Multiple sequence alignment - TraesCS5D01G329700

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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 TraesCS5D01G329700 chr5D 100.000 4114 0 0 1 4114 421541891 421546004 0.000000e+00 7598.0
1 TraesCS5D01G329700 chr5D 90.135 1774 134 15 889 2651 421681192 421679449 0.000000e+00 2268.0
2 TraesCS5D01G329700 chr5D 90.554 487 31 11 3613 4091 421678224 421677745 7.500000e-177 630.0
3 TraesCS5D01G329700 chr5D 95.109 368 18 0 3138 3505 421679448 421679081 7.670000e-162 580.0
4 TraesCS5D01G329700 chr5D 84.065 433 37 13 3687 4099 421672331 421671911 4.990000e-104 388.0
5 TraesCS5D01G329700 chr5D 75.679 773 143 30 928 1665 324350154 324350916 1.090000e-90 344.0
6 TraesCS5D01G329700 chr5D 83.710 221 21 8 852 1058 421591577 421591796 1.170000e-45 195.0
7 TraesCS5D01G329700 chr5D 94.737 114 6 0 3503 3616 421679054 421678941 1.180000e-40 178.0
8 TraesCS5D01G329700 chr5D 82.857 70 11 1 1826 1895 47022435 47022503 1.230000e-05 62.1
9 TraesCS5D01G329700 chr5A 95.600 1659 54 10 2463 4114 535148302 535149948 0.000000e+00 2641.0
10 TraesCS5D01G329700 chr5A 94.422 502 25 2 1965 2466 535145369 535145867 0.000000e+00 769.0
11 TraesCS5D01G329700 chr5A 83.130 575 78 12 868 1430 535182387 535182954 1.320000e-139 507.0
12 TraesCS5D01G329700 chr5A 84.749 518 52 15 326 834 535143324 535143823 1.030000e-135 494.0
13 TraesCS5D01G329700 chr5A 93.851 309 14 2 838 1142 535144951 535145258 1.040000e-125 460.0
14 TraesCS5D01G329700 chr5A 84.171 398 38 9 3687 4071 535274078 535273693 3.020000e-96 363.0
15 TraesCS5D01G329700 chr5A 74.756 820 160 32 910 1693 422019860 422020668 1.430000e-84 324.0
16 TraesCS5D01G329700 chr5A 94.545 110 6 0 1825 1934 535145258 535145367 1.970000e-38 171.0
17 TraesCS5D01G329700 chr5B 90.814 1633 113 15 1892 3505 507919947 507921561 0.000000e+00 2150.0
18 TraesCS5D01G329700 chr5B 88.652 705 58 8 836 1525 507897662 507898359 0.000000e+00 839.0
19 TraesCS5D01G329700 chr5B 87.758 629 57 11 3503 4114 507921588 507922213 0.000000e+00 717.0
20 TraesCS5D01G329700 chr5B 85.114 571 49 25 283 839 507895930 507896478 6.010000e-153 551.0
21 TraesCS5D01G329700 chr5B 83.067 626 75 19 2819 3434 375804490 375805094 1.300000e-149 540.0
22 TraesCS5D01G329700 chr5B 75.702 819 154 30 910 1693 375733629 375734437 6.500000e-98 368.0
23 TraesCS5D01G329700 chr5B 82.597 385 40 13 3690 4066 508152504 508152139 8.580000e-82 315.0
24 TraesCS5D01G329700 chr5B 74.603 567 103 26 936 1466 375653767 375654328 1.160000e-50 211.0
25 TraesCS5D01G329700 chr5B 95.000 40 1 1 784 822 369334925 369334886 1.230000e-05 62.1
26 TraesCS5D01G329700 chr4A 83.815 173 24 3 1824 1996 552458793 552458961 1.180000e-35 161.0
27 TraesCS5D01G329700 chr4A 73.279 247 45 16 334 571 690626512 690626278 2.050000e-08 71.3
28 TraesCS5D01G329700 chr6A 82.199 191 28 5 1794 1983 61671050 61670865 4.260000e-35 159.0
29 TraesCS5D01G329700 chr7B 75.522 335 54 21 328 649 555316299 555316618 5.550000e-29 139.0
30 TraesCS5D01G329700 chr2A 80.102 196 31 5 1800 1991 47781244 47781053 5.550000e-29 139.0
31 TraesCS5D01G329700 chr7A 83.333 126 18 3 1871 1996 669721247 669721369 3.360000e-21 113.0
32 TraesCS5D01G329700 chr7D 72.821 390 67 29 328 702 521688353 521688718 3.380000e-16 97.1
33 TraesCS5D01G329700 chr4B 83.951 81 7 6 342 418 20687409 20687331 5.700000e-09 73.1
34 TraesCS5D01G329700 chr1B 84.722 72 10 1 1890 1961 61055011 61055081 2.050000e-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 TraesCS5D01G329700 chr5D 421541891 421546004 4113 False 7598.0 7598 100.00000 1 4114 1 chr5D.!!$F3 4113
1 TraesCS5D01G329700 chr5D 421677745 421681192 3447 True 914.0 2268 92.63375 889 4091 4 chr5D.!!$R2 3202
2 TraesCS5D01G329700 chr5D 324350154 324350916 762 False 344.0 344 75.67900 928 1665 1 chr5D.!!$F2 737
3 TraesCS5D01G329700 chr5A 535143324 535149948 6624 False 907.0 2641 92.63340 326 4114 5 chr5A.!!$F3 3788
4 TraesCS5D01G329700 chr5A 535182387 535182954 567 False 507.0 507 83.13000 868 1430 1 chr5A.!!$F2 562
5 TraesCS5D01G329700 chr5A 422019860 422020668 808 False 324.0 324 74.75600 910 1693 1 chr5A.!!$F1 783
6 TraesCS5D01G329700 chr5B 507919947 507922213 2266 False 1433.5 2150 89.28600 1892 4114 2 chr5B.!!$F5 2222
7 TraesCS5D01G329700 chr5B 507895930 507898359 2429 False 695.0 839 86.88300 283 1525 2 chr5B.!!$F4 1242
8 TraesCS5D01G329700 chr5B 375804490 375805094 604 False 540.0 540 83.06700 2819 3434 1 chr5B.!!$F3 615
9 TraesCS5D01G329700 chr5B 375733629 375734437 808 False 368.0 368 75.70200 910 1693 1 chr5B.!!$F2 783
10 TraesCS5D01G329700 chr5B 375653767 375654328 561 False 211.0 211 74.60300 936 1466 1 chr5B.!!$F1 530

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
170 171 0.528017 TGCTGCCGTGTTTCAAACAA 59.472 45.0 4.02 0.0 44.16 2.83 F
1395 3067 0.606604 TAGGGTCGACTTGCAGGAAC 59.393 55.0 16.46 0.0 0.00 3.62 F
1863 3541 0.106519 AGCATAGCAATTCGGCCCTT 60.107 50.0 0.00 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1694 3372 1.275421 AAGGGGTAAGCAGAGAGGGC 61.275 60.000 0.0 0.0 0.0 5.19 R
2898 7040 1.277557 AGGTGCATGGAAGTGTCTCTC 59.722 52.381 0.0 0.0 0.0 3.20 R
3858 8766 0.326238 ATTTCCAGGCTCCGAGGGTA 60.326 55.000 0.0 0.0 0.0 3.69 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
110 111 8.761575 AAATGTTGCCACAGTTTAATAGAATG 57.238 30.769 0.00 0.00 37.99 2.67
111 112 6.892658 TGTTGCCACAGTTTAATAGAATGT 57.107 33.333 0.00 0.00 0.00 2.71
112 113 7.283625 TGTTGCCACAGTTTAATAGAATGTT 57.716 32.000 0.00 0.00 0.00 2.71
113 114 7.144661 TGTTGCCACAGTTTAATAGAATGTTG 58.855 34.615 0.00 0.00 0.00 3.33
114 115 7.013750 TGTTGCCACAGTTTAATAGAATGTTGA 59.986 33.333 0.00 0.00 0.00 3.18
115 116 7.701539 TGCCACAGTTTAATAGAATGTTGAT 57.298 32.000 0.00 0.00 0.00 2.57
116 117 8.800370 TGCCACAGTTTAATAGAATGTTGATA 57.200 30.769 0.00 0.00 0.00 2.15
117 118 9.237187 TGCCACAGTTTAATAGAATGTTGATAA 57.763 29.630 0.00 0.00 0.00 1.75
139 140 8.986039 ATAAAATTTCAAAACAATGTTCGTGC 57.014 26.923 0.00 0.00 0.00 5.34
140 141 5.402464 AATTTCAAAACAATGTTCGTGCC 57.598 34.783 0.00 0.00 0.00 5.01
141 142 3.510388 TTCAAAACAATGTTCGTGCCA 57.490 38.095 0.00 0.00 0.00 4.92
142 143 3.510388 TCAAAACAATGTTCGTGCCAA 57.490 38.095 0.00 0.00 0.00 4.52
143 144 4.052159 TCAAAACAATGTTCGTGCCAAT 57.948 36.364 0.00 0.00 0.00 3.16
144 145 3.801050 TCAAAACAATGTTCGTGCCAATG 59.199 39.130 0.00 0.00 0.00 2.82
145 146 3.724508 AAACAATGTTCGTGCCAATGA 57.275 38.095 0.00 0.00 0.00 2.57
146 147 3.724508 AACAATGTTCGTGCCAATGAA 57.275 38.095 0.00 0.00 0.00 2.57
147 148 3.724508 ACAATGTTCGTGCCAATGAAA 57.275 38.095 0.00 0.00 33.11 2.69
148 149 4.052159 ACAATGTTCGTGCCAATGAAAA 57.948 36.364 0.00 0.00 33.11 2.29
149 150 4.630111 ACAATGTTCGTGCCAATGAAAAT 58.370 34.783 0.00 0.00 33.11 1.82
150 151 5.777802 ACAATGTTCGTGCCAATGAAAATA 58.222 33.333 0.00 0.00 33.11 1.40
151 152 6.397272 ACAATGTTCGTGCCAATGAAAATAT 58.603 32.000 0.00 0.00 33.11 1.28
152 153 6.310956 ACAATGTTCGTGCCAATGAAAATATG 59.689 34.615 0.00 0.00 33.11 1.78
153 154 4.172505 TGTTCGTGCCAATGAAAATATGC 58.827 39.130 0.00 0.00 33.11 3.14
154 155 4.082300 TGTTCGTGCCAATGAAAATATGCT 60.082 37.500 0.00 0.00 33.11 3.79
155 156 4.031418 TCGTGCCAATGAAAATATGCTG 57.969 40.909 0.00 0.00 0.00 4.41
156 157 2.536803 CGTGCCAATGAAAATATGCTGC 59.463 45.455 0.00 0.00 0.00 5.25
157 158 2.867975 GTGCCAATGAAAATATGCTGCC 59.132 45.455 0.00 0.00 0.00 4.85
158 159 2.129607 GCCAATGAAAATATGCTGCCG 58.870 47.619 0.00 0.00 0.00 5.69
159 160 2.481795 GCCAATGAAAATATGCTGCCGT 60.482 45.455 0.00 0.00 0.00 5.68
160 161 3.117794 CCAATGAAAATATGCTGCCGTG 58.882 45.455 0.00 0.00 0.00 4.94
161 162 3.429272 CCAATGAAAATATGCTGCCGTGT 60.429 43.478 0.00 0.00 0.00 4.49
162 163 4.175516 CAATGAAAATATGCTGCCGTGTT 58.824 39.130 0.00 0.00 0.00 3.32
163 164 3.932545 TGAAAATATGCTGCCGTGTTT 57.067 38.095 0.00 0.00 0.00 2.83
164 165 3.832276 TGAAAATATGCTGCCGTGTTTC 58.168 40.909 0.00 3.38 0.00 2.78
165 166 3.254411 TGAAAATATGCTGCCGTGTTTCA 59.746 39.130 11.95 11.95 0.00 2.69
166 167 3.932545 AAATATGCTGCCGTGTTTCAA 57.067 38.095 0.00 0.00 0.00 2.69
167 168 3.932545 AATATGCTGCCGTGTTTCAAA 57.067 38.095 0.00 0.00 0.00 2.69
168 169 2.697431 TATGCTGCCGTGTTTCAAAC 57.303 45.000 0.00 0.00 0.00 2.93
169 170 0.743688 ATGCTGCCGTGTTTCAAACA 59.256 45.000 0.00 0.00 39.52 2.83
170 171 0.528017 TGCTGCCGTGTTTCAAACAA 59.472 45.000 4.02 0.00 44.16 2.83
171 172 1.067565 TGCTGCCGTGTTTCAAACAAA 60.068 42.857 4.02 0.00 44.16 2.83
172 173 2.200899 GCTGCCGTGTTTCAAACAAAT 58.799 42.857 4.02 0.00 44.16 2.32
173 174 2.033832 GCTGCCGTGTTTCAAACAAATG 60.034 45.455 4.02 0.00 44.16 2.32
174 175 3.186119 CTGCCGTGTTTCAAACAAATGT 58.814 40.909 4.02 0.00 44.16 2.71
175 176 4.355437 CTGCCGTGTTTCAAACAAATGTA 58.645 39.130 4.02 0.00 44.16 2.29
176 177 4.938080 TGCCGTGTTTCAAACAAATGTAT 58.062 34.783 4.02 0.00 44.16 2.29
177 178 4.742167 TGCCGTGTTTCAAACAAATGTATG 59.258 37.500 4.02 0.00 44.16 2.39
178 179 4.375908 GCCGTGTTTCAAACAAATGTATGC 60.376 41.667 4.02 0.00 44.16 3.14
179 180 4.742167 CCGTGTTTCAAACAAATGTATGCA 59.258 37.500 4.02 0.00 44.16 3.96
180 181 5.332205 CCGTGTTTCAAACAAATGTATGCAC 60.332 40.000 4.02 0.00 44.16 4.57
181 182 5.230936 CGTGTTTCAAACAAATGTATGCACA 59.769 36.000 4.02 0.00 44.16 4.57
182 183 6.237675 CGTGTTTCAAACAAATGTATGCACAA 60.238 34.615 4.02 0.00 44.16 3.33
183 184 7.459486 GTGTTTCAAACAAATGTATGCACAAA 58.541 30.769 4.02 0.00 44.16 2.83
184 185 8.121708 GTGTTTCAAACAAATGTATGCACAAAT 58.878 29.630 4.02 0.00 44.16 2.32
185 186 8.671921 TGTTTCAAACAAATGTATGCACAAATT 58.328 25.926 0.00 0.00 38.72 1.82
186 187 9.157259 GTTTCAAACAAATGTATGCACAAATTC 57.843 29.630 0.00 0.00 38.42 2.17
187 188 8.429493 TTCAAACAAATGTATGCACAAATTCA 57.571 26.923 0.00 0.00 38.42 2.57
188 189 8.429493 TCAAACAAATGTATGCACAAATTCAA 57.571 26.923 0.00 0.00 38.42 2.69
189 190 8.886719 TCAAACAAATGTATGCACAAATTCAAA 58.113 25.926 0.00 0.00 38.42 2.69
190 191 9.499585 CAAACAAATGTATGCACAAATTCAAAA 57.500 25.926 0.00 0.00 38.42 2.44
277 278 8.844441 TTAAAATAGTCAAGTTTTTCCACACG 57.156 30.769 0.00 0.00 0.00 4.49
278 279 6.687081 AAATAGTCAAGTTTTTCCACACGA 57.313 33.333 0.00 0.00 0.00 4.35
279 280 6.687081 AATAGTCAAGTTTTTCCACACGAA 57.313 33.333 0.00 0.00 0.00 3.85
280 281 6.687081 ATAGTCAAGTTTTTCCACACGAAA 57.313 33.333 0.00 0.00 38.74 3.46
281 282 5.379732 AGTCAAGTTTTTCCACACGAAAA 57.620 34.783 0.00 0.00 46.41 2.29
382 391 5.873164 ACTTGGAAGATGTTACCGTGTATTC 59.127 40.000 0.00 0.00 0.00 1.75
383 392 5.408880 TGGAAGATGTTACCGTGTATTCA 57.591 39.130 0.00 0.00 0.00 2.57
384 393 5.795972 TGGAAGATGTTACCGTGTATTCAA 58.204 37.500 0.00 0.00 0.00 2.69
494 504 7.595502 GTGTGCTCTAATGTATATGGTGTACTC 59.404 40.741 0.00 0.00 0.00 2.59
529 539 7.845622 GCAGACATGTGTTGAACAAAATAAAAC 59.154 33.333 1.15 0.00 43.61 2.43
599 612 9.574516 AGAGAAACAAAGAAAACCATATAGTGT 57.425 29.630 0.00 0.00 0.00 3.55
626 642 9.671279 AACAAAGAAAGAAACCAAAGAAATCAT 57.329 25.926 0.00 0.00 0.00 2.45
627 643 9.317936 ACAAAGAAAGAAACCAAAGAAATCATC 57.682 29.630 0.00 0.00 0.00 2.92
737 758 2.249139 AGAAAACCCGACAGTAGAGCT 58.751 47.619 0.00 0.00 0.00 4.09
917 2548 3.449227 CTCCTACAGGCCGCGTCA 61.449 66.667 4.92 0.00 34.44 4.35
1130 2787 2.121538 CGACAGCATCCTCCTCCGA 61.122 63.158 0.00 0.00 0.00 4.55
1137 2794 3.106859 ATCCTCCTCCGATGCCCCT 62.107 63.158 0.00 0.00 0.00 4.79
1200 2857 4.760047 GCCGCATCCACGACTGGT 62.760 66.667 0.00 0.00 38.90 4.00
1317 2989 1.655654 CATCTCTCGTACTGCGCCG 60.656 63.158 4.18 0.00 41.07 6.46
1395 3067 0.606604 TAGGGTCGACTTGCAGGAAC 59.393 55.000 16.46 0.00 0.00 3.62
1491 3169 2.238521 TCCCTGGTGAATTCAAACAGC 58.761 47.619 25.18 10.36 34.04 4.40
1512 3190 1.217942 GGGTGATTCAGGGGCCTAATT 59.782 52.381 0.84 0.00 0.00 1.40
1517 3195 1.089123 TTCAGGGGCCTAATTTGGGT 58.911 50.000 0.84 0.00 0.00 4.51
1519 3197 1.006639 TCAGGGGCCTAATTTGGGTTC 59.993 52.381 0.84 0.00 0.00 3.62
1527 3205 3.566351 CCTAATTTGGGTTCCCTCCATC 58.434 50.000 9.43 0.00 33.82 3.51
1531 3209 1.753903 TTGGGTTCCCTCCATCTTCA 58.246 50.000 9.43 0.00 33.82 3.02
1556 3234 3.228453 GCTTGATGATCATGGTTGGGAT 58.772 45.455 14.30 0.00 0.00 3.85
1601 3279 5.220739 GGATTCTGCCGTCATTGATATATGC 60.221 44.000 0.00 0.00 0.00 3.14
1614 3292 8.977412 TCATTGATATATGCGACTATTTAGGGA 58.023 33.333 0.00 0.00 0.00 4.20
1651 3329 2.507110 TTTCTCTCCGGCCTTGCGAG 62.507 60.000 0.00 1.71 0.00 5.03
1659 3337 3.195698 GCCTTGCGAGCCTTACCG 61.196 66.667 0.00 0.00 0.00 4.02
1694 3372 6.387041 TCTACTTATCATCAACCGGTACAG 57.613 41.667 8.00 0.41 0.00 2.74
1704 3382 2.496817 CGGTACAGCCCTCTCTGC 59.503 66.667 0.00 0.00 37.59 4.26
1744 3422 8.600625 CCATTGAAATTAAATTCAGCACTCATG 58.399 33.333 6.10 6.31 40.21 3.07
1863 3541 0.106519 AGCATAGCAATTCGGCCCTT 60.107 50.000 0.00 0.00 0.00 3.95
2250 3928 4.860022 ACTTGGAAATTACCTCCTCATGG 58.140 43.478 0.00 0.00 33.77 3.66
2261 3939 2.507484 CTCCTCATGGTGTTCTTTGCA 58.493 47.619 0.00 0.00 34.23 4.08
2451 4134 6.054860 AGCTGTGGATGTGACTTTACTTAT 57.945 37.500 0.00 0.00 0.00 1.73
2452 4135 7.093509 TGAGCTGTGGATGTGACTTTACTTATA 60.094 37.037 0.00 0.00 0.00 0.98
2732 6871 1.978580 CCTGGTTCTAGTTCCACACCT 59.021 52.381 4.94 0.00 0.00 4.00
2734 6873 1.616865 TGGTTCTAGTTCCACACCTCG 59.383 52.381 4.94 0.00 0.00 4.63
2783 6922 5.022282 TCGTAGCATCAATGATTCTGGAA 57.978 39.130 5.67 0.00 0.00 3.53
2843 6982 5.821995 TCAACGATTCTGGATATGCATTGAA 59.178 36.000 3.54 0.00 0.00 2.69
2898 7040 4.582656 TCAGTTAAATGGGGCCAATATTCG 59.417 41.667 4.39 0.00 0.00 3.34
3103 7249 7.362660 CCATCATTATCGCTTCCAATGAATGAT 60.363 37.037 0.00 0.00 40.86 2.45
3167 7313 1.826720 GCATGGGGCAGAAATTTGAGA 59.173 47.619 0.00 0.00 43.97 3.27
3420 7566 6.038603 TCAACTCATGCTGAGGTTATATTTGC 59.961 38.462 14.88 0.00 42.87 3.68
3548 7723 7.250569 CCTACGTCGTTCCAACTTTACTATTA 58.749 38.462 1.78 0.00 0.00 0.98
3682 8583 2.097825 AGGCTCAATGCATTCAGGAAC 58.902 47.619 12.58 1.65 45.15 3.62
3907 8821 1.234821 GTTCCGCTGGAATGACACAA 58.765 50.000 12.13 0.00 44.04 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 7.367285 TCAACATTCTATTAAACTGTGGCAAC 58.633 34.615 0.00 0.00 0.00 4.17
90 91 7.517614 TCAACATTCTATTAAACTGTGGCAA 57.482 32.000 0.00 0.00 0.00 4.52
91 92 7.701539 ATCAACATTCTATTAAACTGTGGCA 57.298 32.000 0.00 0.00 0.00 4.92
113 114 9.091255 GCACGAACATTGTTTTGAAATTTTATC 57.909 29.630 13.48 0.00 0.00 1.75
114 115 8.067189 GGCACGAACATTGTTTTGAAATTTTAT 58.933 29.630 13.48 0.00 0.00 1.40
115 116 7.064609 TGGCACGAACATTGTTTTGAAATTTTA 59.935 29.630 13.48 0.00 0.00 1.52
116 117 6.128172 TGGCACGAACATTGTTTTGAAATTTT 60.128 30.769 13.48 0.00 0.00 1.82
117 118 5.352569 TGGCACGAACATTGTTTTGAAATTT 59.647 32.000 13.48 0.00 0.00 1.82
118 119 4.872691 TGGCACGAACATTGTTTTGAAATT 59.127 33.333 13.48 0.00 0.00 1.82
119 120 4.437239 TGGCACGAACATTGTTTTGAAAT 58.563 34.783 13.48 0.00 0.00 2.17
120 121 3.849911 TGGCACGAACATTGTTTTGAAA 58.150 36.364 13.48 1.73 0.00 2.69
121 122 3.510388 TGGCACGAACATTGTTTTGAA 57.490 38.095 13.48 2.00 0.00 2.69
122 123 3.510388 TTGGCACGAACATTGTTTTGA 57.490 38.095 13.48 0.00 0.00 2.69
123 124 3.801050 TCATTGGCACGAACATTGTTTTG 59.199 39.130 3.08 5.72 0.00 2.44
124 125 4.052159 TCATTGGCACGAACATTGTTTT 57.948 36.364 3.08 0.00 0.00 2.43
125 126 3.724508 TCATTGGCACGAACATTGTTT 57.275 38.095 3.08 0.00 0.00 2.83
126 127 3.724508 TTCATTGGCACGAACATTGTT 57.275 38.095 0.63 0.63 0.00 2.83
127 128 3.724508 TTTCATTGGCACGAACATTGT 57.275 38.095 0.00 0.00 0.00 2.71
128 129 6.698107 CATATTTTCATTGGCACGAACATTG 58.302 36.000 0.00 0.00 0.00 2.82
129 130 5.291614 GCATATTTTCATTGGCACGAACATT 59.708 36.000 0.00 0.00 0.00 2.71
130 131 4.805192 GCATATTTTCATTGGCACGAACAT 59.195 37.500 0.00 0.00 0.00 2.71
131 132 4.082300 AGCATATTTTCATTGGCACGAACA 60.082 37.500 0.00 0.00 0.00 3.18
132 133 4.266029 CAGCATATTTTCATTGGCACGAAC 59.734 41.667 0.00 0.00 0.00 3.95
133 134 4.422840 CAGCATATTTTCATTGGCACGAA 58.577 39.130 0.00 0.00 0.00 3.85
134 135 3.734597 GCAGCATATTTTCATTGGCACGA 60.735 43.478 0.00 0.00 0.00 4.35
135 136 2.536803 GCAGCATATTTTCATTGGCACG 59.463 45.455 0.00 0.00 0.00 5.34
136 137 2.867975 GGCAGCATATTTTCATTGGCAC 59.132 45.455 0.00 0.00 0.00 5.01
137 138 2.481622 CGGCAGCATATTTTCATTGGCA 60.482 45.455 0.00 0.00 0.00 4.92
138 139 2.129607 CGGCAGCATATTTTCATTGGC 58.870 47.619 0.00 0.00 0.00 4.52
139 140 3.117794 CACGGCAGCATATTTTCATTGG 58.882 45.455 0.00 0.00 0.00 3.16
140 141 3.772932 ACACGGCAGCATATTTTCATTG 58.227 40.909 0.00 0.00 0.00 2.82
141 142 4.454728 AACACGGCAGCATATTTTCATT 57.545 36.364 0.00 0.00 0.00 2.57
142 143 4.082300 TGAAACACGGCAGCATATTTTCAT 60.082 37.500 0.00 0.00 0.00 2.57
143 144 3.254411 TGAAACACGGCAGCATATTTTCA 59.746 39.130 0.00 1.17 0.00 2.69
144 145 3.832276 TGAAACACGGCAGCATATTTTC 58.168 40.909 0.00 0.00 0.00 2.29
145 146 3.932545 TGAAACACGGCAGCATATTTT 57.067 38.095 0.00 0.00 0.00 1.82
146 147 3.932545 TTGAAACACGGCAGCATATTT 57.067 38.095 0.00 0.00 0.00 1.40
147 148 3.005261 TGTTTGAAACACGGCAGCATATT 59.995 39.130 6.66 0.00 36.25 1.28
148 149 2.556189 TGTTTGAAACACGGCAGCATAT 59.444 40.909 6.66 0.00 36.25 1.78
149 150 1.950216 TGTTTGAAACACGGCAGCATA 59.050 42.857 6.66 0.00 36.25 3.14
150 151 0.743688 TGTTTGAAACACGGCAGCAT 59.256 45.000 6.66 0.00 36.25 3.79
151 152 0.528017 TTGTTTGAAACACGGCAGCA 59.472 45.000 10.72 0.00 41.97 4.41
152 153 1.634702 TTTGTTTGAAACACGGCAGC 58.365 45.000 10.72 0.00 41.97 5.25
153 154 3.186119 ACATTTGTTTGAAACACGGCAG 58.814 40.909 10.72 2.40 41.97 4.85
154 155 3.238108 ACATTTGTTTGAAACACGGCA 57.762 38.095 10.72 0.00 41.97 5.69
155 156 4.375908 GCATACATTTGTTTGAAACACGGC 60.376 41.667 10.72 3.58 41.97 5.68
156 157 4.742167 TGCATACATTTGTTTGAAACACGG 59.258 37.500 10.72 5.82 41.97 4.94
157 158 5.230936 TGTGCATACATTTGTTTGAAACACG 59.769 36.000 10.72 5.12 41.97 4.49
158 159 6.580963 TGTGCATACATTTGTTTGAAACAC 57.419 33.333 10.72 0.00 41.97 3.32
159 160 7.601073 TTTGTGCATACATTTGTTTGAAACA 57.399 28.000 6.66 6.66 36.74 2.83
160 161 9.157259 GAATTTGTGCATACATTTGTTTGAAAC 57.843 29.630 0.14 0.14 36.53 2.78
161 162 8.886719 TGAATTTGTGCATACATTTGTTTGAAA 58.113 25.926 5.48 0.00 36.53 2.69
162 163 8.429493 TGAATTTGTGCATACATTTGTTTGAA 57.571 26.923 5.48 0.00 36.53 2.69
163 164 8.429493 TTGAATTTGTGCATACATTTGTTTGA 57.571 26.923 5.48 0.00 36.53 2.69
164 165 9.499585 TTTTGAATTTGTGCATACATTTGTTTG 57.500 25.926 0.00 0.00 36.53 2.93
251 252 9.291664 CGTGTGGAAAAACTTGACTATTTTAAA 57.708 29.630 0.00 0.00 0.00 1.52
252 253 8.675504 TCGTGTGGAAAAACTTGACTATTTTAA 58.324 29.630 0.00 0.00 0.00 1.52
253 254 8.211116 TCGTGTGGAAAAACTTGACTATTTTA 57.789 30.769 0.00 0.00 0.00 1.52
254 255 7.090953 TCGTGTGGAAAAACTTGACTATTTT 57.909 32.000 0.00 0.00 0.00 1.82
255 256 6.687081 TCGTGTGGAAAAACTTGACTATTT 57.313 33.333 0.00 0.00 0.00 1.40
256 257 6.687081 TTCGTGTGGAAAAACTTGACTATT 57.313 33.333 0.00 0.00 0.00 1.73
257 258 6.687081 TTTCGTGTGGAAAAACTTGACTAT 57.313 33.333 0.00 0.00 41.55 2.12
441 450 2.851263 AAATTCTGGCACACGTAGGA 57.149 45.000 0.00 0.00 0.00 2.94
465 475 6.183361 ACACCATATACATTAGAGCACACCAT 60.183 38.462 0.00 0.00 0.00 3.55
504 514 8.049592 CGTTTTATTTTGTTCAACACATGTCTG 58.950 33.333 0.00 0.00 34.43 3.51
567 577 8.932945 ATGGTTTTCTTTGTTTCTCTCTTTTC 57.067 30.769 0.00 0.00 0.00 2.29
594 607 9.233649 TCTTTGGTTTCTTTCTTTGTTACACTA 57.766 29.630 0.00 0.00 0.00 2.74
595 608 8.117813 TCTTTGGTTTCTTTCTTTGTTACACT 57.882 30.769 0.00 0.00 0.00 3.55
596 609 8.751302 TTCTTTGGTTTCTTTCTTTGTTACAC 57.249 30.769 0.00 0.00 0.00 2.90
597 610 9.936759 ATTTCTTTGGTTTCTTTCTTTGTTACA 57.063 25.926 0.00 0.00 0.00 2.41
600 613 9.671279 ATGATTTCTTTGGTTTCTTTCTTTGTT 57.329 25.926 0.00 0.00 0.00 2.83
626 642 7.227049 ACTCTGGTTTTCTTTGTTTTCTTGA 57.773 32.000 0.00 0.00 0.00 3.02
627 643 8.980143 TTACTCTGGTTTTCTTTGTTTTCTTG 57.020 30.769 0.00 0.00 0.00 3.02
737 758 1.399440 CTCGCTGTACGCTGTAGGTTA 59.601 52.381 7.82 0.00 43.23 2.85
1179 2836 4.451150 GTCGTGGATGCGGCAGGA 62.451 66.667 9.25 0.00 36.38 3.86
1181 2838 3.190849 CAGTCGTGGATGCGGCAG 61.191 66.667 9.25 0.00 39.17 4.85
1200 2857 2.754658 GCGGGAGAGGACGAGGAA 60.755 66.667 0.00 0.00 0.00 3.36
1219 2876 1.379977 TCGAGGATCTCAACGGCCT 60.380 57.895 0.00 0.00 0.00 5.19
1317 2989 3.925090 CCGGGGTAGCATCGGGAC 61.925 72.222 15.32 0.00 40.07 4.46
1491 3169 1.632018 TTAGGCCCCTGAATCACCCG 61.632 60.000 0.00 0.00 0.00 5.28
1517 3195 1.839994 AGCGAATGAAGATGGAGGGAA 59.160 47.619 0.00 0.00 0.00 3.97
1519 3197 1.945394 CAAGCGAATGAAGATGGAGGG 59.055 52.381 0.00 0.00 0.00 4.30
1527 3205 4.275196 ACCATGATCATCAAGCGAATGAAG 59.725 41.667 4.86 0.00 32.06 3.02
1531 3209 3.317149 CCAACCATGATCATCAAGCGAAT 59.683 43.478 4.86 0.00 0.00 3.34
1556 3234 1.684391 TCGCGGAAGATCCCCAAGA 60.684 57.895 6.13 0.00 31.13 3.02
1601 3279 3.278367 TCGCGATTCCCTAAATAGTCG 57.722 47.619 3.71 0.00 0.00 4.18
1614 3292 5.355350 AGAGAAATTTGGAGAAATCGCGATT 59.645 36.000 27.94 27.94 30.02 3.34
1616 3294 4.253685 AGAGAAATTTGGAGAAATCGCGA 58.746 39.130 13.09 13.09 30.02 5.87
1651 3329 3.257127 AGATATCTGAAGCTCGGTAAGGC 59.743 47.826 3.89 0.00 0.00 4.35
1694 3372 1.275421 AAGGGGTAAGCAGAGAGGGC 61.275 60.000 0.00 0.00 0.00 5.19
1704 3382 7.718334 AATTTCAATGGTAAGAAGGGGTAAG 57.282 36.000 0.00 0.00 0.00 2.34
1735 3413 6.543831 GTCCTTTAATTATGTCCATGAGTGCT 59.456 38.462 0.00 0.00 0.00 4.40
1744 3422 9.216117 AGTTATATGCGTCCTTTAATTATGTCC 57.784 33.333 0.00 0.00 0.00 4.02
1800 3478 6.038382 TCCCTCGCGTATATAAATTGCAAAAA 59.962 34.615 5.77 0.00 0.00 1.94
1801 3479 5.527951 TCCCTCGCGTATATAAATTGCAAAA 59.472 36.000 5.77 0.00 0.00 2.44
1802 3480 5.057819 TCCCTCGCGTATATAAATTGCAAA 58.942 37.500 5.77 0.00 0.00 3.68
1803 3481 4.633175 TCCCTCGCGTATATAAATTGCAA 58.367 39.130 5.77 0.00 0.00 4.08
1804 3482 4.260139 TCCCTCGCGTATATAAATTGCA 57.740 40.909 5.77 0.00 0.00 4.08
1805 3483 4.630069 ACATCCCTCGCGTATATAAATTGC 59.370 41.667 5.77 0.00 0.00 3.56
1964 3642 3.544684 TGAATCCCGAACATTCAGGATG 58.455 45.455 9.64 0.00 42.25 3.51
2135 3813 3.557595 CGATTGTCCCTAGCTGATCAAAC 59.442 47.826 0.00 0.00 0.00 2.93
2250 3928 3.253188 TCTGTGGCTAATGCAAAGAACAC 59.747 43.478 14.98 14.98 41.91 3.32
2546 6668 3.391382 AAGCCGGTCCGCTAAGCT 61.391 61.111 5.50 6.33 38.44 3.74
2666 6805 2.183679 GAGAAGGGGAAAGAGCAGAGA 58.816 52.381 0.00 0.00 0.00 3.10
2732 6871 4.689549 TTCCCTGCGTCTCCCCGA 62.690 66.667 0.00 0.00 0.00 5.14
2734 6873 3.003763 ACTTCCCTGCGTCTCCCC 61.004 66.667 0.00 0.00 0.00 4.81
2783 6922 7.491048 ACAGTCAAAAATTAAACTCAACGCATT 59.509 29.630 0.00 0.00 0.00 3.56
2817 6956 6.487668 TCAATGCATATCCAGAATCGTTGAAT 59.512 34.615 0.00 0.00 0.00 2.57
2898 7040 1.277557 AGGTGCATGGAAGTGTCTCTC 59.722 52.381 0.00 0.00 0.00 3.20
3079 7225 7.698506 ATCATTCATTGGAAGCGATAATGAT 57.301 32.000 0.00 0.00 39.67 2.45
3087 7233 6.324819 AGTAAACAATCATTCATTGGAAGCG 58.675 36.000 0.00 0.00 45.70 4.68
3167 7313 5.754890 GTGCATTTTGAAACTCTCCATTTGT 59.245 36.000 0.00 0.00 0.00 2.83
3682 8583 3.624326 TGAAACACGAGCATGGAAAAG 57.376 42.857 0.00 0.00 0.00 2.27
3858 8766 0.326238 ATTTCCAGGCTCCGAGGGTA 60.326 55.000 0.00 0.00 0.00 3.69
3907 8821 3.136641 ACCTTGGTCATGGGAGAGTAT 57.863 47.619 7.63 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.