Multiple sequence alignment - TraesCS2A01G180600

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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 TraesCS2A01G180600 chr2A 100.000 6244 0 0 1 6244 139517430 139523673 0.000000e+00 11531.0
1 TraesCS2A01G180600 chr2A 90.404 792 63 6 5459 6243 156136120 156135335 0.000000e+00 1029.0
2 TraesCS2A01G180600 chr2D 94.086 5309 202 38 1 5268 81660301 81655064 0.000000e+00 7962.0
3 TraesCS2A01G180600 chr2D 93.177 982 60 4 5268 6243 81572542 81571562 0.000000e+00 1435.0
4 TraesCS2A01G180600 chr2D 91.103 798 60 7 5454 6243 643249252 643250046 0.000000e+00 1070.0
5 TraesCS2A01G180600 chr2D 98.182 55 1 0 194 248 81660174 81660120 5.150000e-16 97.1
6 TraesCS2A01G180600 chr2B 89.313 3144 276 34 1107 4222 155176905 155173794 0.000000e+00 3890.0
7 TraesCS2A01G180600 chr2B 89.977 888 78 7 194 1075 155177780 155176898 0.000000e+00 1136.0
8 TraesCS2A01G180600 chr2B 91.905 803 55 6 4659 5455 155159306 155158508 0.000000e+00 1114.0
9 TraesCS2A01G180600 chr2B 92.896 183 8 4 1 179 155177907 155177726 1.730000e-65 261.0
10 TraesCS2A01G180600 chr5A 81.433 3000 380 93 1104 4029 87430506 87427610 0.000000e+00 2290.0
11 TraesCS2A01G180600 chr5A 84.952 1874 208 40 1104 2944 87896254 87894422 0.000000e+00 1831.0
12 TraesCS2A01G180600 chr5A 82.945 1630 169 58 2992 4561 87894341 87892761 0.000000e+00 1369.0
13 TraesCS2A01G180600 chr5A 85.775 942 105 15 194 1131 87897275 87896359 0.000000e+00 970.0
14 TraesCS2A01G180600 chr5A 89.414 529 54 2 4792 5319 87427073 87426546 0.000000e+00 665.0
15 TraesCS2A01G180600 chr5A 86.713 572 57 9 4717 5280 87891725 87891165 8.890000e-173 617.0
16 TraesCS2A01G180600 chr5A 89.373 367 35 3 772 1136 87430935 87430571 5.700000e-125 459.0
17 TraesCS2A01G180600 chr5A 84.451 328 34 9 4068 4379 87427529 87427203 2.190000e-79 307.0
18 TraesCS2A01G180600 chr5A 84.118 170 21 6 1 167 87431591 87431425 6.480000e-35 159.0
19 TraesCS2A01G180600 chr5A 84.146 164 17 5 19 179 87897378 87897221 3.900000e-32 150.0
20 TraesCS2A01G180600 chr5A 82.979 94 16 0 2959 3052 669450173 669450266 1.120000e-12 86.1
21 TraesCS2A01G180600 chr5B 80.807 2777 391 64 1319 4029 101155129 101152429 0.000000e+00 2045.0
22 TraesCS2A01G180600 chr5B 78.646 1536 219 50 3056 4521 364797333 364795837 0.000000e+00 918.0
23 TraesCS2A01G180600 chr5B 78.699 1460 234 50 1191 2619 364799009 364797596 0.000000e+00 902.0
24 TraesCS2A01G180600 chr5B 88.142 565 58 6 4796 5352 101151759 101151196 0.000000e+00 664.0
25 TraesCS2A01G180600 chr5B 83.381 698 100 12 4717 5405 364795777 364795087 3.180000e-177 632.0
26 TraesCS2A01G180600 chr5B 82.489 691 95 11 437 1122 364799760 364799091 3.240000e-162 582.0
27 TraesCS2A01G180600 chr5B 85.316 538 69 9 194 730 101230297 101229769 1.180000e-151 547.0
28 TraesCS2A01G180600 chr5B 87.432 366 43 2 772 1136 101229768 101229405 9.680000e-113 418.0
29 TraesCS2A01G180600 chr5B 87.558 217 17 6 4167 4373 101152114 101151898 6.250000e-60 243.0
30 TraesCS2A01G180600 chr5B 83.408 223 19 11 1104 1316 101229298 101229084 2.300000e-44 191.0
31 TraesCS2A01G180600 chr5D 80.693 2626 352 74 1104 3654 93990280 93987735 0.000000e+00 1897.0
32 TraesCS2A01G180600 chr5D 90.759 790 66 4 5460 6243 545231575 545232363 0.000000e+00 1048.0
33 TraesCS2A01G180600 chr5D 84.972 539 67 12 194 730 93991246 93990720 9.210000e-148 534.0
34 TraesCS2A01G180600 chr5D 89.344 366 36 2 772 1136 93990719 93990356 2.050000e-124 457.0
35 TraesCS2A01G180600 chr5D 84.746 177 20 6 1 173 93991372 93991199 2.990000e-38 171.0
36 TraesCS2A01G180600 chr5D 84.694 98 10 4 2959 3055 297053659 297053752 6.660000e-15 93.5
37 TraesCS2A01G180600 chr1D 91.266 790 63 3 5460 6243 420371421 420370632 0.000000e+00 1072.0
38 TraesCS2A01G180600 chr1D 90.278 792 63 8 5460 6241 49886074 49885287 0.000000e+00 1024.0
39 TraesCS2A01G180600 chr7D 90.668 793 62 5 5459 6243 554965861 554965073 0.000000e+00 1044.0
40 TraesCS2A01G180600 chr7D 90.339 797 63 8 5459 6244 236814253 236813460 0.000000e+00 1033.0
41 TraesCS2A01G180600 chr6B 90.253 790 69 4 5460 6242 55093050 55092262 0.000000e+00 1026.0
42 TraesCS2A01G180600 chr6B 100.000 29 0 0 3012 3040 385586392 385586420 3.000000e-03 54.7
43 TraesCS2A01G180600 chr4D 97.500 40 1 0 2668 2707 84600829 84600868 1.120000e-07 69.4


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 TraesCS2A01G180600 chr2A 139517430 139523673 6243 False 11531.000000 11531 100.000000 1 6244 1 chr2A.!!$F1 6243
1 TraesCS2A01G180600 chr2A 156135335 156136120 785 True 1029.000000 1029 90.404000 5459 6243 1 chr2A.!!$R1 784
2 TraesCS2A01G180600 chr2D 81655064 81660301 5237 True 4029.550000 7962 96.134000 1 5268 2 chr2D.!!$R2 5267
3 TraesCS2A01G180600 chr2D 81571562 81572542 980 True 1435.000000 1435 93.177000 5268 6243 1 chr2D.!!$R1 975
4 TraesCS2A01G180600 chr2D 643249252 643250046 794 False 1070.000000 1070 91.103000 5454 6243 1 chr2D.!!$F1 789
5 TraesCS2A01G180600 chr2B 155173794 155177907 4113 True 1762.333333 3890 90.728667 1 4222 3 chr2B.!!$R2 4221
6 TraesCS2A01G180600 chr2B 155158508 155159306 798 True 1114.000000 1114 91.905000 4659 5455 1 chr2B.!!$R1 796
7 TraesCS2A01G180600 chr5A 87891165 87897378 6213 True 987.400000 1831 84.906200 19 5280 5 chr5A.!!$R2 5261
8 TraesCS2A01G180600 chr5A 87426546 87431591 5045 True 776.000000 2290 85.757800 1 5319 5 chr5A.!!$R1 5318
9 TraesCS2A01G180600 chr5B 101151196 101155129 3933 True 984.000000 2045 85.502333 1319 5352 3 chr5B.!!$R1 4033
10 TraesCS2A01G180600 chr5B 364795087 364799760 4673 True 758.500000 918 80.803750 437 5405 4 chr5B.!!$R3 4968
11 TraesCS2A01G180600 chr5B 101229084 101230297 1213 True 385.333333 547 85.385333 194 1316 3 chr5B.!!$R2 1122
12 TraesCS2A01G180600 chr5D 545231575 545232363 788 False 1048.000000 1048 90.759000 5460 6243 1 chr5D.!!$F2 783
13 TraesCS2A01G180600 chr5D 93987735 93991372 3637 True 764.750000 1897 84.938750 1 3654 4 chr5D.!!$R1 3653
14 TraesCS2A01G180600 chr1D 420370632 420371421 789 True 1072.000000 1072 91.266000 5460 6243 1 chr1D.!!$R2 783
15 TraesCS2A01G180600 chr1D 49885287 49886074 787 True 1024.000000 1024 90.278000 5460 6241 1 chr1D.!!$R1 781
16 TraesCS2A01G180600 chr7D 554965073 554965861 788 True 1044.000000 1044 90.668000 5459 6243 1 chr7D.!!$R2 784
17 TraesCS2A01G180600 chr7D 236813460 236814253 793 True 1033.000000 1033 90.339000 5459 6244 1 chr7D.!!$R1 785
18 TraesCS2A01G180600 chr6B 55092262 55093050 788 True 1026.000000 1026 90.253000 5460 6242 1 chr6B.!!$R1 782

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
906 971 0.179032 AGTGCGGTGATGTCCAACAA 60.179 50.000 0.00 0.0 31.20 2.83 F
919 984 2.297033 GTCCAACAAATGTCATGCCACT 59.703 45.455 0.00 0.0 0.00 4.00 F
1761 2006 0.742635 TTATTCCACGCGCTGCATCA 60.743 50.000 5.73 0.0 0.00 3.07 F
2936 3219 3.640967 AGTCCTTATGCTCAGTCTCATCC 59.359 47.826 0.00 0.0 0.00 3.51 F
3962 4320 2.125350 GCTGTTGCTCCTCCCTCG 60.125 66.667 0.00 0.0 36.03 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1986 0.588252 GATGCAGCGCGTGGAATAAT 59.412 50.000 8.43 0.0 0.00 1.28 R
2298 2558 3.753272 CCGCATGAAGTAAATCATAGGGG 59.247 47.826 0.00 0.0 37.96 4.79 R
3039 3354 2.420705 ACTACTACTCCCTCCGATCCT 58.579 52.381 0.00 0.0 0.00 3.24 R
4591 6220 2.491693 CCGCTCCATGTTAAATGTGGTT 59.508 45.455 0.00 0.0 34.61 3.67 R
5581 7261 0.032017 ACGTGGAGCCCCTTCTATCT 60.032 55.000 0.00 0.0 0.00 1.98 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
126 129 1.341383 CCAATTGGTTCCTAGGCTGCT 60.341 52.381 16.90 0.00 0.00 4.24
127 130 2.092429 CCAATTGGTTCCTAGGCTGCTA 60.092 50.000 16.90 0.00 0.00 3.49
128 131 3.435601 CCAATTGGTTCCTAGGCTGCTAT 60.436 47.826 16.90 0.00 0.00 2.97
129 132 4.202461 CCAATTGGTTCCTAGGCTGCTATA 60.202 45.833 16.90 0.00 0.00 1.31
130 133 5.515534 CCAATTGGTTCCTAGGCTGCTATAT 60.516 44.000 16.90 0.00 0.00 0.86
131 134 4.623932 TTGGTTCCTAGGCTGCTATATG 57.376 45.455 2.96 0.00 0.00 1.78
132 135 2.303022 TGGTTCCTAGGCTGCTATATGC 59.697 50.000 2.96 0.00 43.25 3.14
155 158 9.887629 ATGCATCTAATGAAGTGATATCTTAGG 57.112 33.333 3.98 0.00 0.00 2.69
156 159 9.093458 TGCATCTAATGAAGTGATATCTTAGGA 57.907 33.333 3.98 0.00 0.00 2.94
160 163 9.093458 TCTAATGAAGTGATATCTTAGGATGCA 57.907 33.333 3.98 0.00 33.71 3.96
161 164 9.716531 CTAATGAAGTGATATCTTAGGATGCAA 57.283 33.333 3.98 0.00 33.71 4.08
162 165 8.985315 AATGAAGTGATATCTTAGGATGCAAA 57.015 30.769 3.98 0.00 33.71 3.68
163 166 8.985315 ATGAAGTGATATCTTAGGATGCAAAA 57.015 30.769 3.98 0.00 33.71 2.44
164 167 8.806429 TGAAGTGATATCTTAGGATGCAAAAA 57.194 30.769 3.98 0.00 33.71 1.94
187 190 8.537728 AAAAATATCAACATGGCATCTAAGGA 57.462 30.769 0.00 0.00 0.00 3.36
188 191 8.537728 AAAATATCAACATGGCATCTAAGGAA 57.462 30.769 0.00 0.00 0.00 3.36
189 192 7.756395 AATATCAACATGGCATCTAAGGAAG 57.244 36.000 0.00 0.00 0.00 3.46
190 193 4.574674 TCAACATGGCATCTAAGGAAGT 57.425 40.909 0.00 0.00 0.00 3.01
191 194 4.264253 TCAACATGGCATCTAAGGAAGTG 58.736 43.478 0.00 0.00 0.00 3.16
192 195 4.019411 TCAACATGGCATCTAAGGAAGTGA 60.019 41.667 0.00 0.00 0.00 3.41
272 325 6.788598 ACCATCATGCAAACCATTAATGTA 57.211 33.333 14.25 0.00 29.71 2.29
434 487 6.569127 AAATATGGTGGTGGACATAGTGTA 57.431 37.500 0.00 0.00 33.50 2.90
435 488 3.906720 ATGGTGGTGGACATAGTGTAC 57.093 47.619 0.00 0.00 0.00 2.90
455 508 7.331934 AGTGTACAAGTGTGCATATCTTTGTAG 59.668 37.037 14.09 2.34 42.31 2.74
542 596 8.359642 CAATCTTACCAAAAGTTCTTCCAATCA 58.640 33.333 0.00 0.00 0.00 2.57
544 598 7.885297 TCTTACCAAAAGTTCTTCCAATCATG 58.115 34.615 0.00 0.00 0.00 3.07
665 728 4.498682 GCTTGACAAGTGTTTTGCATCTCT 60.499 41.667 16.39 0.00 0.00 3.10
754 818 9.917118 TGGGTTTATAGAGGGGAAATATTAGTA 57.083 33.333 0.00 0.00 0.00 1.82
891 956 2.783135 TGACAATTGGGAAGAGAGTGC 58.217 47.619 10.83 0.00 0.00 4.40
906 971 0.179032 AGTGCGGTGATGTCCAACAA 60.179 50.000 0.00 0.00 31.20 2.83
919 984 2.297033 GTCCAACAAATGTCATGCCACT 59.703 45.455 0.00 0.00 0.00 4.00
944 1009 4.877378 ATCCAACCAACACGTAGTCTAA 57.123 40.909 0.00 0.00 41.61 2.10
982 1054 5.480422 CCCCTTTATAAAAGCAGGTCAAACT 59.520 40.000 0.00 0.00 0.00 2.66
1010 1083 7.713734 ATTCTTCTCATCAAATGTGGATTGT 57.286 32.000 0.00 0.00 0.00 2.71
1060 1133 7.489239 CCCCCTTGATTTCTTATTTAACCAA 57.511 36.000 0.00 0.00 0.00 3.67
1168 1388 4.314121 TCGAAATTGCCTCCCAAATTTTG 58.686 39.130 1.99 1.99 36.92 2.44
1169 1389 4.039730 TCGAAATTGCCTCCCAAATTTTGA 59.960 37.500 10.72 6.68 36.92 2.69
1170 1390 4.937015 CGAAATTGCCTCCCAAATTTTGAT 59.063 37.500 10.72 0.00 36.92 2.57
1173 1393 7.254522 CGAAATTGCCTCCCAAATTTTGATATG 60.255 37.037 10.72 0.00 36.92 1.78
1174 1394 4.405116 TGCCTCCCAAATTTTGATATGC 57.595 40.909 10.72 8.29 0.00 3.14
1176 1396 4.470664 TGCCTCCCAAATTTTGATATGCTT 59.529 37.500 10.72 0.00 0.00 3.91
1177 1397 5.045724 TGCCTCCCAAATTTTGATATGCTTT 60.046 36.000 10.72 0.00 0.00 3.51
1178 1398 5.882000 GCCTCCCAAATTTTGATATGCTTTT 59.118 36.000 10.72 0.00 0.00 2.27
1179 1399 6.375174 GCCTCCCAAATTTTGATATGCTTTTT 59.625 34.615 10.72 0.00 0.00 1.94
1460 1695 4.646492 AGCATATTCCCTCCATGTGTTTTC 59.354 41.667 0.00 0.00 0.00 2.29
1491 1726 7.905265 AGGAGTTACTACTTTCTAAAAGGGAC 58.095 38.462 0.00 0.00 33.84 4.46
1741 1986 3.452627 ACCAAATTTTGTGGGTGCACTTA 59.547 39.130 17.98 2.89 40.75 2.24
1761 2006 0.742635 TTATTCCACGCGCTGCATCA 60.743 50.000 5.73 0.00 0.00 3.07
1860 2116 4.645588 CAGTTGTTACTAAAAACCACCCCA 59.354 41.667 0.00 0.00 31.96 4.96
1890 2146 8.193438 CACCTAAACTACCTTATGTGTACTACC 58.807 40.741 0.00 0.00 0.00 3.18
1955 2211 5.806818 TGGAAGTATAGATACCTCGAGGAG 58.193 45.833 37.69 13.04 38.94 3.69
1977 2233 7.041167 AGGAGCAAAAGTTGAATAAAAATTGCC 60.041 33.333 0.00 0.00 0.00 4.52
2102 2361 4.210331 AGTCATCTTTGTTGGAAGCTTGT 58.790 39.130 2.10 0.00 0.00 3.16
2356 2616 8.691661 TTAGCTCATTTCTTCAAAAGTAGGTT 57.308 30.769 0.00 0.00 0.00 3.50
2358 2618 8.691661 AGCTCATTTCTTCAAAAGTAGGTTAA 57.308 30.769 0.00 0.00 0.00 2.01
2609 2877 3.802948 TCTGTTCCGAGCCTCTTTATC 57.197 47.619 0.00 0.00 0.00 1.75
2700 2977 4.948341 TCAATTAATTCGGATCGGAGGA 57.052 40.909 0.00 0.00 0.00 3.71
2928 3211 7.913674 AAAACTTAGAAGTCCTTATGCTCAG 57.086 36.000 0.00 0.00 38.57 3.35
2936 3219 3.640967 AGTCCTTATGCTCAGTCTCATCC 59.359 47.826 0.00 0.00 0.00 3.51
3266 3599 6.291377 ACATTTGACTCACTGTGATACTGTT 58.709 36.000 11.45 0.00 0.00 3.16
3887 4244 3.243267 ACAACAAATCAACGGGCTGTTAC 60.243 43.478 12.12 0.00 39.29 2.50
3962 4320 2.125350 GCTGTTGCTCCTCCCTCG 60.125 66.667 0.00 0.00 36.03 4.63
4507 5196 3.064207 GACTCGTGTATGCTTGGACAAA 58.936 45.455 0.00 0.00 0.00 2.83
4509 5198 3.880490 ACTCGTGTATGCTTGGACAAAAA 59.120 39.130 0.00 0.00 0.00 1.94
4591 6220 8.084073 AGTACGTTATGAAGTTGTACTAAAGCA 58.916 33.333 0.00 0.00 42.73 3.91
4637 6266 9.095700 GGAGGGAGTATCTTCTTTAGTGAATAT 57.904 37.037 0.00 0.00 33.73 1.28
4748 6377 6.018433 ACTATGTAATTCCTTTCTGCCCAT 57.982 37.500 0.00 0.00 0.00 4.00
4874 6549 5.389859 TTCGTAACTCGTAGGATCCAAAA 57.610 39.130 15.82 0.00 40.80 2.44
4928 6603 2.419673 GCATAAACCTGCATTTTTGGGC 59.580 45.455 5.69 4.62 41.87 5.36
5337 7015 9.803315 GAGTAATTACACACATCTCTCATGTTA 57.197 33.333 17.65 0.00 0.00 2.41
5447 7127 5.763698 AGGTAAACAAAGTAGGAGAAAGCAC 59.236 40.000 0.00 0.00 0.00 4.40
5467 7147 3.541130 CACATGCGTTCGTACACTAGTAC 59.459 47.826 0.00 0.00 45.67 2.73
5549 7229 1.300963 GGGTCGGGACTAAAACCCC 59.699 63.158 0.00 0.00 44.75 4.95
5563 7243 3.985553 AAACCCCAAACCTTTAGTCCT 57.014 42.857 0.00 0.00 0.00 3.85
5679 7359 0.810648 GATCAAAAGGCATCCACGCA 59.189 50.000 0.00 0.00 0.00 5.24
5708 7388 2.627699 CTGGCAGAAGCAAGGGTTTTTA 59.372 45.455 9.42 0.00 44.61 1.52
5808 7506 5.123227 AGAGAAGTGACCTCTCTTATCTCG 58.877 45.833 7.89 0.00 41.37 4.04
5819 7517 2.428890 CTCTTATCTCGGTGCTTGGTCT 59.571 50.000 0.00 0.00 0.00 3.85
5833 7531 3.303924 GCTTGGTCTACGCTAGCTACTAC 60.304 52.174 13.93 5.92 0.00 2.73
5861 7559 1.733360 GAGAGAACTCGACACGCTAGT 59.267 52.381 0.00 0.00 33.32 2.57
5980 7682 8.814235 ACAACAAGTTTTCGTATATCTATTCGG 58.186 33.333 0.00 0.00 0.00 4.30
5987 7689 3.000623 TCGTATATCTATTCGGCGCTACG 59.999 47.826 7.64 9.76 33.83 3.51
6032 7734 6.051717 AGATCTCTTACAATCCCAAACATCG 58.948 40.000 0.00 0.00 0.00 3.84
6045 7753 4.022416 CCCAAACATCGAAGGTCAATTTCA 60.022 41.667 0.00 0.00 0.00 2.69
6051 7759 5.473162 ACATCGAAGGTCAATTTCAACATGA 59.527 36.000 0.00 0.00 0.00 3.07
6141 7850 2.732366 CGATCATGTGGTAGGAGTTCG 58.268 52.381 0.00 0.00 0.00 3.95
6154 7863 1.078759 GAGTTCGTCCCGCATCTGTG 61.079 60.000 0.00 0.00 0.00 3.66
6196 7905 8.000171 AGGGGGTCAATACATGTATATGAATT 58.000 34.615 18.56 1.06 37.73 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 75 9.706691 ATACTACTGTCCAATATACATTTTCCG 57.293 33.333 0.00 0.00 0.00 4.30
88 91 4.445452 TTGGACGACAATACTACTGTCC 57.555 45.455 2.34 2.34 44.75 4.02
101 104 2.629051 CCTAGGAACCAATTGGACGAC 58.371 52.381 31.22 16.54 38.94 4.34
129 132 9.887629 CCTAAGATATCACTTCATTAGATGCAT 57.112 33.333 0.00 0.00 0.00 3.96
130 133 9.093458 TCCTAAGATATCACTTCATTAGATGCA 57.907 33.333 5.32 0.00 0.00 3.96
134 137 9.093458 TGCATCCTAAGATATCACTTCATTAGA 57.907 33.333 5.32 0.00 0.00 2.10
135 138 9.716531 TTGCATCCTAAGATATCACTTCATTAG 57.283 33.333 5.32 3.22 0.00 1.73
137 140 8.985315 TTTGCATCCTAAGATATCACTTCATT 57.015 30.769 5.32 0.00 0.00 2.57
138 141 8.985315 TTTTGCATCCTAAGATATCACTTCAT 57.015 30.769 5.32 0.00 0.00 2.57
139 142 8.806429 TTTTTGCATCCTAAGATATCACTTCA 57.194 30.769 5.32 0.00 0.00 3.02
162 165 8.537728 TCCTTAGATGCCATGTTGATATTTTT 57.462 30.769 0.00 0.00 0.00 1.94
163 166 8.537728 TTCCTTAGATGCCATGTTGATATTTT 57.462 30.769 0.00 0.00 0.00 1.82
164 167 7.781693 ACTTCCTTAGATGCCATGTTGATATTT 59.218 33.333 0.00 0.00 0.00 1.40
165 168 7.230108 CACTTCCTTAGATGCCATGTTGATATT 59.770 37.037 0.00 0.00 0.00 1.28
166 169 6.713903 CACTTCCTTAGATGCCATGTTGATAT 59.286 38.462 0.00 0.00 0.00 1.63
167 170 6.057533 CACTTCCTTAGATGCCATGTTGATA 58.942 40.000 0.00 0.00 0.00 2.15
168 171 4.885907 CACTTCCTTAGATGCCATGTTGAT 59.114 41.667 0.00 0.00 0.00 2.57
169 172 4.019411 TCACTTCCTTAGATGCCATGTTGA 60.019 41.667 0.00 0.00 0.00 3.18
170 173 4.264253 TCACTTCCTTAGATGCCATGTTG 58.736 43.478 0.00 0.00 0.00 3.33
171 174 4.574674 TCACTTCCTTAGATGCCATGTT 57.425 40.909 0.00 0.00 0.00 2.71
172 175 4.785346 ATCACTTCCTTAGATGCCATGT 57.215 40.909 0.00 0.00 0.00 3.21
173 176 7.012138 GCATATATCACTTCCTTAGATGCCATG 59.988 40.741 0.00 0.00 35.54 3.66
174 177 7.052873 GCATATATCACTTCCTTAGATGCCAT 58.947 38.462 0.00 0.00 35.54 4.40
175 178 6.013466 TGCATATATCACTTCCTTAGATGCCA 60.013 38.462 6.38 0.00 38.92 4.92
176 179 6.409704 TGCATATATCACTTCCTTAGATGCC 58.590 40.000 6.38 0.00 38.92 4.40
177 180 7.986320 AGATGCATATATCACTTCCTTAGATGC 59.014 37.037 0.00 0.00 39.69 3.91
181 184 9.814899 CCTTAGATGCATATATCACTTCCTTAG 57.185 37.037 0.00 0.00 0.00 2.18
182 185 9.547279 TCCTTAGATGCATATATCACTTCCTTA 57.453 33.333 0.00 0.00 0.00 2.69
183 186 8.441311 TCCTTAGATGCATATATCACTTCCTT 57.559 34.615 0.00 0.00 0.00 3.36
184 187 8.441311 TTCCTTAGATGCATATATCACTTCCT 57.559 34.615 0.00 0.00 0.00 3.36
185 188 8.317679 ACTTCCTTAGATGCATATATCACTTCC 58.682 37.037 0.00 0.00 0.00 3.46
186 189 9.149225 CACTTCCTTAGATGCATATATCACTTC 57.851 37.037 0.00 0.00 0.00 3.01
187 190 8.874156 TCACTTCCTTAGATGCATATATCACTT 58.126 33.333 0.00 0.00 0.00 3.16
188 191 8.427902 TCACTTCCTTAGATGCATATATCACT 57.572 34.615 0.00 0.00 0.00 3.41
375 428 4.703093 AGGAAATTTACCACATAACACCCG 59.297 41.667 0.00 0.00 0.00 5.28
434 487 5.412594 CCACTACAAAGATATGCACACTTGT 59.587 40.000 0.00 0.00 0.00 3.16
435 488 5.412594 ACCACTACAAAGATATGCACACTTG 59.587 40.000 0.00 0.00 0.00 3.16
471 524 8.039603 TGTCTTACAAATTTCAGCGATTACAT 57.960 30.769 0.00 0.00 0.00 2.29
696 759 7.337942 AGACATTTATTCCTCTAGCCAAGTTTG 59.662 37.037 0.00 0.00 0.00 2.93
754 818 5.185249 AGTGATCAAACACGTAGTCTACCAT 59.815 40.000 0.00 0.00 41.61 3.55
891 956 2.551887 TGACATTTGTTGGACATCACCG 59.448 45.455 0.00 0.00 0.00 4.94
906 971 2.779430 TGGATAGGAGTGGCATGACATT 59.221 45.455 3.50 0.00 0.00 2.71
919 984 3.167485 ACTACGTGTTGGTTGGATAGGA 58.833 45.455 0.00 0.00 0.00 2.94
944 1009 1.718280 AAGGGGAAAGAGTCGTGAGT 58.282 50.000 0.00 0.00 0.00 3.41
982 1054 9.690913 AATCCACATTTGATGAGAAGAATAGAA 57.309 29.630 0.00 0.00 0.00 2.10
1010 1083 8.639761 GGCTAGTAATCATACCTGAAGTTCTTA 58.360 37.037 4.17 0.00 34.37 2.10
1182 1402 9.799106 ATTAGAACTTGGTATGCTTATATTGCT 57.201 29.630 2.81 0.00 0.00 3.91
1190 1410 9.686683 ACATTCTTATTAGAACTTGGTATGCTT 57.313 29.630 0.00 0.00 42.91 3.91
1191 1411 9.686683 AACATTCTTATTAGAACTTGGTATGCT 57.313 29.630 0.00 0.00 42.91 3.79
1192 1412 9.722056 CAACATTCTTATTAGAACTTGGTATGC 57.278 33.333 0.00 0.00 42.91 3.14
1362 1584 7.086230 AGAGAAAGCATAGCTCTTGAAAATG 57.914 36.000 0.00 0.00 38.25 2.32
1741 1986 0.588252 GATGCAGCGCGTGGAATAAT 59.412 50.000 8.43 0.00 0.00 1.28
1761 2006 9.100554 CATATGGTCATGTGCATGTTTTAAAAT 57.899 29.630 3.52 0.00 39.72 1.82
1860 2116 5.783875 ACACATAAGGTAGTTTAGGTGAGGT 59.216 40.000 14.91 0.00 44.02 3.85
1955 2211 6.857451 CCAGGCAATTTTTATTCAACTTTTGC 59.143 34.615 0.00 0.00 37.94 3.68
2052 2311 6.317789 TGCATAACAAGCATATTCTAAGGC 57.682 37.500 0.00 0.00 37.02 4.35
2202 2461 5.773091 TGGGACAGACCTACACATATAAGA 58.227 41.667 0.00 0.00 38.98 2.10
2297 2557 4.389374 CGCATGAAGTAAATCATAGGGGT 58.611 43.478 0.00 0.00 37.96 4.95
2298 2558 3.753272 CCGCATGAAGTAAATCATAGGGG 59.247 47.826 0.00 0.00 37.96 4.79
2523 2790 9.394477 GTTGACTCTTGTTTTGGATAAATGTAC 57.606 33.333 0.00 0.00 0.00 2.90
2609 2877 7.569240 AGGGAGTACTTAGAATCTTTGGAATG 58.431 38.462 0.00 0.00 0.00 2.67
3010 3325 7.556733 AATTGACGTTGGTTTAGTACAAAGA 57.443 32.000 0.00 0.00 31.87 2.52
3039 3354 2.420705 ACTACTACTCCCTCCGATCCT 58.579 52.381 0.00 0.00 0.00 3.24
3357 3702 7.496591 AGAAATACTACACTCTTAGACCTCTCG 59.503 40.741 0.00 0.00 0.00 4.04
3436 3783 7.201705 GCCAGCTACCTAGTAACAAAATAAAGG 60.202 40.741 0.00 0.00 0.00 3.11
3688 4044 7.290061 AGTACCTACATCAACCATAATTGCAT 58.710 34.615 0.00 0.00 0.00 3.96
3744 4101 6.501781 ACTTACCGTCCATCGTATAAAGAAG 58.498 40.000 0.00 0.00 37.94 2.85
3962 4320 2.674461 GATCGTCCCGGCCGTAAGTC 62.674 65.000 26.12 10.38 0.00 3.01
4111 4754 4.432712 GCGATGGAATTTTTATGTTGCCT 58.567 39.130 0.00 0.00 0.00 4.75
4112 4755 3.555547 GGCGATGGAATTTTTATGTTGCC 59.444 43.478 0.00 0.00 0.00 4.52
4403 5086 9.883142 AATGTTTGAATTTGTTTCTGGAGTTTA 57.117 25.926 0.00 0.00 35.23 2.01
4407 5090 8.492748 CATGAATGTTTGAATTTGTTTCTGGAG 58.507 33.333 0.00 0.00 35.23 3.86
4569 5260 7.013529 GGTTGCTTTAGTACAACTTCATAACG 58.986 38.462 5.91 0.00 44.41 3.18
4571 5262 7.499563 TGTGGTTGCTTTAGTACAACTTCATAA 59.500 33.333 5.91 0.00 44.41 1.90
4573 5264 5.825679 TGTGGTTGCTTTAGTACAACTTCAT 59.174 36.000 5.91 0.00 44.41 2.57
4574 5265 5.186942 TGTGGTTGCTTTAGTACAACTTCA 58.813 37.500 5.91 3.56 44.41 3.02
4575 5266 5.744666 TGTGGTTGCTTTAGTACAACTTC 57.255 39.130 5.91 1.39 44.41 3.01
4578 5269 7.916450 TGTTAAATGTGGTTGCTTTAGTACAAC 59.084 33.333 0.00 0.00 44.29 3.32
4579 5270 7.997482 TGTTAAATGTGGTTGCTTTAGTACAA 58.003 30.769 0.00 0.00 0.00 2.41
4584 6213 6.686630 TCCATGTTAAATGTGGTTGCTTTAG 58.313 36.000 0.00 0.00 34.61 1.85
4591 6220 2.491693 CCGCTCCATGTTAAATGTGGTT 59.508 45.455 0.00 0.00 34.61 3.67
4664 6293 9.289782 GCATCCTCTATAAAGTGTCCATTTTAT 57.710 33.333 11.11 11.11 37.15 1.40
4743 6372 4.211920 TGGCACTAAAACCTATTATGGGC 58.788 43.478 0.00 0.00 0.00 5.36
4853 6528 5.163513 GTTTTTGGATCCTACGAGTTACGA 58.836 41.667 14.23 0.00 45.77 3.43
4874 6549 2.930826 ACAACACCCAATCTCTCGTT 57.069 45.000 0.00 0.00 0.00 3.85
5456 7136 4.870363 TGGGTCGTTTTGTACTAGTGTAC 58.130 43.478 5.39 0.00 46.74 2.90
5467 7147 1.335506 CGGGACAAATGGGTCGTTTTG 60.336 52.381 0.00 0.00 38.70 2.44
5549 7229 2.225727 GCGAACCAGGACTAAAGGTTTG 59.774 50.000 0.00 0.00 45.15 2.93
5579 7259 1.794714 GTGGAGCCCCTTCTATCTCA 58.205 55.000 0.00 0.00 0.00 3.27
5581 7261 0.032017 ACGTGGAGCCCCTTCTATCT 60.032 55.000 0.00 0.00 0.00 1.98
5662 7342 0.810648 GATGCGTGGATGCCTTTTGA 59.189 50.000 0.00 0.00 0.00 2.69
5679 7359 1.749638 GCTTCTGCCAGCTGCTGAT 60.750 57.895 30.10 0.00 45.84 2.90
5726 7423 0.781920 AACCCTCCAAAACCCCCTAC 59.218 55.000 0.00 0.00 0.00 3.18
5808 7506 0.806492 GCTAGCGTAGACCAAGCACC 60.806 60.000 0.00 0.00 33.55 5.01
5819 7517 6.013842 TCTATACGTGTAGTAGCTAGCGTA 57.986 41.667 17.54 13.09 38.94 4.42
5833 7531 4.548536 CGTGTCGAGTTCTCTCTATACGTG 60.549 50.000 0.00 0.00 41.86 4.49
5861 7559 7.775053 AATGGTTCCTTCATTTGCTTACTAA 57.225 32.000 0.00 0.00 31.49 2.24
6025 7727 6.142818 TGTTGAAATTGACCTTCGATGTTT 57.857 33.333 0.00 0.00 0.00 2.83
6032 7734 9.727627 GAGAATATCATGTTGAAATTGACCTTC 57.272 33.333 0.00 0.00 0.00 3.46
6045 7753 6.998074 TCAATAAAGCCGGAGAATATCATGTT 59.002 34.615 5.05 0.00 0.00 2.71
6051 7759 5.639506 CGTCATCAATAAAGCCGGAGAATAT 59.360 40.000 5.05 0.00 0.00 1.28
6141 7850 0.749649 AGATCTCACAGATGCGGGAC 59.250 55.000 0.00 0.00 34.53 4.46
6154 7863 6.007485 ACCCCCTTCTTCAAATTAGATCTC 57.993 41.667 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.