Multiple sequence alignment - TraesCS3D01G364100

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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 TraesCS3D01G364100 chr3D 100.000 4673 0 0 1 4673 477899895 477904567 0.000000e+00 8630.0
1 TraesCS3D01G364100 chr3A 94.639 3917 141 26 792 4673 621317956 621321838 0.000000e+00 6006.0
2 TraesCS3D01G364100 chr3A 83.594 256 35 5 537 789 621316757 621317008 2.810000e-57 233.0
3 TraesCS3D01G364100 chr3B 94.525 1589 64 9 796 2365 637082067 637083651 0.000000e+00 2431.0
4 TraesCS3D01G364100 chr3B 95.365 1467 43 10 2364 3826 637083936 637085381 0.000000e+00 2309.0
5 TraesCS3D01G364100 chr3B 82.280 649 70 26 149 789 637081291 637081902 1.930000e-143 520.0
6 TraesCS3D01G364100 chr3B 90.286 350 17 2 4058 4404 637085776 637086111 4.290000e-120 442.0
7 TraesCS3D01G364100 chr3B 92.500 160 11 1 4514 4672 637086443 637086602 1.310000e-55 228.0
8 TraesCS3D01G364100 chr3B 97.115 104 3 0 4413 4516 637086227 637086330 4.810000e-40 176.0
9 TraesCS3D01G364100 chr2B 83.721 344 49 4 1722 2064 734841064 734840727 7.550000e-83 318.0
10 TraesCS3D01G364100 chrUn 83.285 347 52 5 1719 2064 34095008 34095349 9.760000e-82 315.0
11 TraesCS3D01G364100 chrUn 83.430 344 51 5 1722 2064 234968774 234968436 9.760000e-82 315.0
12 TraesCS3D01G364100 chrUn 77.647 170 27 11 191 359 355070567 355070408 4.980000e-15 93.5
13 TraesCS3D01G364100 chr5D 78.235 170 26 10 191 359 544493275 544493434 1.070000e-16 99.0
14 TraesCS3D01G364100 chr5D 87.931 58 4 2 302 359 223336179 223336233 1.090000e-06 65.8
15 TraesCS3D01G364100 chr5B 77.647 170 27 10 191 359 686844017 686844176 4.980000e-15 93.5
16 TraesCS3D01G364100 chr5B 76.471 170 29 10 191 359 686741376 686741535 1.080000e-11 82.4
17 TraesCS3D01G364100 chr5B 87.931 58 4 2 302 359 249557195 249557141 1.090000e-06 65.8
18 TraesCS3D01G364100 chr5B 97.059 34 0 1 3642 3675 33537295 33537263 6.530000e-04 56.5
19 TraesCS3D01G364100 chr5A 81.609 87 9 6 276 359 295759944 295760026 1.090000e-06 65.8


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 TraesCS3D01G364100 chr3D 477899895 477904567 4672 False 8630.000000 8630 100.000000 1 4673 1 chr3D.!!$F1 4672
1 TraesCS3D01G364100 chr3A 621316757 621321838 5081 False 3119.500000 6006 89.116500 537 4673 2 chr3A.!!$F1 4136
2 TraesCS3D01G364100 chr3B 637081291 637086602 5311 False 1017.666667 2431 92.011833 149 4672 6 chr3B.!!$F1 4523

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
628 635 0.759346 GCTATCCTTCCATCGTGGGT 59.241 55.0 4.52 0.0 38.32 4.51 F
1314 2304 0.597637 ACTTCTGTTCGGTGCGTGAG 60.598 55.0 0.00 0.0 0.00 3.51 F
1872 2869 0.598942 CACACGTTGTCCGGTCATCA 60.599 55.0 1.21 0.0 42.24 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 2615 1.067295 AGGTCAGGATTGGTGAAGCA 58.933 50.000 0.0 0.0 0.00 3.91 R
3085 4369 4.024218 GGATCATCAGTGACAGCTAATTGC 60.024 45.833 0.0 0.0 37.14 3.56 R
3748 5036 4.034510 CCTGACTTTATTTCGGCATCACTC 59.965 45.833 0.0 0.0 0.00 3.51 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
20 21 2.631384 TCCCAAGACCTCTGGATTTGA 58.369 47.619 0.00 0.00 0.00 2.69
21 22 2.305927 TCCCAAGACCTCTGGATTTGAC 59.694 50.000 0.00 0.00 0.00 3.18
22 23 2.040278 CCCAAGACCTCTGGATTTGACA 59.960 50.000 0.00 0.00 0.00 3.58
23 24 3.498481 CCCAAGACCTCTGGATTTGACAA 60.498 47.826 0.00 0.00 0.00 3.18
24 25 4.144297 CCAAGACCTCTGGATTTGACAAA 58.856 43.478 2.48 2.48 0.00 2.83
25 26 4.022849 CCAAGACCTCTGGATTTGACAAAC 60.023 45.833 1.94 0.00 0.00 2.93
26 27 3.756117 AGACCTCTGGATTTGACAAACC 58.244 45.455 1.94 7.55 0.00 3.27
27 28 2.820197 GACCTCTGGATTTGACAAACCC 59.180 50.000 4.13 4.13 0.00 4.11
28 29 2.176798 ACCTCTGGATTTGACAAACCCA 59.823 45.455 13.60 13.60 0.00 4.51
29 30 2.558359 CCTCTGGATTTGACAAACCCAC 59.442 50.000 10.19 0.00 0.00 4.61
30 31 3.221771 CTCTGGATTTGACAAACCCACA 58.778 45.455 10.19 0.00 0.00 4.17
31 32 3.636300 CTCTGGATTTGACAAACCCACAA 59.364 43.478 10.19 1.04 0.00 3.33
32 33 4.026744 TCTGGATTTGACAAACCCACAAA 58.973 39.130 10.19 0.00 37.79 2.83
33 34 4.467795 TCTGGATTTGACAAACCCACAAAA 59.532 37.500 10.19 0.00 37.14 2.44
34 35 5.046304 TCTGGATTTGACAAACCCACAAAAA 60.046 36.000 10.19 0.00 37.14 1.94
117 118 9.661563 TTAATATGTAGGGTTGAAGTGTAAGTG 57.338 33.333 0.00 0.00 0.00 3.16
118 119 5.562298 ATGTAGGGTTGAAGTGTAAGTGT 57.438 39.130 0.00 0.00 0.00 3.55
119 120 4.699637 TGTAGGGTTGAAGTGTAAGTGTG 58.300 43.478 0.00 0.00 0.00 3.82
120 121 3.926058 AGGGTTGAAGTGTAAGTGTGT 57.074 42.857 0.00 0.00 0.00 3.72
121 122 3.541632 AGGGTTGAAGTGTAAGTGTGTG 58.458 45.455 0.00 0.00 0.00 3.82
122 123 3.199071 AGGGTTGAAGTGTAAGTGTGTGA 59.801 43.478 0.00 0.00 0.00 3.58
123 124 4.134563 GGGTTGAAGTGTAAGTGTGTGAT 58.865 43.478 0.00 0.00 0.00 3.06
124 125 5.071250 AGGGTTGAAGTGTAAGTGTGTGATA 59.929 40.000 0.00 0.00 0.00 2.15
125 126 5.761234 GGGTTGAAGTGTAAGTGTGTGATAA 59.239 40.000 0.00 0.00 0.00 1.75
126 127 6.261381 GGGTTGAAGTGTAAGTGTGTGATAAA 59.739 38.462 0.00 0.00 0.00 1.40
127 128 7.130269 GGTTGAAGTGTAAGTGTGTGATAAAC 58.870 38.462 0.00 0.00 0.00 2.01
128 129 7.012044 GGTTGAAGTGTAAGTGTGTGATAAACT 59.988 37.037 0.00 0.00 0.00 2.66
129 130 9.037737 GTTGAAGTGTAAGTGTGTGATAAACTA 57.962 33.333 0.00 0.00 0.00 2.24
130 131 9.772973 TTGAAGTGTAAGTGTGTGATAAACTAT 57.227 29.630 0.00 0.00 0.00 2.12
131 132 9.772973 TGAAGTGTAAGTGTGTGATAAACTATT 57.227 29.630 0.00 0.00 0.00 1.73
177 178 4.593206 TGGAGCTACCCAATATTAGTGGAG 59.407 45.833 11.67 3.47 38.54 3.86
179 180 3.328050 AGCTACCCAATATTAGTGGAGGC 59.672 47.826 11.67 11.40 38.54 4.70
180 181 3.328050 GCTACCCAATATTAGTGGAGGCT 59.672 47.826 11.67 0.00 38.54 4.58
181 182 4.530946 GCTACCCAATATTAGTGGAGGCTA 59.469 45.833 11.67 0.00 38.54 3.93
182 183 5.189934 GCTACCCAATATTAGTGGAGGCTAT 59.810 44.000 11.67 0.00 38.54 2.97
183 184 5.763876 ACCCAATATTAGTGGAGGCTATC 57.236 43.478 11.67 0.00 38.54 2.08
184 185 5.415961 ACCCAATATTAGTGGAGGCTATCT 58.584 41.667 11.67 0.00 38.54 1.98
185 186 5.485708 ACCCAATATTAGTGGAGGCTATCTC 59.514 44.000 11.67 0.00 38.54 2.75
186 187 5.723887 CCCAATATTAGTGGAGGCTATCTCT 59.276 44.000 11.67 0.00 42.10 3.10
187 188 6.897966 CCCAATATTAGTGGAGGCTATCTCTA 59.102 42.308 11.67 0.00 42.10 2.43
188 189 7.069331 CCCAATATTAGTGGAGGCTATCTCTAG 59.931 44.444 11.67 0.00 42.10 2.43
189 190 7.836685 CCAATATTAGTGGAGGCTATCTCTAGA 59.163 40.741 4.09 0.00 42.10 2.43
190 191 9.420118 CAATATTAGTGGAGGCTATCTCTAGAT 57.580 37.037 0.00 0.00 42.10 1.98
303 307 6.815089 AGGTTTTGCATTCAAATTGTACTGA 58.185 32.000 0.00 0.00 41.37 3.41
305 309 6.146021 GGTTTTGCATTCAAATTGTACTGAGG 59.854 38.462 0.00 0.00 41.37 3.86
320 324 6.235664 TGTACTGAGGGTTTAATTTGACCTC 58.764 40.000 0.00 0.00 46.14 3.85
344 348 8.746922 TCATTTCAAGTTTAAAGCATGATGAC 57.253 30.769 0.00 0.00 0.00 3.06
345 349 8.358895 TCATTTCAAGTTTAAAGCATGATGACA 58.641 29.630 0.00 0.00 0.00 3.58
346 350 9.146984 CATTTCAAGTTTAAAGCATGATGACAT 57.853 29.630 0.00 0.00 37.19 3.06
364 368 2.625695 ATGATGGCATGATGTCGTGA 57.374 45.000 3.81 0.00 34.90 4.35
365 369 2.625695 TGATGGCATGATGTCGTGAT 57.374 45.000 3.81 0.00 34.90 3.06
366 370 2.215196 TGATGGCATGATGTCGTGATG 58.785 47.619 3.81 0.00 34.90 3.07
367 371 2.158928 TGATGGCATGATGTCGTGATGA 60.159 45.455 3.81 0.00 34.90 2.92
379 383 7.647228 TGATGTCGTGATGATGAAAAAGAAAA 58.353 30.769 0.00 0.00 0.00 2.29
415 419 9.605275 CAAATCTAAATCTGTCATTACTCCAGA 57.395 33.333 0.00 0.00 39.38 3.86
431 435 4.341520 ACTCCAGATTGTTATAGTCGACCC 59.658 45.833 13.01 0.00 0.00 4.46
434 438 4.040461 CCAGATTGTTATAGTCGACCCCAT 59.960 45.833 13.01 6.05 0.00 4.00
436 440 5.466728 CAGATTGTTATAGTCGACCCCATTG 59.533 44.000 13.01 0.00 0.00 2.82
467 471 1.389609 TACCCCGAGATTCAGGCGAC 61.390 60.000 0.00 0.00 0.00 5.19
535 542 0.820871 ATGTTGCTCTCCTCGAGGAC 59.179 55.000 30.49 20.64 40.04 3.85
538 545 0.894184 TTGCTCTCCTCGAGGACGTT 60.894 55.000 30.49 0.00 40.04 3.99
577 584 5.250543 TGGTGAACTTGATATCCTTCCTTCA 59.749 40.000 0.00 0.00 0.00 3.02
590 597 4.081862 TCCTTCCTTCACGATCGTTGTTAT 60.082 41.667 20.14 0.00 0.00 1.89
620 627 2.305635 TGCTGAACTTGCTATCCTTCCA 59.694 45.455 0.00 0.00 0.00 3.53
628 635 0.759346 GCTATCCTTCCATCGTGGGT 59.241 55.000 4.52 0.00 38.32 4.51
653 660 4.192317 GGGTGTTGCGATTCTAGAGAATT 58.808 43.478 6.24 0.00 44.14 2.17
654 661 4.636206 GGGTGTTGCGATTCTAGAGAATTT 59.364 41.667 6.24 0.00 44.14 1.82
655 662 5.123979 GGGTGTTGCGATTCTAGAGAATTTT 59.876 40.000 6.24 0.00 44.14 1.82
672 679 8.365647 AGAGAATTTTAACTTCTAACCTCGTGA 58.634 33.333 0.00 0.00 33.18 4.35
673 680 8.897872 AGAATTTTAACTTCTAACCTCGTGAA 57.102 30.769 0.00 0.00 31.27 3.18
695 702 7.803189 GTGAAATTGTTATGTGACGACTTTGAT 59.197 33.333 0.00 0.00 0.00 2.57
696 703 8.349245 TGAAATTGTTATGTGACGACTTTGATT 58.651 29.630 0.00 0.00 0.00 2.57
698 705 8.506140 AATTGTTATGTGACGACTTTGATTTG 57.494 30.769 0.00 0.00 0.00 2.32
707 716 6.144402 GTGACGACTTTGATTTGCAAAATCAT 59.856 34.615 17.19 0.00 45.26 2.45
708 717 6.700960 TGACGACTTTGATTTGCAAAATCATT 59.299 30.769 17.19 0.00 45.26 2.57
709 718 7.096106 TGACGACTTTGATTTGCAAAATCATTC 60.096 33.333 17.19 9.31 45.26 2.67
725 734 4.600692 TCATTCGGAGTCTCTTGTTGAA 57.399 40.909 0.00 0.00 0.00 2.69
809 1771 5.287674 AGAGTCGATTCATCACATCCATT 57.712 39.130 10.80 0.00 0.00 3.16
810 1772 5.055144 AGAGTCGATTCATCACATCCATTG 58.945 41.667 10.80 0.00 0.00 2.82
1168 2150 2.285442 AGGTCCCCTTCTTCCCCG 60.285 66.667 0.00 0.00 0.00 5.73
1185 2167 4.162690 GTCGCTCCCCCAATCGCT 62.163 66.667 0.00 0.00 0.00 4.93
1188 2170 3.797353 GCTCCCCCAATCGCTCCA 61.797 66.667 0.00 0.00 0.00 3.86
1190 2172 1.768684 GCTCCCCCAATCGCTCCATA 61.769 60.000 0.00 0.00 0.00 2.74
1192 2174 1.352352 CTCCCCCAATCGCTCCATATT 59.648 52.381 0.00 0.00 0.00 1.28
1196 2178 3.600388 CCCCAATCGCTCCATATTACTC 58.400 50.000 0.00 0.00 0.00 2.59
1303 2292 0.674534 AGCGAGGTCGAACTTCTGTT 59.325 50.000 3.47 0.00 43.02 3.16
1314 2304 0.597637 ACTTCTGTTCGGTGCGTGAG 60.598 55.000 0.00 0.00 0.00 3.51
1455 2445 1.227176 GTACGAGGCCGGGTTCATC 60.227 63.158 2.18 0.00 40.78 2.92
1572 2562 1.952635 GTTCGTCACGGCGTCCTTT 60.953 57.895 10.85 0.00 0.00 3.11
1621 2611 6.539173 ACCAATTCCACTCAAGTATGTGTTA 58.461 36.000 0.00 0.00 31.18 2.41
1625 2615 8.514594 CAATTCCACTCAAGTATGTGTTATTGT 58.485 33.333 0.00 0.00 33.46 2.71
1630 2620 7.017645 CACTCAAGTATGTGTTATTGTGCTTC 58.982 38.462 0.00 0.00 31.18 3.86
1631 2621 6.710295 ACTCAAGTATGTGTTATTGTGCTTCA 59.290 34.615 0.00 0.00 29.27 3.02
1642 2638 1.896220 TGTGCTTCACCAATCCTGAC 58.104 50.000 0.00 0.00 32.73 3.51
1681 2677 2.972625 TGAGGTGTTGATTCCGATGTC 58.027 47.619 0.00 0.00 0.00 3.06
1817 2814 1.372997 GGAAGCGCAGACGTTCAGA 60.373 57.895 11.47 0.00 42.83 3.27
1872 2869 0.598942 CACACGTTGTCCGGTCATCA 60.599 55.000 1.21 0.00 42.24 3.07
1892 2889 0.984230 TGGTTAGTCCCTTCCTGCTG 59.016 55.000 0.00 0.00 34.77 4.41
1940 2938 8.514136 TTGTTTTGTTTTTATGCTTATCCTCG 57.486 30.769 0.00 0.00 0.00 4.63
2140 3138 2.456000 CGGACAACGTATGCTTGCT 58.544 52.632 0.00 0.00 37.93 3.91
2166 3164 7.084486 GTCACCCTTTACTTTTTATCTGCTTG 58.916 38.462 0.00 0.00 0.00 4.01
2226 3224 2.356069 GGCTAATACAGAACTGCTTGCC 59.644 50.000 1.46 5.56 0.00 4.52
2472 3756 3.367395 GGTTCCTTCCTGCTGTTTATTGC 60.367 47.826 0.00 0.00 0.00 3.56
2722 4006 5.678107 GCAATCATAAGAAGCAGTCCAAAGG 60.678 44.000 0.00 0.00 0.00 3.11
2800 4084 4.025730 CGGTATGTCATCCAGTCAAAATCG 60.026 45.833 0.00 0.00 0.00 3.34
3085 4369 0.953727 TGCAAACTAGCAAGCCACTG 59.046 50.000 0.00 0.00 42.46 3.66
3352 4636 9.251440 TCTATTGTCCTCTGTTAAGCTTTAGTA 57.749 33.333 3.20 0.00 0.00 1.82
3494 4778 7.741027 AAATCTATCTATTGACACCATGCAG 57.259 36.000 0.00 0.00 0.00 4.41
3568 4852 8.519799 AGTTTGAGAAGGAATTGAGTACAAAA 57.480 30.769 0.00 0.00 39.54 2.44
3574 4858 9.965824 GAGAAGGAATTGAGTACAAAATTTTCA 57.034 29.630 0.00 0.00 39.54 2.69
3673 4957 4.416516 TGAGGATAACTGGAGTGACTGAA 58.583 43.478 0.00 0.00 0.00 3.02
3674 4958 4.464244 TGAGGATAACTGGAGTGACTGAAG 59.536 45.833 0.00 0.00 0.00 3.02
3677 4963 4.932200 GGATAACTGGAGTGACTGAAGTTG 59.068 45.833 15.88 0.00 33.37 3.16
3725 5013 8.574196 TTGTGAGTTGATCATGTGTATATACG 57.426 34.615 8.33 0.00 40.92 3.06
3748 5036 6.529125 ACGAGGTTACTAACAATATTGACACG 59.471 38.462 22.16 16.86 0.00 4.49
3938 5352 3.153919 TGGTTCACCCAACTGCTATTTC 58.846 45.455 0.00 0.00 41.50 2.17
3951 5367 5.246307 ACTGCTATTTCTGTACCTTGTTCC 58.754 41.667 0.00 0.00 0.00 3.62
3954 5370 5.012664 TGCTATTTCTGTACCTTGTTCCTGA 59.987 40.000 0.00 0.00 0.00 3.86
3965 5381 5.324409 ACCTTGTTCCTGATAAAGCATTGA 58.676 37.500 0.00 0.00 0.00 2.57
3998 5414 4.655963 TGCCTTCTCTGATGCTAAAGTTT 58.344 39.130 0.00 0.00 0.00 2.66
4074 5528 0.834612 TATAAACAGGGTCCCCAGCG 59.165 55.000 3.51 0.00 38.92 5.18
4094 5548 2.079925 GGCAGAAGACACATGAGTTCC 58.920 52.381 0.00 0.00 0.00 3.62
4110 5564 5.362263 TGAGTTCCACTGTTAGGTTTACAC 58.638 41.667 0.00 0.00 0.00 2.90
4113 5567 4.669206 TCCACTGTTAGGTTTACACGAA 57.331 40.909 0.00 0.00 0.00 3.85
4209 5663 4.146961 GCGACATTGTTCAGTTTGTCAATG 59.853 41.667 18.05 18.05 46.85 2.82
4214 5668 7.984002 CATTGTTCAGTTTGTCAATGTTACA 57.016 32.000 14.69 0.00 40.89 2.41
4215 5669 8.404889 CATTGTTCAGTTTGTCAATGTTACAA 57.595 30.769 14.69 0.00 40.89 2.41
4216 5670 7.804614 TTGTTCAGTTTGTCAATGTTACAAC 57.195 32.000 0.00 0.00 36.61 3.32
4217 5671 7.151999 TGTTCAGTTTGTCAATGTTACAACT 57.848 32.000 0.00 0.00 36.61 3.16
4218 5672 7.026562 TGTTCAGTTTGTCAATGTTACAACTG 58.973 34.615 5.12 5.12 36.61 3.16
4219 5673 6.130298 TCAGTTTGTCAATGTTACAACTGG 57.870 37.500 10.08 0.00 36.61 4.00
4220 5674 4.739716 CAGTTTGTCAATGTTACAACTGGC 59.260 41.667 3.88 0.47 36.61 4.85
4221 5675 4.400884 AGTTTGTCAATGTTACAACTGGCA 59.599 37.500 1.72 1.72 36.61 4.92
4222 5676 3.980646 TGTCAATGTTACAACTGGCAC 57.019 42.857 1.72 0.00 0.00 5.01
4320 5791 1.846007 ACAACTTGCACCAGGTTCAA 58.154 45.000 4.45 4.45 31.42 2.69
4357 5828 0.839946 AGCCCGCACTTATTCCAGAT 59.160 50.000 0.00 0.00 0.00 2.90
4359 5830 1.502231 CCCGCACTTATTCCAGATCG 58.498 55.000 0.00 0.00 0.00 3.69
4366 5837 2.039084 ACTTATTCCAGATCGATGCCCC 59.961 50.000 0.54 0.00 0.00 5.80
4493 6071 3.008485 ACAAGGATCTGTTGGAGTTCCTC 59.992 47.826 11.50 0.00 46.44 3.71
4506 6084 3.196685 GGAGTTCCTCAGATACACAGCTT 59.803 47.826 0.00 0.00 31.08 3.74
4652 6346 4.250170 ACCACGGAGGACCCTGGT 62.250 66.667 2.94 0.00 45.87 4.00
4660 6354 4.966787 GGACCCTGGTTTGCGGCA 62.967 66.667 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.305927 GTCAAATCCAGAGGTCTTGGGA 59.694 50.000 0.00 0.00 0.00 4.37
1 2 2.040278 TGTCAAATCCAGAGGTCTTGGG 59.960 50.000 0.00 0.00 0.00 4.12
2 3 3.423539 TGTCAAATCCAGAGGTCTTGG 57.576 47.619 0.00 0.00 0.00 3.61
3 4 4.022849 GGTTTGTCAAATCCAGAGGTCTTG 60.023 45.833 0.40 0.00 0.00 3.02
4 5 4.145052 GGTTTGTCAAATCCAGAGGTCTT 58.855 43.478 0.40 0.00 0.00 3.01
5 6 3.498661 GGGTTTGTCAAATCCAGAGGTCT 60.499 47.826 20.77 0.00 41.48 3.85
6 7 2.820197 GGGTTTGTCAAATCCAGAGGTC 59.180 50.000 20.77 0.00 41.48 3.85
7 8 2.176798 TGGGTTTGTCAAATCCAGAGGT 59.823 45.455 23.82 0.00 46.45 3.85
8 9 2.875296 TGGGTTTGTCAAATCCAGAGG 58.125 47.619 23.82 0.00 46.45 3.69
91 92 9.661563 CACTTACACTTCAACCCTACATATTAA 57.338 33.333 0.00 0.00 0.00 1.40
92 93 8.818860 ACACTTACACTTCAACCCTACATATTA 58.181 33.333 0.00 0.00 0.00 0.98
93 94 7.606456 CACACTTACACTTCAACCCTACATATT 59.394 37.037 0.00 0.00 0.00 1.28
94 95 7.103641 CACACTTACACTTCAACCCTACATAT 58.896 38.462 0.00 0.00 0.00 1.78
95 96 6.042322 ACACACTTACACTTCAACCCTACATA 59.958 38.462 0.00 0.00 0.00 2.29
96 97 5.163237 ACACACTTACACTTCAACCCTACAT 60.163 40.000 0.00 0.00 0.00 2.29
97 98 4.162698 ACACACTTACACTTCAACCCTACA 59.837 41.667 0.00 0.00 0.00 2.74
98 99 4.510340 CACACACTTACACTTCAACCCTAC 59.490 45.833 0.00 0.00 0.00 3.18
99 100 4.406326 TCACACACTTACACTTCAACCCTA 59.594 41.667 0.00 0.00 0.00 3.53
100 101 3.199071 TCACACACTTACACTTCAACCCT 59.801 43.478 0.00 0.00 0.00 4.34
101 102 3.537580 TCACACACTTACACTTCAACCC 58.462 45.455 0.00 0.00 0.00 4.11
102 103 6.854496 TTATCACACACTTACACTTCAACC 57.146 37.500 0.00 0.00 0.00 3.77
103 104 7.916552 AGTTTATCACACACTTACACTTCAAC 58.083 34.615 0.00 0.00 0.00 3.18
104 105 9.772973 ATAGTTTATCACACACTTACACTTCAA 57.227 29.630 0.00 0.00 0.00 2.69
105 106 9.772973 AATAGTTTATCACACACTTACACTTCA 57.227 29.630 0.00 0.00 0.00 3.02
139 140 9.702253 TGGGTAGCTCCAACAATTATTTTATAA 57.298 29.630 0.00 0.00 38.11 0.98
140 141 9.702253 TTGGGTAGCTCCAACAATTATTTTATA 57.298 29.630 2.79 0.00 41.44 0.98
141 142 8.602472 TTGGGTAGCTCCAACAATTATTTTAT 57.398 30.769 2.79 0.00 41.44 1.40
143 144 6.926630 TTGGGTAGCTCCAACAATTATTTT 57.073 33.333 2.79 0.00 41.44 1.82
154 155 4.562767 TCCACTAATATTGGGTAGCTCCA 58.437 43.478 3.68 0.00 38.11 3.86
161 162 5.415961 AGATAGCCTCCACTAATATTGGGT 58.584 41.667 3.68 0.93 34.56 4.51
163 164 6.865834 AGAGATAGCCTCCACTAATATTGG 57.134 41.667 0.00 0.00 42.97 3.16
183 184 8.828644 CATGGTGAAATCTCTTGAAATCTAGAG 58.171 37.037 13.51 13.51 43.82 2.43
184 185 7.281774 GCATGGTGAAATCTCTTGAAATCTAGA 59.718 37.037 0.00 0.00 0.00 2.43
185 186 7.282675 AGCATGGTGAAATCTCTTGAAATCTAG 59.717 37.037 0.00 0.00 0.00 2.43
186 187 7.114754 AGCATGGTGAAATCTCTTGAAATCTA 58.885 34.615 0.00 0.00 0.00 1.98
187 188 5.950549 AGCATGGTGAAATCTCTTGAAATCT 59.049 36.000 0.00 0.00 0.00 2.40
188 189 6.205101 AGCATGGTGAAATCTCTTGAAATC 57.795 37.500 0.00 0.00 0.00 2.17
189 190 7.707624 TTAGCATGGTGAAATCTCTTGAAAT 57.292 32.000 7.89 0.00 0.00 2.17
190 191 7.231317 ACTTTAGCATGGTGAAATCTCTTGAAA 59.769 33.333 7.89 0.00 0.00 2.69
205 207 6.773976 TTAAATTGAGGGACTTTAGCATGG 57.226 37.500 0.00 0.00 41.55 3.66
291 295 9.191995 GTCAAATTAAACCCTCAGTACAATTTG 57.808 33.333 12.51 12.51 43.23 2.32
296 300 6.183361 TGAGGTCAAATTAAACCCTCAGTACA 60.183 38.462 10.41 0.00 45.05 2.90
297 301 6.235664 TGAGGTCAAATTAAACCCTCAGTAC 58.764 40.000 10.41 0.00 45.05 2.73
298 302 6.442541 TGAGGTCAAATTAAACCCTCAGTA 57.557 37.500 10.41 0.00 45.05 2.74
303 307 7.290014 ACTTGAAATGAGGTCAAATTAAACCCT 59.710 33.333 5.72 0.00 34.68 4.34
305 309 8.887036 AACTTGAAATGAGGTCAAATTAAACC 57.113 30.769 1.70 1.70 34.68 3.27
320 324 8.523523 TGTCATCATGCTTTAAACTTGAAATG 57.476 30.769 9.01 6.08 0.00 2.32
321 325 9.146984 CATGTCATCATGCTTTAAACTTGAAAT 57.853 29.630 9.01 0.00 43.66 2.17
322 326 8.523523 CATGTCATCATGCTTTAAACTTGAAA 57.476 30.769 9.01 0.00 43.66 2.69
345 349 2.625695 TCACGACATCATGCCATCAT 57.374 45.000 0.00 0.00 0.00 2.45
346 350 2.158928 TCATCACGACATCATGCCATCA 60.159 45.455 0.00 0.00 0.00 3.07
347 351 2.486918 TCATCACGACATCATGCCATC 58.513 47.619 0.00 0.00 0.00 3.51
348 352 2.625695 TCATCACGACATCATGCCAT 57.374 45.000 0.00 0.00 0.00 4.40
349 353 2.158928 TCATCATCACGACATCATGCCA 60.159 45.455 0.00 0.00 0.00 4.92
350 354 2.486918 TCATCATCACGACATCATGCC 58.513 47.619 0.00 0.00 0.00 4.40
351 355 4.541085 TTTCATCATCACGACATCATGC 57.459 40.909 0.00 0.00 0.00 4.06
352 356 6.778108 TCTTTTTCATCATCACGACATCATG 58.222 36.000 0.00 0.00 0.00 3.07
353 357 6.990341 TCTTTTTCATCATCACGACATCAT 57.010 33.333 0.00 0.00 0.00 2.45
354 358 6.799926 TTCTTTTTCATCATCACGACATCA 57.200 33.333 0.00 0.00 0.00 3.07
355 359 8.679288 ATTTTCTTTTTCATCATCACGACATC 57.321 30.769 0.00 0.00 0.00 3.06
402 406 8.350722 TCGACTATAACAATCTGGAGTAATGAC 58.649 37.037 0.00 0.00 0.00 3.06
403 407 8.350722 GTCGACTATAACAATCTGGAGTAATGA 58.649 37.037 8.70 0.00 0.00 2.57
404 408 7.595502 GGTCGACTATAACAATCTGGAGTAATG 59.404 40.741 16.46 0.00 0.00 1.90
405 409 7.255871 GGGTCGACTATAACAATCTGGAGTAAT 60.256 40.741 16.46 0.00 0.00 1.89
412 416 4.665833 TGGGGTCGACTATAACAATCTG 57.334 45.455 16.46 0.00 0.00 2.90
413 417 5.365605 TCAATGGGGTCGACTATAACAATCT 59.634 40.000 16.46 0.00 0.00 2.40
415 419 5.623956 TCAATGGGGTCGACTATAACAAT 57.376 39.130 16.46 0.00 0.00 2.71
434 438 4.226394 TCTCGGGGTAAGATTCCATTTCAA 59.774 41.667 0.00 0.00 0.00 2.69
436 440 4.417426 TCTCGGGGTAAGATTCCATTTC 57.583 45.455 0.00 0.00 0.00 2.17
449 453 2.363795 TCGCCTGAATCTCGGGGT 60.364 61.111 3.73 0.00 43.24 4.95
453 457 0.108615 ACCTTGTCGCCTGAATCTCG 60.109 55.000 0.00 0.00 0.00 4.04
460 464 0.323629 TTCCCTTACCTTGTCGCCTG 59.676 55.000 0.00 0.00 0.00 4.85
467 471 2.950418 GCCCAATCCTTCCCTTACCTTG 60.950 54.545 0.00 0.00 0.00 3.61
577 584 0.463116 GGGCCCATAACAACGATCGT 60.463 55.000 19.95 16.60 0.00 3.73
590 597 1.114722 CAAGTTCAGCAAAGGGCCCA 61.115 55.000 27.56 0.00 46.50 5.36
620 627 3.948719 AACACCCGCACCCACGAT 61.949 61.111 0.00 0.00 34.06 3.73
628 635 0.739462 CTAGAATCGCAACACCCGCA 60.739 55.000 0.00 0.00 0.00 5.69
634 641 8.547967 AGTTAAAATTCTCTAGAATCGCAACA 57.452 30.769 5.71 0.00 43.41 3.33
653 660 8.441312 ACAATTTCACGAGGTTAGAAGTTAAA 57.559 30.769 0.00 0.00 0.00 1.52
654 661 8.441312 AACAATTTCACGAGGTTAGAAGTTAA 57.559 30.769 0.00 0.00 0.00 2.01
655 662 9.715121 ATAACAATTTCACGAGGTTAGAAGTTA 57.285 29.630 0.00 0.00 0.00 2.24
664 671 4.151689 CGTCACATAACAATTTCACGAGGT 59.848 41.667 0.00 0.00 0.00 3.85
665 672 4.387559 TCGTCACATAACAATTTCACGAGG 59.612 41.667 0.00 0.00 31.75 4.63
672 679 8.967218 CAAATCAAAGTCGTCACATAACAATTT 58.033 29.630 0.00 0.00 0.00 1.82
673 680 7.114811 GCAAATCAAAGTCGTCACATAACAATT 59.885 33.333 0.00 0.00 0.00 2.32
695 702 4.761739 AGAGACTCCGAATGATTTTGCAAA 59.238 37.500 8.05 8.05 0.00 3.68
696 703 4.326826 AGAGACTCCGAATGATTTTGCAA 58.673 39.130 0.00 0.00 0.00 4.08
698 705 4.154918 ACAAGAGACTCCGAATGATTTTGC 59.845 41.667 0.00 0.00 0.00 3.68
707 716 8.311836 AGTTAATATTCAACAAGAGACTCCGAA 58.688 33.333 0.00 0.00 0.00 4.30
708 717 7.837863 AGTTAATATTCAACAAGAGACTCCGA 58.162 34.615 0.00 0.00 0.00 4.55
709 718 7.043986 CGAGTTAATATTCAACAAGAGACTCCG 60.044 40.741 0.00 0.00 0.00 4.63
786 795 6.040842 TCAATGGATGTGATGAATCGACTCTA 59.959 38.462 0.00 0.00 0.00 2.43
787 796 4.952071 ATGGATGTGATGAATCGACTCT 57.048 40.909 0.00 0.00 0.00 3.24
788 797 5.052481 TCAATGGATGTGATGAATCGACTC 58.948 41.667 0.00 0.00 0.00 3.36
789 798 5.027293 TCAATGGATGTGATGAATCGACT 57.973 39.130 0.00 0.00 0.00 4.18
790 799 5.277683 CCTTCAATGGATGTGATGAATCGAC 60.278 44.000 0.00 0.00 31.92 4.20
794 1756 5.763355 ACTCCTTCAATGGATGTGATGAAT 58.237 37.500 0.00 0.00 35.30 2.57
809 1771 2.224079 GTCGTACACGTGTACTCCTTCA 59.776 50.000 40.53 22.56 46.43 3.02
810 1772 2.224079 TGTCGTACACGTGTACTCCTTC 59.776 50.000 40.53 28.63 46.43 3.46
828 1790 5.223382 CGGTTATATCCAGATGTCAGTGTC 58.777 45.833 0.85 0.00 0.00 3.67
829 1791 4.501571 GCGGTTATATCCAGATGTCAGTGT 60.502 45.833 0.85 0.00 0.00 3.55
993 1975 1.200760 CCTCCCACCACATCCACTCA 61.201 60.000 0.00 0.00 0.00 3.41
1168 2150 4.162690 AGCGATTGGGGGAGCGAC 62.163 66.667 0.00 0.00 34.34 5.19
1185 2167 1.830071 GCGGGGAGGGAGTAATATGGA 60.830 57.143 0.00 0.00 0.00 3.41
1188 2170 0.546988 GGGCGGGGAGGGAGTAATAT 60.547 60.000 0.00 0.00 0.00 1.28
1190 2172 2.447959 GGGCGGGGAGGGAGTAAT 60.448 66.667 0.00 0.00 0.00 1.89
1224 2206 1.944234 TACTGCTGATCTCCGCGCAA 61.944 55.000 8.75 0.00 31.24 4.85
1231 2213 8.006590 CGCAAAATTAATAGTACTGCTGATCTC 58.993 37.037 5.39 0.00 0.00 2.75
1303 2292 4.379143 CGTCGACTCACGCACCGA 62.379 66.667 14.70 0.00 42.26 4.69
1314 2304 3.277742 GAACGCCAGCAACGTCGAC 62.278 63.158 5.18 5.18 44.30 4.20
1455 2445 2.262471 GAATGCTCCTGTGCTTGGCG 62.262 60.000 0.00 0.00 0.00 5.69
1572 2562 6.367374 TCCCACACTTTGACATAGTTATCA 57.633 37.500 0.00 0.00 0.00 2.15
1621 2611 2.821969 GTCAGGATTGGTGAAGCACAAT 59.178 45.455 0.00 0.00 35.86 2.71
1625 2615 1.067295 AGGTCAGGATTGGTGAAGCA 58.933 50.000 0.00 0.00 0.00 3.91
1630 2620 5.982890 AAATGTTAAGGTCAGGATTGGTG 57.017 39.130 0.00 0.00 0.00 4.17
1631 2621 5.279456 GCAAAATGTTAAGGTCAGGATTGGT 60.279 40.000 0.00 0.00 0.00 3.67
1642 2638 2.297597 TCAACGGGGCAAAATGTTAAGG 59.702 45.455 0.00 0.00 0.00 2.69
1681 2677 1.285962 ACCAATCCCAGAATGACCAGG 59.714 52.381 0.00 0.00 39.69 4.45
1817 2814 4.096382 GGAAGCAATATCACACAAACGGAT 59.904 41.667 0.00 0.00 0.00 4.18
1872 2869 1.561542 CAGCAGGAAGGGACTAACCAT 59.438 52.381 0.00 0.00 38.49 3.55
1940 2938 5.635417 TGATACCATCTGAGATGATCGAC 57.365 43.478 23.29 10.76 0.00 4.20
2064 3062 4.023980 TGAGACCGTAACTGATCAAGGAT 58.976 43.478 0.00 0.00 0.00 3.24
2140 3138 6.303839 AGCAGATAAAAAGTAAAGGGTGACA 58.696 36.000 0.00 0.00 0.00 3.58
2166 3164 6.399639 TTCTGAAGAAATAACCAAACCCAC 57.600 37.500 0.00 0.00 0.00 4.61
2226 3224 9.125026 AGTTTTGGAATAGTAGCCAGAATAATG 57.875 33.333 0.00 0.00 35.23 1.90
2722 4006 4.092968 CCATGGTTAGACTTTTGCGTAGTC 59.907 45.833 2.57 4.93 41.83 2.59
2800 4084 5.335127 CAGCACCATAATGAGCTGTTTTAC 58.665 41.667 12.63 0.00 46.92 2.01
3085 4369 4.024218 GGATCATCAGTGACAGCTAATTGC 60.024 45.833 0.00 0.00 37.14 3.56
3219 4503 6.500400 ACCAGACCATGTATTGTATGCCTATA 59.500 38.462 0.00 0.00 0.00 1.31
3220 4504 5.310594 ACCAGACCATGTATTGTATGCCTAT 59.689 40.000 0.00 0.00 0.00 2.57
3352 4636 7.931578 TTAGGAATGGAATACACGTTGAAAT 57.068 32.000 0.00 0.00 0.00 2.17
3574 4858 7.985184 AGCAGCATCAAATCATCAAATTTACAT 59.015 29.630 0.00 0.00 0.00 2.29
3688 4974 5.825593 TCAACTCACAAGTTATCTCCCTT 57.174 39.130 0.00 0.00 43.99 3.95
3702 4988 7.539022 CCTCGTATATACACATGATCAACTCAC 59.461 40.741 13.22 0.00 36.48 3.51
3725 5013 7.758528 ACTCGTGTCAATATTGTTAGTAACCTC 59.241 37.037 14.97 1.58 0.00 3.85
3748 5036 4.034510 CCTGACTTTATTTCGGCATCACTC 59.965 45.833 0.00 0.00 0.00 3.51
3938 5352 5.245531 TGCTTTATCAGGAACAAGGTACAG 58.754 41.667 0.00 0.00 0.00 2.74
3954 5370 8.042515 AGGCATAAAACATGTTCAATGCTTTAT 58.957 29.630 33.99 21.64 39.03 1.40
3965 5381 6.626623 GCATCAGAGAAGGCATAAAACATGTT 60.627 38.462 4.92 4.92 0.00 2.71
3998 5414 6.729690 AATTTCATTGTTGTTCCCTTCAGA 57.270 33.333 0.00 0.00 0.00 3.27
4074 5528 2.079925 GGAACTCATGTGTCTTCTGCC 58.920 52.381 0.03 0.00 0.00 4.85
4094 5548 3.805422 TGCTTCGTGTAAACCTAACAGTG 59.195 43.478 0.00 0.00 0.00 3.66
4110 5564 4.282950 AGTTGCATGATATGTTGCTTCG 57.717 40.909 0.00 0.00 39.60 3.79
4113 5567 6.028146 TCAAAAGTTGCATGATATGTTGCT 57.972 33.333 0.00 0.00 39.60 3.91
4209 5663 2.916111 CAATGTCGTGCCAGTTGTAAC 58.084 47.619 0.00 0.00 0.00 2.50
4210 5664 1.265635 GCAATGTCGTGCCAGTTGTAA 59.734 47.619 0.00 0.00 38.66 2.41
4211 5665 0.871722 GCAATGTCGTGCCAGTTGTA 59.128 50.000 0.00 0.00 38.66 2.41
4212 5666 0.819259 AGCAATGTCGTGCCAGTTGT 60.819 50.000 0.00 0.00 46.14 3.32
4213 5667 0.386352 CAGCAATGTCGTGCCAGTTG 60.386 55.000 0.00 0.00 46.14 3.16
4214 5668 0.534877 TCAGCAATGTCGTGCCAGTT 60.535 50.000 0.00 0.00 46.14 3.16
4215 5669 0.534877 TTCAGCAATGTCGTGCCAGT 60.535 50.000 0.00 0.00 46.14 4.00
4216 5670 0.806868 ATTCAGCAATGTCGTGCCAG 59.193 50.000 0.00 0.00 46.14 4.85
4217 5671 1.246649 AATTCAGCAATGTCGTGCCA 58.753 45.000 0.00 0.00 46.14 4.92
4218 5672 1.987770 CAAATTCAGCAATGTCGTGCC 59.012 47.619 0.00 0.00 46.14 5.01
4219 5673 2.406024 CACAAATTCAGCAATGTCGTGC 59.594 45.455 0.00 0.00 45.28 5.34
4220 5674 3.422876 CACACAAATTCAGCAATGTCGTG 59.577 43.478 0.00 0.00 0.00 4.35
4221 5675 3.314913 TCACACAAATTCAGCAATGTCGT 59.685 39.130 0.00 0.00 0.00 4.34
4222 5676 3.665409 GTCACACAAATTCAGCAATGTCG 59.335 43.478 0.00 0.00 0.00 4.35
4320 5791 3.248446 TAGGCGCCCGCAACTTCTT 62.248 57.895 26.15 2.07 44.11 2.52
4357 5828 2.364632 CAACACAATAAGGGGCATCGA 58.635 47.619 0.00 0.00 0.00 3.59
4359 5830 2.102578 AGCAACACAATAAGGGGCATC 58.897 47.619 0.00 0.00 0.00 3.91
4366 5837 2.486982 AGCAGCTCAGCAACACAATAAG 59.513 45.455 0.00 0.00 36.85 1.73
4506 6084 7.490079 CCAGTTACGCAGAGTTATACATAACAA 59.510 37.037 13.19 0.00 43.83 2.83
4521 6214 0.373716 GCGGATTTCCAGTTACGCAG 59.626 55.000 0.00 0.00 45.57 5.18
4643 6337 4.966787 TGCCGCAAACCAGGGTCC 62.967 66.667 0.00 0.00 0.00 4.46
4652 6346 2.494530 GGGGAGTGTTTGCCGCAAA 61.495 57.895 14.60 14.60 38.39 3.68


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

AutoCloner maintained by Alex Coulton.