28 3.769300 GGGACTAAAGGGTCGGTACTAAA 59.231 47.826 0.00 0.00 37.12 1.85
28 29 3.365472 GGGACTAAAGGGTCGGTACTAA 58.635 50.000 0.00 0.00 37.12 2.24
29 30 2.683742 CGGGACTAAAGGGTCGGTACTA 60.684 54.545 0.00 0.00 37.12 1.82
30 31 1.857965 GGGACTAAAGGGTCGGTACT 58.142 55.000 0.00 0.00 37.12 2.73
31 32 0.457443 CGGGACTAAAGGGTCGGTAC 59.543 60.000 0.00 0.00 37.12 3.34
32 33 0.684153 CCGGGACTAAAGGGTCGGTA 60.684 60.000 0.00 0.00 37.12 4.02
33 34 1.986210 CCGGGACTAAAGGGTCGGT 60.986 63.158 0.00 0.00 37.12 4.69
34 35 1.547472 AACCGGGACTAAAGGGTCGG 61.547 60.000 6.32 0.00 42.69 4.79
35 36 0.108472 GAACCGGGACTAAAGGGTCG 60.108 60.000 6.32 0.00 37.12 4.79
36 37 0.978907 TGAACCGGGACTAAAGGGTC 59.021 55.000 6.32 0.00 41.92 4.46
37 38 0.981943 CTGAACCGGGACTAAAGGGT 59.018 55.000 6.32 0.00 0.00 4.34
38 39 0.252197 CCTGAACCGGGACTAAAGGG 59.748 60.000 6.32 0.00 29.82 3.95
39 40 1.272807 TCCTGAACCGGGACTAAAGG 58.727 55.000 6.32 3.89 33.41 3.11
40 41 2.696506 GTTCCTGAACCGGGACTAAAG 58.303 52.381 6.32 0.00 38.83 1.85
41 42 2.845363 GTTCCTGAACCGGGACTAAA 57.155 50.000 6.32 0.00 38.83 1.85
51 52 1.539827 CATTTGTCCCGGTTCCTGAAC 59.460 52.381 0.00 1.33 40.45 3.18
52 53 1.546773 CCATTTGTCCCGGTTCCTGAA 60.547 52.381 0.00 0.00 0.00 3.02
53 54 0.037590 CCATTTGTCCCGGTTCCTGA 59.962 55.000 0.00 0.00 0.00 3.86
54 55 0.965363 CCCATTTGTCCCGGTTCCTG 60.965 60.000 0.00 0.00 0.00 3.86
55 56 1.382629 CCCATTTGTCCCGGTTCCT 59.617 57.895 0.00 0.00 0.00 3.36
56 57 2.348104 GCCCATTTGTCCCGGTTCC 61.348 63.158 0.00 0.00 0.00 3.62
57 58 2.348104 GGCCCATTTGTCCCGGTTC 61.348 63.158 0.00 0.00 0.00 3.62
58 59 2.283604 GGCCCATTTGTCCCGGTT 60.284 61.111 0.00 0.00 0.00 4.44
59 60 1.502527 TAAGGCCCATTTGTCCCGGT 61.503 55.000 0.00 0.00 0.00 5.28
60 61 0.106217 ATAAGGCCCATTTGTCCCGG 60.106 55.000 0.00 0.00 0.00 5.73
61 62 1.032014 CATAAGGCCCATTTGTCCCG 58.968 55.000 0.00 0.00 0.00 5.14
62 63 2.430694 GTTCATAAGGCCCATTTGTCCC 59.569 50.000 0.00 0.00 0.00 4.46
63 64 2.430694 GGTTCATAAGGCCCATTTGTCC 59.569 50.000 0.00 0.00 0.00 4.02
64 65 3.131046 CAGGTTCATAAGGCCCATTTGTC 59.869 47.826 0.00 0.00 0.00 3.18
65 66 3.099141 CAGGTTCATAAGGCCCATTTGT 58.901 45.455 0.00 0.00 0.00 2.83
66 67 2.431782 CCAGGTTCATAAGGCCCATTTG 59.568 50.000 0.00 0.00 0.00 2.32
67 68 2.314549 TCCAGGTTCATAAGGCCCATTT 59.685 45.455 0.00 0.00 0.00 2.32
68 69 1.929494 TCCAGGTTCATAAGGCCCATT 59.071 47.619 0.00 0.00 0.00 3.16
69 70 1.215423 GTCCAGGTTCATAAGGCCCAT 59.785 52.381 0.00 0.00 0.00 4.00
70 71 0.623723 GTCCAGGTTCATAAGGCCCA 59.376 55.000 0.00 0.00 0.00 5.36
71 72 0.623723 TGTCCAGGTTCATAAGGCCC 59.376 55.000 0.00 0.00 0.00 5.80
72 73 2.507407 TTGTCCAGGTTCATAAGGCC 57.493 50.000 0.00 0.00 0.00 5.19
73 74 3.131046 CCATTTGTCCAGGTTCATAAGGC 59.869 47.826 0.00 0.00 0.00 4.35
74 75 3.701040 CCCATTTGTCCAGGTTCATAAGG 59.299 47.826 0.00 0.00 0.00 2.69
75 76 3.131046 GCCCATTTGTCCAGGTTCATAAG 59.869 47.826 0.00 0.00 0.00 1.73
76 77 3.096092 GCCCATTTGTCCAGGTTCATAA 58.904 45.455 0.00 0.00 0.00 1.90
77 78 2.622977 GGCCCATTTGTCCAGGTTCATA 60.623 50.000 0.00 0.00 0.00 2.15
78 79 1.560505 GCCCATTTGTCCAGGTTCAT 58.439 50.000 0.00 0.00 0.00 2.57
79 80 0.541764 GGCCCATTTGTCCAGGTTCA 60.542 55.000 0.00 0.00 0.00 3.18
80 81 0.251787 AGGCCCATTTGTCCAGGTTC 60.252 55.000 0.00 0.00 0.00 3.62
81 82 0.190815 AAGGCCCATTTGTCCAGGTT 59.809 50.000 0.00 0.00 0.00 3.50
82 83 0.190815 AAAGGCCCATTTGTCCAGGT 59.809 50.000 0.00 0.00 0.00 4.00
83 84 1.351076 AAAAGGCCCATTTGTCCAGG 58.649 50.000 0.00 0.00 0.00 4.45
84 85 2.634453 AGAAAAAGGCCCATTTGTCCAG 59.366 45.455 8.01 0.00 28.13 3.86
85 86 2.688477 AGAAAAAGGCCCATTTGTCCA 58.312 42.857 8.01 0.00 28.13 4.02
86 87 3.056107 GGTAGAAAAAGGCCCATTTGTCC 60.056 47.826 8.01 4.95 28.13 4.02
87 88 3.576550 TGGTAGAAAAAGGCCCATTTGTC 59.423 43.478 8.01 4.02 0.00 3.18
88 89 3.578282 CTGGTAGAAAAAGGCCCATTTGT 59.422 43.478 8.01 6.88 0.00 2.83
89 90 3.578282 ACTGGTAGAAAAAGGCCCATTTG 59.422 43.478 8.01 0.00 0.00 2.32
90 91 3.578282 CACTGGTAGAAAAAGGCCCATTT 59.422 43.478 0.00 0.00 0.00 2.32
91 92 3.165071 CACTGGTAGAAAAAGGCCCATT 58.835 45.455 0.00 0.00 0.00 3.16
92 93 2.110011 ACACTGGTAGAAAAAGGCCCAT 59.890 45.455 0.00 0.00 0.00 4.00
93 94 1.497286 ACACTGGTAGAAAAAGGCCCA 59.503 47.619 0.00 0.00 0.00 5.36
94 95 2.160205 GACACTGGTAGAAAAAGGCCC 58.840 52.381 0.00 0.00 0.00 5.80
95 96 2.160205 GGACACTGGTAGAAAAAGGCC 58.840 52.381 0.00 0.00 0.00 5.19
96 97 3.075148 GAGGACACTGGTAGAAAAAGGC 58.925 50.000 0.00 0.00 0.00 4.35
97 98 4.351874 TGAGGACACTGGTAGAAAAAGG 57.648 45.455 0.00 0.00 0.00 3.11
98 99 5.799213 AGATGAGGACACTGGTAGAAAAAG 58.201 41.667 0.00 0.00 0.00 2.27
99 100 5.280011 GGAGATGAGGACACTGGTAGAAAAA 60.280 44.000 0.00 0.00 0.00 1.94
100 101 4.223032 GGAGATGAGGACACTGGTAGAAAA 59.777 45.833 0.00 0.00 0.00 2.29
101 102 3.769844 GGAGATGAGGACACTGGTAGAAA 59.230 47.826 0.00 0.00 0.00 2.52
102 103 3.245622 TGGAGATGAGGACACTGGTAGAA 60.246 47.826 0.00 0.00 0.00 2.10
103 104 2.311841 TGGAGATGAGGACACTGGTAGA 59.688 50.000 0.00 0.00 0.00 2.59
104 105 2.428890 GTGGAGATGAGGACACTGGTAG 59.571 54.545 0.00 0.00 0.00 3.18
105 106 2.457598 GTGGAGATGAGGACACTGGTA 58.542 52.381 0.00 0.00 0.00 3.25
106 107 1.270907 GTGGAGATGAGGACACTGGT 58.729 55.000 0.00 0.00 0.00 4.00
107 108 0.539051 GGTGGAGATGAGGACACTGG 59.461 60.000 0.00 0.00 34.42 4.00
108 109 1.269958 TGGTGGAGATGAGGACACTG 58.730 55.000 0.00 0.00 34.42 3.66
109 110 2.114616 GATGGTGGAGATGAGGACACT 58.885 52.381 0.00 0.00 34.42 3.55
110 111 1.833630 TGATGGTGGAGATGAGGACAC 59.166 52.381 0.00 0.00 0.00 3.67
111 112 2.252535 TGATGGTGGAGATGAGGACA 57.747 50.000 0.00 0.00 0.00 4.02
112 113 2.288702 CGATGATGGTGGAGATGAGGAC 60.289 54.545 0.00 0.00 0.00 3.85
153 157 5.278709 CCGATATTCTGTGTATGCACTCTCT 60.279 44.000 15.25 0.92 45.44 3.10
286 302 0.762842 TATCCCACTATGCTGGCCGT 60.763 55.000 0.00 0.00 0.00 5.68
287 303 0.615331 ATATCCCACTATGCTGGCCG 59.385 55.000 0.00 0.00 0.00 6.13
307 323 1.895131 TGGTTCCCTACGTACACCTTC 59.105 52.381 0.00 0.00 0.00 3.46
361 382 2.300152 GCGGAGGAATCCATGTCATCTA 59.700 50.000 0.61 0.00 0.00 1.98
368 389 2.203056 TGCGCGGAGGAATCCATG 60.203 61.111 8.83 0.00 0.00 3.66
369 390 2.203070 GTGCGCGGAGGAATCCAT 60.203 61.111 8.83 0.00 0.00 3.41
370 391 4.467084 GGTGCGCGGAGGAATCCA 62.467 66.667 8.83 0.00 0.00 3.41
371 392 2.701163 CTAGGTGCGCGGAGGAATCC 62.701 65.000 8.83 1.26 0.00 3.01
372 393 1.300233 CTAGGTGCGCGGAGGAATC 60.300 63.158 8.83 0.00 0.00 2.52
449 480 6.319658 ACCATCTTTGATTGCTATTTCGTGAT 59.680 34.615 0.00 0.00 0.00 3.06
663 704 6.386654 CCTGATATTTTTGCCACGTTTACTT 58.613 36.000 0.00 0.00 0.00 2.24
664 705 5.621329 GCCTGATATTTTTGCCACGTTTACT 60.621 40.000 0.00 0.00 0.00 2.24
665 706 4.561213 GCCTGATATTTTTGCCACGTTTAC 59.439 41.667 0.00 0.00 0.00 2.01
666 707 4.218635 TGCCTGATATTTTTGCCACGTTTA 59.781 37.500 0.00 0.00 0.00 2.01
1629 2773 8.520351 TCTGAATAACAAGTCAAGATCGTTCTA 58.480 33.333 0.00 0.00 0.00 2.10
1634 2778 7.588143 AACTCTGAATAACAAGTCAAGATCG 57.412 36.000 0.00 0.00 0.00 3.69
1669 2816 1.996191 GGTGCGCAAAGAAACAAACAA 59.004 42.857 14.00 0.00 0.00 2.83
1671 2818 0.570272 CGGTGCGCAAAGAAACAAAC 59.430 50.000 14.00 0.00 0.00 2.93
1740 2893 0.387929 AGAAACAGACGACGAAGGCA 59.612 50.000 0.00 0.00 0.00 4.75
1757 2910 0.755698 AGGGCGAGGATAGCGAAAGA 60.756 55.000 0.00 0.00 37.72 2.52
1929 3088 6.317676 GCCAGAGCTTTTGTACAGGATGTAA 61.318 44.000 0.00 0.00 44.88 2.41
2023 3187 7.207383 CGTCCCATAATGTAAGTCTATTGTCA 58.793 38.462 0.00 0.00 0.00 3.58
2024 3188 6.645415 CCGTCCCATAATGTAAGTCTATTGTC 59.355 42.308 0.00 0.00 0.00 3.18
2025 3189 6.325545 TCCGTCCCATAATGTAAGTCTATTGT 59.674 38.462 0.00 0.00 0.00 2.71
2026 3190 6.755206 TCCGTCCCATAATGTAAGTCTATTG 58.245 40.000 0.00 0.00 0.00 1.90
2028 3192 5.480772 CCTCCGTCCCATAATGTAAGTCTAT 59.519 44.000 0.00 0.00 0.00 1.98
2029 3193 4.831155 CCTCCGTCCCATAATGTAAGTCTA 59.169 45.833 0.00 0.00 0.00 2.59
2030 3194 3.641906 CCTCCGTCCCATAATGTAAGTCT 59.358 47.826 0.00 0.00 0.00 3.24
2031 3195 3.640029 TCCTCCGTCCCATAATGTAAGTC 59.360 47.826 0.00 0.00 0.00 3.01
2032 3196 3.641906 CTCCTCCGTCCCATAATGTAAGT 59.358 47.826 0.00 0.00 0.00 2.24
2040 3222 1.229131 AGTACCTCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2053 3235 4.047883 AGGCATCCCTCATAAAAGTACCT 58.952 43.478 0.00 0.00 36.46 3.08
2054 3236 4.439253 AGGCATCCCTCATAAAAGTACC 57.561 45.455 0.00 0.00 36.46 3.34
2085 3267 3.420893 ACATTCGCATCCCTCAGAAAAA 58.579 40.909 0.00 0.00 0.00 1.94
2086 3268 3.071874 ACATTCGCATCCCTCAGAAAA 57.928 42.857 0.00 0.00 0.00 2.29
2087 3269 2.787473 ACATTCGCATCCCTCAGAAA 57.213 45.000 0.00 0.00 0.00 2.52
2088 3270 3.904800 TTACATTCGCATCCCTCAGAA 57.095 42.857 0.00 0.00 0.00 3.02
2089 3271 5.070446 ACTTATTACATTCGCATCCCTCAGA 59.930 40.000 0.00 0.00 0.00 3.27
2090 3272 5.300752 ACTTATTACATTCGCATCCCTCAG 58.699 41.667 0.00 0.00 0.00 3.35
2091 3273 5.290493 ACTTATTACATTCGCATCCCTCA 57.710 39.130 0.00 0.00 0.00 3.86
2092 3274 6.456501 AGTACTTATTACATTCGCATCCCTC 58.543 40.000 0.00 0.00 32.41 4.30
2093 3275 6.420913 AGTACTTATTACATTCGCATCCCT 57.579 37.500 0.00 0.00 32.41 4.20
2094 3276 5.638234 GGAGTACTTATTACATTCGCATCCC 59.362 44.000 0.00 0.00 32.41 3.85
2095 3277 6.145696 GTGGAGTACTTATTACATTCGCATCC 59.854 42.308 0.00 0.00 32.41 3.51
2096 3278 6.924060 AGTGGAGTACTTATTACATTCGCATC 59.076 38.462 0.00 0.00 35.67 3.91
2097 3279 6.817184 AGTGGAGTACTTATTACATTCGCAT 58.183 36.000 0.00 0.00 35.67 4.73
2098 3280 6.216801 AGTGGAGTACTTATTACATTCGCA 57.783 37.500 0.00 0.00 35.67 5.10
2186 3368 0.462047 CGAGTACTGCCCCAATCACC 60.462 60.000 0.00 0.00 0.00 4.02
2205 3387 3.145286 GGTCGATACTGGGTAGTACTCC 58.855 54.545 0.00 0.27 41.92 3.85
2210 3392 0.932211 AGGGGTCGATACTGGGTAGT 59.068 55.000 0.00 0.00 40.99 2.73
2213 3395 0.397254 CAGAGGGGTCGATACTGGGT 60.397 60.000 0.00 0.00 0.00 4.51
2216 3398 4.408182 AAAATCAGAGGGGTCGATACTG 57.592 45.455 0.00 0.00 0.00 2.74
2221 3403 3.502123 AACAAAAATCAGAGGGGTCGA 57.498 42.857 0.00 0.00 0.00 4.20
2232 3414 3.621715 AGATCGGACGGCTAACAAAAATC 59.378 43.478 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.