Multiple sequence alignment - TraesCS5D01G455300

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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 TraesCS5D01G455300 chr5D 100.000 2594 0 0 1 2594 502365906 502363313 0.000000e+00 4791
1 TraesCS5D01G455300 chr5D 97.497 1958 43 4 642 2594 502537477 502535521 0.000000e+00 3339
2 TraesCS5D01G455300 chr5D 75.214 468 66 29 80 525 502187716 502187277 2.650000e-40 176
3 TraesCS5D01G455300 chr5B 96.885 1958 52 6 642 2593 626141008 626139054 0.000000e+00 3269
4 TraesCS5D01G455300 chr5B 92.712 1962 118 20 642 2594 626085308 626083363 0.000000e+00 2808
5 TraesCS5D01G455300 chr5B 92.559 1962 124 15 642 2594 631354584 631352636 0.000000e+00 2795
6 TraesCS5D01G455300 chr5B 89.476 1967 183 15 642 2594 626107352 626105396 0.000000e+00 2464
7 TraesCS5D01G455300 chr5B 91.799 1451 110 7 642 2086 631379056 631377609 0.000000e+00 2012
8 TraesCS5D01G455300 chr5B 89.628 511 47 4 2086 2594 631368714 631368208 0.000000e+00 645
9 TraesCS5D01G455300 chr5B 97.095 241 7 0 399 639 626142273 626142033 8.640000e-110 407
10 TraesCS5D01G455300 chr5B 77.794 689 118 22 1475 2147 631365416 631364747 2.420000e-105 392
11 TraesCS5D01G455300 chr5B 86.012 336 21 3 305 639 626086663 626086353 1.150000e-88 337
12 TraesCS5D01G455300 chr5B 91.026 156 10 1 170 325 631361993 631361842 9.410000e-50 207
13 TraesCS5D01G455300 chr5B 93.671 79 5 0 561 639 631382542 631382464 4.530000e-23 119
14 TraesCS5D01G455300 chr5B 83.824 136 7 2 172 307 626086844 626086724 5.870000e-22 115
15 TraesCS5D01G455300 chr5A 88.493 1964 175 21 642 2594 631085276 631083353 0.000000e+00 2327
16 TraesCS5D01G455300 chr5A 90.027 1093 71 16 1509 2593 631111365 631110303 0.000000e+00 1380
17 TraesCS5D01G455300 chr5A 82.000 350 42 6 293 639 631255545 631255214 7.070000e-71 278
18 TraesCS5D01G455300 chr5A 89.524 210 22 0 642 851 631111572 631111363 1.530000e-67 267
19 TraesCS5D01G455300 chr5A 81.073 317 55 3 684 995 631254160 631253844 5.540000e-62 248
20 TraesCS5D01G455300 chrUn 92.172 396 23 5 1 391 472860550 472860158 1.050000e-153 553
21 TraesCS5D01G455300 chr6A 92.958 71 3 2 173 241 60578247 60578177 4.570000e-18 102
22 TraesCS5D01G455300 chr2D 92.958 71 3 2 173 241 217521607 217521677 4.570000e-18 102
23 TraesCS5D01G455300 chr2A 91.892 74 4 2 170 241 560734083 560734156 4.570000e-18 102


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 TraesCS5D01G455300 chr5D 502363313 502365906 2593 True 4791.000000 4791 100.000000 1 2594 1 chr5D.!!$R2 2593
1 TraesCS5D01G455300 chr5D 502535521 502537477 1956 True 3339.000000 3339 97.497000 642 2594 1 chr5D.!!$R3 1952
2 TraesCS5D01G455300 chr5B 631352636 631354584 1948 True 2795.000000 2795 92.559000 642 2594 1 chr5B.!!$R2 1952
3 TraesCS5D01G455300 chr5B 626105396 626107352 1956 True 2464.000000 2464 89.476000 642 2594 1 chr5B.!!$R1 1952
4 TraesCS5D01G455300 chr5B 626139054 626142273 3219 True 1838.000000 3269 96.990000 399 2593 2 chr5B.!!$R4 2194
5 TraesCS5D01G455300 chr5B 626083363 626086844 3481 True 1086.666667 2808 87.516000 172 2594 3 chr5B.!!$R3 2422
6 TraesCS5D01G455300 chr5B 631377609 631382542 4933 True 1065.500000 2012 92.735000 561 2086 2 chr5B.!!$R6 1525
7 TraesCS5D01G455300 chr5B 631361842 631368714 6872 True 414.666667 645 86.149333 170 2594 3 chr5B.!!$R5 2424
8 TraesCS5D01G455300 chr5A 631083353 631085276 1923 True 2327.000000 2327 88.493000 642 2594 1 chr5A.!!$R1 1952
9 TraesCS5D01G455300 chr5A 631110303 631111572 1269 True 823.500000 1380 89.775500 642 2593 2 chr5A.!!$R2 1951
10 TraesCS5D01G455300 chr5A 631253844 631255545 1701 True 263.000000 278 81.536500 293 995 2 chr5A.!!$R3 702

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
165 166 0.103937 CAAAGGGTGCCTCGCAAAAA 59.896 50.0 0.0 0.0 41.47 1.94 F
879 6133 0.744414 ACAACTTGGCATCGGGATCG 60.744 55.0 0.0 0.0 37.82 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 6811 1.516386 GCACATCGTCGTCGGTCAT 60.516 57.895 1.55 0.0 37.69 3.06 R
2161 7632 3.896272 CCACTAACCTGGACCTCCTATAC 59.104 52.174 0.00 0.0 36.82 1.47 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
55 56 4.660938 AGGAGGCGGCGGCTTTTT 62.661 61.111 36.47 21.51 38.98 1.94
72 73 0.658897 TTTTTCGTGTGCCCTCGTTC 59.341 50.000 0.00 0.00 0.00 3.95
73 74 1.161563 TTTTCGTGTGCCCTCGTTCC 61.162 55.000 0.00 0.00 0.00 3.62
75 76 4.657824 CGTGTGCCCTCGTTCCGT 62.658 66.667 0.00 0.00 0.00 4.69
77 78 2.280524 TGTGCCCTCGTTCCGTTG 60.281 61.111 0.00 0.00 0.00 4.10
78 79 3.047877 GTGCCCTCGTTCCGTTGG 61.048 66.667 0.00 0.00 0.00 3.77
81 82 4.323477 CCCTCGTTCCGTTGGCCA 62.323 66.667 0.00 0.00 0.00 5.36
82 83 2.046314 CCTCGTTCCGTTGGCCAT 60.046 61.111 6.09 0.00 0.00 4.40
83 84 1.674322 CCTCGTTCCGTTGGCCATT 60.674 57.895 6.09 0.00 0.00 3.16
84 85 1.241315 CCTCGTTCCGTTGGCCATTT 61.241 55.000 6.09 0.00 0.00 2.32
85 86 1.444836 CTCGTTCCGTTGGCCATTTA 58.555 50.000 6.09 0.00 0.00 1.40
87 88 1.161843 CGTTCCGTTGGCCATTTACT 58.838 50.000 6.09 0.00 0.00 2.24
88 89 1.538075 CGTTCCGTTGGCCATTTACTT 59.462 47.619 6.09 0.00 0.00 2.24
90 91 2.279935 TCCGTTGGCCATTTACTTGT 57.720 45.000 6.09 0.00 0.00 3.16
94 95 3.491792 CCGTTGGCCATTTACTTGTTTGT 60.492 43.478 6.09 0.00 0.00 2.83
96 97 4.208253 CGTTGGCCATTTACTTGTTTGTTC 59.792 41.667 6.09 0.00 0.00 3.18
97 98 5.112686 GTTGGCCATTTACTTGTTTGTTCA 58.887 37.500 6.09 0.00 0.00 3.18
98 99 5.543507 TGGCCATTTACTTGTTTGTTCAT 57.456 34.783 0.00 0.00 0.00 2.57
99 100 6.656632 TGGCCATTTACTTGTTTGTTCATA 57.343 33.333 0.00 0.00 0.00 2.15
100 101 6.451393 TGGCCATTTACTTGTTTGTTCATAC 58.549 36.000 0.00 0.00 0.00 2.39
101 102 5.571357 GGCCATTTACTTGTTTGTTCATACG 59.429 40.000 0.00 0.00 0.00 3.06
102 103 6.375377 GCCATTTACTTGTTTGTTCATACGA 58.625 36.000 0.00 0.00 0.00 3.43
103 104 6.523201 GCCATTTACTTGTTTGTTCATACGAG 59.477 38.462 8.40 8.40 32.98 4.18
104 105 7.572353 GCCATTTACTTGTTTGTTCATACGAGA 60.572 37.037 14.36 0.00 31.52 4.04
105 106 8.286800 CCATTTACTTGTTTGTTCATACGAGAA 58.713 33.333 14.36 3.73 31.52 2.87
106 107 9.318041 CATTTACTTGTTTGTTCATACGAGAAG 57.682 33.333 14.36 4.82 31.52 2.85
107 108 5.344207 ACTTGTTTGTTCATACGAGAAGC 57.656 39.130 14.36 0.00 31.52 3.86
108 109 5.057149 ACTTGTTTGTTCATACGAGAAGCT 58.943 37.500 14.36 0.00 31.52 3.74
109 110 5.527582 ACTTGTTTGTTCATACGAGAAGCTT 59.472 36.000 0.00 0.00 31.52 3.74
110 111 5.591643 TGTTTGTTCATACGAGAAGCTTC 57.408 39.130 19.11 19.11 0.00 3.86
111 112 5.053811 TGTTTGTTCATACGAGAAGCTTCA 58.946 37.500 27.57 7.97 0.00 3.02
112 113 5.050363 TGTTTGTTCATACGAGAAGCTTCAC 60.050 40.000 27.57 20.43 0.00 3.18
113 114 3.242518 TGTTCATACGAGAAGCTTCACG 58.757 45.455 34.65 34.65 44.83 4.35
114 115 3.057806 TGTTCATACGAGAAGCTTCACGA 60.058 43.478 40.13 27.51 42.55 4.35
115 116 4.106197 GTTCATACGAGAAGCTTCACGAT 58.894 43.478 40.13 28.22 42.55 3.73
116 117 3.953766 TCATACGAGAAGCTTCACGATC 58.046 45.455 40.13 23.47 42.55 3.69
117 118 3.377172 TCATACGAGAAGCTTCACGATCA 59.623 43.478 40.13 27.63 42.55 2.92
118 119 2.724977 ACGAGAAGCTTCACGATCAA 57.275 45.000 40.13 0.00 42.55 2.57
119 120 2.600731 ACGAGAAGCTTCACGATCAAG 58.399 47.619 40.13 19.12 42.55 3.02
120 121 2.229062 ACGAGAAGCTTCACGATCAAGA 59.771 45.455 40.13 0.00 42.55 3.02
121 122 3.245797 CGAGAAGCTTCACGATCAAGAA 58.754 45.455 33.72 0.00 42.55 2.52
122 123 3.862267 CGAGAAGCTTCACGATCAAGAAT 59.138 43.478 33.72 8.19 42.55 2.40
123 124 4.259730 CGAGAAGCTTCACGATCAAGAATG 60.260 45.833 33.72 7.01 42.55 2.67
124 125 3.373439 AGAAGCTTCACGATCAAGAATGC 59.627 43.478 27.57 0.00 0.00 3.56
125 126 1.662629 AGCTTCACGATCAAGAATGCG 59.337 47.619 0.00 0.00 0.00 4.73
126 127 1.394917 GCTTCACGATCAAGAATGCGT 59.605 47.619 0.00 0.00 37.48 5.24
130 131 2.654749 ACGATCAAGAATGCGTGAGA 57.345 45.000 0.00 0.00 36.00 3.27
131 132 2.959516 ACGATCAAGAATGCGTGAGAA 58.040 42.857 0.00 0.00 36.00 2.87
132 133 2.926200 ACGATCAAGAATGCGTGAGAAG 59.074 45.455 0.00 0.00 36.00 2.85
133 134 2.283617 CGATCAAGAATGCGTGAGAAGG 59.716 50.000 0.00 0.00 36.00 3.46
134 135 2.099141 TCAAGAATGCGTGAGAAGGG 57.901 50.000 0.00 0.00 0.00 3.95
135 136 1.347707 TCAAGAATGCGTGAGAAGGGT 59.652 47.619 0.00 0.00 0.00 4.34
136 137 1.466167 CAAGAATGCGTGAGAAGGGTG 59.534 52.381 0.00 0.00 0.00 4.61
137 138 0.687354 AGAATGCGTGAGAAGGGTGT 59.313 50.000 0.00 0.00 0.00 4.16
138 139 1.899814 AGAATGCGTGAGAAGGGTGTA 59.100 47.619 0.00 0.00 0.00 2.90
139 140 2.301870 AGAATGCGTGAGAAGGGTGTAA 59.698 45.455 0.00 0.00 0.00 2.41
140 141 2.094762 ATGCGTGAGAAGGGTGTAAC 57.905 50.000 0.00 0.00 0.00 2.50
141 142 0.753867 TGCGTGAGAAGGGTGTAACA 59.246 50.000 0.00 0.00 39.98 2.41
142 143 1.145803 GCGTGAGAAGGGTGTAACAC 58.854 55.000 0.00 0.00 44.26 3.32
152 153 2.227194 GGGTGTAACACTGACAAAGGG 58.773 52.381 0.00 0.00 37.19 3.95
154 155 2.616842 GGTGTAACACTGACAAAGGGTG 59.383 50.000 0.00 0.00 43.84 4.61
155 156 2.032924 GTGTAACACTGACAAAGGGTGC 59.967 50.000 0.00 0.00 43.84 5.01
156 157 1.607148 GTAACACTGACAAAGGGTGCC 59.393 52.381 0.00 0.00 43.84 5.01
157 158 0.258774 AACACTGACAAAGGGTGCCT 59.741 50.000 0.00 0.00 43.84 4.75
158 159 0.179018 ACACTGACAAAGGGTGCCTC 60.179 55.000 0.00 0.00 42.62 4.70
159 160 1.071471 ACTGACAAAGGGTGCCTCG 59.929 57.895 0.00 0.00 30.89 4.63
160 161 2.281484 TGACAAAGGGTGCCTCGC 60.281 61.111 0.00 0.00 30.89 5.03
161 162 2.281484 GACAAAGGGTGCCTCGCA 60.281 61.111 0.00 0.00 35.60 5.10
162 163 1.896660 GACAAAGGGTGCCTCGCAA 60.897 57.895 0.00 0.00 41.47 4.85
163 164 1.452145 GACAAAGGGTGCCTCGCAAA 61.452 55.000 0.00 0.00 41.47 3.68
164 165 1.040339 ACAAAGGGTGCCTCGCAAAA 61.040 50.000 0.00 0.00 41.47 2.44
165 166 0.103937 CAAAGGGTGCCTCGCAAAAA 59.896 50.000 0.00 0.00 41.47 1.94
210 211 2.357517 GTGGGCGTGACTGTCAGG 60.358 66.667 22.41 22.41 35.54 3.86
213 214 2.421739 GGCGTGACTGTCAGGTGT 59.578 61.111 25.73 0.00 34.95 4.16
238 239 5.438761 AAACTCTAGTTTTGGTGCATGTC 57.561 39.130 2.24 0.00 45.07 3.06
239 240 3.067106 ACTCTAGTTTTGGTGCATGTCG 58.933 45.455 0.00 0.00 0.00 4.35
240 241 3.244078 ACTCTAGTTTTGGTGCATGTCGA 60.244 43.478 0.00 0.00 0.00 4.20
241 242 3.734463 TCTAGTTTTGGTGCATGTCGAA 58.266 40.909 0.00 0.00 0.00 3.71
242 243 4.323417 TCTAGTTTTGGTGCATGTCGAAT 58.677 39.130 0.00 0.00 0.00 3.34
243 244 3.287312 AGTTTTGGTGCATGTCGAATG 57.713 42.857 0.00 0.00 0.00 2.67
244 245 2.884012 AGTTTTGGTGCATGTCGAATGA 59.116 40.909 10.52 0.00 0.00 2.57
245 246 3.507233 AGTTTTGGTGCATGTCGAATGAT 59.493 39.130 10.52 0.00 0.00 2.45
246 247 3.763097 TTTGGTGCATGTCGAATGATC 57.237 42.857 10.52 0.00 0.00 2.92
270 271 4.794278 TGCGTGATCACTTAACTTCCTA 57.206 40.909 22.95 0.00 0.00 2.94
273 274 4.745620 GCGTGATCACTTAACTTCCTATCC 59.254 45.833 22.95 0.00 0.00 2.59
275 276 6.238953 GCGTGATCACTTAACTTCCTATCCTA 60.239 42.308 22.95 0.00 0.00 2.94
287 288 1.806461 CTATCCTAGCGCGGCTTCCA 61.806 60.000 8.83 0.00 40.44 3.53
338 402 1.267261 CGTTTGTCACCGAGAGAGACT 59.733 52.381 0.00 0.00 37.03 3.24
339 403 2.287668 CGTTTGTCACCGAGAGAGACTT 60.288 50.000 0.00 0.00 37.03 3.01
355 419 2.741985 TTGTGCGTGCCAGGATCG 60.742 61.111 0.00 0.00 0.00 3.69
418 483 3.547413 CCACATTAACGATGCTGCATCTG 60.547 47.826 32.62 27.48 38.59 2.90
447 512 1.488705 TTGTTCTCCGGCACCAGGAT 61.489 55.000 0.00 0.00 37.13 3.24
569 636 7.817478 TCATGTACGTATGTCAAGACTGAAATT 59.183 33.333 0.00 0.00 31.53 1.82
639 706 2.605338 CGACACAATCCAGGCAAAAGTG 60.605 50.000 0.00 0.00 0.00 3.16
716 5848 2.301870 TCGTTTACCATGCTGTCCTTCT 59.698 45.455 0.00 0.00 0.00 2.85
721 5853 1.277557 ACCATGCTGTCCTTCTCTCAC 59.722 52.381 0.00 0.00 0.00 3.51
872 6126 3.059352 AGTGGAGTACAACTTGGCATC 57.941 47.619 0.00 0.00 0.00 3.91
879 6133 0.744414 ACAACTTGGCATCGGGATCG 60.744 55.000 0.00 0.00 37.82 3.69
909 6163 4.286297 TGGCCCCTAATAGATGATTTCG 57.714 45.455 0.00 0.00 0.00 3.46
1076 6338 2.133858 TCTTCTTCCCCTCCAACCTT 57.866 50.000 0.00 0.00 0.00 3.50
1290 6641 1.677637 GGAAGTCCCCGCTCGAGATT 61.678 60.000 18.75 0.00 0.00 2.40
1456 6811 2.171209 CTGTCCGGTGATGCCTGTCA 62.171 60.000 0.00 0.00 34.25 3.58
1839 7208 9.582431 AAGTTGATCATGTCATTGATTTTGATC 57.418 29.630 19.31 19.31 39.75 2.92
2161 7632 3.365969 GCGGTTGGACTAGATGTTTTTGG 60.366 47.826 0.00 0.00 0.00 3.28
2297 7772 2.093306 TCGATGTGTGGTAAGGCTTG 57.907 50.000 10.69 0.00 0.00 4.01
2391 7870 5.899547 AGTTTCAACAAAAGGGGAGAGATTT 59.100 36.000 0.00 0.00 0.00 2.17
2392 7871 5.789643 TTCAACAAAAGGGGAGAGATTTG 57.210 39.130 0.00 0.00 38.42 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.324943 CGCCTCCTCCTCCAGAAAAA 59.675 55.000 0.00 0.00 0.00 1.94
27 28 1.553690 CCGCCTCCTCCTCCAGAAAA 61.554 60.000 0.00 0.00 0.00 2.29
29 30 2.364317 CCGCCTCCTCCTCCAGAA 60.364 66.667 0.00 0.00 0.00 3.02
38 39 4.660938 AAAAAGCCGCCGCCTCCT 62.661 61.111 0.00 0.00 34.57 3.69
53 54 0.658897 GAACGAGGGCACACGAAAAA 59.341 50.000 14.16 0.00 34.36 1.94
55 56 1.595929 GGAACGAGGGCACACGAAA 60.596 57.895 14.16 0.00 34.36 3.46
56 57 2.029964 GGAACGAGGGCACACGAA 59.970 61.111 14.16 0.00 34.36 3.85
69 70 2.295070 ACAAGTAAATGGCCAACGGAAC 59.705 45.455 10.96 4.09 0.00 3.62
72 73 3.056304 CAAACAAGTAAATGGCCAACGG 58.944 45.455 10.96 4.32 0.00 4.44
73 74 3.712187 ACAAACAAGTAAATGGCCAACG 58.288 40.909 10.96 0.00 0.00 4.10
75 76 5.344743 TGAACAAACAAGTAAATGGCCAA 57.655 34.783 10.96 0.00 0.00 4.52
77 78 5.571357 CGTATGAACAAACAAGTAAATGGCC 59.429 40.000 0.00 0.00 0.00 5.36
78 79 6.375377 TCGTATGAACAAACAAGTAAATGGC 58.625 36.000 0.00 0.00 0.00 4.40
79 80 7.802738 TCTCGTATGAACAAACAAGTAAATGG 58.197 34.615 0.00 0.00 0.00 3.16
80 81 9.318041 CTTCTCGTATGAACAAACAAGTAAATG 57.682 33.333 0.00 0.00 0.00 2.32
81 82 8.015658 GCTTCTCGTATGAACAAACAAGTAAAT 58.984 33.333 0.00 0.00 0.00 1.40
82 83 7.225931 AGCTTCTCGTATGAACAAACAAGTAAA 59.774 33.333 0.00 0.00 0.00 2.01
83 84 6.704493 AGCTTCTCGTATGAACAAACAAGTAA 59.296 34.615 0.00 0.00 0.00 2.24
84 85 6.220930 AGCTTCTCGTATGAACAAACAAGTA 58.779 36.000 0.00 0.00 0.00 2.24
85 86 5.057149 AGCTTCTCGTATGAACAAACAAGT 58.943 37.500 0.00 0.00 0.00 3.16
87 88 5.525745 TGAAGCTTCTCGTATGAACAAACAA 59.474 36.000 26.09 0.00 0.00 2.83
88 89 5.050363 GTGAAGCTTCTCGTATGAACAAACA 60.050 40.000 26.09 0.00 0.00 2.83
90 91 4.149922 CGTGAAGCTTCTCGTATGAACAAA 59.850 41.667 32.20 6.49 38.81 2.83
94 95 3.842732 TCGTGAAGCTTCTCGTATGAA 57.157 42.857 35.99 21.96 42.70 2.57
96 97 3.695816 TGATCGTGAAGCTTCTCGTATG 58.304 45.455 35.99 19.76 42.70 2.39
97 98 4.096532 TCTTGATCGTGAAGCTTCTCGTAT 59.903 41.667 35.99 29.17 42.70 3.06
98 99 3.439129 TCTTGATCGTGAAGCTTCTCGTA 59.561 43.478 35.99 26.87 42.70 3.43
99 100 2.229062 TCTTGATCGTGAAGCTTCTCGT 59.771 45.455 35.99 27.26 42.70 4.18
100 101 2.868662 TCTTGATCGTGAAGCTTCTCG 58.131 47.619 33.86 33.86 43.27 4.04
101 102 4.493872 GCATTCTTGATCGTGAAGCTTCTC 60.494 45.833 26.09 21.29 0.00 2.87
102 103 3.373439 GCATTCTTGATCGTGAAGCTTCT 59.627 43.478 26.09 6.84 0.00 2.85
103 104 3.678662 GCATTCTTGATCGTGAAGCTTC 58.321 45.455 19.89 19.89 0.00 3.86
104 105 2.094894 CGCATTCTTGATCGTGAAGCTT 59.905 45.455 0.00 0.00 0.00 3.74
105 106 1.662629 CGCATTCTTGATCGTGAAGCT 59.337 47.619 6.41 0.00 0.00 3.74
106 107 1.394917 ACGCATTCTTGATCGTGAAGC 59.605 47.619 6.41 8.24 33.59 3.86
111 112 2.654749 TCTCACGCATTCTTGATCGT 57.345 45.000 0.00 0.00 35.35 3.73
112 113 2.283617 CCTTCTCACGCATTCTTGATCG 59.716 50.000 0.00 0.00 0.00 3.69
113 114 2.611292 CCCTTCTCACGCATTCTTGATC 59.389 50.000 0.00 0.00 0.00 2.92
114 115 2.026822 ACCCTTCTCACGCATTCTTGAT 60.027 45.455 0.00 0.00 0.00 2.57
115 116 1.347707 ACCCTTCTCACGCATTCTTGA 59.652 47.619 0.00 0.00 0.00 3.02
116 117 1.466167 CACCCTTCTCACGCATTCTTG 59.534 52.381 0.00 0.00 0.00 3.02
117 118 1.072331 ACACCCTTCTCACGCATTCTT 59.928 47.619 0.00 0.00 0.00 2.52
118 119 0.687354 ACACCCTTCTCACGCATTCT 59.313 50.000 0.00 0.00 0.00 2.40
119 120 2.380084 TACACCCTTCTCACGCATTC 57.620 50.000 0.00 0.00 0.00 2.67
120 121 2.224426 TGTTACACCCTTCTCACGCATT 60.224 45.455 0.00 0.00 0.00 3.56
121 122 1.346395 TGTTACACCCTTCTCACGCAT 59.654 47.619 0.00 0.00 0.00 4.73
122 123 0.753867 TGTTACACCCTTCTCACGCA 59.246 50.000 0.00 0.00 0.00 5.24
123 124 1.145803 GTGTTACACCCTTCTCACGC 58.854 55.000 3.79 0.00 0.00 5.34
124 125 2.035449 TCAGTGTTACACCCTTCTCACG 59.965 50.000 12.28 0.00 34.49 4.35
125 126 3.181469 TGTCAGTGTTACACCCTTCTCAC 60.181 47.826 12.28 0.00 34.49 3.51
126 127 3.035363 TGTCAGTGTTACACCCTTCTCA 58.965 45.455 12.28 1.25 34.49 3.27
127 128 3.746045 TGTCAGTGTTACACCCTTCTC 57.254 47.619 12.28 0.00 34.49 2.87
128 129 4.451900 CTTTGTCAGTGTTACACCCTTCT 58.548 43.478 12.28 0.00 34.49 2.85
129 130 3.564225 CCTTTGTCAGTGTTACACCCTTC 59.436 47.826 12.28 1.73 34.49 3.46
130 131 3.551846 CCTTTGTCAGTGTTACACCCTT 58.448 45.455 12.28 0.00 34.49 3.95
131 132 2.158667 CCCTTTGTCAGTGTTACACCCT 60.159 50.000 12.28 0.00 34.49 4.34
132 133 2.227194 CCCTTTGTCAGTGTTACACCC 58.773 52.381 12.28 1.34 34.49 4.61
133 134 2.616842 CACCCTTTGTCAGTGTTACACC 59.383 50.000 12.28 0.00 34.49 4.16
134 135 2.032924 GCACCCTTTGTCAGTGTTACAC 59.967 50.000 7.50 7.50 33.96 2.90
135 136 2.294074 GCACCCTTTGTCAGTGTTACA 58.706 47.619 0.00 0.00 33.96 2.41
136 137 1.607148 GGCACCCTTTGTCAGTGTTAC 59.393 52.381 0.00 0.00 33.96 2.50
137 138 1.493022 AGGCACCCTTTGTCAGTGTTA 59.507 47.619 0.00 0.00 33.96 2.41
138 139 0.258774 AGGCACCCTTTGTCAGTGTT 59.741 50.000 0.00 0.00 33.96 3.32
139 140 0.179018 GAGGCACCCTTTGTCAGTGT 60.179 55.000 0.00 0.00 31.76 3.55
140 141 1.230635 CGAGGCACCCTTTGTCAGTG 61.231 60.000 0.00 0.00 31.76 3.66
141 142 1.071471 CGAGGCACCCTTTGTCAGT 59.929 57.895 0.00 0.00 31.76 3.41
142 143 2.328099 GCGAGGCACCCTTTGTCAG 61.328 63.158 0.00 0.00 31.76 3.51
143 144 2.281484 GCGAGGCACCCTTTGTCA 60.281 61.111 0.00 0.00 31.76 3.58
144 145 1.452145 TTTGCGAGGCACCCTTTGTC 61.452 55.000 0.00 0.00 38.71 3.18
145 146 1.040339 TTTTGCGAGGCACCCTTTGT 61.040 50.000 0.00 0.00 38.71 2.83
146 147 0.103937 TTTTTGCGAGGCACCCTTTG 59.896 50.000 0.00 0.00 38.71 2.77
147 148 2.510664 TTTTTGCGAGGCACCCTTT 58.489 47.368 0.00 0.00 38.71 3.11
148 149 4.268720 TTTTTGCGAGGCACCCTT 57.731 50.000 0.00 0.00 38.71 3.95
163 164 3.181466 GGCACCCTTTGTCAGTGATTTTT 60.181 43.478 0.00 0.00 33.21 1.94
164 165 2.365293 GGCACCCTTTGTCAGTGATTTT 59.635 45.455 0.00 0.00 33.21 1.82
165 166 1.963515 GGCACCCTTTGTCAGTGATTT 59.036 47.619 0.00 0.00 33.21 2.17
166 167 1.133513 TGGCACCCTTTGTCAGTGATT 60.134 47.619 0.00 0.00 33.77 2.57
167 168 0.478072 TGGCACCCTTTGTCAGTGAT 59.522 50.000 0.00 0.00 33.77 3.06
168 169 0.478072 ATGGCACCCTTTGTCAGTGA 59.522 50.000 0.00 0.00 45.14 3.41
169 170 1.331214 AATGGCACCCTTTGTCAGTG 58.669 50.000 0.00 0.00 45.14 3.66
170 171 2.086610 AAATGGCACCCTTTGTCAGT 57.913 45.000 0.00 0.00 45.14 3.41
238 239 2.053627 TGATCACGCATCGATCATTCG 58.946 47.619 0.00 0.00 43.30 3.34
242 243 2.584492 AAGTGATCACGCATCGATCA 57.416 45.000 19.85 5.77 45.36 2.92
243 244 4.045104 AGTTAAGTGATCACGCATCGATC 58.955 43.478 19.85 6.93 39.82 3.69
244 245 4.046938 AGTTAAGTGATCACGCATCGAT 57.953 40.909 19.85 0.00 33.61 3.59
245 246 3.503827 AGTTAAGTGATCACGCATCGA 57.496 42.857 19.85 2.19 33.61 3.59
246 247 3.000322 GGAAGTTAAGTGATCACGCATCG 60.000 47.826 19.85 0.00 33.61 3.84
270 271 2.441822 GATGGAAGCCGCGCTAGGAT 62.442 60.000 5.56 0.00 38.25 3.24
273 274 3.032609 CGATGGAAGCCGCGCTAG 61.033 66.667 5.56 0.00 38.25 3.42
287 288 7.491372 CACTGTTGTATGTATTTAGGTGACGAT 59.509 37.037 0.00 0.00 0.00 3.73
338 402 2.741985 CGATCCTGGCACGCACAA 60.742 61.111 0.00 0.00 0.00 3.33
339 403 4.758251 CCGATCCTGGCACGCACA 62.758 66.667 6.79 0.00 0.00 4.57
372 436 8.790718 TGGAAAATTGATCTCTCTCAGAAAAAG 58.209 33.333 0.00 0.00 33.62 2.27
378 443 7.627298 AATGTGGAAAATTGATCTCTCTCAG 57.373 36.000 0.00 0.00 0.00 3.35
384 449 7.166473 GCATCGTTAATGTGGAAAATTGATCTC 59.834 37.037 0.00 0.00 37.71 2.75
418 483 1.572941 GGAGAACAAAACGGCCGAC 59.427 57.895 35.90 13.02 0.00 4.79
447 512 0.034896 GGAAGAAGTTGACCTCCGCA 59.965 55.000 0.00 0.00 0.00 5.69
639 706 1.503542 CAAACGCACCATCCAGCTC 59.496 57.895 0.00 0.00 0.00 4.09
716 5848 6.512741 GCGAAGAAATTGTTGGTAAAGTGAGA 60.513 38.462 0.00 0.00 0.00 3.27
721 5853 6.143919 GGAAAGCGAAGAAATTGTTGGTAAAG 59.856 38.462 0.00 0.00 0.00 1.85
872 6126 0.108615 GCCATCCTATCACGATCCCG 60.109 60.000 0.00 0.00 42.50 5.14
879 6133 4.362677 TCTATTAGGGGCCATCCTATCAC 58.637 47.826 4.39 0.00 38.99 3.06
909 6163 7.147976 GGAAATTATTATGTCCTGGATGTTGC 58.852 38.462 0.00 0.00 35.54 4.17
1076 6338 1.943340 CATCACCGAGATCTGAGACGA 59.057 52.381 0.00 0.00 33.72 4.20
1121 6470 3.289834 GATTGCCGCCGCCATGAT 61.290 61.111 0.00 0.00 0.00 2.45
1290 6641 3.073503 CCTCCATCATTGCCCAATAGAGA 59.926 47.826 0.00 0.00 0.00 3.10
1456 6811 1.516386 GCACATCGTCGTCGGTCAT 60.516 57.895 1.55 0.00 37.69 3.06
1839 7208 7.494625 ACAAACCATCCTCATAACAGTATTACG 59.505 37.037 0.00 0.00 0.00 3.18
2161 7632 3.896272 CCACTAACCTGGACCTCCTATAC 59.104 52.174 0.00 0.00 36.82 1.47


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

AutoCloner maintained by Alex Coulton.