Multiple sequence alignment - TraesCS5D01G421600

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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 TraesCS5D01G421600 chr5D 100.000 2336 0 0 1 2336 481762114 481759779 0.000000e+00 4314
1 TraesCS5D01G421600 chr5D 85.289 1244 106 36 920 2100 481564304 481563075 0.000000e+00 1212
2 TraesCS5D01G421600 chr5D 85.425 789 82 17 920 1697 481643432 481642666 0.000000e+00 789
3 TraesCS5D01G421600 chr5D 88.506 174 16 1 707 876 481643840 481643667 8.460000e-50 207
4 TraesCS5D01G421600 chr5D 84.298 121 17 2 1940 2058 481738961 481738841 1.470000e-22 117
5 TraesCS5D01G421600 chr5A 91.030 1427 91 13 920 2336 601341927 601340528 0.000000e+00 1892
6 TraesCS5D01G421600 chr5A 87.573 1022 83 19 920 1912 600503643 600502637 0.000000e+00 1144
7 TraesCS5D01G421600 chr5A 83.617 1233 130 48 635 1839 601087026 601085838 0.000000e+00 1092
8 TraesCS5D01G421600 chr5A 87.578 805 84 8 1534 2336 601255751 601254961 0.000000e+00 918
9 TraesCS5D01G421600 chr5A 92.140 598 44 3 920 1516 601256332 601255737 0.000000e+00 841
10 TraesCS5D01G421600 chr5A 87.755 637 43 14 4 631 601342886 601342276 0.000000e+00 712
11 TraesCS5D01G421600 chr5A 88.845 502 39 6 963 1449 601166999 601166500 3.320000e-168 601
12 TraesCS5D01G421600 chr5A 80.676 828 112 26 1073 1879 601483987 601483187 1.190000e-167 599
13 TraesCS5D01G421600 chr5A 90.499 421 36 1 215 631 601257310 601256890 9.430000e-154 553
14 TraesCS5D01G421600 chr5A 87.111 450 47 6 1696 2141 601245793 601245351 1.250000e-137 499
15 TraesCS5D01G421600 chr5A 88.104 269 15 3 635 901 601342168 601341915 1.050000e-78 303
16 TraesCS5D01G421600 chr5A 93.782 193 12 0 439 631 601087308 601087116 8.170000e-75 291
17 TraesCS5D01G421600 chr5A 89.848 197 19 1 1844 2040 601254476 601254281 3.850000e-63 252
18 TraesCS5D01G421600 chr5A 90.110 182 15 1 690 871 601098774 601098596 1.400000e-57 233
19 TraesCS5D01G421600 chr5A 85.222 203 16 5 14 216 601257602 601257414 1.830000e-46 196
20 TraesCS5D01G421600 chr5A 85.279 197 17 8 689 876 600504069 600503876 2.370000e-45 193
21 TraesCS5D01G421600 chr5A 79.630 270 43 5 2069 2336 601254279 601254020 1.430000e-42 183
22 TraesCS5D01G421600 chr5A 92.000 125 9 1 2212 2336 601245328 601245205 8.580000e-40 174
23 TraesCS5D01G421600 chr5A 76.699 309 47 10 12 312 601485002 601484711 5.200000e-32 148
24 TraesCS5D01G421600 chr5A 86.232 138 14 5 1920 2055 601498510 601498376 6.730000e-31 145
25 TraesCS5D01G421600 chr5A 77.959 245 40 3 641 871 601484891 601484647 8.700000e-30 141
26 TraesCS5D01G421600 chr5A 88.073 109 11 2 1735 1842 601254720 601254613 6.780000e-26 128
27 TraesCS5D01G421600 chr5A 77.368 190 32 7 1947 2134 601097323 601097143 4.110000e-18 102
28 TraesCS5D01G421600 chr5B 90.974 1407 106 12 936 2336 590806038 590804647 0.000000e+00 1875
29 TraesCS5D01G421600 chr5B 88.144 1029 78 20 919 1913 590183549 590182531 0.000000e+00 1184
30 TraesCS5D01G421600 chr5B 87.220 626 35 15 14 631 590807166 590806578 0.000000e+00 671
31 TraesCS5D01G421600 chr5B 94.650 243 12 1 635 876 590806471 590806229 2.190000e-100 375
32 TraesCS5D01G421600 chr5B 93.333 135 9 0 439 573 590503167 590503033 1.420000e-47 200
33 TraesCS5D01G421600 chr5B 84.118 170 14 7 2005 2171 590181891 590181732 4.020000e-33 152
34 TraesCS5D01G421600 chr5B 82.993 147 22 3 1914 2058 590387905 590387760 1.880000e-26 130


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 TraesCS5D01G421600 chr5D 481759779 481762114 2335 True 4314.000000 4314 100.000000 1 2336 1 chr5D.!!$R3 2335
1 TraesCS5D01G421600 chr5D 481563075 481564304 1229 True 1212.000000 1212 85.289000 920 2100 1 chr5D.!!$R1 1180
2 TraesCS5D01G421600 chr5D 481642666 481643840 1174 True 498.000000 789 86.965500 707 1697 2 chr5D.!!$R4 990
3 TraesCS5D01G421600 chr5A 601340528 601342886 2358 True 969.000000 1892 88.963000 4 2336 3 chr5A.!!$R8 2332
4 TraesCS5D01G421600 chr5A 601085838 601087308 1470 True 691.500000 1092 88.699500 439 1839 2 chr5A.!!$R4 1400
5 TraesCS5D01G421600 chr5A 600502637 600504069 1432 True 668.500000 1144 86.426000 689 1912 2 chr5A.!!$R3 1223
6 TraesCS5D01G421600 chr5A 601254020 601257602 3582 True 438.714286 918 87.570000 14 2336 7 chr5A.!!$R7 2322
7 TraesCS5D01G421600 chr5A 601245205 601245793 588 True 336.500000 499 89.555500 1696 2336 2 chr5A.!!$R6 640
8 TraesCS5D01G421600 chr5A 601483187 601485002 1815 True 296.000000 599 78.444667 12 1879 3 chr5A.!!$R9 1867
9 TraesCS5D01G421600 chr5B 590804647 590807166 2519 True 973.666667 1875 90.948000 14 2336 3 chr5B.!!$R4 2322
10 TraesCS5D01G421600 chr5B 590181732 590183549 1817 True 668.000000 1184 86.131000 919 2171 2 chr5B.!!$R3 1252

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
76 77 0.987294 ACATGCCTTGCTACTGTCCT 59.013 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 3419 0.625316 TCCTGGGCAACACATAGCAT 59.375 50.0 0.0 0.0 39.74 3.79 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
64 65 9.897744 CGATAAAATTGAATGTATAACATGCCT 57.102 29.630 0.00 0.00 37.97 4.75
73 74 5.097742 TGTATAACATGCCTTGCTACTGT 57.902 39.130 0.00 0.00 0.00 3.55
74 75 5.116180 TGTATAACATGCCTTGCTACTGTC 58.884 41.667 0.00 0.00 0.00 3.51
75 76 1.826385 AACATGCCTTGCTACTGTCC 58.174 50.000 0.00 0.00 0.00 4.02
76 77 0.987294 ACATGCCTTGCTACTGTCCT 59.013 50.000 0.00 0.00 0.00 3.85
77 78 2.187958 ACATGCCTTGCTACTGTCCTA 58.812 47.619 0.00 0.00 0.00 2.94
78 79 2.093447 ACATGCCTTGCTACTGTCCTAC 60.093 50.000 0.00 0.00 0.00 3.18
79 80 1.938585 TGCCTTGCTACTGTCCTACT 58.061 50.000 0.00 0.00 0.00 2.57
80 81 1.550524 TGCCTTGCTACTGTCCTACTG 59.449 52.381 0.00 0.00 0.00 2.74
81 82 1.825474 GCCTTGCTACTGTCCTACTGA 59.175 52.381 0.00 0.00 0.00 3.41
82 83 2.233922 GCCTTGCTACTGTCCTACTGAA 59.766 50.000 0.00 0.00 0.00 3.02
83 84 3.306780 GCCTTGCTACTGTCCTACTGAAA 60.307 47.826 0.00 0.00 0.00 2.69
84 85 4.624125 GCCTTGCTACTGTCCTACTGAAAT 60.624 45.833 0.00 0.00 0.00 2.17
85 86 5.395324 GCCTTGCTACTGTCCTACTGAAATA 60.395 44.000 0.00 0.00 0.00 1.40
86 87 6.686632 GCCTTGCTACTGTCCTACTGAAATAT 60.687 42.308 0.00 0.00 0.00 1.28
87 88 7.275920 CCTTGCTACTGTCCTACTGAAATATT 58.724 38.462 0.00 0.00 0.00 1.28
88 89 7.225538 CCTTGCTACTGTCCTACTGAAATATTG 59.774 40.741 0.00 0.00 0.00 1.90
89 90 7.418337 TGCTACTGTCCTACTGAAATATTGA 57.582 36.000 0.00 0.00 0.00 2.57
90 91 7.492524 TGCTACTGTCCTACTGAAATATTGAG 58.507 38.462 0.00 0.00 0.00 3.02
91 92 6.926272 GCTACTGTCCTACTGAAATATTGAGG 59.074 42.308 0.00 0.00 0.00 3.86
92 93 5.675538 ACTGTCCTACTGAAATATTGAGGC 58.324 41.667 0.00 0.00 0.00 4.70
93 94 5.036117 TGTCCTACTGAAATATTGAGGCC 57.964 43.478 0.00 0.00 0.00 5.19
94 95 4.721776 TGTCCTACTGAAATATTGAGGCCT 59.278 41.667 3.86 3.86 0.00 5.19
114 127 3.804325 CCTATCTTGTGTTGGTGCTATCG 59.196 47.826 0.00 0.00 0.00 2.92
133 146 7.277760 TGCTATCGCGTATTAGCATTTTGATAT 59.722 33.333 25.69 4.23 40.21 1.63
135 148 9.973246 CTATCGCGTATTAGCATTTTGATATTT 57.027 29.630 5.77 0.00 36.85 1.40
136 149 8.659569 ATCGCGTATTAGCATTTTGATATTTG 57.340 30.769 5.77 0.00 36.85 2.32
139 152 9.376171 CGCGTATTAGCATTTTGATATTTGTTA 57.624 29.630 0.00 0.00 36.85 2.41
167 180 4.908601 TTTGATTCTCAAGCTCCACCTA 57.091 40.909 0.00 0.00 37.70 3.08
203 216 7.762159 CCTTTGTCCTTAGTCTACTCAAAGATC 59.238 40.741 16.68 0.00 41.14 2.75
220 338 6.661377 TCAAAGATCTCTAGTGCTCTAGTTGT 59.339 38.462 19.48 8.80 42.88 3.32
312 442 6.472686 ACTCTCTGTCTTGTCAGTAGTTTT 57.527 37.500 0.00 0.00 36.85 2.43
365 495 5.012148 ACATGGTAGTATTGTGGATAGGCTC 59.988 44.000 0.00 0.00 0.00 4.70
459 589 2.419673 TGAATGTCCTAACAAGCATGCG 59.580 45.455 13.01 0.84 39.30 4.73
599 729 7.867403 GCCAAGATGTTTTCAGTTATTCAGAAA 59.133 33.333 0.00 0.00 31.43 2.52
622 752 3.316029 TCAGAACATTGCTTCAGGTTGTG 59.684 43.478 0.00 0.00 36.28 3.33
631 761 3.053693 TGCTTCAGGTTGTGGCCTTATAT 60.054 43.478 3.32 0.00 36.58 0.86
632 762 3.316308 GCTTCAGGTTGTGGCCTTATATG 59.684 47.826 3.32 0.00 36.58 1.78
633 763 4.526970 CTTCAGGTTGTGGCCTTATATGT 58.473 43.478 3.32 0.00 36.58 2.29
777 1029 8.088981 TCTTCTTTCCACACTCTGTAATTAGTC 58.911 37.037 0.00 0.00 0.00 2.59
883 1142 8.472413 TGACTTGGATATTACGCTAAGTAGTTT 58.528 33.333 0.00 0.00 36.56 2.66
884 1143 9.956720 GACTTGGATATTACGCTAAGTAGTTTA 57.043 33.333 0.00 0.00 36.56 2.01
892 1151 7.712264 TTACGCTAAGTAGTTTAACAAAGCA 57.288 32.000 0.00 0.00 36.56 3.91
893 1152 5.982324 ACGCTAAGTAGTTTAACAAAGCAC 58.018 37.500 0.00 0.00 32.12 4.40
894 1153 5.049886 ACGCTAAGTAGTTTAACAAAGCACC 60.050 40.000 0.00 0.00 32.12 5.01
895 1154 5.616204 CGCTAAGTAGTTTAACAAAGCACCC 60.616 44.000 0.00 0.00 32.12 4.61
896 1155 5.239963 GCTAAGTAGTTTAACAAAGCACCCA 59.760 40.000 0.00 0.00 32.60 4.51
898 1365 5.767816 AGTAGTTTAACAAAGCACCCAAG 57.232 39.130 0.00 0.00 0.00 3.61
900 1367 3.371034 AGTTTAACAAAGCACCCAAGGT 58.629 40.909 0.00 0.00 35.62 3.50
906 1373 3.304829 ACAAAGCACCCAAGGTAATTGT 58.695 40.909 5.61 5.61 37.17 2.71
907 1374 3.320826 ACAAAGCACCCAAGGTAATTGTC 59.679 43.478 5.61 0.00 37.17 3.18
908 1375 2.969821 AGCACCCAAGGTAATTGTCA 57.030 45.000 0.00 0.00 37.17 3.58
910 1377 3.571590 AGCACCCAAGGTAATTGTCAAA 58.428 40.909 0.00 0.00 37.17 2.69
911 1378 3.964031 AGCACCCAAGGTAATTGTCAAAA 59.036 39.130 0.00 0.00 37.17 2.44
912 1379 4.407296 AGCACCCAAGGTAATTGTCAAAAA 59.593 37.500 0.00 0.00 37.17 1.94
1101 1845 2.965147 GCTAAAGCAGAGAGAGGAGGAT 59.035 50.000 0.00 0.00 41.59 3.24
1325 2069 1.817740 CGGGAATGTCAAACCACACCT 60.818 52.381 0.00 0.00 0.00 4.00
1350 2094 2.295349 TCAGTAACGAACACTGGAGGAC 59.705 50.000 13.19 0.00 42.98 3.85
1414 2169 2.016762 ACCCTCCCTCGGTGATAGT 58.983 57.895 0.00 0.00 30.39 2.12
1460 2219 0.954452 GTGACCTTGCCTCACTTTGG 59.046 55.000 0.00 0.00 35.99 3.28
1490 2250 6.295719 ACGAGTTCCTTTGTCCATAGTTAT 57.704 37.500 0.00 0.00 0.00 1.89
1514 2275 8.721019 ATTTTATATTGGGTTTGTCAGCATTG 57.279 30.769 0.00 0.00 0.00 2.82
1518 2279 1.680735 TGGGTTTGTCAGCATTGTCAC 59.319 47.619 0.00 0.00 0.00 3.67
1561 2322 3.432933 CAGCATTGTGTTAAAATGGCCAC 59.567 43.478 8.16 0.00 35.88 5.01
1581 2345 2.200067 CAGAATGACACTCATCGCCTC 58.800 52.381 0.00 0.00 39.69 4.70
1796 2587 3.574396 TGGTCAAGTGACTACTGAAGAGG 59.426 47.826 11.07 0.00 44.20 3.69
1851 2651 5.187687 TCTTCAAACCTGTCGGTACTTTTT 58.812 37.500 0.00 0.00 44.73 1.94
1862 2662 7.041644 CCTGTCGGTACTTTTTCATTTGAACTA 60.042 37.037 0.00 0.00 33.13 2.24
1875 2675 7.878547 TCATTTGAACTATGCATGGTATTGA 57.121 32.000 16.75 9.91 0.00 2.57
1903 2705 5.124457 AGACAACTTATATGCTGGTGCTTTG 59.876 40.000 0.00 0.00 40.48 2.77
1932 2761 8.830580 TCTTTTACTCACAGAGAATTCAAGTTG 58.169 33.333 8.44 0.00 33.32 3.16
1977 2806 4.931661 ATGAAATATCTGCCTTTGCCAG 57.068 40.909 0.00 0.00 36.33 4.85
1983 2812 1.303074 CTGCCTTTGCCAGCTCTCA 60.303 57.895 0.00 0.00 36.33 3.27
1991 2820 2.071778 TGCCAGCTCTCAAAACCTTT 57.928 45.000 0.00 0.00 0.00 3.11
1997 2826 3.067180 CAGCTCTCAAAACCTTTGCAGAA 59.933 43.478 0.00 0.00 0.00 3.02
2058 3410 7.120923 ACCATGTCCACGTCTTATATAAGTT 57.879 36.000 19.58 5.54 34.93 2.66
2067 3419 9.146984 CCACGTCTTATATAAGTTGAGTTTTGA 57.853 33.333 19.58 0.00 34.93 2.69
2079 3432 6.441274 AGTTGAGTTTTGATGCTATGTGTTG 58.559 36.000 0.00 0.00 0.00 3.33
2093 3447 3.168035 TGTGTTGCCCAGGAATTGTAT 57.832 42.857 0.00 0.00 0.00 2.29
2094 3448 3.505386 TGTGTTGCCCAGGAATTGTATT 58.495 40.909 0.00 0.00 0.00 1.89
2095 3449 3.900601 TGTGTTGCCCAGGAATTGTATTT 59.099 39.130 0.00 0.00 0.00 1.40
2096 3450 4.244862 GTGTTGCCCAGGAATTGTATTTG 58.755 43.478 0.00 0.00 0.00 2.32
2097 3451 3.900601 TGTTGCCCAGGAATTGTATTTGT 59.099 39.130 0.00 0.00 0.00 2.83
2098 3452 5.047660 GTGTTGCCCAGGAATTGTATTTGTA 60.048 40.000 0.00 0.00 0.00 2.41
2099 3453 5.719085 TGTTGCCCAGGAATTGTATTTGTAT 59.281 36.000 0.00 0.00 0.00 2.29
2102 3456 6.638610 TGCCCAGGAATTGTATTTGTATTTG 58.361 36.000 0.00 0.00 0.00 2.32
2135 3489 3.904136 AGTATTGCTCAAGTGTGTTGC 57.096 42.857 0.00 0.00 0.00 4.17
2140 3495 1.845809 GCTCAAGTGTGTTGCTCGGG 61.846 60.000 0.00 0.00 0.00 5.14
2141 3496 1.227823 TCAAGTGTGTTGCTCGGGG 60.228 57.895 0.00 0.00 0.00 5.73
2165 3520 7.363530 GGGGAAAATGGTAAAGATTGTTAGGAC 60.364 40.741 0.00 0.00 0.00 3.85
2186 3541 1.117150 GATAGGCAACGGGACTACCA 58.883 55.000 0.00 0.00 40.84 3.25
2194 3549 3.369157 GCAACGGGACTACCAGAAATAGT 60.369 47.826 0.00 0.00 40.22 2.12
2197 3552 5.121380 ACGGGACTACCAGAAATAGTAGA 57.879 43.478 4.30 0.00 40.22 2.59
2200 3555 5.768662 CGGGACTACCAGAAATAGTAGATGA 59.231 44.000 4.30 0.00 40.22 2.92
2203 3558 8.483758 GGGACTACCAGAAATAGTAGATGAAAA 58.516 37.037 4.30 0.00 39.85 2.29
2218 3575 5.014858 AGATGAAAAGGATTCTGTGTGCAT 58.985 37.500 0.00 0.00 0.00 3.96
2225 3582 4.655963 AGGATTCTGTGTGCATAAAGTGT 58.344 39.130 0.01 0.00 0.00 3.55
2237 3594 6.206438 TGTGCATAAAGTGTTGTGTATGTCAT 59.794 34.615 0.00 0.00 0.00 3.06
2283 3640 7.768807 AGCTACTAGTTATATTCAGGTCCAG 57.231 40.000 0.00 0.00 0.00 3.86
2287 3644 6.583562 ACTAGTTATATTCAGGTCCAGCAAC 58.416 40.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.959721 GTGACCATACATAATTACTCCCAATAT 57.040 33.333 0.00 0.00 0.00 1.28
6 7 9.166222 AGTGACCATACATAATTACTCCCAATA 57.834 33.333 0.00 0.00 0.00 1.90
7 8 7.939039 CAGTGACCATACATAATTACTCCCAAT 59.061 37.037 0.00 0.00 0.00 3.16
8 9 7.126573 TCAGTGACCATACATAATTACTCCCAA 59.873 37.037 0.00 0.00 0.00 4.12
9 10 6.613679 TCAGTGACCATACATAATTACTCCCA 59.386 38.462 0.00 0.00 0.00 4.37
10 11 7.062749 TCAGTGACCATACATAATTACTCCC 57.937 40.000 0.00 0.00 0.00 4.30
62 63 4.537135 TTTCAGTAGGACAGTAGCAAGG 57.463 45.455 0.00 0.00 0.00 3.61
64 65 7.847096 TCAATATTTCAGTAGGACAGTAGCAA 58.153 34.615 0.00 0.00 0.00 3.91
73 74 7.019388 AGATAGGCCTCAATATTTCAGTAGGA 58.981 38.462 9.68 0.00 0.00 2.94
74 75 7.251321 AGATAGGCCTCAATATTTCAGTAGG 57.749 40.000 9.68 0.00 0.00 3.18
75 76 8.153550 ACAAGATAGGCCTCAATATTTCAGTAG 58.846 37.037 9.68 0.00 0.00 2.57
76 77 7.933577 CACAAGATAGGCCTCAATATTTCAGTA 59.066 37.037 9.68 0.00 0.00 2.74
77 78 6.769822 CACAAGATAGGCCTCAATATTTCAGT 59.230 38.462 9.68 0.00 0.00 3.41
78 79 6.769822 ACACAAGATAGGCCTCAATATTTCAG 59.230 38.462 9.68 0.00 0.00 3.02
79 80 6.662755 ACACAAGATAGGCCTCAATATTTCA 58.337 36.000 9.68 0.00 0.00 2.69
80 81 7.420800 CAACACAAGATAGGCCTCAATATTTC 58.579 38.462 9.68 0.00 0.00 2.17
81 82 6.322201 CCAACACAAGATAGGCCTCAATATTT 59.678 38.462 9.68 0.00 0.00 1.40
82 83 5.829924 CCAACACAAGATAGGCCTCAATATT 59.170 40.000 9.68 0.00 0.00 1.28
83 84 5.103940 ACCAACACAAGATAGGCCTCAATAT 60.104 40.000 9.68 0.00 0.00 1.28
84 85 4.227300 ACCAACACAAGATAGGCCTCAATA 59.773 41.667 9.68 0.00 0.00 1.90
85 86 3.010584 ACCAACACAAGATAGGCCTCAAT 59.989 43.478 9.68 0.00 0.00 2.57
86 87 2.375174 ACCAACACAAGATAGGCCTCAA 59.625 45.455 9.68 0.00 0.00 3.02
87 88 1.985159 ACCAACACAAGATAGGCCTCA 59.015 47.619 9.68 0.00 0.00 3.86
88 89 2.359900 CACCAACACAAGATAGGCCTC 58.640 52.381 9.68 0.00 0.00 4.70
89 90 1.614317 GCACCAACACAAGATAGGCCT 60.614 52.381 11.78 11.78 0.00 5.19
90 91 0.811281 GCACCAACACAAGATAGGCC 59.189 55.000 0.00 0.00 0.00 5.19
91 92 1.826385 AGCACCAACACAAGATAGGC 58.174 50.000 0.00 0.00 0.00 3.93
92 93 3.804325 CGATAGCACCAACACAAGATAGG 59.196 47.826 0.00 0.00 0.00 2.57
203 216 6.689241 CACGAATAACAACTAGAGCACTAGAG 59.311 42.308 22.92 16.44 46.34 2.43
459 589 4.313282 ACAAACCGAGGAAGTTAAGCTAC 58.687 43.478 0.00 0.00 0.00 3.58
599 729 4.022589 CACAACCTGAAGCAATGTTCTGAT 60.023 41.667 0.00 0.00 0.00 2.90
622 752 9.927668 AACAAATATTGCAATACATATAAGGCC 57.072 29.630 21.10 0.00 0.00 5.19
757 1001 6.665992 ACAGACTAATTACAGAGTGTGGAA 57.334 37.500 7.81 0.00 40.36 3.53
871 1130 5.379827 GGTGCTTTGTTAAACTACTTAGCG 58.620 41.667 0.00 0.00 31.93 4.26
883 1142 4.896482 ACAATTACCTTGGGTGCTTTGTTA 59.104 37.500 0.00 0.00 39.30 2.41
884 1143 3.709141 ACAATTACCTTGGGTGCTTTGTT 59.291 39.130 0.00 0.00 39.30 2.83
886 1145 3.320541 TGACAATTACCTTGGGTGCTTTG 59.679 43.478 0.00 3.71 39.30 2.77
888 1147 3.237268 TGACAATTACCTTGGGTGCTT 57.763 42.857 0.00 0.00 39.30 3.91
890 1149 4.329462 TTTTGACAATTACCTTGGGTGC 57.671 40.909 0.00 0.00 39.30 5.01
917 1384 0.106015 AGCAGACCTTGGGTGCTTTT 60.106 50.000 11.50 0.00 32.14 2.27
1101 1845 0.664761 GTTGCTGAGCTTCTGTTGCA 59.335 50.000 5.83 0.00 0.00 4.08
1325 2069 4.556233 CTCCAGTGTTCGTTACTGATTCA 58.444 43.478 14.75 0.00 46.52 2.57
1350 2094 1.265095 GGCATGCTGTATCAATCACCG 59.735 52.381 18.92 0.00 0.00 4.94
1357 2101 2.212812 TTGGTTGGCATGCTGTATCA 57.787 45.000 18.92 6.86 0.00 2.15
1414 2169 2.472029 TGAAACCCTTTTTCCTTGCCA 58.528 42.857 0.00 0.00 0.00 4.92
1460 2219 1.301479 AAAGGAACTCGTCGTGGCC 60.301 57.895 0.00 0.00 38.49 5.36
1490 2250 7.675062 ACAATGCTGACAAACCCAATATAAAA 58.325 30.769 0.00 0.00 0.00 1.52
1514 2275 1.337823 ACAGCTATGGACGTTGGTGAC 60.338 52.381 11.06 0.00 0.00 3.67
1518 2279 2.151202 ACAAACAGCTATGGACGTTGG 58.849 47.619 0.00 0.00 0.00 3.77
1561 2322 2.159128 AGAGGCGATGAGTGTCATTCTG 60.159 50.000 0.00 0.00 37.20 3.02
1581 2345 8.622948 AAACTGATCACCCTTTAAAGACTTAG 57.377 34.615 16.98 7.71 0.00 2.18
1636 2404 9.520515 TGTAGAAATAAGAGCAATTCCTTCTTT 57.479 29.630 2.11 0.00 33.51 2.52
1796 2587 3.409026 TCTCTCCCTTTCTTTGACAGC 57.591 47.619 0.00 0.00 0.00 4.40
1851 2651 7.774625 TCTCAATACCATGCATAGTTCAAATGA 59.225 33.333 2.32 1.46 0.00 2.57
1862 2662 6.835174 AGTTGTCTATCTCAATACCATGCAT 58.165 36.000 0.00 0.00 0.00 3.96
1875 2675 6.042552 AGCACCAGCATATAAGTTGTCTATCT 59.957 38.462 0.00 0.00 45.49 1.98
1895 2697 5.646606 TGTGAGTAAAAGAAACAAAGCACC 58.353 37.500 0.00 0.00 0.00 5.01
1903 2705 9.657121 CTTGAATTCTCTGTGAGTAAAAGAAAC 57.343 33.333 7.05 0.00 30.43 2.78
1932 2761 1.904287 TGTGGGCATGTTAGGTTGAC 58.096 50.000 0.00 0.00 0.00 3.18
1977 2806 3.715628 TTCTGCAAAGGTTTTGAGAGC 57.284 42.857 5.77 0.00 0.00 4.09
1983 2812 3.711190 AGGGTGAATTCTGCAAAGGTTTT 59.289 39.130 7.05 0.00 0.00 2.43
1991 2820 4.574674 ATGTAAGAGGGTGAATTCTGCA 57.425 40.909 7.05 0.00 0.00 4.41
1997 2826 7.918076 TGAAGAGTTTATGTAAGAGGGTGAAT 58.082 34.615 0.00 0.00 0.00 2.57
2058 3410 4.321156 GGCAACACATAGCATCAAAACTCA 60.321 41.667 0.00 0.00 0.00 3.41
2067 3419 0.625316 TCCTGGGCAACACATAGCAT 59.375 50.000 0.00 0.00 39.74 3.79
2079 3432 6.048509 CCAAATACAAATACAATTCCTGGGC 58.951 40.000 0.00 0.00 0.00 5.36
2095 3449 9.687210 CAATACTATTAGAGCGTACCAAATACA 57.313 33.333 0.00 0.00 32.79 2.29
2096 3450 8.645487 GCAATACTATTAGAGCGTACCAAATAC 58.355 37.037 0.00 0.00 0.00 1.89
2097 3451 8.582437 AGCAATACTATTAGAGCGTACCAAATA 58.418 33.333 0.00 0.00 0.00 1.40
2098 3452 7.442656 AGCAATACTATTAGAGCGTACCAAAT 58.557 34.615 0.00 0.00 0.00 2.32
2099 3453 6.812998 AGCAATACTATTAGAGCGTACCAAA 58.187 36.000 0.00 0.00 0.00 3.28
2102 3456 6.010294 TGAGCAATACTATTAGAGCGTACC 57.990 41.667 0.00 0.00 0.00 3.34
2135 3489 3.359695 TCTTTACCATTTTCCCCCGAG 57.640 47.619 0.00 0.00 0.00 4.63
2140 3495 7.396339 AGTCCTAACAATCTTTACCATTTTCCC 59.604 37.037 0.00 0.00 0.00 3.97
2141 3496 8.244113 CAGTCCTAACAATCTTTACCATTTTCC 58.756 37.037 0.00 0.00 0.00 3.13
2165 3520 1.068741 GGTAGTCCCGTTGCCTATCAG 59.931 57.143 0.00 0.00 0.00 2.90
2194 3549 5.559770 TGCACACAGAATCCTTTTCATCTA 58.440 37.500 0.00 0.00 0.00 1.98
2197 3552 6.839124 TTATGCACACAGAATCCTTTTCAT 57.161 33.333 0.00 0.00 0.00 2.57
2200 3555 6.040842 ACACTTTATGCACACAGAATCCTTTT 59.959 34.615 0.00 0.00 0.00 2.27
2203 3558 4.655963 ACACTTTATGCACACAGAATCCT 58.344 39.130 0.00 0.00 0.00 3.24
2218 3575 9.984190 TGTAACTATGACATACACAACACTTTA 57.016 29.630 0.00 0.00 0.00 1.85
2225 3582 7.992008 TCGAGATGTAACTATGACATACACAA 58.008 34.615 0.00 0.00 37.65 3.33
2274 3631 1.451504 CCTGTGTTGCTGGACCTGA 59.548 57.895 1.91 0.00 38.33 3.86
2283 3640 1.748493 TCTTTGTTGACCCTGTGTTGC 59.252 47.619 0.00 0.00 0.00 4.17
2287 3644 6.633500 TTTATCTTCTTTGTTGACCCTGTG 57.367 37.500 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.