Multiple sequence alignment - TraesCS7B01G161500

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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 TraesCS7B01G161500 chr7B 100.000 5632 0 0 1 5632 220871311 220865680 0.000000e+00 10401.0
1 TraesCS7B01G161500 chr7D 93.742 5705 214 59 4 5625 244957167 244951523 0.000000e+00 8425.0
2 TraesCS7B01G161500 chr7A 93.896 3342 139 30 2331 5632 261224157 261220841 0.000000e+00 4981.0
3 TraesCS7B01G161500 chr7A 92.910 2144 92 22 317 2418 261226279 261224154 0.000000e+00 3062.0
4 TraesCS7B01G161500 chr7A 81.973 294 42 8 4 297 261226726 261226444 7.290000e-59 239.0
5 TraesCS7B01G161500 chr7A 100.000 32 0 0 385 416 126042144 126042175 6.090000e-05 60.2
6 TraesCS7B01G161500 chr2A 88.075 1174 106 10 2627 3789 14848713 14847563 0.000000e+00 1362.0
7 TraesCS7B01G161500 chr5D 100.000 32 0 0 386 417 166628442 166628473 6.090000e-05 60.2
8 TraesCS7B01G161500 chr4B 97.222 36 0 1 382 416 476358113 476358148 6.090000e-05 60.2
9 TraesCS7B01G161500 chr4B 97.059 34 0 1 382 414 269174156 269174123 7.880000e-04 56.5
10 TraesCS7B01G161500 chr1D 100.000 32 0 0 385 416 349811066 349811097 6.090000e-05 60.2
11 TraesCS7B01G161500 chr1D 97.059 34 1 0 383 416 329729668 329729701 2.190000e-04 58.4
12 TraesCS7B01G161500 chr1A 87.273 55 3 4 387 440 63336182 63336131 6.090000e-05 60.2
13 TraesCS7B01G161500 chr6A 100.000 31 0 0 386 416 572483316 572483346 2.190000e-04 58.4
14 TraesCS7B01G161500 chr2B 100.000 31 0 0 385 415 457680330 457680360 2.190000e-04 58.4


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 TraesCS7B01G161500 chr7B 220865680 220871311 5631 True 10401.000000 10401 100.000 1 5632 1 chr7B.!!$R1 5631
1 TraesCS7B01G161500 chr7D 244951523 244957167 5644 True 8425.000000 8425 93.742 4 5625 1 chr7D.!!$R1 5621
2 TraesCS7B01G161500 chr7A 261220841 261226726 5885 True 2760.666667 4981 89.593 4 5632 3 chr7A.!!$R1 5628
3 TraesCS7B01G161500 chr2A 14847563 14848713 1150 True 1362.000000 1362 88.075 2627 3789 1 chr2A.!!$R1 1162

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
686 845 0.035458 ACACTGCTAACTCACTGCCC 59.965 55.000 0.00 0.0 0.00 5.36 F
759 919 0.036732 TGGAAAGAGAATGCCGTGCT 59.963 50.000 0.00 0.0 0.00 4.40 F
1985 2183 0.329261 TGCATTGCCTTCAGGTAGCT 59.671 50.000 6.12 0.0 37.57 3.32 F
2260 2460 1.197721 GTGCCAGTTCCAAAGTCATCG 59.802 52.381 0.00 0.0 0.00 3.84 F
3763 4057 0.740737 GTGTTCAGGCTGCTGTGTTT 59.259 50.000 10.34 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2183 0.250510 TGTTTGGCTACCACGATGCA 60.251 50.000 0.00 0.0 30.78 3.96 R
2303 2503 0.469331 TCCGTGAGAACCACAGGAGT 60.469 55.000 0.00 0.0 45.98 3.85 R
3283 3567 3.275999 GGGCTATTAACAACATCGTGGT 58.724 45.455 0.00 0.0 0.00 4.16 R
4244 4540 2.610859 GAGCTCCCCAAGGTCCCA 60.611 66.667 0.87 0.0 45.05 4.37 R
5578 5920 0.038526 TCCTTCCTTCGTTCACTCGC 60.039 55.000 0.00 0.0 0.00 5.03 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
160 161 6.945435 TCCTCAGCATCAAGTTACCATTTTAA 59.055 34.615 0.00 0.00 0.00 1.52
163 164 9.474920 CTCAGCATCAAGTTACCATTTTAAAAA 57.525 29.630 4.44 0.00 0.00 1.94
187 188 9.476202 AAAAGACTTGTAAAATGTTCCTAATGC 57.524 29.630 0.00 0.00 0.00 3.56
188 189 8.409358 AAGACTTGTAAAATGTTCCTAATGCT 57.591 30.769 0.00 0.00 0.00 3.79
189 190 7.820648 AGACTTGTAAAATGTTCCTAATGCTG 58.179 34.615 0.00 0.00 0.00 4.41
190 191 6.924111 ACTTGTAAAATGTTCCTAATGCTGG 58.076 36.000 0.00 0.00 0.00 4.85
191 192 6.493458 ACTTGTAAAATGTTCCTAATGCTGGT 59.507 34.615 0.00 0.00 0.00 4.00
192 193 6.909550 TGTAAAATGTTCCTAATGCTGGTT 57.090 33.333 0.00 0.00 0.00 3.67
193 194 7.296628 TGTAAAATGTTCCTAATGCTGGTTT 57.703 32.000 0.00 0.00 0.00 3.27
194 195 8.410673 TGTAAAATGTTCCTAATGCTGGTTTA 57.589 30.769 0.00 0.00 0.00 2.01
195 196 8.301002 TGTAAAATGTTCCTAATGCTGGTTTAC 58.699 33.333 0.00 0.00 0.00 2.01
294 296 7.526608 TCCGAACTTCTTTACAGCAAATATTG 58.473 34.615 0.00 0.00 0.00 1.90
297 299 8.629986 CGAACTTCTTTACAGCAAATATTGTTG 58.370 33.333 5.54 5.54 45.86 3.33
298 300 9.677567 GAACTTCTTTACAGCAAATATTGTTGA 57.322 29.630 12.84 0.00 43.54 3.18
302 304 9.979578 TTCTTTACAGCAAATATTGTTGAATGT 57.020 25.926 12.84 4.53 43.54 2.71
303 305 9.979578 TCTTTACAGCAAATATTGTTGAATGTT 57.020 25.926 12.84 0.00 43.54 2.71
306 338 7.878477 ACAGCAAATATTGTTGAATGTTCTG 57.122 32.000 12.84 1.74 43.54 3.02
314 461 9.740239 AATATTGTTGAATGTTCTGCATACATC 57.260 29.630 13.19 8.76 36.67 3.06
315 462 6.822667 TTGTTGAATGTTCTGCATACATCT 57.177 33.333 13.19 6.01 36.67 2.90
363 513 4.902443 TGCTGGTTTTCACGAACATTTA 57.098 36.364 0.00 0.00 0.00 1.40
378 528 8.160342 CACGAACATTTACACTACATAGAACAC 58.840 37.037 0.00 0.00 0.00 3.32
390 540 9.424319 CACTACATAGAACACTCAACAATACTT 57.576 33.333 0.00 0.00 0.00 2.24
391 541 9.640963 ACTACATAGAACACTCAACAATACTTC 57.359 33.333 0.00 0.00 0.00 3.01
392 542 7.907214 ACATAGAACACTCAACAATACTTCC 57.093 36.000 0.00 0.00 0.00 3.46
393 543 7.680730 ACATAGAACACTCAACAATACTTCCT 58.319 34.615 0.00 0.00 0.00 3.36
394 544 7.819900 ACATAGAACACTCAACAATACTTCCTC 59.180 37.037 0.00 0.00 0.00 3.71
395 545 5.552178 AGAACACTCAACAATACTTCCTCC 58.448 41.667 0.00 0.00 0.00 4.30
396 546 3.926616 ACACTCAACAATACTTCCTCCG 58.073 45.455 0.00 0.00 0.00 4.63
397 547 3.323979 ACACTCAACAATACTTCCTCCGT 59.676 43.478 0.00 0.00 0.00 4.69
398 548 4.525487 ACACTCAACAATACTTCCTCCGTA 59.475 41.667 0.00 0.00 0.00 4.02
399 549 5.011329 ACACTCAACAATACTTCCTCCGTAA 59.989 40.000 0.00 0.00 0.00 3.18
400 550 5.929992 CACTCAACAATACTTCCTCCGTAAA 59.070 40.000 0.00 0.00 0.00 2.01
401 551 6.090898 CACTCAACAATACTTCCTCCGTAAAG 59.909 42.308 0.00 0.00 0.00 1.85
402 552 6.014840 ACTCAACAATACTTCCTCCGTAAAGA 60.015 38.462 0.00 0.00 0.00 2.52
403 553 6.761312 TCAACAATACTTCCTCCGTAAAGAA 58.239 36.000 0.00 0.00 0.00 2.52
404 554 7.218614 TCAACAATACTTCCTCCGTAAAGAAA 58.781 34.615 0.00 0.00 0.00 2.52
405 555 7.881232 TCAACAATACTTCCTCCGTAAAGAAAT 59.119 33.333 0.00 0.00 0.00 2.17
406 556 9.158233 CAACAATACTTCCTCCGTAAAGAAATA 57.842 33.333 0.00 0.00 0.00 1.40
407 557 9.901172 AACAATACTTCCTCCGTAAAGAAATAT 57.099 29.630 0.00 0.00 0.00 1.28
413 563 7.927092 ACTTCCTCCGTAAAGAAATATAAGAGC 59.073 37.037 0.00 0.00 0.00 4.09
414 564 7.356089 TCCTCCGTAAAGAAATATAAGAGCA 57.644 36.000 0.00 0.00 0.00 4.26
417 567 9.360093 CCTCCGTAAAGAAATATAAGAGCATAG 57.640 37.037 0.00 0.00 0.00 2.23
465 617 3.808728 TCACTATTCATAAGGCTGCACC 58.191 45.455 0.50 0.00 39.61 5.01
522 674 3.490933 GCTTTAATCGCCATTTTCTCCCC 60.491 47.826 0.00 0.00 0.00 4.81
533 685 6.374053 CGCCATTTTCTCCCCAAAATAAAATT 59.626 34.615 0.00 0.00 34.77 1.82
557 710 6.240894 TGTGATTTTCTCAGCAGTTTAGGAT 58.759 36.000 0.00 0.00 33.51 3.24
578 737 6.070136 AGGATTCCTAGTTCTTTCCACCTTAC 60.070 42.308 2.49 0.00 28.47 2.34
597 756 1.144057 CGGGACCCACTACTCATGC 59.856 63.158 12.15 0.00 0.00 4.06
671 830 3.635373 TCCGCTAGATATTTTCCGACACT 59.365 43.478 0.00 0.00 0.00 3.55
686 845 0.035458 ACACTGCTAACTCACTGCCC 59.965 55.000 0.00 0.00 0.00 5.36
688 847 0.322975 ACTGCTAACTCACTGCCCAG 59.677 55.000 0.00 0.00 0.00 4.45
759 919 0.036732 TGGAAAGAGAATGCCGTGCT 59.963 50.000 0.00 0.00 0.00 4.40
796 956 4.292178 CAGCGGATCGGCCTCCTC 62.292 72.222 20.46 1.26 32.77 3.71
890 1071 2.585247 GCGGCGATAAGAAGCGGT 60.585 61.111 12.98 0.00 34.37 5.68
1254 1444 4.814294 GCGGATTGCGACGGAGGT 62.814 66.667 0.29 0.00 0.00 3.85
1512 1705 4.803426 GAGGTGGCTGTCTCGGCG 62.803 72.222 0.00 0.00 36.46 6.46
1578 1771 4.873129 GAGATGGCGCGGCGAGAA 62.873 66.667 28.54 10.89 0.00 2.87
1788 1981 2.815308 GACCGCCTCCGTGATGAT 59.185 61.111 0.00 0.00 0.00 2.45
1830 2023 3.407967 TTCGCCCCACCCTCATCC 61.408 66.667 0.00 0.00 0.00 3.51
1985 2183 0.329261 TGCATTGCCTTCAGGTAGCT 59.671 50.000 6.12 0.00 37.57 3.32
2046 2246 2.224079 TGTAACACTACTCGGTCACGAC 59.776 50.000 0.00 0.00 45.59 4.34
2236 2436 6.299141 ACCTATTGGCGTTCAGATGAATAAT 58.701 36.000 0.00 1.84 34.90 1.28
2260 2460 1.197721 GTGCCAGTTCCAAAGTCATCG 59.802 52.381 0.00 0.00 0.00 3.84
2263 2463 2.778299 CCAGTTCCAAAGTCATCGGAA 58.222 47.619 0.00 0.00 36.46 4.30
2373 2657 2.634453 TGTCAGCCAGAGAAGTGATTGA 59.366 45.455 0.00 0.00 0.00 2.57
2476 2760 1.927487 AGAATGCAGTTGCCATGGAA 58.073 45.000 18.40 0.00 41.18 3.53
2538 2822 4.160252 GGTTGGCTGATAATGAATGGTGTT 59.840 41.667 0.00 0.00 0.00 3.32
2572 2856 4.320494 CCAACAGTGCAAATTAGACTGGAC 60.320 45.833 13.22 4.43 41.23 4.02
2713 2997 7.467811 GCCTGATGGTGAACAGTATTTATTCAG 60.468 40.741 0.00 0.00 33.16 3.02
2756 3040 9.632638 ACATTGCTATCTATACAGTTTCCATTT 57.367 29.630 0.00 0.00 0.00 2.32
3763 4057 0.740737 GTGTTCAGGCTGCTGTGTTT 59.259 50.000 10.34 0.00 0.00 2.83
3885 4179 2.010145 TTAGGTGCTCTCAATCACGC 57.990 50.000 0.00 0.00 34.20 5.34
4003 4297 5.876460 GCAATTTTGTCAGCCCTGATAATTT 59.124 36.000 8.05 3.92 42.18 1.82
4115 4411 7.095523 GCTCTTGCAATTGTGATATGTTTGTTT 60.096 33.333 7.40 0.00 39.41 2.83
4131 4427 7.591006 TGTTTGTTTGATATAGTTCTCGTCC 57.409 36.000 0.00 0.00 0.00 4.79
4132 4428 7.383687 TGTTTGTTTGATATAGTTCTCGTCCT 58.616 34.615 0.00 0.00 0.00 3.85
4244 4540 1.378250 GAGCCATGTGCCTGCTTCT 60.378 57.895 2.95 0.00 42.71 2.85
4248 4547 1.001764 CATGTGCCTGCTTCTGGGA 60.002 57.895 0.00 0.00 0.00 4.37
4332 4631 1.038130 AAGGATCGTCCCGACTGGAG 61.038 60.000 1.06 0.00 46.38 3.86
4334 4633 2.043852 ATCGTCCCGACTGGAGCT 60.044 61.111 0.00 0.00 46.38 4.09
4339 4638 1.076727 TCCCGACTGGAGCTGAGAA 59.923 57.895 0.00 0.00 38.61 2.87
4385 4684 1.521681 GCTCGCGCTAAACAGGGAT 60.522 57.895 5.56 0.00 0.00 3.85
4445 4748 0.099436 GGCATGAACCGATGAACAGC 59.901 55.000 0.00 0.00 0.00 4.40
4448 4751 2.677836 GCATGAACCGATGAACAGCTAA 59.322 45.455 0.00 0.00 0.00 3.09
4449 4752 3.485877 GCATGAACCGATGAACAGCTAAC 60.486 47.826 0.00 0.00 0.00 2.34
4450 4753 2.695359 TGAACCGATGAACAGCTAACC 58.305 47.619 0.00 0.00 0.00 2.85
4451 4754 2.007608 GAACCGATGAACAGCTAACCC 58.992 52.381 0.00 0.00 0.00 4.11
4453 4756 0.108329 CCGATGAACAGCTAACCCGT 60.108 55.000 0.00 0.00 0.00 5.28
4457 4760 2.450609 TGAACAGCTAACCCGTCTTC 57.549 50.000 0.00 0.00 0.00 2.87
4458 4761 1.968493 TGAACAGCTAACCCGTCTTCT 59.032 47.619 0.00 0.00 0.00 2.85
4461 4764 3.487120 ACAGCTAACCCGTCTTCTTTT 57.513 42.857 0.00 0.00 0.00 2.27
4480 4786 3.795623 TTACTCCTCATAGACGGTTGC 57.204 47.619 0.00 0.00 0.00 4.17
4609 4915 1.060266 CAAGTCGAATGAAGCGCTCAG 59.940 52.381 12.06 0.00 37.52 3.35
4666 4976 2.584418 CTCGCAGCACGGAGATGG 60.584 66.667 0.00 0.00 43.89 3.51
4767 5081 2.674852 CAGAGGATCATTTCACGGTGTG 59.325 50.000 8.17 0.00 37.82 3.82
4788 5102 5.820947 TGTGTTTCTTTTGTAAGAGACCTCC 59.179 40.000 6.23 0.00 42.11 4.30
4883 5197 7.481642 GTCTCATCTTTCATGCTCATGATTTT 58.518 34.615 12.72 0.00 46.12 1.82
4934 5252 8.567285 ACCAACTAGTAATTGAGATCCAAAAG 57.433 34.615 0.00 0.00 38.43 2.27
5006 5326 3.354948 TGAACATATCAAGGTGCTGCT 57.645 42.857 0.00 0.00 34.30 4.24
5007 5327 4.486125 TGAACATATCAAGGTGCTGCTA 57.514 40.909 0.00 0.00 34.30 3.49
5008 5328 4.445453 TGAACATATCAAGGTGCTGCTAG 58.555 43.478 0.00 0.00 34.30 3.42
5009 5329 3.482156 ACATATCAAGGTGCTGCTAGG 57.518 47.619 0.00 0.00 0.00 3.02
5026 5346 4.948621 TGCTAGGTCTTACTCCTAACTGAC 59.051 45.833 0.00 0.00 37.15 3.51
5099 5419 2.762043 AGAGAGAGGAAGGCGGCC 60.762 66.667 12.11 12.11 0.00 6.13
5159 5479 3.760035 CGGTAGAGGCGGCACACT 61.760 66.667 13.08 10.07 0.00 3.55
5271 5591 2.032170 TGCACGCAACAAAGCAGAT 58.968 47.368 0.00 0.00 32.48 2.90
5272 5592 1.233919 TGCACGCAACAAAGCAGATA 58.766 45.000 0.00 0.00 32.48 1.98
5273 5593 1.811965 TGCACGCAACAAAGCAGATAT 59.188 42.857 0.00 0.00 32.48 1.63
5277 5597 4.671508 GCACGCAACAAAGCAGATATAACA 60.672 41.667 0.00 0.00 0.00 2.41
5302 5622 1.801332 CCGTCCGTCAGTCGAGATT 59.199 57.895 0.00 0.00 42.86 2.40
5305 5625 1.790838 CGTCCGTCAGTCGAGATTGAC 60.791 57.143 15.81 15.81 42.43 3.18
5306 5626 0.809385 TCCGTCAGTCGAGATTGACC 59.191 55.000 18.66 5.91 42.76 4.02
5433 5772 0.321346 TGCCGATGAGCTTCTTGACA 59.679 50.000 0.00 0.00 0.00 3.58
5564 5906 1.001269 ACACGGGAGATCGAGACCA 60.001 57.895 0.00 0.00 0.00 4.02
5578 5920 5.926214 TCGAGACCAATCGATCTAACTAG 57.074 43.478 0.00 0.00 46.20 2.57
5628 5970 0.463295 CTGCATGCCGAGAGATTGGT 60.463 55.000 16.68 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 6.842121 GCAGTAAAGATGCATCGGAAGAAAAA 60.842 38.462 20.67 0.00 43.31 1.94
118 119 2.799412 GAGGAGCAGTAAAGATGCATCG 59.201 50.000 20.67 6.84 46.31 3.84
122 123 1.939255 GCTGAGGAGCAGTAAAGATGC 59.061 52.381 0.00 0.00 46.62 3.91
163 164 8.299570 CAGCATTAGGAACATTTTACAAGTCTT 58.700 33.333 0.00 0.00 0.00 3.01
164 165 7.094205 CCAGCATTAGGAACATTTTACAAGTCT 60.094 37.037 0.00 0.00 0.00 3.24
165 166 7.029563 CCAGCATTAGGAACATTTTACAAGTC 58.970 38.462 0.00 0.00 0.00 3.01
166 167 6.493458 ACCAGCATTAGGAACATTTTACAAGT 59.507 34.615 0.00 0.00 0.00 3.16
167 168 6.924111 ACCAGCATTAGGAACATTTTACAAG 58.076 36.000 0.00 0.00 0.00 3.16
168 169 6.909550 ACCAGCATTAGGAACATTTTACAA 57.090 33.333 0.00 0.00 0.00 2.41
169 170 6.909550 AACCAGCATTAGGAACATTTTACA 57.090 33.333 0.00 0.00 0.00 2.41
170 171 8.520351 AGTAAACCAGCATTAGGAACATTTTAC 58.480 33.333 0.00 0.00 0.00 2.01
171 172 8.519526 CAGTAAACCAGCATTAGGAACATTTTA 58.480 33.333 0.00 0.00 0.00 1.52
176 177 3.756434 GCAGTAAACCAGCATTAGGAACA 59.244 43.478 0.00 0.00 0.00 3.18
177 178 4.010349 AGCAGTAAACCAGCATTAGGAAC 58.990 43.478 0.00 0.00 0.00 3.62
178 179 4.019321 AGAGCAGTAAACCAGCATTAGGAA 60.019 41.667 0.00 0.00 0.00 3.36
180 181 3.878778 AGAGCAGTAAACCAGCATTAGG 58.121 45.455 0.00 0.00 0.00 2.69
182 183 4.937620 CAGAAGAGCAGTAAACCAGCATTA 59.062 41.667 0.00 0.00 0.00 1.90
183 184 3.755378 CAGAAGAGCAGTAAACCAGCATT 59.245 43.478 0.00 0.00 0.00 3.56
184 185 3.008375 TCAGAAGAGCAGTAAACCAGCAT 59.992 43.478 0.00 0.00 0.00 3.79
185 186 2.368548 TCAGAAGAGCAGTAAACCAGCA 59.631 45.455 0.00 0.00 0.00 4.41
186 187 3.045601 TCAGAAGAGCAGTAAACCAGC 57.954 47.619 0.00 0.00 0.00 4.85
187 188 3.862267 CGATCAGAAGAGCAGTAAACCAG 59.138 47.826 0.00 0.00 0.00 4.00
188 189 3.258372 ACGATCAGAAGAGCAGTAAACCA 59.742 43.478 0.00 0.00 0.00 3.67
189 190 3.851098 ACGATCAGAAGAGCAGTAAACC 58.149 45.455 0.00 0.00 0.00 3.27
190 191 6.946229 TTTACGATCAGAAGAGCAGTAAAC 57.054 37.500 0.00 0.00 35.91 2.01
191 192 7.956420 TTTTTACGATCAGAAGAGCAGTAAA 57.044 32.000 0.00 0.00 37.36 2.01
268 270 7.865706 ATATTTGCTGTAAAGAAGTTCGGAT 57.134 32.000 0.00 0.00 0.00 4.18
271 273 8.629986 CAACAATATTTGCTGTAAAGAAGTTCG 58.370 33.333 0.00 0.00 0.00 3.95
285 287 6.709145 TGCAGAACATTCAACAATATTTGC 57.291 33.333 0.00 0.00 0.00 3.68
294 296 9.793252 AATTTAGATGTATGCAGAACATTCAAC 57.207 29.630 16.21 6.23 39.21 3.18
333 482 4.155826 TCGTGAAAACCAGCATTAGGAATG 59.844 41.667 0.00 0.00 41.85 2.67
346 496 6.717413 TGTAGTGTAAATGTTCGTGAAAACC 58.283 36.000 0.00 0.00 0.00 3.27
347 497 9.525007 CTATGTAGTGTAAATGTTCGTGAAAAC 57.475 33.333 0.00 0.00 0.00 2.43
363 513 8.585881 AGTATTGTTGAGTGTTCTATGTAGTGT 58.414 33.333 0.00 0.00 0.00 3.55
378 528 6.395629 TCTTTACGGAGGAAGTATTGTTGAG 58.604 40.000 0.00 0.00 0.00 3.02
390 540 7.356089 TGCTCTTATATTTCTTTACGGAGGA 57.644 36.000 0.00 0.00 0.00 3.71
391 541 9.360093 CTATGCTCTTATATTTCTTTACGGAGG 57.640 37.037 0.00 0.00 0.00 4.30
392 542 9.915629 ACTATGCTCTTATATTTCTTTACGGAG 57.084 33.333 0.00 0.00 0.00 4.63
465 617 3.921119 AGCTTATGATCTCGAGCTCAG 57.079 47.619 22.11 11.37 41.34 3.35
533 685 5.620206 TCCTAAACTGCTGAGAAAATCACA 58.380 37.500 0.00 0.00 33.22 3.58
557 710 4.020839 CGGTAAGGTGGAAAGAACTAGGAA 60.021 45.833 0.00 0.00 0.00 3.36
578 737 1.823295 CATGAGTAGTGGGTCCCGG 59.177 63.158 2.65 0.00 0.00 5.73
635 794 3.443925 CGGAGCTCGCTGAGGTGA 61.444 66.667 7.83 0.00 40.67 4.02
671 830 1.003355 GCTGGGCAGTGAGTTAGCA 60.003 57.895 0.00 0.00 0.00 3.49
790 950 0.998945 AGAGGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
791 951 0.478507 GAGAGGAGGAGGAGGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
792 952 0.996762 GGAGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
793 953 1.541672 GGAGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
794 954 0.998945 AGGGAGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
795 955 0.996762 GAGGGAGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
796 956 1.541672 GAGGGAGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
797 957 1.150536 CGAGGGAGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
798 958 3.063197 GCGAGGGAGAGGAGGAGGA 62.063 68.421 0.00 0.00 0.00 3.71
845 1026 0.937304 GCTTATGCAATCCGAAGCGA 59.063 50.000 0.00 0.00 35.40 4.93
1028 1218 3.760035 AGTAGTCGCACGGCCAGG 61.760 66.667 2.24 0.00 0.00 4.45
1242 1432 4.287781 TCGCAACCTCCGTCGCAA 62.288 61.111 0.00 0.00 0.00 4.85
1985 2183 0.250510 TGTTTGGCTACCACGATGCA 60.251 50.000 0.00 0.00 30.78 3.96
2236 2436 2.173782 TGACTTTGGAACTGGCACCTTA 59.826 45.455 0.00 0.00 0.00 2.69
2260 2460 4.157840 ACAAAGGAATGGACGCTAAATTCC 59.842 41.667 10.28 10.28 46.52 3.01
2263 2463 5.813080 GTACAAAGGAATGGACGCTAAAT 57.187 39.130 0.00 0.00 0.00 1.40
2303 2503 0.469331 TCCGTGAGAACCACAGGAGT 60.469 55.000 0.00 0.00 45.98 3.85
2452 2736 1.725641 TGGCAACTGCATTCTACTCG 58.274 50.000 3.76 0.00 44.36 4.18
2476 2760 0.620556 AACAACCCGATCCATGAGCT 59.379 50.000 0.00 0.00 0.00 4.09
2538 2822 2.703536 TGCACTGTTGGTAGAGGAGAAA 59.296 45.455 0.00 0.00 0.00 2.52
2572 2856 0.595095 GCCAACACCAGCTCAGAAAG 59.405 55.000 0.00 0.00 0.00 2.62
2713 2997 2.921634 TGTCGATGTAGTCAGCAGAC 57.078 50.000 0.05 0.05 45.31 3.51
2756 3040 7.837689 AGGCATACCGAATACTATTATCAGGTA 59.162 37.037 8.23 8.23 42.76 3.08
3224 3508 4.379339 TTTTTCAAAAGGAGGGTGAACG 57.621 40.909 0.00 0.00 31.21 3.95
3283 3567 3.275999 GGGCTATTAACAACATCGTGGT 58.724 45.455 0.00 0.00 0.00 4.16
3554 3843 8.980610 CAACATTGAATTTTGATCAACAGCTAA 58.019 29.630 7.89 0.00 39.43 3.09
3885 4179 6.437477 TCTGTATGGTGGCCTATAACTATCAG 59.563 42.308 3.32 7.22 0.00 2.90
4003 4297 2.780592 TGGTGGGCCTTTATATACAGCA 59.219 45.455 4.53 1.98 34.45 4.41
4107 4403 7.383687 AGGACGAGAACTATATCAAACAAACA 58.616 34.615 0.00 0.00 0.00 2.83
4244 4540 2.610859 GAGCTCCCCAAGGTCCCA 60.611 66.667 0.87 0.00 45.05 4.37
4248 4547 3.827752 GGAAGAGCTCCCCAAGGT 58.172 61.111 10.93 0.00 38.44 3.50
4334 4633 2.359107 CTTGCGGCAGGCTTCTCA 60.359 61.111 1.67 0.00 44.05 3.27
4339 4638 4.845580 CGATCCTTGCGGCAGGCT 62.846 66.667 6.57 0.69 44.05 4.58
4445 4748 5.047519 TGAGGAGTAAAAGAAGACGGGTTAG 60.048 44.000 0.00 0.00 0.00 2.34
4448 4751 3.236896 TGAGGAGTAAAAGAAGACGGGT 58.763 45.455 0.00 0.00 0.00 5.28
4449 4752 3.955650 TGAGGAGTAAAAGAAGACGGG 57.044 47.619 0.00 0.00 0.00 5.28
4450 4753 6.267070 GTCTATGAGGAGTAAAAGAAGACGG 58.733 44.000 0.00 0.00 0.00 4.79
4451 4754 5.966503 CGTCTATGAGGAGTAAAAGAAGACG 59.033 44.000 6.65 6.65 45.01 4.18
4453 4756 5.950549 ACCGTCTATGAGGAGTAAAAGAAGA 59.049 40.000 0.00 0.00 0.00 2.87
4457 4760 4.567159 GCAACCGTCTATGAGGAGTAAAAG 59.433 45.833 0.00 0.00 0.00 2.27
4458 4761 4.020928 TGCAACCGTCTATGAGGAGTAAAA 60.021 41.667 0.00 0.00 0.00 1.52
4461 4764 2.730382 TGCAACCGTCTATGAGGAGTA 58.270 47.619 0.00 0.00 0.00 2.59
4480 4786 4.383649 CACCAGAAACGCATGAGAAAATTG 59.616 41.667 2.50 0.00 0.00 2.32
4565 4871 2.046700 CGGCCTTTCACCCGCTTA 60.047 61.111 0.00 0.00 37.85 3.09
4757 5068 5.411977 TCTTACAAAAGAAACACACCGTGAA 59.588 36.000 5.28 0.00 38.81 3.18
4759 5070 5.064198 TCTCTTACAAAAGAAACACACCGTG 59.936 40.000 0.00 0.00 41.19 4.94
4760 5071 5.064325 GTCTCTTACAAAAGAAACACACCGT 59.936 40.000 0.00 0.00 41.19 4.83
4761 5072 5.499047 GTCTCTTACAAAAGAAACACACCG 58.501 41.667 0.00 0.00 41.19 4.94
4762 5073 5.589050 AGGTCTCTTACAAAAGAAACACACC 59.411 40.000 0.00 0.00 41.19 4.16
4767 5081 4.760715 GGGGAGGTCTCTTACAAAAGAAAC 59.239 45.833 0.00 0.00 41.19 2.78
4788 5102 3.492102 TGTGTTCTGAGGAGAAAAGGG 57.508 47.619 0.00 0.00 40.00 3.95
4883 5197 5.997746 GGTTAAGCAGCAGTATCCATTCATA 59.002 40.000 0.00 0.00 0.00 2.15
4934 5252 4.394729 TCTTGGGAGTACATTGTTTGTCC 58.605 43.478 0.00 0.00 39.87 4.02
4978 5298 8.081633 CAGCACCTTGATATGTTCAAAAGTTAA 58.918 33.333 0.00 0.00 43.64 2.01
4986 5306 3.354948 AGCAGCACCTTGATATGTTCA 57.645 42.857 0.00 0.00 0.00 3.18
5006 5326 5.014966 ACCAGTCAGTTAGGAGTAAGACCTA 59.985 44.000 0.00 0.00 38.76 3.08
5007 5327 4.202695 ACCAGTCAGTTAGGAGTAAGACCT 60.203 45.833 0.00 0.00 41.05 3.85
5008 5328 4.087907 ACCAGTCAGTTAGGAGTAAGACC 58.912 47.826 0.00 0.00 0.00 3.85
5009 5329 4.765856 TGACCAGTCAGTTAGGAGTAAGAC 59.234 45.833 0.00 0.00 34.14 3.01
5026 5346 2.047844 CGGCCAGACACTGACCAG 60.048 66.667 2.24 0.00 33.52 4.00
5174 5494 0.112218 CCATGTGGGGGAACAAGACA 59.888 55.000 0.00 0.00 32.81 3.41
5302 5622 2.110213 GTTCGTGCACCCTGGTCA 59.890 61.111 12.15 0.00 0.00 4.02
5305 5625 2.203139 TGTGTTCGTGCACCCTGG 60.203 61.111 12.15 0.00 38.52 4.45
5306 5626 0.603707 ATCTGTGTTCGTGCACCCTG 60.604 55.000 12.15 0.00 38.52 4.45
5365 5697 3.105514 CGTTACGTACGGCAAGGAA 57.894 52.632 21.06 0.81 46.42 3.36
5433 5772 2.103042 GCTGCTCACGGCGATCTTT 61.103 57.895 16.62 0.00 45.43 2.52
5564 5906 5.512473 GTTCACTCGCTAGTTAGATCGATT 58.488 41.667 0.00 0.00 31.97 3.34
5578 5920 0.038526 TCCTTCCTTCGTTCACTCGC 60.039 55.000 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.