Multiple sequence alignment - TraesCS5A01G355800

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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 TraesCS5A01G355800 chr5A 100.000 3282 0 0 1 3282 558253176 558249895 0.000000e+00 6061
1 TraesCS5A01G355800 chr5D 94.817 1505 68 5 945 2442 441887712 441886211 0.000000e+00 2338
2 TraesCS5A01G355800 chr5D 89.915 823 51 13 2486 3282 441886213 441885397 0.000000e+00 1031
3 TraesCS5A01G355800 chr5D 84.340 894 72 32 1 857 441890048 441889186 0.000000e+00 813
4 TraesCS5A01G355800 chr5B 93.883 1455 67 4 1006 2447 537906766 537905321 0.000000e+00 2174
5 TraesCS5A01G355800 chr5B 90.974 842 55 9 2450 3282 537905245 537904416 0.000000e+00 1114
6 TraesCS5A01G355800 chr5B 86.257 342 34 9 32 367 537907434 537907100 3.110000e-95 359
7 TraesCS5A01G355800 chr5B 94.118 136 5 1 894 1026 537906932 537906797 1.540000e-48 204
8 TraesCS5A01G355800 chr1B 78.593 327 48 14 520 830 120466619 120466939 2.580000e-46 196


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 TraesCS5A01G355800 chr5A 558249895 558253176 3281 True 6061.00 6061 100.000000 1 3282 1 chr5A.!!$R1 3281
1 TraesCS5A01G355800 chr5D 441885397 441890048 4651 True 1394.00 2338 89.690667 1 3282 3 chr5D.!!$R1 3281
2 TraesCS5A01G355800 chr5B 537904416 537907434 3018 True 962.75 2174 91.308000 32 3282 4 chr5B.!!$R1 3250

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
310 317 0.317519 GTTTTGCGGTCGGTTTGAGG 60.318 55.0 0.0 0.0 0.0 3.86 F
1506 3021 0.249120 TTTCATCATCCGGTGCGACT 59.751 50.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 3609 0.472471 AACTTTGCGGGAGACAGGAA 59.528 50.0 0.00 0.0 33.47 3.36 R
2993 4610 0.714439 GACGAGTTTTACCAGCGCTC 59.286 55.0 7.13 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
52 53 0.465705 CCCCGCTGCTTCATCTCTTA 59.534 55.000 0.00 0.00 0.00 2.10
57 58 3.265791 CGCTGCTTCATCTCTTAAGGTT 58.734 45.455 1.85 0.00 0.00 3.50
58 59 3.063180 CGCTGCTTCATCTCTTAAGGTTG 59.937 47.826 1.85 0.00 0.00 3.77
59 60 4.006319 GCTGCTTCATCTCTTAAGGTTGT 58.994 43.478 1.85 0.00 0.00 3.32
84 87 5.343307 TTTGCTCTTTGCCTTTTCTCTTT 57.657 34.783 0.00 0.00 42.00 2.52
90 93 6.860539 GCTCTTTGCCTTTTCTCTTTTCTAAG 59.139 38.462 0.00 0.00 35.15 2.18
114 117 1.616025 ATTGGGGGTTTGGGGCATG 60.616 57.895 0.00 0.00 0.00 4.06
170 173 5.293324 GTGTGTTGATTTTTCCAAAAGGGTC 59.707 40.000 0.00 0.00 38.11 4.46
177 180 8.845413 TGATTTTTCCAAAAGGGTCAATATTG 57.155 30.769 9.29 9.29 38.11 1.90
242 247 7.076842 ACAACACTGAATAAAATCGAGATGG 57.923 36.000 0.00 0.00 0.00 3.51
243 248 6.655003 ACAACACTGAATAAAATCGAGATGGT 59.345 34.615 0.00 0.00 0.00 3.55
276 283 0.456142 TCGCAGTGCAGATACGTGAC 60.456 55.000 16.83 0.00 0.00 3.67
279 286 1.698165 CAGTGCAGATACGTGACGTT 58.302 50.000 18.28 4.02 41.54 3.99
310 317 0.317519 GTTTTGCGGTCGGTTTGAGG 60.318 55.000 0.00 0.00 0.00 3.86
317 324 2.203669 TCGGTTTGAGGGGGTCGA 60.204 61.111 0.00 0.00 0.00 4.20
346 353 5.798434 GTGTTGTGAGTTTGTAAACCTTGAC 59.202 40.000 4.00 0.00 39.71 3.18
347 354 5.106078 TGTTGTGAGTTTGTAAACCTTGACC 60.106 40.000 4.00 0.00 39.71 4.02
358 365 0.841289 ACCTTGACCGAACCTTTGGA 59.159 50.000 0.00 0.00 35.58 3.53
360 367 1.812571 CCTTGACCGAACCTTTGGATG 59.187 52.381 0.00 0.00 35.58 3.51
361 368 2.552155 CCTTGACCGAACCTTTGGATGA 60.552 50.000 0.00 0.00 35.58 2.92
362 369 3.347216 CTTGACCGAACCTTTGGATGAT 58.653 45.455 0.00 0.00 35.58 2.45
363 370 4.513442 CTTGACCGAACCTTTGGATGATA 58.487 43.478 0.00 0.00 35.58 2.15
364 371 4.561500 TGACCGAACCTTTGGATGATAA 57.438 40.909 0.00 0.00 35.58 1.75
365 372 4.258543 TGACCGAACCTTTGGATGATAAC 58.741 43.478 0.00 0.00 35.58 1.89
366 373 4.019681 TGACCGAACCTTTGGATGATAACT 60.020 41.667 0.00 0.00 35.58 2.24
369 376 6.113411 ACCGAACCTTTGGATGATAACTTAG 58.887 40.000 0.00 0.00 35.58 2.18
378 385 9.774742 CTTTGGATGATAACTTAGTAACTTTGC 57.225 33.333 0.00 0.00 0.00 3.68
397 404 2.301870 TGCCTTACCAGTCTCGTTGAAT 59.698 45.455 0.00 0.00 0.00 2.57
399 406 4.020928 TGCCTTACCAGTCTCGTTGAATAA 60.021 41.667 0.00 0.00 0.00 1.40
413 420 4.570369 CGTTGAATAAATGAAATTGGGGGC 59.430 41.667 0.00 0.00 36.10 5.80
426 433 3.009714 GGGGCGGGAGTTCCTTCT 61.010 66.667 0.00 0.00 35.95 2.85
427 434 1.688187 GGGGCGGGAGTTCCTTCTA 60.688 63.158 0.00 0.00 35.95 2.10
428 435 1.687297 GGGGCGGGAGTTCCTTCTAG 61.687 65.000 0.00 0.00 35.95 2.43
430 437 0.460722 GGCGGGAGTTCCTTCTAGAC 59.539 60.000 0.00 0.00 35.95 2.59
432 439 1.135053 GCGGGAGTTCCTTCTAGACAC 60.135 57.143 0.00 0.00 35.95 3.67
433 440 2.448453 CGGGAGTTCCTTCTAGACACT 58.552 52.381 0.00 0.00 35.95 3.55
435 442 4.015084 CGGGAGTTCCTTCTAGACACTTA 58.985 47.826 0.00 0.00 35.95 2.24
436 443 4.645588 CGGGAGTTCCTTCTAGACACTTAT 59.354 45.833 0.00 0.00 35.95 1.73
437 444 5.127356 CGGGAGTTCCTTCTAGACACTTATT 59.873 44.000 0.00 0.00 35.95 1.40
439 446 7.395617 GGGAGTTCCTTCTAGACACTTATTTT 58.604 38.462 0.00 0.00 35.95 1.82
441 448 8.937884 GGAGTTCCTTCTAGACACTTATTTTTC 58.062 37.037 0.00 0.00 0.00 2.29
443 450 9.713713 AGTTCCTTCTAGACACTTATTTTTCTC 57.286 33.333 0.00 0.00 0.00 2.87
463 489 6.952773 TCTCTCTCTCTCTATAAACTTGGC 57.047 41.667 0.00 0.00 0.00 4.52
530 556 4.357399 TCTTCTATACCTTAGCTAGCCCCT 59.643 45.833 12.13 0.00 0.00 4.79
531 557 5.554747 TCTTCTATACCTTAGCTAGCCCCTA 59.445 44.000 12.13 0.00 0.00 3.53
532 558 5.190357 TCTATACCTTAGCTAGCCCCTAC 57.810 47.826 12.13 0.00 0.00 3.18
533 559 4.856765 TCTATACCTTAGCTAGCCCCTACT 59.143 45.833 12.13 0.00 0.00 2.57
536 562 3.574749 ACCTTAGCTAGCCCCTACTAAC 58.425 50.000 12.13 0.00 0.00 2.34
542 568 3.850774 AGCTAGCCCCTACTAACCTTTTT 59.149 43.478 12.13 0.00 0.00 1.94
543 569 4.080469 AGCTAGCCCCTACTAACCTTTTTC 60.080 45.833 12.13 0.00 0.00 2.29
548 574 4.263816 GCCCCTACTAACCTTTTTCCTCTT 60.264 45.833 0.00 0.00 0.00 2.85
561 587 9.700831 ACCTTTTTCCTCTTAATATGTAAGCAT 57.299 29.630 0.00 0.00 39.03 3.79
573 599 6.683974 ATATGTAAGCATTTGTCACCTCAC 57.316 37.500 0.00 0.00 36.58 3.51
574 600 3.814625 TGTAAGCATTTGTCACCTCACA 58.185 40.909 0.00 0.00 0.00 3.58
600 626 5.570262 CAACAAATGCTCACTTCAACATG 57.430 39.130 0.00 0.00 0.00 3.21
606 632 2.291465 TGCTCACTTCAACATGCAACTC 59.709 45.455 0.00 0.00 0.00 3.01
646 672 5.750067 CCACCTAAATATGAAAAGCATGCAC 59.250 40.000 21.98 8.73 37.87 4.57
652 678 5.762825 ATATGAAAAGCATGCACGAGAAT 57.237 34.783 21.98 8.59 37.87 2.40
660 686 4.171005 AGCATGCACGAGAATTTTCATTG 58.829 39.130 21.98 0.00 0.00 2.82
816 851 6.155827 TGCAAATATTCCTACAACAAAGTGC 58.844 36.000 0.00 0.00 0.00 4.40
819 854 6.515272 AATATTCCTACAACAAAGTGCAGG 57.485 37.500 0.00 0.00 0.00 4.85
821 856 0.598065 CCTACAACAAAGTGCAGGGC 59.402 55.000 0.00 0.00 0.00 5.19
829 864 2.025981 ACAAAGTGCAGGGCATCATCTA 60.026 45.455 0.00 0.00 41.91 1.98
848 883 7.556844 TCATCTACTCCCTCTGTAAACAAATC 58.443 38.462 0.00 0.00 0.00 2.17
852 887 9.096823 TCTACTCCCTCTGTAAACAAATCTAAA 57.903 33.333 0.00 0.00 0.00 1.85
857 892 9.010029 TCCCTCTGTAAACAAATCTAAAACATC 57.990 33.333 0.00 0.00 0.00 3.06
879 914 9.256228 ACATCTTAGATCACTAAAGGTCTTACA 57.744 33.333 0.00 0.00 38.01 2.41
886 921 9.574516 AGATCACTAAAGGTCTTACATTTGTTT 57.425 29.630 0.00 0.00 32.79 2.83
889 924 9.059260 TCACTAAAGGTCTTACATTTGTTTACC 57.941 33.333 0.34 0.00 32.79 2.85
890 925 9.063615 CACTAAAGGTCTTACATTTGTTTACCT 57.936 33.333 0.34 5.83 32.79 3.08
916 951 5.866092 GGAAGTAGTAGTTTTAGAACGGTGG 59.134 44.000 0.00 0.00 40.75 4.61
1175 2690 1.956170 ACGCAGCAAGGAGAACACG 60.956 57.895 0.00 0.00 0.00 4.49
1301 2816 1.480954 TCCATTACCCTTGCTCTCGAC 59.519 52.381 0.00 0.00 0.00 4.20
1373 2888 2.353109 CCAGATCGACAAGCAGAAGTCA 60.353 50.000 0.00 0.00 34.48 3.41
1421 2936 0.318441 CTCTTTCGACTGGCACCTCA 59.682 55.000 0.00 0.00 0.00 3.86
1506 3021 0.249120 TTTCATCATCCGGTGCGACT 59.751 50.000 0.00 0.00 0.00 4.18
1517 3032 0.869880 GGTGCGACTTGTTTGTTGCC 60.870 55.000 4.67 0.00 44.46 4.52
1520 3035 1.199852 GCGACTTGTTTGTTGCCACG 61.200 55.000 0.00 0.00 40.48 4.94
1545 3060 1.378646 GGTAGCTTTGCTCCCACCC 60.379 63.158 0.00 0.00 40.44 4.61
1571 3086 4.115199 GAGGTGCCCAAGCCGGAT 62.115 66.667 5.05 0.00 38.69 4.18
1578 3093 1.972660 GCCCAAGCCGGATGTACTCT 61.973 60.000 5.05 0.00 36.56 3.24
1613 3128 2.693074 TCTTCTTCAAACCAAGTTGGGC 59.307 45.455 25.59 0.00 43.37 5.36
1615 3130 0.744281 CTTCAAACCAAGTTGGGCGT 59.256 50.000 25.59 7.96 43.37 5.68
1826 3341 2.887151 CCAAGAGGGAGGTTGACAAT 57.113 50.000 0.00 0.00 40.01 2.71
1842 3357 5.557576 TGACAATATGGAGGAGGATGAAG 57.442 43.478 0.00 0.00 0.00 3.02
1904 3431 3.653344 TGATGAAGAGGACGAACAAGTG 58.347 45.455 0.00 0.00 0.00 3.16
2042 3569 1.001158 GATCTAGCCGAGCAGTACCAC 60.001 57.143 0.00 0.00 0.00 4.16
2075 3602 4.077188 GAGGCGTGCGTGCAGTTC 62.077 66.667 0.00 0.00 36.28 3.01
2105 3632 2.615493 CCTGTCTCCCGCAAAGTTACAT 60.615 50.000 0.00 0.00 0.00 2.29
2115 3642 6.017440 TCCCGCAAAGTTACATATCTTATTGC 60.017 38.462 0.00 0.00 0.00 3.56
2116 3643 5.845953 CCGCAAAGTTACATATCTTATTGCG 59.154 40.000 19.07 19.07 43.85 4.85
2117 3644 6.418956 CGCAAAGTTACATATCTTATTGCGT 58.581 36.000 18.11 0.00 41.61 5.24
2225 3752 2.947852 ACACGTCTTGCTAGCTACTTG 58.052 47.619 17.23 16.03 0.00 3.16
2302 3829 8.547967 TTGAATGTATGGTCTTTAGACTCAAC 57.452 34.615 9.56 6.12 44.20 3.18
2310 3837 6.588204 TGGTCTTTAGACTCAACTTTAAGCA 58.412 36.000 9.56 0.00 44.20 3.91
2316 3843 4.973168 AGACTCAACTTTAAGCACATGGA 58.027 39.130 0.00 0.00 0.00 3.41
2355 3882 3.564225 CGTTCAAAGTGCTAGTTCCCTTT 59.436 43.478 0.00 0.00 0.00 3.11
2434 3961 2.032799 GTGCTGATGTGACCGTGAAAAA 59.967 45.455 0.00 0.00 0.00 1.94
2447 3974 8.550376 GTGACCGTGAAAAACAGTTTTATACTA 58.450 33.333 11.76 0.00 37.07 1.82
2448 3975 8.767085 TGACCGTGAAAAACAGTTTTATACTAG 58.233 33.333 11.76 9.87 37.07 2.57
2478 4078 6.704310 AGTACCATACGGTTCACAAGTATTT 58.296 36.000 0.00 0.00 46.31 1.40
2479 4079 6.815142 AGTACCATACGGTTCACAAGTATTTC 59.185 38.462 0.00 0.00 46.31 2.17
2525 4125 7.613585 TCATGGTATTGTTTGAATCTTTGCAT 58.386 30.769 0.00 0.00 0.00 3.96
2613 4224 7.710907 TGTAATGTATGGAGATTACAGCAACTC 59.289 37.037 0.00 0.00 43.32 3.01
2638 4249 5.090652 TCTTACAATGTGCTTCGAAACAC 57.909 39.130 21.82 21.82 37.31 3.32
2648 4259 3.690139 TGCTTCGAAACACTACCAACAAA 59.310 39.130 0.00 0.00 0.00 2.83
2660 4271 6.482308 ACACTACCAACAAAGATGTCAACTAC 59.518 38.462 0.00 0.00 39.40 2.73
2661 4272 5.995897 ACTACCAACAAAGATGTCAACTACC 59.004 40.000 0.00 0.00 39.40 3.18
2703 4320 5.068198 CAGACAAGACATGGGATTAATTGGG 59.932 44.000 0.00 0.00 0.00 4.12
2707 4324 5.937975 AGACATGGGATTAATTGGGTTTG 57.062 39.130 0.00 0.00 0.00 2.93
2728 4345 7.014038 GGTTTGGGTCGAGATCTATCTAACTAA 59.986 40.741 0.00 0.00 37.25 2.24
2800 4417 2.932614 CTCTGGATAGAACCTTGCAACG 59.067 50.000 0.00 0.00 31.21 4.10
2828 4445 1.061111 TCTCATCCCACCATCTCCCAT 60.061 52.381 0.00 0.00 0.00 4.00
2911 4528 3.770040 CCAGCGACCACCGGATCA 61.770 66.667 9.46 0.00 39.04 2.92
2920 4537 1.176527 CCACCGGATCAACATTGCTT 58.823 50.000 9.46 0.00 0.00 3.91
2952 4569 1.612991 CGGGATGACCACATTCACCAA 60.613 52.381 0.00 0.00 40.22 3.67
2993 4610 2.094700 TCTTCGTCGACATCCTCCAAAG 60.095 50.000 17.16 5.67 0.00 2.77
2999 4616 0.107945 GACATCCTCCAAAGAGCGCT 60.108 55.000 11.27 11.27 38.96 5.92
3000 4617 0.392193 ACATCCTCCAAAGAGCGCTG 60.392 55.000 18.48 0.00 38.96 5.18
3036 4653 2.657237 GAGGAGGTGGTGTGACGG 59.343 66.667 0.00 0.00 0.00 4.79
3089 4706 1.397692 CTCCGTCTTCGTGAGGTAGAC 59.602 57.143 2.39 2.39 38.75 2.59
3090 4707 1.162698 CCGTCTTCGTGAGGTAGACA 58.837 55.000 11.43 0.00 40.67 3.41
3104 4730 2.355946 AGACAGTGCACGGTCTGAT 58.644 52.632 39.90 23.64 46.76 2.90
3105 4731 0.681733 AGACAGTGCACGGTCTGATT 59.318 50.000 39.90 23.32 46.76 2.57
3106 4732 1.893137 AGACAGTGCACGGTCTGATTA 59.107 47.619 39.90 0.00 46.76 1.75
3107 4733 2.497675 AGACAGTGCACGGTCTGATTAT 59.502 45.455 39.90 22.36 46.76 1.28
3174 4800 2.450476 GAGTTGCTTGGGAATGACCAT 58.550 47.619 0.00 0.00 40.91 3.55
3181 4807 2.519302 GGAATGACCATGGGCCGG 60.519 66.667 17.19 0.00 38.79 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 87 4.479156 AACCCCCAATCCAAACTTAGAA 57.521 40.909 0.00 0.00 0.00 2.10
90 93 0.690192 CCCAAACCCCCAATCCAAAC 59.310 55.000 0.00 0.00 0.00 2.93
114 117 7.787725 ATTATGAAACGGAAGGAGAATACAC 57.212 36.000 0.00 0.00 0.00 2.90
242 247 4.138817 CACTGCGACGTACACATAAAAAC 58.861 43.478 0.00 0.00 0.00 2.43
243 248 3.363182 GCACTGCGACGTACACATAAAAA 60.363 43.478 0.00 0.00 0.00 1.94
255 262 1.514228 ACGTATCTGCACTGCGACG 60.514 57.895 13.06 13.06 0.00 5.12
276 283 2.411547 GCAAAACTCATGTCTCCGAACG 60.412 50.000 0.00 0.00 0.00 3.95
279 286 1.428448 CGCAAAACTCATGTCTCCGA 58.572 50.000 0.00 0.00 0.00 4.55
310 317 0.673644 CACAACACCTGATCGACCCC 60.674 60.000 0.00 0.00 0.00 4.95
317 324 5.067283 GGTTTACAAACTCACAACACCTGAT 59.933 40.000 4.93 0.00 38.89 2.90
346 353 6.113411 ACTAAGTTATCATCCAAAGGTTCGG 58.887 40.000 0.00 0.00 0.00 4.30
347 354 8.601476 GTTACTAAGTTATCATCCAAAGGTTCG 58.399 37.037 0.00 0.00 0.00 3.95
358 365 9.392259 GGTAAGGCAAAGTTACTAAGTTATCAT 57.608 33.333 0.00 0.00 32.02 2.45
360 367 8.782339 TGGTAAGGCAAAGTTACTAAGTTATC 57.218 34.615 0.00 0.00 32.02 1.75
361 368 8.380867 ACTGGTAAGGCAAAGTTACTAAGTTAT 58.619 33.333 0.00 0.00 30.08 1.89
362 369 7.738847 ACTGGTAAGGCAAAGTTACTAAGTTA 58.261 34.615 0.00 0.00 30.08 2.24
363 370 6.598503 ACTGGTAAGGCAAAGTTACTAAGTT 58.401 36.000 0.00 0.00 30.08 2.66
364 371 6.042897 AGACTGGTAAGGCAAAGTTACTAAGT 59.957 38.462 0.00 0.00 31.58 2.24
365 372 6.465084 AGACTGGTAAGGCAAAGTTACTAAG 58.535 40.000 0.00 0.00 31.58 2.18
366 373 6.429521 AGACTGGTAAGGCAAAGTTACTAA 57.570 37.500 0.00 0.00 31.58 2.24
369 376 3.678548 CGAGACTGGTAAGGCAAAGTTAC 59.321 47.826 0.00 0.00 31.58 2.50
378 385 6.816640 TCATTTATTCAACGAGACTGGTAAGG 59.183 38.462 0.00 0.00 0.00 2.69
397 404 1.007238 TCCCGCCCCCAATTTCATTTA 59.993 47.619 0.00 0.00 0.00 1.40
399 406 0.687427 CTCCCGCCCCCAATTTCATT 60.687 55.000 0.00 0.00 0.00 2.57
413 420 2.448453 AGTGTCTAGAAGGAACTCCCG 58.552 52.381 0.00 0.00 38.49 5.14
426 433 9.747898 AGAGAGAGAGAGAAAAATAAGTGTCTA 57.252 33.333 0.00 0.00 0.00 2.59
427 434 8.650143 AGAGAGAGAGAGAAAAATAAGTGTCT 57.350 34.615 0.00 0.00 0.00 3.41
437 444 8.254508 GCCAAGTTTATAGAGAGAGAGAGAAAA 58.745 37.037 0.00 0.00 0.00 2.29
439 446 6.322712 GGCCAAGTTTATAGAGAGAGAGAGAA 59.677 42.308 0.00 0.00 0.00 2.87
441 448 5.596361 TGGCCAAGTTTATAGAGAGAGAGAG 59.404 44.000 0.61 0.00 0.00 3.20
443 450 5.860941 TGGCCAAGTTTATAGAGAGAGAG 57.139 43.478 0.61 0.00 0.00 3.20
460 486 6.969993 AGTTAAAATCACTAACTTTGGCCA 57.030 33.333 0.00 0.00 36.42 5.36
521 547 3.928005 AAAAGGTTAGTAGGGGCTAGC 57.072 47.619 6.04 6.04 0.00 3.42
542 568 9.109393 GTGACAAATGCTTACATATTAAGAGGA 57.891 33.333 8.14 0.00 34.62 3.71
543 569 8.345565 GGTGACAAATGCTTACATATTAAGAGG 58.654 37.037 8.14 0.00 34.62 3.69
548 574 7.826744 TGTGAGGTGACAAATGCTTACATATTA 59.173 33.333 0.00 0.00 34.62 0.98
561 587 2.822561 TGTTGCTTTGTGAGGTGACAAA 59.177 40.909 0.00 0.00 42.26 2.83
562 588 2.441410 TGTTGCTTTGTGAGGTGACAA 58.559 42.857 0.00 0.00 33.96 3.18
600 626 2.987889 GCCTTTTGCTATGCAGAGTTGC 60.988 50.000 10.55 0.00 43.35 4.17
606 632 0.174162 GTGGGCCTTTTGCTATGCAG 59.826 55.000 4.53 0.00 40.61 4.41
614 640 5.930837 TTCATATTTAGGTGGGCCTTTTG 57.069 39.130 4.53 0.00 44.18 2.44
635 661 4.619973 TGAAAATTCTCGTGCATGCTTTT 58.380 34.783 20.33 14.54 0.00 2.27
638 664 4.171005 CAATGAAAATTCTCGTGCATGCT 58.829 39.130 20.33 0.00 0.00 3.79
708 737 9.357652 ACTGAAAAATATGTATGATTGTTGTGC 57.642 29.630 0.00 0.00 0.00 4.57
803 838 1.317613 TGCCCTGCACTTTGTTGTAG 58.682 50.000 0.00 0.00 31.71 2.74
804 839 1.885887 GATGCCCTGCACTTTGTTGTA 59.114 47.619 0.00 0.00 43.04 2.41
812 847 1.415659 GAGTAGATGATGCCCTGCACT 59.584 52.381 0.00 0.00 43.04 4.40
819 854 2.324541 ACAGAGGGAGTAGATGATGCC 58.675 52.381 0.00 0.00 0.00 4.40
821 856 6.471233 TGTTTACAGAGGGAGTAGATGATG 57.529 41.667 0.00 0.00 0.00 3.07
829 864 7.996644 TGTTTTAGATTTGTTTACAGAGGGAGT 59.003 33.333 0.00 0.00 0.00 3.85
860 895 9.574516 AAACAAATGTAAGACCTTTAGTGATCT 57.425 29.630 0.00 0.00 0.00 2.75
863 898 9.059260 GGTAAACAAATGTAAGACCTTTAGTGA 57.941 33.333 4.88 0.00 0.00 3.41
864 899 9.063615 AGGTAAACAAATGTAAGACCTTTAGTG 57.936 33.333 7.70 0.00 33.39 2.74
867 902 9.729281 CCTAGGTAAACAAATGTAAGACCTTTA 57.271 33.333 15.15 3.16 36.50 1.85
868 903 8.442374 TCCTAGGTAAACAAATGTAAGACCTTT 58.558 33.333 9.08 0.00 36.50 3.11
869 904 7.981142 TCCTAGGTAAACAAATGTAAGACCTT 58.019 34.615 9.08 0.00 36.50 3.50
870 905 7.563724 TCCTAGGTAAACAAATGTAAGACCT 57.436 36.000 9.08 14.62 37.85 3.85
871 906 7.881751 ACTTCCTAGGTAAACAAATGTAAGACC 59.118 37.037 9.08 4.20 0.00 3.85
872 907 8.843885 ACTTCCTAGGTAAACAAATGTAAGAC 57.156 34.615 9.08 0.00 0.00 3.01
874 909 9.939802 ACTACTTCCTAGGTAAACAAATGTAAG 57.060 33.333 9.08 2.87 0.00 2.34
877 912 9.097946 ACTACTACTTCCTAGGTAAACAAATGT 57.902 33.333 9.08 0.00 0.00 2.71
878 913 9.939802 AACTACTACTTCCTAGGTAAACAAATG 57.060 33.333 9.08 0.00 0.00 2.32
886 921 9.167311 CGTTCTAAAACTACTACTTCCTAGGTA 57.833 37.037 9.08 0.00 32.95 3.08
887 922 7.121907 CCGTTCTAAAACTACTACTTCCTAGGT 59.878 40.741 9.08 0.00 32.95 3.08
888 923 7.121907 ACCGTTCTAAAACTACTACTTCCTAGG 59.878 40.741 0.82 0.82 32.95 3.02
889 924 7.967303 CACCGTTCTAAAACTACTACTTCCTAG 59.033 40.741 0.00 0.00 32.95 3.02
890 925 7.094205 CCACCGTTCTAAAACTACTACTTCCTA 60.094 40.741 0.00 0.00 32.95 2.94
891 926 6.294955 CCACCGTTCTAAAACTACTACTTCCT 60.295 42.308 0.00 0.00 32.95 3.36
916 951 7.166638 CGCATATGAATCGATTCCTATACACTC 59.833 40.741 30.16 16.44 35.97 3.51
995 2459 4.141459 GGAGTTAGGATTTTAGAGTGGGGG 60.141 50.000 0.00 0.00 0.00 5.40
1132 2647 2.440409 AGCCATCCACAATGAACAGAC 58.560 47.619 0.00 0.00 37.59 3.51
1175 2690 2.044946 ATGCTCTTCCCGTTGGGC 60.045 61.111 0.00 0.00 43.94 5.36
1301 2816 2.114670 ATGGCGCGAAACATCCTGG 61.115 57.895 12.10 0.00 0.00 4.45
1486 3001 1.134401 AGTCGCACCGGATGATGAAAT 60.134 47.619 9.46 0.00 0.00 2.17
1517 3032 3.927163 AAAGCTACCGACGGCCGTG 62.927 63.158 39.65 25.40 36.31 4.94
1520 3035 3.497031 GCAAAGCTACCGACGGCC 61.497 66.667 15.39 2.42 0.00 6.13
1533 3048 3.961414 GGTCGGGGTGGGAGCAAA 61.961 66.667 0.00 0.00 32.38 3.68
1571 3086 2.176045 TCTCCGAATTGCCAGAGTACA 58.824 47.619 0.00 0.00 0.00 2.90
1578 3093 3.055167 TGAAGAAGATCTCCGAATTGCCA 60.055 43.478 0.00 0.00 0.00 4.92
1613 3128 2.051971 TCGAACGTCACGTCCACG 60.052 61.111 1.67 10.68 39.99 4.94
1615 3130 2.121564 GACCTCGAACGTCACGTCCA 62.122 60.000 1.67 0.00 39.99 4.02
1826 3341 4.842948 CCTTCATCTTCATCCTCCTCCATA 59.157 45.833 0.00 0.00 0.00 2.74
1842 3357 0.809385 TCGTCCGTGTCTCCTTCATC 59.191 55.000 0.00 0.00 0.00 2.92
1904 3431 2.974698 AAGTGCTGCAGCCACGTC 60.975 61.111 34.64 18.92 41.18 4.34
1925 3452 1.208614 GTACCTATCCGCCGCTACG 59.791 63.158 0.00 0.00 0.00 3.51
2042 3569 0.671781 CCTCCTTCAGGCGACAACAG 60.672 60.000 0.00 0.00 34.56 3.16
2062 3589 4.993945 GCACGAACTGCACGCACG 62.994 66.667 0.00 0.00 46.29 5.34
2075 3602 1.519455 GGGAGACAGGAATCGCACG 60.519 63.158 0.00 0.00 0.00 5.34
2077 3604 2.892640 CGGGAGACAGGAATCGCA 59.107 61.111 0.00 0.00 0.00 5.10
2082 3609 0.472471 AACTTTGCGGGAGACAGGAA 59.528 50.000 0.00 0.00 33.47 3.36
2105 3632 4.814234 CAGCCTTTGGTACGCAATAAGATA 59.186 41.667 0.00 0.00 0.00 1.98
2116 3643 6.769990 GCTATATGCTTCCAGCCTTTGGTAC 61.770 48.000 0.00 0.00 41.51 3.34
2117 3644 4.746702 GCTATATGCTTCCAGCCTTTGGTA 60.747 45.833 0.00 0.00 41.51 3.25
2153 3680 2.820059 TGAGCTCGTTCACAACATCT 57.180 45.000 9.64 0.00 0.00 2.90
2225 3752 4.760204 ACAAGGTCTAACATTTGTGTAGCC 59.240 41.667 0.00 0.00 32.90 3.93
2284 3811 8.372459 TGCTTAAAGTTGAGTCTAAAGACCATA 58.628 33.333 6.50 0.00 45.85 2.74
2302 3829 5.840243 TCAATGGATCCATGTGCTTAAAG 57.160 39.130 27.97 9.41 36.68 1.85
2316 3843 4.201657 TGAACGAATGCAGATCAATGGAT 58.798 39.130 0.00 0.00 36.13 3.41
2355 3882 8.389779 TGAGAATAAAAACATGAGTACTTGCA 57.610 30.769 0.00 0.00 0.00 4.08
2460 4060 5.801380 ACAGGAAATACTTGTGAACCGTAT 58.199 37.500 0.00 0.00 37.43 3.06
2604 4215 5.506317 GCACATTGTAAGAAAGAGTTGCTGT 60.506 40.000 0.00 0.00 0.00 4.40
2613 4224 6.140737 GTGTTTCGAAGCACATTGTAAGAAAG 59.859 38.462 32.14 0.00 39.55 2.62
2638 4249 5.995282 TGGTAGTTGACATCTTTGTTGGTAG 59.005 40.000 0.00 0.00 35.79 3.18
2648 4259 5.710984 CGTAGAGTTTGGTAGTTGACATCT 58.289 41.667 0.00 0.00 0.00 2.90
2660 4271 2.476619 CTGTCAACTGCGTAGAGTTTGG 59.523 50.000 7.78 0.00 33.75 3.28
2661 4272 3.182572 GTCTGTCAACTGCGTAGAGTTTG 59.817 47.826 7.78 1.51 33.75 2.93
2703 4320 6.394025 AGTTAGATAGATCTCGACCCAAAC 57.606 41.667 0.00 0.00 38.32 2.93
2707 4324 9.452287 AATACTTAGTTAGATAGATCTCGACCC 57.548 37.037 0.00 0.00 38.32 4.46
2728 4345 4.465886 ACGAGCCTCTGACAGATAATACT 58.534 43.478 5.42 0.00 0.00 2.12
2800 4417 1.134401 TGGTGGGATGAGAAGCGAATC 60.134 52.381 0.00 0.00 0.00 2.52
2828 4445 3.893326 TCTTTGCAAGATCGAGATGGA 57.107 42.857 0.00 0.00 31.20 3.41
2911 4528 2.996734 CCCGGCCCAAGCAATGTT 60.997 61.111 0.00 0.00 42.56 2.71
2937 4554 1.680735 GCAACTTGGTGAATGTGGTCA 59.319 47.619 0.00 0.00 0.00 4.02
2993 4610 0.714439 GACGAGTTTTACCAGCGCTC 59.286 55.000 7.13 0.00 0.00 5.03
2999 4616 1.069022 CGAGGACGACGAGTTTTACCA 60.069 52.381 0.00 0.00 42.66 3.25
3000 4617 1.197721 TCGAGGACGACGAGTTTTACC 59.802 52.381 0.00 0.00 43.81 2.85
3031 4648 2.362503 ACCGAGATGCTCCCGTCA 60.363 61.111 0.00 0.00 0.00 4.35
3036 4653 2.037620 ATGCCTGACCGAGATGCTCC 62.038 60.000 0.00 0.00 0.00 4.70
3089 4706 3.804325 CCTAATAATCAGACCGTGCACTG 59.196 47.826 16.19 11.43 35.72 3.66
3090 4707 3.704566 TCCTAATAATCAGACCGTGCACT 59.295 43.478 16.19 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.