Multiple sequence alignment - TraesCS2D01G523300

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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 TraesCS2D01G523300 chr2D 100.000 2405 0 0 1 2405 612324383 612326787 0.000000e+00 4442.0
1 TraesCS2D01G523300 chr2D 94.012 501 22 3 180 674 612183899 612184397 0.000000e+00 752.0
2 TraesCS2D01G523300 chr2D 85.534 712 46 24 769 1444 612184455 612185145 0.000000e+00 691.0
3 TraesCS2D01G523300 chr2D 82.353 136 20 4 2072 2206 259719712 259719844 5.430000e-22 115.0
4 TraesCS2D01G523300 chr2B 89.764 1905 101 44 548 2405 747076802 747078659 0.000000e+00 2351.0
5 TraesCS2D01G523300 chr2B 88.717 904 41 13 548 1423 746680083 746680953 0.000000e+00 1048.0
6 TraesCS2D01G523300 chr2B 93.333 375 20 2 182 555 747076293 747076663 1.260000e-152 549.0
7 TraesCS2D01G523300 chr2B 85.867 375 32 9 180 550 746679570 746679927 1.740000e-101 379.0
8 TraesCS2D01G523300 chr2B 77.114 201 33 12 2071 2266 74333050 74333242 1.180000e-18 104.0
9 TraesCS2D01G523300 chr2B 87.037 54 4 2 131 181 710747524 710747471 9.290000e-05 58.4
10 TraesCS2D01G523300 chr2A 81.103 2122 166 129 210 2189 744407846 744409874 0.000000e+00 1480.0
11 TraesCS2D01G523300 chr2A 92.050 239 16 2 2167 2405 744409896 744410131 1.380000e-87 333.0
12 TraesCS2D01G523300 chr7A 85.950 121 14 3 2073 2192 464286395 464286277 2.510000e-25 126.0
13 TraesCS2D01G523300 chr7A 85.950 121 14 3 2073 2192 519203336 519203218 2.510000e-25 126.0
14 TraesCS2D01G523300 chr7A 82.707 133 19 4 2075 2206 246978216 246978345 5.430000e-22 115.0
15 TraesCS2D01G523300 chr5A 84.874 119 13 4 2075 2192 362376143 362376029 5.430000e-22 115.0
16 TraesCS2D01G523300 chr7B 82.443 131 21 2 2076 2206 479060951 479060823 1.950000e-21 113.0
17 TraesCS2D01G523300 chr1D 82.963 135 14 9 2076 2206 431804831 431804702 1.950000e-21 113.0
18 TraesCS2D01G523300 chr4A 92.727 55 1 1 131 182 601761895 601761949 2.560000e-10 76.8
19 TraesCS2D01G523300 chr1B 92.593 54 1 1 131 181 677585847 677585900 9.220000e-10 75.0
20 TraesCS2D01G523300 chrUn 90.909 55 2 2 130 181 109026148 109026094 1.190000e-08 71.3


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 TraesCS2D01G523300 chr2D 612324383 612326787 2404 False 4442.0 4442 100.0000 1 2405 1 chr2D.!!$F2 2404
1 TraesCS2D01G523300 chr2D 612183899 612185145 1246 False 721.5 752 89.7730 180 1444 2 chr2D.!!$F3 1264
2 TraesCS2D01G523300 chr2B 747076293 747078659 2366 False 1450.0 2351 91.5485 182 2405 2 chr2B.!!$F3 2223
3 TraesCS2D01G523300 chr2B 746679570 746680953 1383 False 713.5 1048 87.2920 180 1423 2 chr2B.!!$F2 1243
4 TraesCS2D01G523300 chr2A 744407846 744410131 2285 False 906.5 1480 86.5765 210 2405 2 chr2A.!!$F1 2195

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
34 35 0.744281 CCGGTTGAAGCCAAGTGTTT 59.256 50.000 0.0 0.0 32.06 2.83 F
35 36 1.136110 CCGGTTGAAGCCAAGTGTTTT 59.864 47.619 0.0 0.0 32.06 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1178 1474 0.950116 GCCATCAGCTGCCTATTCAC 59.050 55.000 9.47 0.0 38.99 3.18 R
1863 2263 1.148273 GCGTGGCCCATAATCAGGA 59.852 57.895 0.00 0.0 0.00 3.86 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 4.459331 CGTGCAATCCGCCGGTTG 62.459 66.667 1.63 8.51 41.33 3.77
22 23 3.053291 GTGCAATCCGCCGGTTGA 61.053 61.111 18.37 0.00 41.33 3.18
24 25 2.331893 TGCAATCCGCCGGTTGAAG 61.332 57.895 18.37 0.00 41.33 3.02
25 26 2.485122 CAATCCGCCGGTTGAAGC 59.515 61.111 1.63 0.00 0.00 3.86
27 28 3.561120 AATCCGCCGGTTGAAGCCA 62.561 57.895 1.63 0.00 0.00 4.75
29 30 3.737172 CCGCCGGTTGAAGCCAAG 61.737 66.667 1.90 0.00 32.06 3.61
30 31 2.978010 CGCCGGTTGAAGCCAAGT 60.978 61.111 1.90 0.00 32.06 3.16
31 32 2.644992 GCCGGTTGAAGCCAAGTG 59.355 61.111 1.90 0.00 32.06 3.16
32 33 2.193536 GCCGGTTGAAGCCAAGTGT 61.194 57.895 1.90 0.00 32.06 3.55
33 34 1.734388 GCCGGTTGAAGCCAAGTGTT 61.734 55.000 1.90 0.00 32.06 3.32
34 35 0.744281 CCGGTTGAAGCCAAGTGTTT 59.256 50.000 0.00 0.00 32.06 2.83
35 36 1.136110 CCGGTTGAAGCCAAGTGTTTT 59.864 47.619 0.00 0.00 32.06 2.43
36 37 2.459934 CGGTTGAAGCCAAGTGTTTTC 58.540 47.619 0.00 0.00 32.06 2.29
37 38 2.798145 CGGTTGAAGCCAAGTGTTTTCC 60.798 50.000 0.00 0.00 32.06 3.13
38 39 2.430694 GGTTGAAGCCAAGTGTTTTCCT 59.569 45.455 0.00 0.00 32.06 3.36
39 40 3.118775 GGTTGAAGCCAAGTGTTTTCCTT 60.119 43.478 0.00 0.00 32.06 3.36
40 41 4.098807 GGTTGAAGCCAAGTGTTTTCCTTA 59.901 41.667 0.00 0.00 32.06 2.69
41 42 5.281727 GTTGAAGCCAAGTGTTTTCCTTAG 58.718 41.667 0.00 0.00 32.06 2.18
42 43 4.787551 TGAAGCCAAGTGTTTTCCTTAGA 58.212 39.130 0.00 0.00 0.00 2.10
43 44 5.197451 TGAAGCCAAGTGTTTTCCTTAGAA 58.803 37.500 0.00 0.00 0.00 2.10
44 45 5.067283 TGAAGCCAAGTGTTTTCCTTAGAAC 59.933 40.000 0.00 0.00 0.00 3.01
45 46 4.532834 AGCCAAGTGTTTTCCTTAGAACA 58.467 39.130 0.00 0.00 33.67 3.18
46 47 4.953579 AGCCAAGTGTTTTCCTTAGAACAA 59.046 37.500 0.00 0.00 37.49 2.83
47 48 5.598417 AGCCAAGTGTTTTCCTTAGAACAAT 59.402 36.000 0.00 0.00 37.49 2.71
48 49 6.775629 AGCCAAGTGTTTTCCTTAGAACAATA 59.224 34.615 0.00 0.00 37.49 1.90
49 50 6.861572 GCCAAGTGTTTTCCTTAGAACAATAC 59.138 38.462 0.00 0.00 37.49 1.89
50 51 7.469456 GCCAAGTGTTTTCCTTAGAACAATACA 60.469 37.037 0.00 0.00 37.49 2.29
51 52 8.576442 CCAAGTGTTTTCCTTAGAACAATACAT 58.424 33.333 0.00 0.00 37.49 2.29
52 53 9.612620 CAAGTGTTTTCCTTAGAACAATACATC 57.387 33.333 0.00 0.00 37.49 3.06
53 54 9.574516 AAGTGTTTTCCTTAGAACAATACATCT 57.425 29.630 0.00 0.00 37.49 2.90
54 55 9.574516 AGTGTTTTCCTTAGAACAATACATCTT 57.425 29.630 0.00 0.00 37.49 2.40
80 81 9.607988 TTTTTCTAGTACAATGTCACTTGAGAA 57.392 29.630 0.00 0.00 30.24 2.87
81 82 9.607988 TTTTCTAGTACAATGTCACTTGAGAAA 57.392 29.630 0.00 11.98 30.07 2.52
82 83 9.607988 TTTCTAGTACAATGTCACTTGAGAAAA 57.392 29.630 12.80 4.17 29.53 2.29
83 84 9.607988 TTCTAGTACAATGTCACTTGAGAAAAA 57.392 29.630 0.00 0.00 30.24 1.94
104 105 5.689383 AAAAACGCAGTCAACATAGACAT 57.311 34.783 0.00 0.00 45.00 3.06
105 106 6.795098 AAAAACGCAGTCAACATAGACATA 57.205 33.333 0.00 0.00 45.00 2.29
106 107 6.408858 AAAACGCAGTCAACATAGACATAG 57.591 37.500 0.00 0.00 45.00 2.23
107 108 4.983671 ACGCAGTCAACATAGACATAGA 57.016 40.909 0.00 0.00 29.74 1.98
108 109 4.926244 ACGCAGTCAACATAGACATAGAG 58.074 43.478 0.00 0.00 29.74 2.43
109 110 4.640647 ACGCAGTCAACATAGACATAGAGA 59.359 41.667 0.00 0.00 29.74 3.10
110 111 5.211454 CGCAGTCAACATAGACATAGAGAG 58.789 45.833 0.00 0.00 40.98 3.20
111 112 5.008118 CGCAGTCAACATAGACATAGAGAGA 59.992 44.000 0.00 0.00 40.98 3.10
112 113 6.205784 GCAGTCAACATAGACATAGAGAGAC 58.794 44.000 0.00 0.00 40.98 3.36
113 114 6.426327 CAGTCAACATAGACATAGAGAGACG 58.574 44.000 0.00 0.00 40.98 4.18
114 115 5.529430 AGTCAACATAGACATAGAGAGACGG 59.471 44.000 0.00 0.00 40.98 4.79
115 116 5.297278 GTCAACATAGACATAGAGAGACGGT 59.703 44.000 0.00 0.00 38.40 4.83
116 117 6.482641 GTCAACATAGACATAGAGAGACGGTA 59.517 42.308 0.00 0.00 38.40 4.02
117 118 7.012138 GTCAACATAGACATAGAGAGACGGTAA 59.988 40.741 0.00 0.00 38.40 2.85
118 119 7.555195 TCAACATAGACATAGAGAGACGGTAAA 59.445 37.037 0.00 0.00 0.00 2.01
119 120 7.876936 ACATAGACATAGAGAGACGGTAAAA 57.123 36.000 0.00 0.00 0.00 1.52
120 121 8.466617 ACATAGACATAGAGAGACGGTAAAAT 57.533 34.615 0.00 0.00 0.00 1.82
121 122 8.569641 ACATAGACATAGAGAGACGGTAAAATC 58.430 37.037 0.00 0.00 0.00 2.17
122 123 6.394025 AGACATAGAGAGACGGTAAAATCC 57.606 41.667 0.00 0.00 0.00 3.01
123 124 6.130569 AGACATAGAGAGACGGTAAAATCCT 58.869 40.000 0.00 0.00 0.00 3.24
124 125 7.288560 AGACATAGAGAGACGGTAAAATCCTA 58.711 38.462 0.00 0.00 0.00 2.94
125 126 7.229106 AGACATAGAGAGACGGTAAAATCCTAC 59.771 40.741 0.00 0.00 0.00 3.18
126 127 7.061688 ACATAGAGAGACGGTAAAATCCTACT 58.938 38.462 0.00 0.00 0.00 2.57
127 128 7.229106 ACATAGAGAGACGGTAAAATCCTACTC 59.771 40.741 0.00 0.00 0.00 2.59
128 129 5.757988 AGAGAGACGGTAAAATCCTACTCT 58.242 41.667 0.00 0.00 38.86 3.24
129 130 5.824097 AGAGAGACGGTAAAATCCTACTCTC 59.176 44.000 18.27 18.27 44.36 3.20
130 131 5.757988 AGAGACGGTAAAATCCTACTCTCT 58.242 41.667 0.00 0.00 34.98 3.10
131 132 6.189133 AGAGACGGTAAAATCCTACTCTCTT 58.811 40.000 0.00 0.00 34.98 2.85
132 133 6.664384 AGAGACGGTAAAATCCTACTCTCTTT 59.336 38.462 0.00 0.00 34.98 2.52
133 134 7.833183 AGAGACGGTAAAATCCTACTCTCTTTA 59.167 37.037 0.00 0.00 34.98 1.85
134 135 8.358582 AGACGGTAAAATCCTACTCTCTTTAA 57.641 34.615 0.00 0.00 0.00 1.52
135 136 8.979534 AGACGGTAAAATCCTACTCTCTTTAAT 58.020 33.333 0.00 0.00 0.00 1.40
159 160 8.739649 ATACAAAGTTAGTACAAAGTCGAGTC 57.260 34.615 0.00 0.00 0.00 3.36
160 161 6.567050 ACAAAGTTAGTACAAAGTCGAGTCA 58.433 36.000 0.00 0.00 0.00 3.41
161 162 7.037438 ACAAAGTTAGTACAAAGTCGAGTCAA 58.963 34.615 0.00 0.00 0.00 3.18
162 163 7.709613 ACAAAGTTAGTACAAAGTCGAGTCAAT 59.290 33.333 0.00 0.00 0.00 2.57
163 164 8.548721 CAAAGTTAGTACAAAGTCGAGTCAATT 58.451 33.333 0.00 0.00 0.00 2.32
164 165 8.658499 AAGTTAGTACAAAGTCGAGTCAATTT 57.342 30.769 0.00 0.00 0.00 1.82
165 166 8.658499 AGTTAGTACAAAGTCGAGTCAATTTT 57.342 30.769 0.00 0.00 0.00 1.82
166 167 8.548721 AGTTAGTACAAAGTCGAGTCAATTTTG 58.451 33.333 0.00 0.00 35.47 2.44
167 168 6.920569 AGTACAAAGTCGAGTCAATTTTGT 57.079 33.333 9.34 9.34 42.59 2.83
168 169 6.715464 AGTACAAAGTCGAGTCAATTTTGTG 58.285 36.000 13.29 0.00 40.83 3.33
169 170 5.811399 ACAAAGTCGAGTCAATTTTGTGA 57.189 34.783 4.10 0.00 39.65 3.58
170 171 5.569413 ACAAAGTCGAGTCAATTTTGTGAC 58.431 37.500 4.10 0.00 46.90 3.67
176 177 2.989422 GTCAATTTTGTGACGGAGGG 57.011 50.000 0.00 0.00 38.68 4.30
177 178 2.500229 GTCAATTTTGTGACGGAGGGA 58.500 47.619 0.00 0.00 38.68 4.20
178 179 2.484264 GTCAATTTTGTGACGGAGGGAG 59.516 50.000 0.00 0.00 38.68 4.30
190 191 3.385115 ACGGAGGGAGTATTTGGATTCT 58.615 45.455 0.00 0.00 0.00 2.40
196 197 7.518188 GGAGGGAGTATTTGGATTCTGAAATA 58.482 38.462 0.00 0.00 0.00 1.40
206 207 7.781324 TTGGATTCTGAAATAAAGCCTTCTT 57.219 32.000 0.00 0.00 32.17 2.52
288 294 6.491745 TCTCTTAATCTATCAAGGACGATGCT 59.508 38.462 0.00 0.00 0.00 3.79
412 437 6.314648 GGCCACACAACTAAACTAATACTACC 59.685 42.308 0.00 0.00 0.00 3.18
461 486 3.062763 GGATCGATCTCGTACGTCCTAA 58.937 50.000 23.96 0.00 40.80 2.69
463 488 2.205074 TCGATCTCGTACGTCCTAACC 58.795 52.381 16.05 0.00 40.80 2.85
865 1133 2.224305 ACTCACCCAACTGTTAGTCTGC 60.224 50.000 0.00 0.00 0.00 4.26
866 1134 2.037772 CTCACCCAACTGTTAGTCTGCT 59.962 50.000 0.00 0.00 0.00 4.24
867 1135 2.146342 CACCCAACTGTTAGTCTGCTG 58.854 52.381 0.00 0.00 0.00 4.41
869 1137 1.271054 CCCAACTGTTAGTCTGCTGCT 60.271 52.381 0.00 0.00 0.00 4.24
870 1138 2.028112 CCCAACTGTTAGTCTGCTGCTA 60.028 50.000 0.00 0.00 0.00 3.49
871 1139 3.257393 CCAACTGTTAGTCTGCTGCTAG 58.743 50.000 0.00 0.00 0.00 3.42
924 1201 1.460497 TGTGGGTGTGGGCACTCTA 60.460 57.895 0.00 0.00 46.03 2.43
947 1224 2.286067 GCTACAGCTCGATACGTACGTT 60.286 50.000 27.92 14.22 38.21 3.99
956 1233 4.521010 TCGATACGTACGTTCATAAGCTG 58.479 43.478 27.92 7.44 0.00 4.24
1017 1297 3.440415 ATGTCGTCGAGCAGCCGA 61.440 61.111 0.00 2.24 36.06 5.54
1178 1474 1.523758 AGTACCAGCTGCTTTTTCCG 58.476 50.000 8.66 0.00 0.00 4.30
1246 1563 2.987821 GAGAGTTAGCCTTCGTGTTGTC 59.012 50.000 0.00 0.00 0.00 3.18
1281 1598 2.203907 AGGGTGCTGCAGGAGACT 60.204 61.111 17.12 10.82 46.44 3.24
1332 1649 2.486042 GACGACCTCAGCGAGACC 59.514 66.667 7.07 0.00 0.00 3.85
1460 1824 4.634133 TGCGTCCGTGACACCGTC 62.634 66.667 0.00 0.00 32.09 4.79
1471 1835 4.403137 CACCGTCCGTCGCCGTTA 62.403 66.667 2.59 0.00 38.35 3.18
1501 1865 3.488467 GAGCTAGCATGCCCCTGGG 62.488 68.421 18.83 5.50 38.57 4.45
1570 1938 7.459795 TTTTTCCTTGAGGTTTTTGCATTTT 57.540 28.000 0.00 0.00 36.34 1.82
1574 1942 7.118496 TCCTTGAGGTTTTTGCATTTTCTTA 57.882 32.000 0.00 0.00 36.34 2.10
1863 2263 5.180492 TGATTAAGATCGGTCGCTTGTTTTT 59.820 36.000 0.00 0.00 34.91 1.94
1867 2267 0.941542 TCGGTCGCTTGTTTTTCCTG 59.058 50.000 0.00 0.00 0.00 3.86
1926 2326 3.867857 TGGATGTATGCATACGTGTGTT 58.132 40.909 31.31 12.61 38.80 3.32
1946 2346 3.052455 TGTGTCTTGTGTCTTGTGTGT 57.948 42.857 0.00 0.00 0.00 3.72
1947 2347 2.741517 TGTGTCTTGTGTCTTGTGTGTG 59.258 45.455 0.00 0.00 0.00 3.82
2021 2434 6.840780 AATTTTGGAGCACAATTAGCTAGT 57.159 33.333 4.71 0.00 43.58 2.57
2024 2437 6.985188 TTTGGAGCACAATTAGCTAGTTAG 57.015 37.500 0.61 0.00 43.58 2.34
2032 2445 4.102681 ACAATTAGCTAGTTAGGGGCGATT 59.897 41.667 0.61 0.00 0.00 3.34
2049 2462 4.569564 GGCGATTATTTGTACGAAGAACCT 59.430 41.667 5.05 0.00 0.00 3.50
2050 2463 5.490213 GCGATTATTTGTACGAAGAACCTG 58.510 41.667 5.05 0.55 0.00 4.00
2051 2464 5.490213 CGATTATTTGTACGAAGAACCTGC 58.510 41.667 5.05 0.00 0.00 4.85
2052 2465 5.062934 CGATTATTTGTACGAAGAACCTGCA 59.937 40.000 5.05 0.00 0.00 4.41
2061 2474 1.888512 GAAGAACCTGCATGCCTCAAA 59.111 47.619 16.68 0.00 0.00 2.69
2064 2477 2.298163 AGAACCTGCATGCCTCAAAAAG 59.702 45.455 16.68 3.39 0.00 2.27
2102 2517 5.587289 TGTTTGGTTCATGACTAACTTTGC 58.413 37.500 0.00 0.00 0.00 3.68
2128 2543 3.981211 ACTAACTTTAGGCAAACGACGA 58.019 40.909 0.00 0.00 35.08 4.20
2130 2545 1.505425 ACTTTAGGCAAACGACGACC 58.495 50.000 0.00 0.00 0.00 4.79
2131 2546 1.202557 ACTTTAGGCAAACGACGACCA 60.203 47.619 0.00 0.00 0.00 4.02
2139 2554 1.730064 CAAACGACGACCACCCATAAG 59.270 52.381 0.00 0.00 0.00 1.73
2147 2562 2.028476 CGACCACCCATAAGAAGTGTGA 60.028 50.000 0.00 0.00 0.00 3.58
2216 2674 0.179084 CCCTATGACGACACGCCAAT 60.179 55.000 0.00 0.00 0.00 3.16
2255 2713 1.538687 GGCAACCTCAGGCTGCAAAT 61.539 55.000 20.84 0.00 37.83 2.32
2261 2719 1.614903 CCTCAGGCTGCAAATCAAACA 59.385 47.619 10.34 0.00 0.00 2.83
2262 2720 2.232941 CCTCAGGCTGCAAATCAAACAT 59.767 45.455 10.34 0.00 0.00 2.71
2266 2724 4.705991 TCAGGCTGCAAATCAAACATATGA 59.294 37.500 10.34 0.00 0.00 2.15
2274 2732 8.929827 TGCAAATCAAACATATGACCTTAATG 57.070 30.769 10.38 2.45 30.82 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.485122 CTTCAACCGGCGGATTGC 59.515 61.111 35.78 0.00 45.38 3.56
8 9 2.485122 GCTTCAACCGGCGGATTG 59.515 61.111 35.78 29.22 0.00 2.67
10 11 3.561120 TTGGCTTCAACCGGCGGAT 62.561 57.895 35.78 20.37 0.00 4.18
12 13 3.737172 CTTGGCTTCAACCGGCGG 61.737 66.667 27.06 27.06 0.00 6.13
13 14 2.978010 ACTTGGCTTCAACCGGCG 60.978 61.111 0.00 0.00 0.00 6.46
14 15 1.734388 AACACTTGGCTTCAACCGGC 61.734 55.000 0.00 0.00 0.00 6.13
15 16 0.744281 AAACACTTGGCTTCAACCGG 59.256 50.000 0.00 0.00 0.00 5.28
16 17 2.459934 GAAAACACTTGGCTTCAACCG 58.540 47.619 0.00 0.00 0.00 4.44
17 18 2.430694 AGGAAAACACTTGGCTTCAACC 59.569 45.455 0.00 0.00 0.00 3.77
18 19 3.801114 AGGAAAACACTTGGCTTCAAC 57.199 42.857 0.00 0.00 0.00 3.18
19 20 5.197451 TCTAAGGAAAACACTTGGCTTCAA 58.803 37.500 0.00 0.00 0.00 2.69
21 22 5.067283 TGTTCTAAGGAAAACACTTGGCTTC 59.933 40.000 0.00 0.00 32.81 3.86
22 23 4.953579 TGTTCTAAGGAAAACACTTGGCTT 59.046 37.500 0.00 0.00 32.81 4.35
24 25 4.911514 TGTTCTAAGGAAAACACTTGGC 57.088 40.909 0.00 0.00 32.81 4.52
25 26 7.936584 TGTATTGTTCTAAGGAAAACACTTGG 58.063 34.615 0.00 0.00 35.24 3.61
27 28 9.574516 AGATGTATTGTTCTAAGGAAAACACTT 57.425 29.630 0.00 0.00 35.24 3.16
54 55 9.607988 TTCTCAAGTGACATTGTACTAGAAAAA 57.392 29.630 0.00 0.00 0.00 1.94
55 56 9.607988 TTTCTCAAGTGACATTGTACTAGAAAA 57.392 29.630 0.00 0.00 31.62 2.29
56 57 9.607988 TTTTCTCAAGTGACATTGTACTAGAAA 57.392 29.630 0.00 13.39 32.18 2.52
57 58 9.607988 TTTTTCTCAAGTGACATTGTACTAGAA 57.392 29.630 0.00 0.00 0.00 2.10
82 83 5.689383 ATGTCTATGTTGACTGCGTTTTT 57.311 34.783 0.00 0.00 37.79 1.94
83 84 6.163476 TCTATGTCTATGTTGACTGCGTTTT 58.837 36.000 0.00 0.00 37.79 2.43
84 85 5.720202 TCTATGTCTATGTTGACTGCGTTT 58.280 37.500 0.00 0.00 37.79 3.60
85 86 5.125578 TCTCTATGTCTATGTTGACTGCGTT 59.874 40.000 0.00 0.00 37.79 4.84
86 87 4.640647 TCTCTATGTCTATGTTGACTGCGT 59.359 41.667 0.00 0.00 37.79 5.24
87 88 5.008118 TCTCTCTATGTCTATGTTGACTGCG 59.992 44.000 0.00 0.00 37.79 5.18
88 89 6.205784 GTCTCTCTATGTCTATGTTGACTGC 58.794 44.000 0.00 0.00 37.79 4.40
89 90 6.426327 CGTCTCTCTATGTCTATGTTGACTG 58.574 44.000 0.00 0.00 37.79 3.51
90 91 5.529430 CCGTCTCTCTATGTCTATGTTGACT 59.471 44.000 0.00 0.00 37.79 3.41
91 92 5.297278 ACCGTCTCTCTATGTCTATGTTGAC 59.703 44.000 0.00 0.00 37.47 3.18
92 93 5.437946 ACCGTCTCTCTATGTCTATGTTGA 58.562 41.667 0.00 0.00 0.00 3.18
93 94 5.759506 ACCGTCTCTCTATGTCTATGTTG 57.240 43.478 0.00 0.00 0.00 3.33
94 95 7.876936 TTTACCGTCTCTCTATGTCTATGTT 57.123 36.000 0.00 0.00 0.00 2.71
95 96 7.876936 TTTTACCGTCTCTCTATGTCTATGT 57.123 36.000 0.00 0.00 0.00 2.29
96 97 8.024285 GGATTTTACCGTCTCTCTATGTCTATG 58.976 40.741 0.00 0.00 0.00 2.23
97 98 7.945664 AGGATTTTACCGTCTCTCTATGTCTAT 59.054 37.037 0.00 0.00 34.73 1.98
98 99 7.288560 AGGATTTTACCGTCTCTCTATGTCTA 58.711 38.462 0.00 0.00 34.73 2.59
99 100 6.130569 AGGATTTTACCGTCTCTCTATGTCT 58.869 40.000 0.00 0.00 34.73 3.41
100 101 6.394025 AGGATTTTACCGTCTCTCTATGTC 57.606 41.667 0.00 0.00 34.73 3.06
101 102 7.061688 AGTAGGATTTTACCGTCTCTCTATGT 58.938 38.462 0.00 0.00 34.73 2.29
102 103 7.446013 AGAGTAGGATTTTACCGTCTCTCTATG 59.554 40.741 0.00 0.00 38.94 2.23
103 104 7.519927 AGAGTAGGATTTTACCGTCTCTCTAT 58.480 38.462 0.00 0.00 38.94 1.98
104 105 6.897986 AGAGTAGGATTTTACCGTCTCTCTA 58.102 40.000 0.00 0.00 38.94 2.43
105 106 5.757988 AGAGTAGGATTTTACCGTCTCTCT 58.242 41.667 0.00 0.00 38.94 3.10
106 107 6.063640 GAGAGTAGGATTTTACCGTCTCTC 57.936 45.833 17.73 17.73 44.46 3.20
107 108 5.757988 AGAGAGTAGGATTTTACCGTCTCT 58.242 41.667 0.00 0.00 42.32 3.10
108 109 6.453926 AAGAGAGTAGGATTTTACCGTCTC 57.546 41.667 0.00 0.00 36.90 3.36
109 110 6.854091 AAAGAGAGTAGGATTTTACCGTCT 57.146 37.500 0.00 0.00 34.73 4.18
133 134 9.189723 GACTCGACTTTGTACTAACTTTGTATT 57.810 33.333 0.00 0.00 0.00 1.89
134 135 8.355169 TGACTCGACTTTGTACTAACTTTGTAT 58.645 33.333 0.00 0.00 0.00 2.29
135 136 7.706159 TGACTCGACTTTGTACTAACTTTGTA 58.294 34.615 0.00 0.00 0.00 2.41
136 137 6.567050 TGACTCGACTTTGTACTAACTTTGT 58.433 36.000 0.00 0.00 0.00 2.83
137 138 7.459394 TTGACTCGACTTTGTACTAACTTTG 57.541 36.000 0.00 0.00 0.00 2.77
138 139 8.658499 AATTGACTCGACTTTGTACTAACTTT 57.342 30.769 0.00 0.00 0.00 2.66
139 140 8.658499 AAATTGACTCGACTTTGTACTAACTT 57.342 30.769 0.00 0.00 0.00 2.66
140 141 8.548721 CAAAATTGACTCGACTTTGTACTAACT 58.451 33.333 0.00 0.00 0.00 2.24
141 142 8.333186 ACAAAATTGACTCGACTTTGTACTAAC 58.667 33.333 4.36 0.00 38.19 2.34
142 143 8.332464 CACAAAATTGACTCGACTTTGTACTAA 58.668 33.333 5.69 0.00 37.95 2.24
143 144 7.707464 TCACAAAATTGACTCGACTTTGTACTA 59.293 33.333 5.69 0.00 37.95 1.82
144 145 6.537301 TCACAAAATTGACTCGACTTTGTACT 59.463 34.615 5.69 0.00 37.95 2.73
145 146 6.627671 GTCACAAAATTGACTCGACTTTGTAC 59.372 38.462 5.69 2.93 42.36 2.90
146 147 6.508880 CGTCACAAAATTGACTCGACTTTGTA 60.509 38.462 5.69 0.00 43.30 2.41
147 148 5.569413 GTCACAAAATTGACTCGACTTTGT 58.431 37.500 0.77 0.77 42.36 2.83
148 149 4.666176 CGTCACAAAATTGACTCGACTTTG 59.334 41.667 0.00 0.00 43.30 2.77
149 150 4.260620 CCGTCACAAAATTGACTCGACTTT 60.261 41.667 0.00 0.00 43.30 2.66
150 151 3.247648 CCGTCACAAAATTGACTCGACTT 59.752 43.478 0.00 0.00 43.30 3.01
151 152 2.800544 CCGTCACAAAATTGACTCGACT 59.199 45.455 0.00 0.00 43.30 4.18
152 153 2.798283 TCCGTCACAAAATTGACTCGAC 59.202 45.455 0.00 1.09 43.30 4.20
153 154 3.057019 CTCCGTCACAAAATTGACTCGA 58.943 45.455 0.00 0.00 43.30 4.04
154 155 2.157668 CCTCCGTCACAAAATTGACTCG 59.842 50.000 0.00 1.83 43.30 4.18
155 156 2.484264 CCCTCCGTCACAAAATTGACTC 59.516 50.000 0.00 0.00 43.30 3.36
156 157 2.105821 TCCCTCCGTCACAAAATTGACT 59.894 45.455 0.00 0.00 43.30 3.41
157 158 2.484264 CTCCCTCCGTCACAAAATTGAC 59.516 50.000 0.00 0.00 42.24 3.18
158 159 2.105821 ACTCCCTCCGTCACAAAATTGA 59.894 45.455 0.00 0.00 0.00 2.57
159 160 2.504367 ACTCCCTCCGTCACAAAATTG 58.496 47.619 0.00 0.00 0.00 2.32
160 161 2.951229 ACTCCCTCCGTCACAAAATT 57.049 45.000 0.00 0.00 0.00 1.82
161 162 4.569719 AATACTCCCTCCGTCACAAAAT 57.430 40.909 0.00 0.00 0.00 1.82
162 163 4.069304 CAAATACTCCCTCCGTCACAAAA 58.931 43.478 0.00 0.00 0.00 2.44
163 164 3.558321 CCAAATACTCCCTCCGTCACAAA 60.558 47.826 0.00 0.00 0.00 2.83
164 165 2.027561 CCAAATACTCCCTCCGTCACAA 60.028 50.000 0.00 0.00 0.00 3.33
165 166 1.553248 CCAAATACTCCCTCCGTCACA 59.447 52.381 0.00 0.00 0.00 3.58
166 167 1.829222 TCCAAATACTCCCTCCGTCAC 59.171 52.381 0.00 0.00 0.00 3.67
167 168 2.241281 TCCAAATACTCCCTCCGTCA 57.759 50.000 0.00 0.00 0.00 4.35
168 169 3.388350 AGAATCCAAATACTCCCTCCGTC 59.612 47.826 0.00 0.00 0.00 4.79
169 170 3.134804 CAGAATCCAAATACTCCCTCCGT 59.865 47.826 0.00 0.00 0.00 4.69
170 171 3.388024 TCAGAATCCAAATACTCCCTCCG 59.612 47.826 0.00 0.00 0.00 4.63
171 172 5.373812 TTCAGAATCCAAATACTCCCTCC 57.626 43.478 0.00 0.00 0.00 4.30
172 173 8.980481 TTATTTCAGAATCCAAATACTCCCTC 57.020 34.615 0.00 0.00 0.00 4.30
173 174 9.413734 CTTTATTTCAGAATCCAAATACTCCCT 57.586 33.333 0.00 0.00 0.00 4.20
174 175 8.138074 GCTTTATTTCAGAATCCAAATACTCCC 58.862 37.037 0.00 0.00 0.00 4.30
175 176 8.138074 GGCTTTATTTCAGAATCCAAATACTCC 58.862 37.037 0.00 0.00 0.00 3.85
176 177 8.907885 AGGCTTTATTTCAGAATCCAAATACTC 58.092 33.333 0.00 0.00 0.00 2.59
177 178 8.829373 AGGCTTTATTTCAGAATCCAAATACT 57.171 30.769 0.00 0.00 0.00 2.12
178 179 9.521503 GAAGGCTTTATTTCAGAATCCAAATAC 57.478 33.333 0.00 0.00 0.00 1.89
190 191 9.241919 TGTATCAATGAAGAAGGCTTTATTTCA 57.758 29.630 18.55 18.55 38.00 2.69
196 197 7.472334 AACATGTATCAATGAAGAAGGCTTT 57.528 32.000 0.00 0.00 33.61 3.51
364 389 1.337703 TGGATTTTGTCTGCACTGTGC 59.662 47.619 25.15 25.15 45.29 4.57
420 445 8.181573 TCGATCCAGTAAATGCTTGTTTATTTC 58.818 33.333 0.00 0.00 0.00 2.17
947 1224 0.595053 GCGCGCTAGACAGCTTATGA 60.595 55.000 26.67 0.00 46.26 2.15
969 1246 4.521062 ATCGCTCGCTCACAGCCC 62.521 66.667 0.00 0.00 38.18 5.19
971 1248 3.318555 CGATCGCTCGCTCACAGC 61.319 66.667 0.26 0.00 38.20 4.40
972 1249 1.653835 CTCGATCGCTCGCTCACAG 60.654 63.158 11.09 0.00 44.65 3.66
973 1250 2.405191 CTCGATCGCTCGCTCACA 59.595 61.111 11.09 0.00 44.65 3.58
1178 1474 0.950116 GCCATCAGCTGCCTATTCAC 59.050 55.000 9.47 0.00 38.99 3.18
1209 1505 1.271934 CTCTCAGTGACACTGGACTGG 59.728 57.143 30.39 17.16 45.94 4.00
1281 1598 1.153369 GCTCCGGATGTAGCTGCAA 60.153 57.895 9.07 0.00 35.80 4.08
1468 1832 6.483385 TGCTAGCTCGTAGTATGATCTAAC 57.517 41.667 17.23 1.90 0.00 2.34
1520 1888 1.536766 TGCACGTACGTACACTAGCTT 59.463 47.619 22.34 0.00 0.00 3.74
1863 2263 1.148273 GCGTGGCCCATAATCAGGA 59.852 57.895 0.00 0.00 0.00 3.86
1926 2326 2.741517 CACACACAAGACACAAGACACA 59.258 45.455 0.00 0.00 0.00 3.72
1946 2346 2.232696 ACACTACACACAGTCACACACA 59.767 45.455 0.00 0.00 0.00 3.72
1947 2347 2.603110 CACACTACACACAGTCACACAC 59.397 50.000 0.00 0.00 0.00 3.82
2021 2434 4.669206 TCGTACAAATAATCGCCCCTAA 57.331 40.909 0.00 0.00 0.00 2.69
2024 2437 3.460103 TCTTCGTACAAATAATCGCCCC 58.540 45.455 0.00 0.00 0.00 5.80
2032 2445 4.094294 GCATGCAGGTTCTTCGTACAAATA 59.906 41.667 14.21 0.00 0.00 1.40
2049 2462 5.664294 ATATTCACTTTTTGAGGCATGCA 57.336 34.783 21.36 0.00 34.94 3.96
2050 2463 6.698766 CCTAATATTCACTTTTTGAGGCATGC 59.301 38.462 9.90 9.90 34.94 4.06
2051 2464 7.205297 CCCTAATATTCACTTTTTGAGGCATG 58.795 38.462 0.00 0.00 34.94 4.06
2052 2465 6.183360 GCCCTAATATTCACTTTTTGAGGCAT 60.183 38.462 0.00 0.00 34.94 4.40
2061 2474 6.440328 ACCAAACATGCCCTAATATTCACTTT 59.560 34.615 0.00 0.00 0.00 2.66
2064 2477 5.852282 ACCAAACATGCCCTAATATTCAC 57.148 39.130 0.00 0.00 0.00 3.18
2102 2517 4.273969 TCGTTTGCCTAAAGTTAGTTGTGG 59.726 41.667 0.00 0.00 0.00 4.17
2128 2543 2.289444 CGTCACACTTCTTATGGGTGGT 60.289 50.000 0.00 0.00 35.53 4.16
2130 2545 3.313012 TCGTCACACTTCTTATGGGTG 57.687 47.619 0.00 0.00 37.05 4.61
2131 2546 3.070446 TGTTCGTCACACTTCTTATGGGT 59.930 43.478 0.00 0.00 0.00 4.51
2139 2554 3.042887 GCCATTTTGTTCGTCACACTTC 58.957 45.455 0.00 0.00 33.98 3.01
2147 2562 0.387565 GTGGTGGCCATTTTGTTCGT 59.612 50.000 9.72 0.00 35.28 3.85
2197 2655 0.179084 ATTGGCGTGTCGTCATAGGG 60.179 55.000 0.00 0.00 42.26 3.53
2261 2719 5.529800 GGCCGTAACAACATTAAGGTCATAT 59.470 40.000 0.00 0.00 30.28 1.78
2262 2720 4.877251 GGCCGTAACAACATTAAGGTCATA 59.123 41.667 0.00 0.00 30.28 2.15
2266 2724 2.040679 AGGGCCGTAACAACATTAAGGT 59.959 45.455 0.00 0.00 0.00 3.50
2274 2732 1.198408 GTAAAGCAGGGCCGTAACAAC 59.802 52.381 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.