Multiple sequence alignment - TraesCS7D01G199700

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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 TraesCS7D01G199700 chr7D 100.000 3035 0 0 1 3035 156690617 156687583 0 5605
1 TraesCS7D01G199700 chr7A 90.782 3081 167 44 1 3035 211644089 211641080 0 4008
2 TraesCS7D01G199700 chr7B 92.504 1761 96 21 532 2272 118981997 118980253 0 2488
3 TraesCS7D01G199700 chr7B 95.811 740 18 6 2301 3035 118980253 118979522 0 1182


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 TraesCS7D01G199700 chr7D 156687583 156690617 3034 True 5605 5605 100.0000 1 3035 1 chr7D.!!$R1 3034
1 TraesCS7D01G199700 chr7A 211641080 211644089 3009 True 4008 4008 90.7820 1 3035 1 chr7A.!!$R1 3034
2 TraesCS7D01G199700 chr7B 118979522 118981997 2475 True 1835 2488 94.1575 532 3035 2 chr7B.!!$R1 2503

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
499 515 0.380378 TTTCTTCCGTTGCAGCACAC 59.620 50.0 0.00 0.0 0.0 3.82 F
1241 1277 0.032416 GCTGTCAGTACCCCCTCCTA 60.032 60.0 0.93 0.0 0.0 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1959 2007 1.117994 CCTGCACATAGGCTCTGAGA 58.882 55.000 9.28 0.00 34.04 3.27 R
2067 2115 1.472082 TGCACTTGACCACAACAGTTG 59.528 47.619 12.03 12.03 32.27 3.16 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
38 41 0.405973 AGCTTTCCCTTTCCCTGGTC 59.594 55.000 0.00 0.00 0.00 4.02
103 106 1.156736 AAAAGACCTCGAACCATGCG 58.843 50.000 0.00 0.00 0.00 4.73
209 212 7.733969 AGTCACATGCATCTACTCATTTAGAT 58.266 34.615 0.00 0.00 39.05 1.98
210 213 8.209584 AGTCACATGCATCTACTCATTTAGATT 58.790 33.333 0.00 0.00 36.79 2.40
211 214 8.494347 GTCACATGCATCTACTCATTTAGATTC 58.506 37.037 0.00 0.00 36.79 2.52
212 215 7.658982 TCACATGCATCTACTCATTTAGATTCC 59.341 37.037 0.00 0.00 36.79 3.01
213 216 6.648310 ACATGCATCTACTCATTTAGATTCCG 59.352 38.462 0.00 0.00 36.79 4.30
214 217 4.991056 TGCATCTACTCATTTAGATTCCGC 59.009 41.667 0.00 0.00 36.79 5.54
215 218 4.390297 GCATCTACTCATTTAGATTCCGCC 59.610 45.833 0.00 0.00 36.79 6.13
216 219 5.541845 CATCTACTCATTTAGATTCCGCCA 58.458 41.667 0.00 0.00 36.79 5.69
217 220 5.607939 TCTACTCATTTAGATTCCGCCAA 57.392 39.130 0.00 0.00 0.00 4.52
218 221 5.357257 TCTACTCATTTAGATTCCGCCAAC 58.643 41.667 0.00 0.00 0.00 3.77
219 222 3.279434 ACTCATTTAGATTCCGCCAACC 58.721 45.455 0.00 0.00 0.00 3.77
220 223 3.054361 ACTCATTTAGATTCCGCCAACCT 60.054 43.478 0.00 0.00 0.00 3.50
221 224 3.541632 TCATTTAGATTCCGCCAACCTC 58.458 45.455 0.00 0.00 0.00 3.85
222 225 2.413310 TTTAGATTCCGCCAACCTCC 57.587 50.000 0.00 0.00 0.00 4.30
223 226 1.580059 TTAGATTCCGCCAACCTCCT 58.420 50.000 0.00 0.00 0.00 3.69
224 227 2.464796 TAGATTCCGCCAACCTCCTA 57.535 50.000 0.00 0.00 0.00 2.94
225 228 1.580059 AGATTCCGCCAACCTCCTAA 58.420 50.000 0.00 0.00 0.00 2.69
226 229 1.913419 AGATTCCGCCAACCTCCTAAA 59.087 47.619 0.00 0.00 0.00 1.85
227 230 2.014857 GATTCCGCCAACCTCCTAAAC 58.985 52.381 0.00 0.00 0.00 2.01
228 231 0.766131 TTCCGCCAACCTCCTAAACA 59.234 50.000 0.00 0.00 0.00 2.83
229 232 0.988832 TCCGCCAACCTCCTAAACAT 59.011 50.000 0.00 0.00 0.00 2.71
230 233 1.353022 TCCGCCAACCTCCTAAACATT 59.647 47.619 0.00 0.00 0.00 2.71
231 234 1.472480 CCGCCAACCTCCTAAACATTG 59.528 52.381 0.00 0.00 0.00 2.82
251 254 1.940613 GTCCATCGCCCTATTGTTGTC 59.059 52.381 0.00 0.00 0.00 3.18
259 262 0.390603 CCTATTGTTGTCGTCGGCCA 60.391 55.000 2.24 0.00 0.00 5.36
309 312 4.320546 TCCATGGATGTGAACCAAGAAT 57.679 40.909 11.44 0.00 40.93 2.40
336 339 2.884012 ACTCGGCAATCAATGTTTGTCA 59.116 40.909 9.01 0.00 0.00 3.58
376 392 4.979943 TTTTTCTTTACCCCGAACGTTT 57.020 36.364 0.46 0.00 0.00 3.60
396 412 5.359493 GTTTTACGGTAATTTTGCTTTGCG 58.641 37.500 0.73 0.00 0.00 4.85
402 418 1.130955 AATTTTGCTTTGCGTGCTCG 58.869 45.000 3.31 3.31 40.37 5.03
419 435 2.592194 CTCGCTAAGAAACGTGTGCTA 58.408 47.619 0.00 0.00 0.00 3.49
421 437 1.059264 CGCTAAGAAACGTGTGCTAGC 59.941 52.381 8.10 8.10 0.00 3.42
422 438 2.338500 GCTAAGAAACGTGTGCTAGCT 58.662 47.619 17.23 0.00 0.00 3.32
433 449 4.023107 ACGTGTGCTAGCTATAGTATGTGG 60.023 45.833 17.23 0.00 0.00 4.17
436 452 5.692204 GTGTGCTAGCTATAGTATGTGGTTG 59.308 44.000 17.23 0.00 0.00 3.77
451 467 4.825422 TGTGGTTGAGATTTGCTCTAGAG 58.175 43.478 15.85 15.85 44.27 2.43
485 501 8.474025 TGAATGTTGTGTTAGGATTTGTTTCTT 58.526 29.630 0.00 0.00 0.00 2.52
486 502 8.871686 AATGTTGTGTTAGGATTTGTTTCTTC 57.128 30.769 0.00 0.00 0.00 2.87
488 504 5.682943 TGTGTTAGGATTTGTTTCTTCCG 57.317 39.130 0.00 0.00 34.61 4.30
489 505 5.127491 TGTGTTAGGATTTGTTTCTTCCGT 58.873 37.500 0.00 0.00 34.61 4.69
499 515 0.380378 TTTCTTCCGTTGCAGCACAC 59.620 50.000 0.00 0.00 0.00 3.82
500 516 0.746204 TTCTTCCGTTGCAGCACACA 60.746 50.000 0.00 0.00 0.00 3.72
505 521 1.499056 CGTTGCAGCACACAGATCC 59.501 57.895 0.00 0.00 0.00 3.36
506 522 1.229975 CGTTGCAGCACACAGATCCA 61.230 55.000 0.00 0.00 0.00 3.41
508 524 1.542915 GTTGCAGCACACAGATCCATT 59.457 47.619 0.00 0.00 0.00 3.16
513 529 3.011818 CAGCACACAGATCCATTTGCTA 58.988 45.455 7.04 0.00 38.24 3.49
521 537 6.319658 ACACAGATCCATTTGCTAGTAATTGG 59.680 38.462 21.72 21.72 34.14 3.16
527 543 6.727394 TCCATTTGCTAGTAATTGGTAAGGT 58.273 36.000 24.69 0.00 34.36 3.50
528 544 6.601613 TCCATTTGCTAGTAATTGGTAAGGTG 59.398 38.462 24.69 6.76 34.36 4.00
529 545 6.601613 CCATTTGCTAGTAATTGGTAAGGTGA 59.398 38.462 20.26 0.00 0.00 4.02
530 546 7.415206 CCATTTGCTAGTAATTGGTAAGGTGAC 60.415 40.741 20.26 0.00 0.00 3.67
553 569 3.680937 TCGCACGGTATTTCTTAACTTGG 59.319 43.478 0.00 0.00 0.00 3.61
568 584 6.879458 TCTTAACTTGGCTTCACTTAATCTCC 59.121 38.462 0.00 0.00 0.00 3.71
598 614 2.058705 TCCCCCACACTACACAATCAA 58.941 47.619 0.00 0.00 0.00 2.57
610 626 2.362077 ACACAATCAAGTGAGCCCAAAC 59.638 45.455 0.57 0.00 42.05 2.93
615 631 3.410631 TCAAGTGAGCCCAAACGATTA 57.589 42.857 0.00 0.00 0.00 1.75
621 637 2.682856 TGAGCCCAAACGATTAATCAGC 59.317 45.455 15.57 7.62 0.00 4.26
625 641 3.002759 GCCCAAACGATTAATCAGCTCTC 59.997 47.826 15.57 0.00 0.00 3.20
650 667 2.285083 TCCGACCAAAATATTCGCCAG 58.715 47.619 0.00 0.00 0.00 4.85
652 669 3.118702 TCCGACCAAAATATTCGCCAGTA 60.119 43.478 0.00 0.00 0.00 2.74
653 670 3.001939 CCGACCAAAATATTCGCCAGTAC 59.998 47.826 0.00 0.00 0.00 2.73
671 688 2.217510 ACGGCCGAGTATATCCATCT 57.782 50.000 35.90 0.00 0.00 2.90
673 690 3.899726 ACGGCCGAGTATATCCATCTAT 58.100 45.455 35.90 0.00 0.00 1.98
675 692 4.138290 CGGCCGAGTATATCCATCTATCT 58.862 47.826 24.07 0.00 0.00 1.98
677 694 5.179742 CGGCCGAGTATATCCATCTATCTAC 59.820 48.000 24.07 0.00 0.00 2.59
678 695 6.300703 GGCCGAGTATATCCATCTATCTACT 58.699 44.000 0.00 0.00 0.00 2.57
704 721 6.418585 ACTACTTTTCGTAAGCTAATTGGC 57.581 37.500 5.52 5.52 37.18 4.52
713 730 4.985409 CGTAAGCTAATTGGCCTAAGAGAG 59.015 45.833 10.54 0.00 0.00 3.20
714 731 5.452077 CGTAAGCTAATTGGCCTAAGAGAGT 60.452 44.000 10.54 0.00 0.00 3.24
716 733 6.561519 AAGCTAATTGGCCTAAGAGAGTAA 57.438 37.500 10.54 0.00 0.00 2.24
718 735 6.764379 AGCTAATTGGCCTAAGAGAGTAATC 58.236 40.000 10.54 0.00 0.00 1.75
719 736 6.556874 AGCTAATTGGCCTAAGAGAGTAATCT 59.443 38.462 10.54 0.00 0.00 2.40
720 737 7.071824 AGCTAATTGGCCTAAGAGAGTAATCTT 59.928 37.037 10.54 0.00 42.20 2.40
768 791 3.614176 CGTATGCGATCATATCCACTTGG 59.386 47.826 0.00 0.00 41.33 3.61
788 813 2.047655 CTACGAAAGCCGGGTGCA 60.048 61.111 7.07 0.00 44.83 4.57
849 874 1.067354 CATTTCAGCCAAGCAAGTCCC 60.067 52.381 0.00 0.00 0.00 4.46
1220 1248 5.068460 CCAGAAGTCAGGTAAAGATCTCGAT 59.932 44.000 0.00 0.00 0.00 3.59
1228 1264 4.160439 AGGTAAAGATCTCGATTGCTGTCA 59.840 41.667 0.00 0.00 0.00 3.58
1229 1265 4.505922 GGTAAAGATCTCGATTGCTGTCAG 59.494 45.833 0.00 0.00 0.00 3.51
1231 1267 4.991153 AAGATCTCGATTGCTGTCAGTA 57.009 40.909 0.00 0.00 0.00 2.74
1233 1269 2.941453 TCTCGATTGCTGTCAGTACC 57.059 50.000 0.93 0.00 0.00 3.34
1236 1272 0.462047 CGATTGCTGTCAGTACCCCC 60.462 60.000 0.93 0.00 0.00 5.40
1237 1273 0.912486 GATTGCTGTCAGTACCCCCT 59.088 55.000 0.93 0.00 0.00 4.79
1238 1274 0.912486 ATTGCTGTCAGTACCCCCTC 59.088 55.000 0.93 0.00 0.00 4.30
1239 1275 1.198759 TTGCTGTCAGTACCCCCTCC 61.199 60.000 0.93 0.00 0.00 4.30
1240 1276 1.306226 GCTGTCAGTACCCCCTCCT 60.306 63.158 0.93 0.00 0.00 3.69
1241 1277 0.032416 GCTGTCAGTACCCCCTCCTA 60.032 60.000 0.93 0.00 0.00 2.94
1242 1278 1.777941 CTGTCAGTACCCCCTCCTAC 58.222 60.000 0.00 0.00 0.00 3.18
1250 1286 2.286121 CCCCTCCTACCCTTGGCA 60.286 66.667 0.00 0.00 0.00 4.92
1269 1305 6.899393 TGGCAGTTTATTTCTTGATTGAGT 57.101 33.333 0.00 0.00 0.00 3.41
1282 1318 2.415168 TGATTGAGTGAAACGAATCGGC 59.585 45.455 7.80 0.00 45.86 5.54
1329 1371 1.074072 ATGGCTTGGCGTTGTACCA 59.926 52.632 0.00 0.00 34.65 3.25
1368 1410 5.777732 AGATAAGAGTAGATCCGCTGGATTT 59.222 40.000 10.72 8.26 43.27 2.17
1385 1427 2.010582 TTTTGGCCTGTTCGTGGTGC 62.011 55.000 3.32 0.00 0.00 5.01
1441 1484 4.084537 GCTACGGTCGATATCCATGTTTTG 60.085 45.833 0.00 0.00 0.00 2.44
1569 1614 0.110238 CGCGTGGATTGTTGGTGAAG 60.110 55.000 0.00 0.00 0.00 3.02
1583 1628 3.426615 TGGTGAAGTTATGCGGGATTTT 58.573 40.909 0.00 0.00 0.00 1.82
1782 1830 6.839124 AACAAACCTTATCTGCATTGATGA 57.161 33.333 0.00 0.00 0.00 2.92
1827 1875 6.202570 GCAGCTCATCTTAATCTTGTTAGAGG 59.797 42.308 0.00 0.00 32.92 3.69
1911 1959 2.614969 AAGATGGGGAGGGCAGCA 60.615 61.111 0.00 0.00 0.00 4.41
2048 2096 4.093556 CCCGAAATGAAGCACTTTAGTCTC 59.906 45.833 0.00 0.00 0.00 3.36
2067 2115 3.562141 TCTCTCTGTGACTCGCTATTAGC 59.438 47.826 5.56 5.56 38.02 3.09
2143 2191 7.492524 GCGTCCATAATTCAGAGGATATCATA 58.507 38.462 4.83 0.00 31.91 2.15
2213 2261 2.583024 TGTGATGGTTGATGGCTTCA 57.417 45.000 0.00 0.00 0.00 3.02
2330 2378 6.066690 ACTGCAGACATTTGGATATTGCTAT 58.933 36.000 23.35 0.00 0.00 2.97
2412 2460 6.347888 GGAATTTGTGAATTTTGTGAGCATGG 60.348 38.462 0.00 0.00 35.65 3.66
2431 2479 4.293662 TGGATGTGCTGTGGTATTTGTA 57.706 40.909 0.00 0.00 0.00 2.41
2491 2544 4.339247 CCACATTTTATCTAACAGCCCAGG 59.661 45.833 0.00 0.00 0.00 4.45
2721 2775 3.903467 TCTCCTCTCTTATACAGCTGCA 58.097 45.455 15.27 0.00 0.00 4.41
2833 2887 5.146010 TGCCAAAATAAAATGGACAGTCC 57.854 39.130 13.35 13.35 39.12 3.85
2947 3003 4.641094 GTCGAATCCTTTCTAGAGTCCTCA 59.359 45.833 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 41 2.466867 CGGAAATTGTGAGGGTCCG 58.533 57.895 0.00 0.00 44.60 4.79
75 78 7.393841 TGGTTCGAGGTCTTTTTCTTTAAAA 57.606 32.000 0.00 0.00 34.64 1.52
103 106 1.243902 TGAAATTTGTCCTCCACGGC 58.756 50.000 0.00 0.00 0.00 5.68
188 191 6.648310 CGGAATCTAAATGAGTAGATGCATGT 59.352 38.462 2.46 1.37 39.44 3.21
209 212 0.766131 TGTTTAGGAGGTTGGCGGAA 59.234 50.000 0.00 0.00 0.00 4.30
210 213 0.988832 ATGTTTAGGAGGTTGGCGGA 59.011 50.000 0.00 0.00 0.00 5.54
211 214 1.472480 CAATGTTTAGGAGGTTGGCGG 59.528 52.381 0.00 0.00 0.00 6.13
212 215 2.159382 ACAATGTTTAGGAGGTTGGCG 58.841 47.619 0.00 0.00 0.00 5.69
213 216 2.492088 GGACAATGTTTAGGAGGTTGGC 59.508 50.000 0.00 0.00 0.00 4.52
214 217 3.761897 TGGACAATGTTTAGGAGGTTGG 58.238 45.455 0.00 0.00 0.00 3.77
215 218 4.094887 CGATGGACAATGTTTAGGAGGTTG 59.905 45.833 0.00 0.00 0.00 3.77
216 219 4.261801 CGATGGACAATGTTTAGGAGGTT 58.738 43.478 0.00 0.00 0.00 3.50
217 220 3.873910 CGATGGACAATGTTTAGGAGGT 58.126 45.455 0.00 0.00 0.00 3.85
218 221 2.614057 GCGATGGACAATGTTTAGGAGG 59.386 50.000 0.00 0.00 0.00 4.30
219 222 2.614057 GGCGATGGACAATGTTTAGGAG 59.386 50.000 0.00 0.00 0.00 3.69
220 223 2.639065 GGCGATGGACAATGTTTAGGA 58.361 47.619 0.00 0.00 0.00 2.94
221 224 1.676006 GGGCGATGGACAATGTTTAGG 59.324 52.381 0.00 0.00 0.00 2.69
222 225 2.643551 AGGGCGATGGACAATGTTTAG 58.356 47.619 0.00 0.00 0.00 1.85
223 226 2.799126 AGGGCGATGGACAATGTTTA 57.201 45.000 0.00 0.00 0.00 2.01
224 227 2.799126 TAGGGCGATGGACAATGTTT 57.201 45.000 0.00 0.00 0.00 2.83
225 228 2.951642 CAATAGGGCGATGGACAATGTT 59.048 45.455 0.00 0.00 0.00 2.71
226 229 2.092429 ACAATAGGGCGATGGACAATGT 60.092 45.455 0.00 0.00 0.00 2.71
227 230 2.575532 ACAATAGGGCGATGGACAATG 58.424 47.619 0.00 0.00 0.00 2.82
228 231 2.951642 CAACAATAGGGCGATGGACAAT 59.048 45.455 0.00 0.00 0.00 2.71
229 232 2.290641 ACAACAATAGGGCGATGGACAA 60.291 45.455 0.00 0.00 0.00 3.18
230 233 1.280710 ACAACAATAGGGCGATGGACA 59.719 47.619 0.00 0.00 0.00 4.02
231 234 1.940613 GACAACAATAGGGCGATGGAC 59.059 52.381 0.00 0.00 0.00 4.02
259 262 0.463654 ACACGGATTATGGTGCGCAT 60.464 50.000 15.91 0.00 37.68 4.73
306 309 1.202114 TGATTGCCGAGTTGCCAATTC 59.798 47.619 0.00 0.00 0.00 2.17
309 312 1.067706 CATTGATTGCCGAGTTGCCAA 60.068 47.619 0.00 0.00 0.00 4.52
328 331 3.529533 CAAAGCAAATGGGTGACAAACA 58.470 40.909 0.00 0.00 0.00 2.83
336 339 2.934886 AACATGCAAAGCAAATGGGT 57.065 40.000 0.00 0.00 43.62 4.51
362 365 1.789506 CCGTAAAACGTTCGGGGTAA 58.210 50.000 16.76 0.00 40.58 2.85
369 372 6.736807 AAGCAAAATTACCGTAAAACGTTC 57.263 33.333 0.00 0.00 40.58 3.95
376 392 3.975670 CACGCAAAGCAAAATTACCGTAA 59.024 39.130 0.00 0.00 0.00 3.18
396 412 1.136611 CACACGTTTCTTAGCGAGCAC 60.137 52.381 0.00 0.00 0.00 4.40
402 418 2.338500 AGCTAGCACACGTTTCTTAGC 58.662 47.619 18.83 9.64 0.00 3.09
408 424 5.977725 CACATACTATAGCTAGCACACGTTT 59.022 40.000 18.83 0.00 0.00 3.60
412 428 5.455056 ACCACATACTATAGCTAGCACAC 57.545 43.478 18.83 0.00 0.00 3.82
419 435 6.708054 GCAAATCTCAACCACATACTATAGCT 59.292 38.462 0.00 0.00 0.00 3.32
421 437 8.147058 AGAGCAAATCTCAACCACATACTATAG 58.853 37.037 0.00 0.00 44.35 1.31
422 438 8.023021 AGAGCAAATCTCAACCACATACTATA 57.977 34.615 0.00 0.00 44.35 1.31
456 472 7.288810 ACAAATCCTAACACAACATTCATGT 57.711 32.000 0.00 0.00 44.20 3.21
461 477 7.926018 GGAAGAAACAAATCCTAACACAACATT 59.074 33.333 0.00 0.00 0.00 2.71
466 482 5.127491 ACGGAAGAAACAAATCCTAACACA 58.873 37.500 0.00 0.00 0.00 3.72
470 486 4.580995 TGCAACGGAAGAAACAAATCCTAA 59.419 37.500 0.00 0.00 0.00 2.69
485 501 0.950555 GATCTGTGTGCTGCAACGGA 60.951 55.000 20.61 20.61 0.00 4.69
486 502 1.499056 GATCTGTGTGCTGCAACGG 59.501 57.895 2.77 10.32 0.00 4.44
488 504 1.171308 ATGGATCTGTGTGCTGCAAC 58.829 50.000 2.77 5.97 0.00 4.17
489 505 1.913778 AATGGATCTGTGTGCTGCAA 58.086 45.000 2.77 0.00 0.00 4.08
499 515 6.949352 ACCAATTACTAGCAAATGGATCTG 57.051 37.500 15.51 0.00 0.00 2.90
500 516 7.721399 CCTTACCAATTACTAGCAAATGGATCT 59.279 37.037 15.51 0.00 0.00 2.75
505 521 7.336931 AGTCACCTTACCAATTACTAGCAAATG 59.663 37.037 0.00 0.00 0.00 2.32
506 522 7.402862 AGTCACCTTACCAATTACTAGCAAAT 58.597 34.615 0.00 0.00 0.00 2.32
508 524 6.368779 AGTCACCTTACCAATTACTAGCAA 57.631 37.500 0.00 0.00 0.00 3.91
513 529 3.259876 TGCGAGTCACCTTACCAATTACT 59.740 43.478 0.00 0.00 0.00 2.24
521 537 0.523072 TACCGTGCGAGTCACCTTAC 59.477 55.000 0.00 0.00 42.69 2.34
527 543 2.736144 AAGAAATACCGTGCGAGTCA 57.264 45.000 0.00 0.00 0.00 3.41
528 544 4.171754 AGTTAAGAAATACCGTGCGAGTC 58.828 43.478 0.00 0.00 0.00 3.36
529 545 4.184079 AGTTAAGAAATACCGTGCGAGT 57.816 40.909 0.00 0.00 0.00 4.18
530 546 4.201685 CCAAGTTAAGAAATACCGTGCGAG 60.202 45.833 0.00 0.00 0.00 5.03
541 557 8.691661 AGATTAAGTGAAGCCAAGTTAAGAAA 57.308 30.769 0.00 0.00 0.00 2.52
553 569 6.587273 AGAACTATGGGAGATTAAGTGAAGC 58.413 40.000 0.00 0.00 0.00 3.86
568 584 1.916181 AGTGTGGGGGAAGAACTATGG 59.084 52.381 0.00 0.00 0.00 2.74
598 614 3.941483 CTGATTAATCGTTTGGGCTCACT 59.059 43.478 10.80 0.00 0.00 3.41
610 626 2.723658 GAGCACGAGAGCTGATTAATCG 59.276 50.000 10.80 6.90 46.75 3.34
615 631 1.140589 CGGAGCACGAGAGCTGATT 59.859 57.895 6.51 0.00 46.75 2.57
625 641 2.285602 CGAATATTTTGGTCGGAGCACG 60.286 50.000 9.78 4.64 46.11 5.34
650 667 3.015327 AGATGGATATACTCGGCCGTAC 58.985 50.000 27.15 5.61 0.00 3.67
652 669 2.217510 AGATGGATATACTCGGCCGT 57.782 50.000 27.15 9.68 0.00 5.68
653 670 4.138290 AGATAGATGGATATACTCGGCCG 58.862 47.826 22.12 22.12 0.00 6.13
656 673 8.832521 GTTGAGTAGATAGATGGATATACTCGG 58.167 40.741 11.50 0.00 46.60 4.63
671 688 8.954350 AGCTTACGAAAAGTAGTTGAGTAGATA 58.046 33.333 0.00 0.00 36.56 1.98
673 690 7.211966 AGCTTACGAAAAGTAGTTGAGTAGA 57.788 36.000 0.00 0.00 36.56 2.59
675 692 9.918630 AATTAGCTTACGAAAAGTAGTTGAGTA 57.081 29.630 0.00 0.00 36.56 2.59
677 694 8.169268 CCAATTAGCTTACGAAAAGTAGTTGAG 58.831 37.037 0.00 0.00 36.56 3.02
678 695 7.360607 GCCAATTAGCTTACGAAAAGTAGTTGA 60.361 37.037 0.00 0.00 36.56 3.18
768 791 1.810030 CACCCGGCTTTCGTAGAGC 60.810 63.158 0.00 0.00 38.43 4.09
849 874 1.595109 TGTGGTTGCTCAGTCGCTG 60.595 57.895 1.02 1.02 0.00 5.18
1061 1088 2.232298 GAAGAGCGAGTGAGGGGGTG 62.232 65.000 0.00 0.00 0.00 4.61
1062 1089 1.985116 GAAGAGCGAGTGAGGGGGT 60.985 63.158 0.00 0.00 0.00 4.95
1063 1090 1.261238 AAGAAGAGCGAGTGAGGGGG 61.261 60.000 0.00 0.00 0.00 5.40
1066 1093 0.179150 CGGAAGAAGAGCGAGTGAGG 60.179 60.000 0.00 0.00 0.00 3.86
1067 1094 0.523966 ACGGAAGAAGAGCGAGTGAG 59.476 55.000 0.00 0.00 0.00 3.51
1068 1095 0.959553 AACGGAAGAAGAGCGAGTGA 59.040 50.000 0.00 0.00 0.00 3.41
1220 1248 1.198759 GGAGGGGGTACTGACAGCAA 61.199 60.000 1.25 0.00 0.00 3.91
1228 1264 0.342313 CAAGGGTAGGAGGGGGTACT 59.658 60.000 0.00 0.00 0.00 2.73
1229 1265 0.693430 CCAAGGGTAGGAGGGGGTAC 60.693 65.000 0.00 0.00 0.00 3.34
1231 1267 2.459710 CCAAGGGTAGGAGGGGGT 59.540 66.667 0.00 0.00 0.00 4.95
1233 1269 2.286121 TGCCAAGGGTAGGAGGGG 60.286 66.667 0.00 0.00 0.00 4.79
1236 1272 3.933861 ATAAACTGCCAAGGGTAGGAG 57.066 47.619 5.37 0.00 39.75 3.69
1237 1273 4.291249 AGAAATAAACTGCCAAGGGTAGGA 59.709 41.667 5.37 0.00 39.75 2.94
1238 1274 4.600062 AGAAATAAACTGCCAAGGGTAGG 58.400 43.478 5.37 0.00 39.75 3.18
1239 1275 5.710099 TCAAGAAATAAACTGCCAAGGGTAG 59.290 40.000 0.00 0.00 41.23 3.18
1240 1276 5.636123 TCAAGAAATAAACTGCCAAGGGTA 58.364 37.500 0.00 0.00 0.00 3.69
1241 1277 4.479158 TCAAGAAATAAACTGCCAAGGGT 58.521 39.130 0.00 0.00 0.00 4.34
1242 1278 5.665916 ATCAAGAAATAAACTGCCAAGGG 57.334 39.130 0.00 0.00 0.00 3.95
1250 1286 8.836413 TCGTTTCACTCAATCAAGAAATAAACT 58.164 29.630 0.00 0.00 33.18 2.66
1269 1305 2.045731 GGGGGCCGATTCGTTTCA 60.046 61.111 5.20 0.00 0.00 2.69
1291 1327 6.033341 GCCATGTAATAATCAAACAAGCGAA 58.967 36.000 0.00 0.00 0.00 4.70
1368 1410 2.904866 GCACCACGAACAGGCCAA 60.905 61.111 5.01 0.00 0.00 4.52
1500 1544 3.245052 CCAAATGGTTCTCTTCTCACCCT 60.245 47.826 0.00 0.00 0.00 4.34
1569 1614 2.939460 ACTGCAAAATCCCGCATAAC 57.061 45.000 0.00 0.00 37.54 1.89
1911 1959 1.980765 TCATGGTTCTCAAGCACTCCT 59.019 47.619 0.00 0.00 42.32 3.69
1959 2007 1.117994 CCTGCACATAGGCTCTGAGA 58.882 55.000 9.28 0.00 34.04 3.27
2048 2096 3.699779 TGCTAATAGCGAGTCACAGAG 57.300 47.619 7.84 0.00 46.26 3.35
2067 2115 1.472082 TGCACTTGACCACAACAGTTG 59.528 47.619 12.03 12.03 32.27 3.16
2143 2191 9.014297 CATGGTTCTTTCAATAAGAGGTACTTT 57.986 33.333 0.00 0.00 41.55 2.66
2213 2261 9.865321 CCACAATCTCAATGAAACAGATATTTT 57.135 29.630 0.00 0.00 0.00 1.82
2299 2347 2.223340 CCAAATGTCTGCAGTAATCGCC 60.223 50.000 14.67 0.00 0.00 5.54
2330 2378 5.451242 GGAACACACTTCAAAATACCAGCAA 60.451 40.000 0.00 0.00 0.00 3.91
2412 2460 4.261801 ACCTACAAATACCACAGCACATC 58.738 43.478 0.00 0.00 0.00 3.06
2465 2515 6.668645 TGGGCTGTTAGATAAAATGTGGTAT 58.331 36.000 0.00 0.00 0.00 2.73
2491 2544 5.470368 TGCATCTGAGTACTACAACAAGAC 58.530 41.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.