Multiple sequence alignment - TraesCS6B01G193400

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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 TraesCS6B01G193400 chr6B 100.000 5244 0 0 1 5244 228238417 228243660 0.000000e+00 9684.0
1 TraesCS6B01G193400 chr6B 76.099 933 179 38 2940 3844 8787583 8786667 1.040000e-121 448.0
2 TraesCS6B01G193400 chr6B 76.025 317 59 16 3543 3851 671166177 671165870 1.180000e-31 148.0
3 TraesCS6B01G193400 chr6A 93.161 5264 212 66 52 5242 168114140 168119328 0.000000e+00 7590.0
4 TraesCS6B01G193400 chr6A 98.214 56 1 0 4396 4451 168118449 168118504 1.200000e-16 99.0
5 TraesCS6B01G193400 chr6D 97.011 2643 73 4 2607 5244 129782557 129785198 0.000000e+00 4438.0
6 TraesCS6B01G193400 chr6D 94.115 1937 74 19 651 2571 129780650 129782562 0.000000e+00 2909.0
7 TraesCS6B01G193400 chr6D 85.981 321 17 10 50 347 129780019 129780334 8.470000e-83 318.0
8 TraesCS6B01G193400 chr6D 89.017 173 17 2 376 547 129780333 129780504 4.110000e-51 213.0
9 TraesCS6B01G193400 chr5A 79.367 979 176 23 2907 3869 4957894 4956926 0.000000e+00 665.0
10 TraesCS6B01G193400 chr5A 77.215 632 130 13 3223 3847 29906563 29905939 1.800000e-94 357.0
11 TraesCS6B01G193400 chr5A 90.909 44 3 1 4202 4244 575706082 575706039 2.040000e-04 58.4
12 TraesCS6B01G193400 chr5A 90.909 44 3 1 4202 4244 576084920 576084877 2.040000e-04 58.4
13 TraesCS6B01G193400 chr5A 90.909 44 3 1 4202 4244 576272511 576272554 2.040000e-04 58.4
14 TraesCS6B01G193400 chr5B 78.247 970 185 21 2916 3869 7707654 7706695 2.700000e-167 599.0
15 TraesCS6B01G193400 chr5B 90.909 44 3 1 4202 4244 560441483 560441440 2.040000e-04 58.4
16 TraesCS6B01G193400 chr5B 90.476 42 3 1 4202 4242 561061827 561061786 3.000000e-03 54.7
17 TraesCS6B01G193400 chr7A 77.007 274 47 8 3223 3485 15525081 15524813 5.470000e-30 143.0
18 TraesCS6B01G193400 chr5D 72.990 311 66 16 3538 3839 458180772 458180471 5.590000e-15 93.5
19 TraesCS6B01G193400 chr5D 90.909 44 3 1 4202 4244 458094833 458094790 2.040000e-04 58.4
20 TraesCS6B01G193400 chr5D 100.000 30 0 0 4215 4244 458180083 458180054 7.340000e-04 56.5


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 TraesCS6B01G193400 chr6B 228238417 228243660 5243 False 9684.0 9684 100.0000 1 5244 1 chr6B.!!$F1 5243
1 TraesCS6B01G193400 chr6B 8786667 8787583 916 True 448.0 448 76.0990 2940 3844 1 chr6B.!!$R1 904
2 TraesCS6B01G193400 chr6A 168114140 168119328 5188 False 3844.5 7590 95.6875 52 5242 2 chr6A.!!$F1 5190
3 TraesCS6B01G193400 chr6D 129780019 129785198 5179 False 1969.5 4438 91.5310 50 5244 4 chr6D.!!$F1 5194
4 TraesCS6B01G193400 chr5A 4956926 4957894 968 True 665.0 665 79.3670 2907 3869 1 chr5A.!!$R1 962
5 TraesCS6B01G193400 chr5A 29905939 29906563 624 True 357.0 357 77.2150 3223 3847 1 chr5A.!!$R2 624
6 TraesCS6B01G193400 chr5B 7706695 7707654 959 True 599.0 599 78.2470 2916 3869 1 chr5B.!!$R1 953

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
33 34 0.108709 CCAAAATGGGCGGTCACATG 60.109 55.0 0.00 0.0 32.67 3.21 F
34 35 0.737019 CAAAATGGGCGGTCACATGC 60.737 55.0 0.00 0.0 0.00 4.06 F
789 906 1.139989 CCATCACGACTGACACACAC 58.860 55.0 0.00 0.0 0.00 3.82 F
2584 2746 0.319900 ACAGTGCGAATCGAGCAGTT 60.320 50.0 6.91 0.0 45.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1385 1503 0.616964 TCTCTCCTGTCCTGCATGCT 60.617 55.0 20.33 0.00 0.00 3.79 R
1780 1906 0.745845 CGTGGCTTCATGGCTAGCTT 60.746 55.0 15.72 0.00 42.34 3.74 R
2631 2793 0.538118 CCACGAAAATCGGTCCCCTA 59.462 55.0 4.66 0.00 45.59 3.53 R
4244 4440 1.856539 ATCTTGTCCTGGGGCCACAG 61.857 60.0 29.29 29.29 38.21 3.66 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
22 23 1.906995 GGGGGATGTGCCAAAATGG 59.093 57.895 0.00 0.00 41.55 3.16
23 24 1.625417 GGGGGATGTGCCAAAATGGG 61.625 60.000 0.00 0.00 38.19 4.00
30 31 2.261361 GCCAAAATGGGCGGTCAC 59.739 61.111 0.00 0.00 45.40 3.67
31 32 2.569354 GCCAAAATGGGCGGTCACA 61.569 57.895 0.00 0.00 45.40 3.58
32 33 1.887344 GCCAAAATGGGCGGTCACAT 61.887 55.000 0.00 0.00 45.40 3.21
33 34 0.108709 CCAAAATGGGCGGTCACATG 60.109 55.000 0.00 0.00 32.67 3.21
34 35 0.737019 CAAAATGGGCGGTCACATGC 60.737 55.000 0.00 0.00 0.00 4.06
35 36 1.184322 AAAATGGGCGGTCACATGCA 61.184 50.000 0.00 0.00 0.00 3.96
36 37 1.876497 AAATGGGCGGTCACATGCAC 61.876 55.000 0.00 0.00 34.29 4.57
42 43 2.033448 GGTCACATGCACCGGGAA 59.967 61.111 6.32 0.00 0.00 3.97
43 44 2.040544 GGTCACATGCACCGGGAAG 61.041 63.158 6.32 0.00 0.00 3.46
44 45 1.302511 GTCACATGCACCGGGAAGT 60.303 57.895 6.32 0.00 0.00 3.01
45 46 1.302431 TCACATGCACCGGGAAGTG 60.302 57.895 6.32 7.42 40.88 3.16
46 47 1.302431 CACATGCACCGGGAAGTGA 60.302 57.895 6.32 0.00 40.34 3.41
47 48 1.302511 ACATGCACCGGGAAGTGAC 60.303 57.895 6.32 0.00 40.34 3.67
48 49 1.302431 CATGCACCGGGAAGTGACA 60.302 57.895 6.32 0.00 40.34 3.58
165 168 2.350772 CGTGCTTCAAGGTTCCAATGTC 60.351 50.000 0.00 0.00 0.00 3.06
237 240 3.181489 CGGTCGACTAGCCAACTTTCTAT 60.181 47.826 16.46 0.00 0.00 1.98
238 241 4.677250 CGGTCGACTAGCCAACTTTCTATT 60.677 45.833 16.46 0.00 0.00 1.73
239 242 4.567159 GGTCGACTAGCCAACTTTCTATTG 59.433 45.833 16.46 0.00 0.00 1.90
242 245 2.678336 ACTAGCCAACTTTCTATTGCGC 59.322 45.455 0.00 0.00 0.00 6.09
266 290 2.327343 GCAACTGGCATCAGCGACA 61.327 57.895 0.00 0.00 44.59 4.35
267 291 1.651240 GCAACTGGCATCAGCGACAT 61.651 55.000 0.00 0.00 44.59 3.06
285 309 6.599244 AGCGACATTTATTTTGAGATGAAGGA 59.401 34.615 0.00 0.00 0.00 3.36
340 364 4.320608 AACAAAGATCAAATGTGGCGTT 57.679 36.364 0.00 0.00 0.00 4.84
359 383 3.180980 CGTTCGCTCAAACTTTTCGTAGA 59.819 43.478 0.00 0.00 0.00 2.59
379 403 4.273318 AGAAGAAAATATCTGGTGCACCC 58.727 43.478 32.62 15.42 38.79 4.61
389 413 1.303317 GGTGCACCCGGTCTCAATT 60.303 57.895 26.31 0.00 0.00 2.32
390 414 1.586154 GGTGCACCCGGTCTCAATTG 61.586 60.000 26.31 0.00 0.00 2.32
395 419 2.436417 CACCCGGTCTCAATTGTCATT 58.564 47.619 5.13 0.00 0.00 2.57
399 423 3.426159 CCCGGTCTCAATTGTCATTTTCG 60.426 47.826 5.13 2.52 0.00 3.46
400 424 3.435327 CCGGTCTCAATTGTCATTTTCGA 59.565 43.478 5.13 0.00 0.00 3.71
450 474 2.756760 AGGGCATGCAAACAATGAGTAG 59.243 45.455 21.36 0.00 0.00 2.57
457 482 2.223144 GCAAACAATGAGTAGCGACACA 59.777 45.455 0.00 0.00 0.00 3.72
486 511 6.381801 AGTATTCAAATCCAAACTGAAAGCG 58.618 36.000 0.00 0.00 37.60 4.68
493 518 1.192980 CCAAACTGAAAGCGCAATTGC 59.807 47.619 20.76 20.76 37.60 3.56
510 535 6.764094 GCAATTGCGAAACACAAATGATATT 58.236 32.000 15.87 0.00 31.00 1.28
561 649 8.542497 TTAGCTTACTATTCAACACGTGATTT 57.458 30.769 25.01 3.65 35.70 2.17
566 654 6.861065 ACTATTCAACACGTGATTTGTCTT 57.139 33.333 25.01 0.19 35.70 3.01
625 715 9.748708 CTTTTACAGTGATTCAATTCTTTCCAA 57.251 29.630 0.00 0.00 0.00 3.53
629 719 5.922544 CAGTGATTCAATTCTTTCCAACACC 59.077 40.000 0.00 0.00 0.00 4.16
641 734 6.094061 TCTTTCCAACACCTTTTTGTAAACG 58.906 36.000 0.00 0.00 0.00 3.60
661 769 1.738099 CTAGACAGGTGCACGCCAC 60.738 63.158 11.45 2.74 43.90 5.01
684 792 2.047061 ACCATAGGGCGTCATGTACAT 58.953 47.619 1.41 1.41 37.90 2.29
702 819 6.764379 TGTACATACACTCTTCAAATGGACA 58.236 36.000 0.00 0.00 38.70 4.02
717 834 9.487790 TTCAAATGGACATTTTATTTCCAAGAC 57.512 29.630 7.51 0.00 42.71 3.01
733 850 6.024552 TCCAAGACAAATGATTTGGTTAGC 57.975 37.500 20.69 6.01 44.81 3.09
750 867 3.082579 GCTAGCCAGGTACGCAGCT 62.083 63.158 2.29 7.24 39.37 4.24
767 884 2.416202 CAGCTAATCATCGTGTTGCACA 59.584 45.455 0.00 0.00 33.40 4.57
789 906 1.139989 CCATCACGACTGACACACAC 58.860 55.000 0.00 0.00 0.00 3.82
881 998 2.125350 GAGCACTTGGGAGAGCCG 60.125 66.667 0.00 0.00 39.93 5.52
882 999 2.604686 AGCACTTGGGAGAGCCGA 60.605 61.111 0.00 0.00 39.93 5.54
928 1045 5.719173 GCTAGCTAGCTAACTAATCAGCAT 58.281 41.667 33.71 0.00 45.62 3.79
941 1058 6.352516 ACTAATCAGCATAAGAACAGAAGGG 58.647 40.000 0.00 0.00 0.00 3.95
946 1063 4.161189 CAGCATAAGAACAGAAGGGAGAGA 59.839 45.833 0.00 0.00 0.00 3.10
1363 1481 2.284995 ACCCCAGTGAGCCTCTCC 60.285 66.667 0.00 0.00 0.00 3.71
1374 1492 3.055530 GTGAGCCTCTCCATCTTTTCTCA 60.056 47.826 0.00 0.00 0.00 3.27
1376 1494 2.238395 AGCCTCTCCATCTTTTCTCACC 59.762 50.000 0.00 0.00 0.00 4.02
1385 1503 4.935205 CCATCTTTTCTCACCACAACGATA 59.065 41.667 0.00 0.00 0.00 2.92
1473 1599 2.294233 TCACATGGCTGAGAAAAGTTGC 59.706 45.455 0.00 0.00 0.00 4.17
1475 1601 2.961062 ACATGGCTGAGAAAAGTTGCTT 59.039 40.909 0.00 0.00 0.00 3.91
1476 1602 3.005155 ACATGGCTGAGAAAAGTTGCTTC 59.995 43.478 0.00 0.00 0.00 3.86
1478 1604 1.873591 GGCTGAGAAAAGTTGCTTCGA 59.126 47.619 0.00 0.00 0.00 3.71
1821 1947 0.886490 CTCTCCGTGCTTGCTTGGTT 60.886 55.000 0.00 0.00 0.00 3.67
1827 1953 2.139917 CGTGCTTGCTTGGTTGTACTA 58.860 47.619 0.00 0.00 0.00 1.82
1879 2010 1.447140 GTCATACCTGCCGTCGCAA 60.447 57.895 0.00 0.00 46.66 4.85
2017 2148 1.635663 GCGACCCGGACAAGAACATG 61.636 60.000 0.73 0.00 0.00 3.21
2121 2252 1.277495 ACGTAACGTAAGCACACCGC 61.277 55.000 0.00 0.00 38.73 5.68
2134 2265 4.410400 ACCGCCCTTGCTACCTGC 62.410 66.667 0.00 0.00 43.25 4.85
2135 2266 4.101448 CCGCCCTTGCTACCTGCT 62.101 66.667 0.00 0.00 43.37 4.24
2136 2267 2.731571 CCGCCCTTGCTACCTGCTA 61.732 63.158 0.00 0.00 43.37 3.49
2153 2291 5.358160 ACCTGCTAAGCAATAATCTTGTTCC 59.642 40.000 0.00 0.00 38.41 3.62
2346 2490 1.331756 CAACAACTCGCAGTGCTTCTT 59.668 47.619 14.33 0.00 0.00 2.52
2545 2689 2.796193 CCGTCCATGCCTGATCCGA 61.796 63.158 0.00 0.00 0.00 4.55
2555 2699 1.875813 CTGATCCGACAGAGCACGC 60.876 63.158 0.00 0.00 35.51 5.34
2563 2725 1.337817 GACAGAGCACGCAGTACACG 61.338 60.000 6.75 6.75 41.61 4.49
2567 2729 0.386352 GAGCACGCAGTACACGTACA 60.386 55.000 12.77 0.00 41.61 2.90
2568 2730 0.386858 AGCACGCAGTACACGTACAG 60.387 55.000 12.77 2.99 41.61 2.74
2569 2731 0.662374 GCACGCAGTACACGTACAGT 60.662 55.000 12.77 4.21 41.61 3.55
2578 2740 3.010088 CACGTACAGTGCGAATCGA 57.990 52.632 18.66 0.00 44.72 3.59
2579 2741 0.907837 CACGTACAGTGCGAATCGAG 59.092 55.000 18.66 0.00 44.72 4.04
2580 2742 0.797249 ACGTACAGTGCGAATCGAGC 60.797 55.000 18.66 0.00 0.00 5.03
2581 2743 0.796870 CGTACAGTGCGAATCGAGCA 60.797 55.000 6.91 0.00 42.99 4.26
2582 2744 0.917259 GTACAGTGCGAATCGAGCAG 59.083 55.000 6.91 0.00 46.10 4.24
2584 2746 0.319900 ACAGTGCGAATCGAGCAGTT 60.320 50.000 6.91 0.00 45.00 3.16
2585 2747 1.067846 ACAGTGCGAATCGAGCAGTTA 60.068 47.619 6.91 0.00 45.00 2.24
2586 2748 1.992667 CAGTGCGAATCGAGCAGTTAA 59.007 47.619 6.91 0.00 45.00 2.01
2587 2749 2.604914 CAGTGCGAATCGAGCAGTTAAT 59.395 45.455 6.91 0.00 45.00 1.40
2588 2750 3.062639 CAGTGCGAATCGAGCAGTTAATT 59.937 43.478 6.91 0.00 45.00 1.40
2589 2751 4.267690 CAGTGCGAATCGAGCAGTTAATTA 59.732 41.667 6.91 0.00 45.00 1.40
2590 2752 4.267928 AGTGCGAATCGAGCAGTTAATTAC 59.732 41.667 6.91 0.00 45.00 1.89
2591 2753 4.267928 GTGCGAATCGAGCAGTTAATTACT 59.732 41.667 6.91 0.00 46.10 2.24
2624 2786 6.092533 CACATAGTACATGACATGACTTTGCA 59.907 38.462 22.19 6.57 30.60 4.08
2631 2793 4.717233 TGACATGACTTTGCACTTTTGT 57.283 36.364 0.00 0.00 0.00 2.83
2775 2943 8.948853 TGATCAAGTTGCTTTTAATAAGTTCG 57.051 30.769 0.00 0.00 0.00 3.95
2782 2950 8.565416 AGTTGCTTTTAATAAGTTCGCTTAGTT 58.435 29.630 0.00 0.00 42.32 2.24
2783 2951 9.815936 GTTGCTTTTAATAAGTTCGCTTAGTTA 57.184 29.630 0.00 0.00 42.32 2.24
2833 3017 1.817099 CCCCATCGTGAGCAAGCTC 60.817 63.158 14.90 14.90 43.01 4.09
2905 3089 0.179073 AGAAGATGATGAACGGGCGG 60.179 55.000 0.00 0.00 0.00 6.13
3994 4190 1.739049 GCTGGACATCCTCTCCTCG 59.261 63.158 0.00 0.00 36.82 4.63
4244 4440 2.286872 CCAACAGCATCTCCATCTGAC 58.713 52.381 0.00 0.00 0.00 3.51
4258 4454 3.249189 TGACTGTGGCCCCAGGAC 61.249 66.667 20.06 13.05 36.75 3.85
4268 4464 1.202818 GGCCCCAGGACAAGATATCAC 60.203 57.143 5.32 0.00 0.00 3.06
4513 4744 3.527533 TGTACCGTATCATTTGGAGCAC 58.472 45.455 0.00 0.00 0.00 4.40
4821 5052 7.025963 GCTAATAATACTGATTGCCATGCTTC 58.974 38.462 0.00 0.00 0.00 3.86
4825 5056 3.301794 ACTGATTGCCATGCTTCCATA 57.698 42.857 0.00 0.00 0.00 2.74
4827 5058 4.025360 ACTGATTGCCATGCTTCCATAAA 58.975 39.130 0.00 0.00 0.00 1.40
4832 5063 6.885376 TGATTGCCATGCTTCCATAAATTTTT 59.115 30.769 0.00 0.00 0.00 1.94
4867 5098 3.756117 CAGGGGAGCAGAGTTTACTTTT 58.244 45.455 0.00 0.00 0.00 2.27
4877 5108 7.280356 AGCAGAGTTTACTTTTCTTACTTCCA 58.720 34.615 0.00 0.00 0.00 3.53
4879 5110 7.012044 GCAGAGTTTACTTTTCTTACTTCCACA 59.988 37.037 0.00 0.00 0.00 4.17
4912 5145 1.073964 CATGGTGTCTTCTGCAGTCG 58.926 55.000 14.67 6.14 0.00 4.18
4964 5197 3.492313 GTCAATTGGCATCGACAGAAAC 58.508 45.455 4.85 0.00 0.00 2.78
5177 5410 2.040939 TCAAGTGAGTTACCCGTGGAA 58.959 47.619 0.00 0.00 0.00 3.53
5192 5425 3.065371 CCGTGGAAGATGGCTCAAAATAC 59.935 47.826 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.625417 CCCATTTTGGCACATCCCCC 61.625 60.000 0.00 0.00 39.30 5.40
5 6 1.906995 CCCATTTTGGCACATCCCC 59.093 57.895 0.00 0.00 39.30 4.81
14 15 0.108709 CATGTGACCGCCCATTTTGG 60.109 55.000 0.00 0.00 37.25 3.28
15 16 0.737019 GCATGTGACCGCCCATTTTG 60.737 55.000 0.00 0.00 0.00 2.44
16 17 1.184322 TGCATGTGACCGCCCATTTT 61.184 50.000 0.00 0.00 0.00 1.82
17 18 1.606025 TGCATGTGACCGCCCATTT 60.606 52.632 0.00 0.00 0.00 2.32
18 19 2.035469 TGCATGTGACCGCCCATT 59.965 55.556 0.00 0.00 0.00 3.16
19 20 2.751436 GTGCATGTGACCGCCCAT 60.751 61.111 0.00 0.00 0.00 4.00
25 26 2.033448 TTCCCGGTGCATGTGACC 59.967 61.111 0.00 6.08 0.00 4.02
26 27 1.302511 ACTTCCCGGTGCATGTGAC 60.303 57.895 0.00 0.00 0.00 3.67
27 28 1.302431 CACTTCCCGGTGCATGTGA 60.302 57.895 0.00 0.00 0.00 3.58
28 29 1.302431 TCACTTCCCGGTGCATGTG 60.302 57.895 0.00 2.97 37.16 3.21
29 30 1.302511 GTCACTTCCCGGTGCATGT 60.303 57.895 0.00 0.00 37.16 3.21
30 31 0.888736 TTGTCACTTCCCGGTGCATG 60.889 55.000 0.00 0.00 37.16 4.06
31 32 0.606401 CTTGTCACTTCCCGGTGCAT 60.606 55.000 0.00 0.00 37.16 3.96
32 33 1.227823 CTTGTCACTTCCCGGTGCA 60.228 57.895 0.00 0.00 37.16 4.57
33 34 2.617274 GCTTGTCACTTCCCGGTGC 61.617 63.158 0.00 0.00 37.16 5.01
34 35 1.966451 GGCTTGTCACTTCCCGGTG 60.966 63.158 0.00 0.00 38.44 4.94
35 36 0.834687 TAGGCTTGTCACTTCCCGGT 60.835 55.000 0.00 0.00 0.00 5.28
36 37 0.391263 GTAGGCTTGTCACTTCCCGG 60.391 60.000 0.00 0.00 0.00 5.73
37 38 0.608640 AGTAGGCTTGTCACTTCCCG 59.391 55.000 0.00 0.00 0.00 5.14
38 39 1.623811 TCAGTAGGCTTGTCACTTCCC 59.376 52.381 0.00 0.00 0.00 3.97
39 40 3.265791 CATCAGTAGGCTTGTCACTTCC 58.734 50.000 0.00 0.00 0.00 3.46
40 41 3.931578 ACATCAGTAGGCTTGTCACTTC 58.068 45.455 0.00 0.00 0.00 3.01
41 42 5.683876 ATACATCAGTAGGCTTGTCACTT 57.316 39.130 0.00 0.00 32.86 3.16
42 43 5.894393 AGTATACATCAGTAGGCTTGTCACT 59.106 40.000 5.50 0.00 32.86 3.41
43 44 6.150396 AGTATACATCAGTAGGCTTGTCAC 57.850 41.667 5.50 0.00 32.86 3.67
44 45 6.459710 CGAAGTATACATCAGTAGGCTTGTCA 60.460 42.308 5.50 0.00 32.17 3.58
45 46 5.915758 CGAAGTATACATCAGTAGGCTTGTC 59.084 44.000 5.50 0.00 32.17 3.18
46 47 5.360144 ACGAAGTATACATCAGTAGGCTTGT 59.640 40.000 5.50 0.00 41.94 3.16
47 48 5.687730 CACGAAGTATACATCAGTAGGCTTG 59.312 44.000 5.50 0.00 41.61 4.01
48 49 5.736492 GCACGAAGTATACATCAGTAGGCTT 60.736 44.000 5.50 0.00 41.61 4.35
136 139 0.307760 CCTTGAAGCACGTTCCACAC 59.692 55.000 0.00 0.00 33.75 3.82
137 140 0.107410 ACCTTGAAGCACGTTCCACA 60.107 50.000 0.00 0.00 33.75 4.17
165 168 3.589654 TTGAACGAGCAGGAGGGCG 62.590 63.158 0.00 0.00 39.27 6.13
242 245 0.179137 CTGATGCCAGTTGCTGCATG 60.179 55.000 1.84 0.00 42.00 4.06
252 276 3.976793 AATAAATGTCGCTGATGCCAG 57.023 42.857 0.00 0.00 43.22 4.85
258 282 6.983474 TCATCTCAAAATAAATGTCGCTGA 57.017 33.333 0.00 0.00 0.00 4.26
285 309 8.207350 TCCAGCAGCCTAAAGAATATATACTT 57.793 34.615 0.00 0.00 0.00 2.24
319 343 4.298332 GAACGCCACATTTGATCTTTGTT 58.702 39.130 0.00 0.00 0.00 2.83
340 364 4.613944 TCTTCTACGAAAAGTTTGAGCGA 58.386 39.130 11.27 0.00 0.00 4.93
359 383 3.016736 CGGGTGCACCAGATATTTTCTT 58.983 45.455 35.78 0.00 40.22 2.52
372 396 0.889186 ACAATTGAGACCGGGTGCAC 60.889 55.000 13.59 8.80 0.00 4.57
379 403 4.388773 TCTCGAAAATGACAATTGAGACCG 59.611 41.667 13.59 6.26 0.00 4.79
450 474 4.742438 TTTGAATACTTTCCTGTGTCGC 57.258 40.909 0.00 0.00 0.00 5.19
457 482 8.477419 TTCAGTTTGGATTTGAATACTTTCCT 57.523 30.769 0.00 0.00 0.00 3.36
486 511 4.650545 ATCATTTGTGTTTCGCAATTGC 57.349 36.364 20.76 20.76 36.10 3.56
493 518 8.861033 ATTCCATCAATATCATTTGTGTTTCG 57.139 30.769 0.00 0.00 0.00 3.46
510 535 9.699410 ATCTAGATTTGGTTGTAAATTCCATCA 57.301 29.630 0.00 0.00 30.78 3.07
625 715 6.108015 TGTCTAGACGTTTACAAAAAGGTGT 58.892 36.000 17.85 0.77 42.22 4.16
629 719 6.646636 CACCTGTCTAGACGTTTACAAAAAG 58.353 40.000 17.85 5.60 0.00 2.27
641 734 1.446272 GGCGTGCACCTGTCTAGAC 60.446 63.158 16.32 16.32 0.00 2.59
661 769 2.839486 ACATGACGCCCTATGGTATG 57.161 50.000 0.00 0.00 0.00 2.39
717 834 5.450965 CCTGGCTAGCTAACCAAATCATTTG 60.451 44.000 16.49 2.80 40.32 2.32
733 850 0.744874 TTAGCTGCGTACCTGGCTAG 59.255 55.000 0.00 0.00 38.31 3.42
750 867 1.737236 GGCTGTGCAACACGATGATTA 59.263 47.619 0.00 0.00 45.67 1.75
767 884 1.293498 GTGTCAGTCGTGATGGGCT 59.707 57.895 0.00 0.00 34.36 5.19
789 906 0.717896 CGATGTGTTTCACGTGCGTG 60.718 55.000 17.44 17.44 46.64 5.34
881 998 3.223589 GGCCGGCCTCTCTCTCTC 61.224 72.222 38.76 7.31 0.00 3.20
882 999 4.851214 GGGCCGGCCTCTCTCTCT 62.851 72.222 42.70 0.00 36.10 3.10
916 1033 6.825721 CCCTTCTGTTCTTATGCTGATTAGTT 59.174 38.462 0.00 0.00 0.00 2.24
928 1045 4.856509 TCGATCTCTCCCTTCTGTTCTTA 58.143 43.478 0.00 0.00 0.00 2.10
941 1058 1.018148 TCGAGCTGGTTCGATCTCTC 58.982 55.000 5.51 0.00 44.00 3.20
1201 1318 1.187087 GACCTCTCCTTGGTCGTCAT 58.813 55.000 0.00 0.00 43.55 3.06
1344 1461 2.681778 AGAGGCTCACTGGGGTCG 60.682 66.667 18.26 0.00 0.00 4.79
1363 1481 5.446473 GCTATCGTTGTGGTGAGAAAAGATG 60.446 44.000 0.00 0.00 0.00 2.90
1374 1492 1.372582 CTGCATGCTATCGTTGTGGT 58.627 50.000 20.33 0.00 0.00 4.16
1376 1494 1.328680 GTCCTGCATGCTATCGTTGTG 59.671 52.381 20.33 0.00 0.00 3.33
1385 1503 0.616964 TCTCTCCTGTCCTGCATGCT 60.617 55.000 20.33 0.00 0.00 3.79
1429 1554 0.813184 ATCAAATCAACCGCTGGCTG 59.187 50.000 0.00 0.00 0.00 4.85
1430 1555 1.549203 AATCAAATCAACCGCTGGCT 58.451 45.000 0.00 0.00 0.00 4.75
1431 1556 2.368655 AAATCAAATCAACCGCTGGC 57.631 45.000 0.00 0.00 0.00 4.85
1432 1557 4.150451 GTGAAAAATCAAATCAACCGCTGG 59.850 41.667 0.00 0.00 0.00 4.85
1778 1904 2.216898 GTGGCTTCATGGCTAGCTTAG 58.783 52.381 15.72 4.61 42.34 2.18
1779 1905 1.473257 CGTGGCTTCATGGCTAGCTTA 60.473 52.381 15.72 4.59 42.34 3.09
1780 1906 0.745845 CGTGGCTTCATGGCTAGCTT 60.746 55.000 15.72 0.00 42.34 3.74
1793 1919 3.753434 CACGGAGAGAGCGTGGCT 61.753 66.667 0.00 0.00 43.88 4.75
1821 1947 4.442332 CGCCATGGTTAGTTCCATAGTACA 60.442 45.833 14.67 0.00 45.23 2.90
1948 2079 3.036084 CGCTCGTGGAACTTGCGT 61.036 61.111 0.00 0.00 45.82 5.24
2017 2148 4.941309 ACCGGGCGTTTGTGGTCC 62.941 66.667 6.32 0.00 0.00 4.46
2107 2238 3.173167 AAGGGCGGTGTGCTTACGT 62.173 57.895 0.00 0.00 45.43 3.57
2108 2239 2.358247 AAGGGCGGTGTGCTTACG 60.358 61.111 0.00 0.00 45.43 3.18
2109 2240 2.978018 GCAAGGGCGGTGTGCTTAC 61.978 63.158 0.00 0.00 45.43 2.34
2110 2241 1.832719 TAGCAAGGGCGGTGTGCTTA 61.833 55.000 2.33 0.00 46.25 3.09
2111 2242 3.190738 TAGCAAGGGCGGTGTGCTT 62.191 57.895 2.33 0.00 46.25 3.91
2153 2291 3.425404 CACCGGCAATCGTTAGAATTTG 58.575 45.455 0.00 0.00 37.11 2.32
2346 2490 4.776322 CGATGGCCGGGAAGTGCA 62.776 66.667 2.18 0.00 33.91 4.57
2414 2558 2.767505 GTTGATGACGTTGAAGGAGGT 58.232 47.619 0.00 0.00 0.00 3.85
2500 2644 0.820226 CACTCTCAAGCATCTCGGGA 59.180 55.000 0.00 0.00 0.00 5.14
2545 2689 1.371758 CGTGTACTGCGTGCTCTGT 60.372 57.895 0.00 0.00 0.00 3.41
2555 2699 2.040714 TTCGCACTGTACGTGTACTG 57.959 50.000 15.74 13.45 45.57 2.74
2563 2725 0.917259 CTGCTCGATTCGCACTGTAC 59.083 55.000 0.00 0.00 33.19 2.90
2567 2729 2.363788 TTAACTGCTCGATTCGCACT 57.636 45.000 0.00 0.00 33.19 4.40
2568 2730 3.658351 AATTAACTGCTCGATTCGCAC 57.342 42.857 0.00 0.00 33.19 5.34
2569 2731 4.430007 AGTAATTAACTGCTCGATTCGCA 58.570 39.130 0.00 0.00 36.93 5.10
2592 2754 5.324784 TGTCATGTACTATGTGGTCTCAC 57.675 43.478 0.00 0.00 43.87 3.51
2593 2755 5.656416 TCATGTCATGTACTATGTGGTCTCA 59.344 40.000 12.54 0.00 0.00 3.27
2594 2756 5.980116 GTCATGTCATGTACTATGTGGTCTC 59.020 44.000 12.54 0.00 0.00 3.36
2595 2757 5.658634 AGTCATGTCATGTACTATGTGGTCT 59.341 40.000 12.54 0.00 0.00 3.85
2596 2758 5.907207 AGTCATGTCATGTACTATGTGGTC 58.093 41.667 12.54 0.00 0.00 4.02
2597 2759 5.939764 AGTCATGTCATGTACTATGTGGT 57.060 39.130 12.54 0.00 0.00 4.16
2598 2760 6.457392 GCAAAGTCATGTCATGTACTATGTGG 60.457 42.308 12.54 0.86 0.00 4.17
2599 2761 6.092533 TGCAAAGTCATGTCATGTACTATGTG 59.907 38.462 12.54 12.74 0.00 3.21
2600 2762 6.092670 GTGCAAAGTCATGTCATGTACTATGT 59.907 38.462 12.54 2.83 0.00 2.29
2601 2763 6.314648 AGTGCAAAGTCATGTCATGTACTATG 59.685 38.462 12.54 7.98 35.61 2.23
2602 2764 6.409704 AGTGCAAAGTCATGTCATGTACTAT 58.590 36.000 12.54 4.37 35.61 2.12
2603 2765 5.793817 AGTGCAAAGTCATGTCATGTACTA 58.206 37.500 12.54 0.00 35.61 1.82
2604 2766 4.645535 AGTGCAAAGTCATGTCATGTACT 58.354 39.130 12.54 11.29 33.10 2.73
2605 2767 5.362556 AAGTGCAAAGTCATGTCATGTAC 57.637 39.130 12.54 9.39 0.00 2.90
2606 2768 6.183360 ACAAAAGTGCAAAGTCATGTCATGTA 60.183 34.615 12.54 0.00 0.00 2.29
2607 2769 4.924305 AAAGTGCAAAGTCATGTCATGT 57.076 36.364 12.54 0.00 0.00 3.21
2608 2770 5.045215 ACAAAAGTGCAAAGTCATGTCATG 58.955 37.500 6.47 6.47 0.00 3.07
2609 2771 5.266733 ACAAAAGTGCAAAGTCATGTCAT 57.733 34.783 0.00 0.00 0.00 3.06
2624 2786 3.801307 AAATCGGTCCCCTACAAAAGT 57.199 42.857 0.00 0.00 0.00 2.66
2631 2793 0.538118 CCACGAAAATCGGTCCCCTA 59.462 55.000 4.66 0.00 45.59 3.53
2741 2909 3.754965 AGCAACTTGATCAAAGGCTGTA 58.245 40.909 20.84 0.00 40.51 2.74
2775 2943 7.128976 GCATGCACTCTCTTAATTAACTAAGC 58.871 38.462 14.21 0.00 0.00 3.09
2782 2950 5.297527 CACCATGCATGCACTCTCTTAATTA 59.702 40.000 25.37 0.00 0.00 1.40
2783 2951 4.097437 CACCATGCATGCACTCTCTTAATT 59.903 41.667 25.37 0.00 0.00 1.40
2784 2952 3.630769 CACCATGCATGCACTCTCTTAAT 59.369 43.478 25.37 0.00 0.00 1.40
2786 2954 2.635714 CACCATGCATGCACTCTCTTA 58.364 47.619 25.37 0.00 0.00 2.10
2788 2956 1.030488 GCACCATGCATGCACTCTCT 61.030 55.000 25.37 3.10 44.26 3.10
2905 3089 2.501610 GCCTCCTCCACCGTCATC 59.498 66.667 0.00 0.00 0.00 2.92
3611 3807 2.351111 CCTCGTCCGACTTGTAGTAGAC 59.649 54.545 0.00 0.00 31.69 2.59
4244 4440 1.856539 ATCTTGTCCTGGGGCCACAG 61.857 60.000 29.29 29.29 38.21 3.66
4258 4454 7.548427 CCTAATCCTACATGCAGTGATATCTTG 59.452 40.741 3.98 4.06 0.00 3.02
4268 4464 8.099537 ACATCTTATTCCTAATCCTACATGCAG 58.900 37.037 0.00 0.00 0.00 4.41
4513 4744 5.233050 TGTGATTGTTTTGTTTTGTATGGCG 59.767 36.000 0.00 0.00 0.00 5.69
4821 5052 8.087750 TGCTTCACTCTGGTTAAAAATTTATGG 58.912 33.333 0.00 0.00 0.00 2.74
4825 5056 6.462909 CCCTGCTTCACTCTGGTTAAAAATTT 60.463 38.462 0.00 0.00 0.00 1.82
4827 5058 4.524328 CCCTGCTTCACTCTGGTTAAAAAT 59.476 41.667 0.00 0.00 0.00 1.82
4832 5063 0.984230 CCCCTGCTTCACTCTGGTTA 59.016 55.000 0.00 0.00 0.00 2.85
4867 5098 4.014406 TGCTCGACTATGTGGAAGTAAGA 58.986 43.478 0.00 0.00 0.00 2.10
4877 5108 1.603931 CCATGCGATGCTCGACTATGT 60.604 52.381 9.32 0.00 43.74 2.29
4879 5110 0.676184 ACCATGCGATGCTCGACTAT 59.324 50.000 9.32 0.00 43.74 2.12
4892 5125 0.801251 GACTGCAGAAGACACCATGC 59.199 55.000 23.35 0.00 39.14 4.06
4896 5129 2.029844 GCCGACTGCAGAAGACACC 61.030 63.158 23.35 0.00 40.77 4.16
4929 5162 4.804108 CCAATTGACGACAGCCAAAATTA 58.196 39.130 7.12 0.00 0.00 1.40
4931 5164 2.610232 GCCAATTGACGACAGCCAAAAT 60.610 45.455 7.12 0.00 0.00 1.82
4964 5197 2.408050 AGCGTCACAGCTCTTTACAAG 58.592 47.619 0.00 0.00 45.67 3.16
5171 5404 3.242413 CGTATTTTGAGCCATCTTCCACG 60.242 47.826 0.00 0.00 0.00 4.94
5177 5410 2.550978 CGACCGTATTTTGAGCCATCT 58.449 47.619 0.00 0.00 0.00 2.90
5192 5425 2.671396 CTCTTTCATAACAACCCGACCG 59.329 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.