Multiple sequence alignment - TraesCS7D01G193600

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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 TraesCS7D01G193600 chr7D 100.000 2226 0 0 1584 3809 150604169 150601944 0.000000e+00 4111.0
1 TraesCS7D01G193600 chr7D 100.000 1397 0 0 1 1397 150605752 150604356 0.000000e+00 2580.0
2 TraesCS7D01G193600 chr4B 94.328 1569 74 7 1704 3269 402763460 402761904 0.000000e+00 2390.0
3 TraesCS7D01G193600 chr4B 91.892 518 28 3 881 1397 402764190 402763686 0.000000e+00 712.0
4 TraesCS7D01G193600 chr4B 91.129 372 26 4 3298 3667 402759355 402758989 7.350000e-137 497.0
5 TraesCS7D01G193600 chr4B 84.426 122 13 6 1584 1704 402763629 402763513 8.650000e-22 115.0
6 TraesCS7D01G193600 chr7B 94.882 1270 53 5 1704 2971 112338884 112337625 0.000000e+00 1975.0
7 TraesCS7D01G193600 chr7B 91.273 825 38 11 586 1397 112339913 112339110 0.000000e+00 1094.0
8 TraesCS7D01G193600 chr7B 92.203 590 17 6 1 589 112342412 112341851 0.000000e+00 808.0
9 TraesCS7D01G193600 chr7B 86.822 516 36 16 3298 3809 112335540 112335053 7.190000e-152 547.0
10 TraesCS7D01G193600 chr7B 92.395 263 15 3 3010 3269 112337620 112337360 1.670000e-98 370.0
11 TraesCS7D01G193600 chr7B 85.246 122 13 5 1584 1704 112339054 112338937 1.860000e-23 121.0
12 TraesCS7D01G193600 chr7A 96.499 1171 41 0 1704 2874 150419891 150418721 0.000000e+00 1936.0
13 TraesCS7D01G193600 chr7A 87.414 437 29 12 902 1319 150420589 150420160 2.660000e-131 479.0
14 TraesCS7D01G193600 chr7A 81.495 562 45 27 3086 3611 150418601 150418063 1.270000e-109 407.0
15 TraesCS7D01G193600 chr7A 85.526 228 33 0 222 449 150427937 150427710 4.920000e-59 239.0
16 TraesCS7D01G193600 chr7A 84.577 201 25 6 180 374 150425027 150424827 1.080000e-45 195.0
17 TraesCS7D01G193600 chr7A 95.946 74 3 0 3736 3809 150418020 150417947 1.860000e-23 121.0
18 TraesCS7D01G193600 chr7A 97.436 39 1 0 3633 3671 150418059 150418021 2.460000e-07 67.6
19 TraesCS7D01G193600 chr3B 95.122 41 2 0 36 76 589905978 589906018 8.830000e-07 65.8
20 TraesCS7D01G193600 chr3A 95.122 41 2 0 36 76 308867058 308867098 8.830000e-07 65.8
21 TraesCS7D01G193600 chr5B 94.872 39 2 0 38 76 481767780 481767742 1.140000e-05 62.1


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 TraesCS7D01G193600 chr7D 150601944 150605752 3808 True 3345.500000 4111 100.000000 1 3809 2 chr7D.!!$R1 3808
1 TraesCS7D01G193600 chr4B 402758989 402764190 5201 True 928.500000 2390 90.443750 881 3667 4 chr4B.!!$R1 2786
2 TraesCS7D01G193600 chr7B 112335053 112342412 7359 True 819.166667 1975 90.470167 1 3809 6 chr7B.!!$R1 3808
3 TraesCS7D01G193600 chr7A 150417947 150420589 2642 True 602.120000 1936 91.758000 902 3809 5 chr7A.!!$R1 2907
4 TraesCS7D01G193600 chr7A 150424827 150427937 3110 True 217.000000 239 85.051500 180 449 2 chr7A.!!$R2 269

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
864 2807 0.03831 TCTCTCTCCCTCTGTCGCAA 59.962 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2846 5686 1.515088 AGAACTCAGCGCACGATCG 60.515 57.895 14.88 14.88 0.0 3.69 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
28 29 9.184523 ACATTCAGGATATACGAAAATTTTCCA 57.815 29.630 22.15 12.52 33.68 3.53
32 33 7.996066 TCAGGATATACGAAAATTTTCCATGGA 59.004 33.333 22.15 11.44 33.68 3.41
86 88 7.753580 CGGAGGGAGTACAAAATTATTTCAAAC 59.246 37.037 0.00 0.00 0.00 2.93
87 89 8.033038 GGAGGGAGTACAAAATTATTTCAAACC 58.967 37.037 0.00 0.00 0.00 3.27
88 90 7.599171 AGGGAGTACAAAATTATTTCAAACCG 58.401 34.615 0.00 0.00 0.00 4.44
89 91 7.449086 AGGGAGTACAAAATTATTTCAAACCGA 59.551 33.333 0.00 0.00 0.00 4.69
90 92 7.753580 GGGAGTACAAAATTATTTCAAACCGAG 59.246 37.037 0.00 0.00 0.00 4.63
91 93 8.294577 GGAGTACAAAATTATTTCAAACCGAGT 58.705 33.333 0.00 0.00 0.00 4.18
164 166 3.971871 CAGCAAATCAAACGTTCGCTAAA 59.028 39.130 0.00 0.00 0.00 1.85
166 168 3.118972 GCAAATCAAACGTTCGCTAAACC 59.881 43.478 0.00 0.00 34.11 3.27
177 179 1.134818 TCGCTAAACCGCATGAGTGAT 60.135 47.619 0.00 0.00 0.00 3.06
178 180 1.004610 CGCTAAACCGCATGAGTGATG 60.005 52.381 0.00 0.00 34.84 3.07
201 203 7.800155 TGACAATATAATTTGGCATCTCGAA 57.200 32.000 0.00 0.00 39.69 3.71
221 223 4.863689 CGAATGTTTGATTTGCCATGCTTA 59.136 37.500 0.00 0.00 0.00 3.09
340 342 2.916527 AATCCTGCCTTGATGCCCGG 62.917 60.000 0.00 0.00 0.00 5.73
374 376 2.202797 CCATGAGCTCCCACGACG 60.203 66.667 12.15 0.00 0.00 5.12
456 458 3.216292 AACCACCAGCACGGCAAC 61.216 61.111 0.00 0.00 39.03 4.17
488 490 4.505808 CACTTGCAGTTCTGATCTCTGAT 58.494 43.478 3.84 0.00 0.00 2.90
490 492 3.538634 TGCAGTTCTGATCTCTGATGG 57.461 47.619 3.84 0.00 0.00 3.51
491 493 2.211806 GCAGTTCTGATCTCTGATGGC 58.788 52.381 3.84 0.00 0.00 4.40
492 494 2.419713 GCAGTTCTGATCTCTGATGGCA 60.420 50.000 3.84 0.00 0.00 4.92
493 495 3.459145 CAGTTCTGATCTCTGATGGCAG 58.541 50.000 0.00 0.00 43.67 4.85
503 505 2.415624 TCTGATGGCAGATCATTCCCT 58.584 47.619 0.00 0.00 45.88 4.20
504 506 2.105993 TCTGATGGCAGATCATTCCCTG 59.894 50.000 0.00 0.00 45.88 4.45
505 507 2.105993 CTGATGGCAGATCATTCCCTGA 59.894 50.000 0.00 0.00 45.17 3.86
514 516 1.750193 TCATTCCCTGAAACGATGGC 58.250 50.000 0.00 0.00 0.00 4.40
541 543 1.794714 CAGATACCTACCAGCCCACT 58.205 55.000 0.00 0.00 0.00 4.00
546 548 0.905337 ACCTACCAGCCCACTCTCAC 60.905 60.000 0.00 0.00 0.00 3.51
620 2563 1.199327 GAACTCCCGCTTAAACCTTGC 59.801 52.381 0.00 0.00 0.00 4.01
661 2604 3.270027 CTGAATAGACATTTCACCCGCA 58.730 45.455 0.00 0.00 0.00 5.69
662 2605 3.680490 TGAATAGACATTTCACCCGCAA 58.320 40.909 0.00 0.00 0.00 4.85
721 2664 6.219473 AGTATATCAACACAGCACTGCTATC 58.781 40.000 2.39 0.00 36.40 2.08
751 2694 3.108144 CAAAGAGAAAAACACTGCCGTG 58.892 45.455 6.73 6.73 46.63 4.94
771 2714 1.098050 GGCTGTTTGGGCTATGTGAG 58.902 55.000 0.00 0.00 0.00 3.51
781 2724 1.443407 CTATGTGAGTCGGGCCCAG 59.557 63.158 24.92 15.19 0.00 4.45
812 2755 6.878389 AGCCATTTAACAAACCCAATAATGTG 59.122 34.615 0.00 0.00 0.00 3.21
854 2797 6.472016 AGAAAACATTCTTTCTCTCTCTCCC 58.528 40.000 0.00 0.00 40.84 4.30
864 2807 0.038310 TCTCTCTCCCTCTGTCGCAA 59.962 55.000 0.00 0.00 0.00 4.85
978 2937 4.135153 CCTCTCCCCGTGCACGAG 62.135 72.222 39.10 27.69 43.02 4.18
1039 2998 2.358737 GCCACCACCTCCAGAACG 60.359 66.667 0.00 0.00 0.00 3.95
1297 3280 0.682209 TCCAGGTACGGTGCTAGGTC 60.682 60.000 0.00 0.00 0.00 3.85
1323 3306 0.179056 TCGATTGATTTCTCCCCGGC 60.179 55.000 0.00 0.00 0.00 6.13
1326 3309 1.921869 ATTGATTTCTCCCCGGCGGT 61.922 55.000 26.32 3.39 0.00 5.68
1634 3634 9.031360 CGCTCTTAACAAGCTCAATAAATAGTA 57.969 33.333 0.00 0.00 37.62 1.82
1663 3668 4.322650 GGTGGTTGTTGAAATGTGCCATAT 60.323 41.667 0.00 0.00 0.00 1.78
1664 3669 4.864247 GTGGTTGTTGAAATGTGCCATATC 59.136 41.667 0.00 0.00 0.00 1.63
1691 3697 2.762887 TGTGATTTTCCCACTTGTGCAA 59.237 40.909 0.00 0.00 35.66 4.08
2202 4641 4.341502 GGCGTGCGGCACAACAAT 62.342 61.111 30.23 0.00 46.16 2.71
2562 5402 1.448013 GCTGGGCTACACGGAGAAC 60.448 63.158 0.00 0.00 0.00 3.01
2793 5633 2.924290 GTTCAACGAGATCCTGCTACAC 59.076 50.000 0.00 0.00 0.00 2.90
2797 5637 0.817654 CGAGATCCTGCTACACACCA 59.182 55.000 0.00 0.00 0.00 4.17
2867 5707 0.319900 ATCGTGCGCTGAGTTCTGTT 60.320 50.000 9.73 0.00 0.00 3.16
2868 5708 0.312729 TCGTGCGCTGAGTTCTGTTA 59.687 50.000 9.73 0.00 0.00 2.41
2869 5709 1.136690 CGTGCGCTGAGTTCTGTTAA 58.863 50.000 9.73 0.00 0.00 2.01
2883 5723 7.180229 TGAGTTCTGTTAATGATCTAGGAACCA 59.820 37.037 0.00 0.00 34.30 3.67
2884 5724 7.331791 AGTTCTGTTAATGATCTAGGAACCAC 58.668 38.462 0.00 0.00 34.30 4.16
2901 5741 0.673437 CACGAATTTTGGGCCAGTGT 59.327 50.000 6.23 0.00 0.00 3.55
2902 5742 1.883275 CACGAATTTTGGGCCAGTGTA 59.117 47.619 6.23 0.00 0.00 2.90
2903 5743 2.095263 CACGAATTTTGGGCCAGTGTAG 60.095 50.000 6.23 0.67 0.00 2.74
2911 5751 2.030562 GCCAGTGTAGGTGCGTGT 59.969 61.111 0.00 0.00 0.00 4.49
2912 5752 1.290955 GCCAGTGTAGGTGCGTGTA 59.709 57.895 0.00 0.00 0.00 2.90
2913 5753 1.012486 GCCAGTGTAGGTGCGTGTAC 61.012 60.000 0.00 0.00 0.00 2.90
2914 5754 0.315886 CCAGTGTAGGTGCGTGTACA 59.684 55.000 0.00 0.00 0.00 2.90
2915 5755 1.067142 CCAGTGTAGGTGCGTGTACAT 60.067 52.381 0.00 0.00 31.95 2.29
2916 5756 2.259618 CAGTGTAGGTGCGTGTACATC 58.740 52.381 0.00 0.00 31.95 3.06
2917 5757 1.135489 AGTGTAGGTGCGTGTACATCG 60.135 52.381 0.00 6.16 31.95 3.84
2935 5775 4.393062 ACATCGATGATTCTTTTGCTCGTT 59.607 37.500 31.33 0.07 0.00 3.85
2936 5776 4.584029 TCGATGATTCTTTTGCTCGTTC 57.416 40.909 0.00 0.00 0.00 3.95
2964 5804 4.653868 ACGATCAGGATACGAGATAGGTT 58.346 43.478 0.00 0.00 46.39 3.50
2977 5817 4.367450 GAGATAGGTTGTGATGAGAGCAC 58.633 47.826 0.00 0.00 36.81 4.40
2979 5819 0.036952 AGGTTGTGATGAGAGCACCG 60.037 55.000 0.00 0.00 35.43 4.94
2980 5820 1.639298 GGTTGTGATGAGAGCACCGC 61.639 60.000 0.00 0.00 35.43 5.68
2987 5827 1.830587 ATGAGAGCACCGCTGGTTCA 61.831 55.000 0.00 0.83 39.88 3.18
3045 5896 2.923121 TGCTGGGAGTATGAATTGCTC 58.077 47.619 0.00 0.00 0.00 4.26
3069 5920 8.480133 TCTGAGGTCCTAGAAGGTATAATTTC 57.520 38.462 0.00 0.00 36.53 2.17
3092 5943 6.154445 TCCTGACGAATCTGTAAGTTGTAAC 58.846 40.000 0.00 0.00 33.76 2.50
3122 5976 4.615588 AGAGATTGCTAGTTATCAGGGC 57.384 45.455 8.35 0.00 0.00 5.19
3160 6027 6.601217 GCCTGGACTCTCTTTTTCATTCTTAT 59.399 38.462 0.00 0.00 0.00 1.73
3161 6028 7.121907 GCCTGGACTCTCTTTTTCATTCTTATT 59.878 37.037 0.00 0.00 0.00 1.40
3278 6148 5.126869 TGATGTTTCTGAAAGTTCCAAGCAA 59.873 36.000 2.48 0.00 33.76 3.91
3282 6152 5.751243 TTCTGAAAGTTCCAAGCAACTAC 57.249 39.130 0.00 0.00 35.45 2.73
3283 6153 5.036117 TCTGAAAGTTCCAAGCAACTACT 57.964 39.130 0.00 0.00 35.45 2.57
3284 6154 5.437060 TCTGAAAGTTCCAAGCAACTACTT 58.563 37.500 0.00 0.00 35.45 2.24
3286 6156 4.947388 TGAAAGTTCCAAGCAACTACTTGT 59.053 37.500 3.82 0.00 44.55 3.16
3289 6159 4.386711 AGTTCCAAGCAACTACTTGTACC 58.613 43.478 3.82 0.00 44.55 3.34
3290 6160 4.131596 GTTCCAAGCAACTACTTGTACCA 58.868 43.478 3.82 0.00 44.55 3.25
3292 6162 2.484264 CCAAGCAACTACTTGTACCAGC 59.516 50.000 3.82 0.00 44.55 4.85
3293 6163 3.138304 CAAGCAACTACTTGTACCAGCA 58.862 45.455 0.00 0.00 41.74 4.41
3296 6166 3.576982 AGCAACTACTTGTACCAGCAGTA 59.423 43.478 0.46 0.00 0.00 2.74
3300 8776 6.761714 GCAACTACTTGTACCAGCAGTATTAT 59.238 38.462 0.46 0.00 32.28 1.28
3303 8779 7.717568 ACTACTTGTACCAGCAGTATTATCAG 58.282 38.462 0.00 0.00 32.28 2.90
3309 8785 4.701765 ACCAGCAGTATTATCAGCTTCTG 58.298 43.478 0.00 0.00 34.61 3.02
3313 8789 5.814188 CAGCAGTATTATCAGCTTCTGTCAA 59.186 40.000 0.00 0.00 34.61 3.18
3360 8836 5.690409 GTGAAGTTCTATTCTGACGTGTTCA 59.310 40.000 4.17 0.00 0.00 3.18
3409 8891 1.961277 GTCAGCACAACAGGGGTCG 60.961 63.158 0.00 0.00 0.00 4.79
3419 8901 0.966370 ACAGGGGTCGTCTACTGCTC 60.966 60.000 0.00 0.00 34.40 4.26
3491 8977 2.758009 GAGGCATCTGATCTTGCTCTC 58.242 52.381 13.15 13.11 38.88 3.20
3518 9004 4.127566 GCACAAATTGCCACCATATTCT 57.872 40.909 0.00 0.00 46.63 2.40
3531 9017 6.294508 GCCACCATATTCTTGTGTTTGTAGTT 60.295 38.462 0.00 0.00 0.00 2.24
3540 9026 1.082366 GTTTGTAGTTGGCGTGGCG 60.082 57.895 0.00 0.00 0.00 5.69
3546 9032 2.457743 TAGTTGGCGTGGCGGATGTT 62.458 55.000 0.00 0.00 0.00 2.71
3612 9102 2.327568 CGCAAGGTTTGTGCTTATTGG 58.672 47.619 0.00 0.00 39.95 3.16
3667 9163 0.533308 TTTGCTTAGTGGCGTCCGTT 60.533 50.000 0.00 0.00 34.52 4.44
3690 9186 1.577468 TTTGTGTGTGCGAGGTAGTG 58.423 50.000 0.00 0.00 0.00 2.74
3692 9188 2.027625 GTGTGTGCGAGGTAGTGGC 61.028 63.158 0.00 0.00 0.00 5.01
3693 9189 2.809601 GTGTGCGAGGTAGTGGCG 60.810 66.667 0.00 0.00 31.05 5.69
3694 9190 3.299977 TGTGCGAGGTAGTGGCGT 61.300 61.111 0.00 0.00 31.05 5.68
3695 9191 2.506438 GTGCGAGGTAGTGGCGTC 60.506 66.667 0.00 0.00 31.05 5.19
3697 9193 4.849329 GCGAGGTAGTGGCGTCCG 62.849 72.222 0.00 0.00 0.00 4.79
3698 9194 3.437795 CGAGGTAGTGGCGTCCGT 61.438 66.667 0.00 0.00 0.00 4.69
3699 9195 2.181021 GAGGTAGTGGCGTCCGTG 59.819 66.667 0.00 0.00 0.00 4.94
3700 9196 2.599578 AGGTAGTGGCGTCCGTGT 60.600 61.111 0.00 0.00 0.00 4.49
3701 9197 2.151049 GAGGTAGTGGCGTCCGTGTT 62.151 60.000 0.00 0.00 0.00 3.32
3720 9216 0.179004 TTGGCTGTCCGTGGTTGATT 60.179 50.000 0.00 0.00 34.14 2.57
3739 9235 0.109153 TCGTGAGTATAGCCGGGCTA 59.891 55.000 29.55 29.55 45.55 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.016610 CCTCCGTCCAAAATTCTTGTTTTAGA 60.017 38.462 0.00 0.00 30.56 2.10
41 42 6.149633 CCTCCGTCCAAAATTCTTGTTTTAG 58.850 40.000 0.00 0.00 30.56 1.85
42 43 5.010213 CCCTCCGTCCAAAATTCTTGTTTTA 59.990 40.000 0.00 0.00 30.56 1.52
43 44 4.202212 CCCTCCGTCCAAAATTCTTGTTTT 60.202 41.667 0.00 0.00 0.00 2.43
164 166 2.408271 ATTGTCATCACTCATGCGGT 57.592 45.000 0.00 0.00 31.70 5.68
166 168 7.536281 CCAAATTATATTGTCATCACTCATGCG 59.464 37.037 0.00 0.00 31.70 4.73
177 179 7.800155 TTCGAGATGCCAAATTATATTGTCA 57.200 32.000 0.00 0.00 0.00 3.58
178 180 8.292448 ACATTCGAGATGCCAAATTATATTGTC 58.708 33.333 7.28 0.00 0.00 3.18
200 202 7.507733 TTTTAAGCATGGCAAATCAAACATT 57.492 28.000 0.00 0.00 0.00 2.71
201 203 7.608761 AGATTTTAAGCATGGCAAATCAAACAT 59.391 29.630 12.19 0.00 37.87 2.71
221 223 2.476821 ACGAACCGAACGTCAGATTTT 58.523 42.857 0.00 0.00 39.87 1.82
340 342 2.202810 GGCTCTGCACCTACTCGC 60.203 66.667 0.00 0.00 0.00 5.03
384 386 0.670854 GACAGAAGCCCAAGACGTCC 60.671 60.000 13.01 0.00 0.00 4.79
456 458 1.813859 CTGCAAGTGCCATGGGATG 59.186 57.895 15.13 8.28 41.18 3.51
488 490 2.726821 GTTTCAGGGAATGATCTGCCA 58.273 47.619 0.00 0.00 37.89 4.92
490 492 2.632377 TCGTTTCAGGGAATGATCTGC 58.368 47.619 0.00 0.00 37.89 4.26
491 493 3.562973 CCATCGTTTCAGGGAATGATCTG 59.437 47.826 0.00 0.00 37.89 2.90
492 494 3.813443 CCATCGTTTCAGGGAATGATCT 58.187 45.455 0.00 0.00 37.89 2.75
493 495 2.291741 GCCATCGTTTCAGGGAATGATC 59.708 50.000 0.00 0.00 37.89 2.92
495 497 1.750193 GCCATCGTTTCAGGGAATGA 58.250 50.000 0.00 0.00 35.62 2.57
496 498 0.378257 CGCCATCGTTTCAGGGAATG 59.622 55.000 0.00 0.00 0.00 2.67
497 499 2.780595 CGCCATCGTTTCAGGGAAT 58.219 52.632 0.00 0.00 0.00 3.01
498 500 4.294523 CGCCATCGTTTCAGGGAA 57.705 55.556 0.00 0.00 0.00 3.97
514 516 0.030369 GGTAGGTATCTGCGTCCACG 59.970 60.000 0.00 0.00 43.27 4.94
541 543 0.748450 AGACGTTGAAACCGGTGAGA 59.252 50.000 8.52 0.00 0.00 3.27
546 548 2.139210 GTCGAGACGTTGAAACCGG 58.861 57.895 0.00 0.00 0.00 5.28
573 575 1.818674 ACCGATTGATTGTCCTTTGGC 59.181 47.619 0.00 0.00 0.00 4.52
620 2563 4.053295 CAGCTTTGGTTCTCAACAATTGG 58.947 43.478 10.83 0.00 34.67 3.16
685 2628 9.388506 CTGTGTTGATATACTCTCCTGAAAAAT 57.611 33.333 0.00 0.00 0.00 1.82
751 2694 0.323360 TCACATAGCCCAAACAGCCC 60.323 55.000 0.00 0.00 0.00 5.19
781 2724 2.480037 GGTTTGTTAAATGGCTGCTTGC 59.520 45.455 0.00 0.00 41.94 4.01
812 2755 0.827368 CTCTACTGGCCTCTGTTCCC 59.173 60.000 3.32 0.00 0.00 3.97
815 2758 3.391296 TGTTTTCTCTACTGGCCTCTGTT 59.609 43.478 3.32 0.00 0.00 3.16
912 2861 1.595058 AAGGGGATCGAGGAGAGGGT 61.595 60.000 0.00 0.00 0.00 4.34
978 2937 2.280457 GCGTGGAGGGAGCTATGC 60.280 66.667 0.00 0.00 0.00 3.14
1209 3180 1.986575 GCTCCTCAAGCGCATTCACC 61.987 60.000 11.47 0.00 42.21 4.02
1280 3263 1.134560 GAAGACCTAGCACCGTACCTG 59.865 57.143 0.00 0.00 0.00 4.00
1297 3280 4.276926 GGGGAGAAATCAATCGATTGGAAG 59.723 45.833 32.03 11.95 41.12 3.46
1349 3332 2.278857 CCCAGAGACGAATCCGCG 60.279 66.667 0.00 0.00 39.95 6.46
1634 3634 1.786937 TTTCAACAACCACCATGGCT 58.213 45.000 13.04 0.00 42.67 4.75
1663 3668 2.170166 GTGGGAAAATCACATGCCAGA 58.830 47.619 0.00 0.00 37.75 3.86
1664 3669 2.173519 AGTGGGAAAATCACATGCCAG 58.826 47.619 0.00 0.00 37.75 4.85
1678 3683 2.158986 CCAAAATGTTGCACAAGTGGGA 60.159 45.455 2.00 0.00 33.01 4.37
1712 4151 3.656045 GGGCCAACACGACAACGG 61.656 66.667 4.39 0.00 44.46 4.44
1714 4153 2.589442 TCGGGCCAACACGACAAC 60.589 61.111 4.39 0.00 33.69 3.32
1743 4182 2.711922 GGATCCTGACGCCGACACT 61.712 63.158 3.84 0.00 0.00 3.55
2202 4641 3.859650 GAACGAGTCGAGGAACACA 57.140 52.632 21.50 0.00 0.00 3.72
2534 4973 2.427245 TAGCCCAGCTCCTTCTCGC 61.427 63.158 0.00 0.00 40.44 5.03
2846 5686 1.515088 AGAACTCAGCGCACGATCG 60.515 57.895 14.88 14.88 0.00 3.69
2867 5707 7.282224 CCAAAATTCGTGGTTCCTAGATCATTA 59.718 37.037 0.00 0.00 0.00 1.90
2868 5708 6.095440 CCAAAATTCGTGGTTCCTAGATCATT 59.905 38.462 0.00 0.00 0.00 2.57
2869 5709 5.590259 CCAAAATTCGTGGTTCCTAGATCAT 59.410 40.000 0.00 0.00 0.00 2.45
2883 5723 2.159382 CTACACTGGCCCAAAATTCGT 58.841 47.619 0.00 0.00 0.00 3.85
2884 5724 1.472480 CCTACACTGGCCCAAAATTCG 59.528 52.381 0.00 0.00 0.00 3.34
2901 5741 2.018515 TCATCGATGTACACGCACCTA 58.981 47.619 24.09 0.00 0.00 3.08
2902 5742 0.815095 TCATCGATGTACACGCACCT 59.185 50.000 24.09 0.00 0.00 4.00
2903 5743 1.852942 ATCATCGATGTACACGCACC 58.147 50.000 24.09 0.00 0.00 5.01
2911 5751 5.109210 ACGAGCAAAAGAATCATCGATGTA 58.891 37.500 24.09 12.00 34.46 2.29
2912 5752 3.935203 ACGAGCAAAAGAATCATCGATGT 59.065 39.130 24.09 6.77 34.46 3.06
2913 5753 4.526970 ACGAGCAAAAGAATCATCGATG 57.473 40.909 19.61 19.61 34.46 3.84
2914 5754 4.259970 CGAACGAGCAAAAGAATCATCGAT 60.260 41.667 0.00 0.00 34.46 3.59
2915 5755 3.060761 CGAACGAGCAAAAGAATCATCGA 59.939 43.478 0.00 0.00 34.46 3.59
2916 5756 3.181530 ACGAACGAGCAAAAGAATCATCG 60.182 43.478 0.14 0.00 36.32 3.84
2917 5757 4.143115 TGACGAACGAGCAAAAGAATCATC 60.143 41.667 0.14 0.00 0.00 2.92
2936 5776 1.865340 TCGTATCCTGATCGTCTGACG 59.135 52.381 23.33 23.33 44.19 4.35
2947 5787 5.241728 TCATCACAACCTATCTCGTATCCTG 59.758 44.000 0.00 0.00 0.00 3.86
2951 5791 5.048364 GCTCTCATCACAACCTATCTCGTAT 60.048 44.000 0.00 0.00 0.00 3.06
2964 5804 1.079612 CAGCGGTGCTCTCATCACA 60.080 57.895 0.00 0.00 36.40 3.58
2977 5817 1.659794 CCCAAACTTGAACCAGCGG 59.340 57.895 0.00 0.00 0.00 5.52
2979 5819 0.961753 CTCCCCAAACTTGAACCAGC 59.038 55.000 0.00 0.00 0.00 4.85
2980 5820 2.656947 TCTCCCCAAACTTGAACCAG 57.343 50.000 0.00 0.00 0.00 4.00
2987 5827 4.140924 ACTCCAAATCTTCTCCCCAAACTT 60.141 41.667 0.00 0.00 0.00 2.66
3045 5896 7.511028 AGGAAATTATACCTTCTAGGACCTCAG 59.489 40.741 0.00 0.00 37.67 3.35
3069 5920 6.157211 AGTTACAACTTACAGATTCGTCAGG 58.843 40.000 0.00 0.00 35.21 3.86
3092 5943 9.376075 TGATAACTAGCAATCTCTTTCTGAAAG 57.624 33.333 21.29 21.29 39.88 2.62
3102 5953 4.202305 ACAGCCCTGATAACTAGCAATCTC 60.202 45.833 1.69 0.00 0.00 2.75
3122 5976 0.746063 TCCAGGCAAGCAAAACACAG 59.254 50.000 0.00 0.00 0.00 3.66
3160 6027 2.733858 GCATTGATTTCGGCGGCTAAAA 60.734 45.455 12.62 10.37 0.00 1.52
3161 6028 1.202245 GCATTGATTTCGGCGGCTAAA 60.202 47.619 11.07 11.07 0.00 1.85
3278 6148 7.655521 TGATAATACTGCTGGTACAAGTAGT 57.344 36.000 22.62 22.62 38.70 2.73
3282 6152 5.605534 AGCTGATAATACTGCTGGTACAAG 58.394 41.667 0.00 0.00 41.92 3.16
3283 6153 5.614324 AGCTGATAATACTGCTGGTACAA 57.386 39.130 0.00 0.00 41.92 2.41
3284 6154 5.363868 AGAAGCTGATAATACTGCTGGTACA 59.636 40.000 0.00 0.00 42.48 2.90
3286 6156 5.363868 ACAGAAGCTGATAATACTGCTGGTA 59.636 40.000 0.82 0.00 40.80 3.25
3289 6159 5.354767 TGACAGAAGCTGATAATACTGCTG 58.645 41.667 0.82 0.00 42.48 4.41
3290 6160 5.604758 TGACAGAAGCTGATAATACTGCT 57.395 39.130 0.82 0.00 44.49 4.24
3292 6162 8.877808 TGTATTGACAGAAGCTGATAATACTG 57.122 34.615 22.59 0.00 40.19 2.74
3296 6166 8.844244 GGAAATGTATTGACAGAAGCTGATAAT 58.156 33.333 0.82 4.34 39.50 1.28
3300 8776 5.559770 TGGAAATGTATTGACAGAAGCTGA 58.440 37.500 0.82 0.00 39.50 4.26
3303 8779 8.538409 AATTTTGGAAATGTATTGACAGAAGC 57.462 30.769 0.00 0.00 39.50 3.86
3360 8836 6.641169 TCGCATCTAGATTTACTCACTGAT 57.359 37.500 1.33 0.00 0.00 2.90
3409 8891 0.374410 GTCCGACGAGAGCAGTAGAC 59.626 60.000 0.00 0.00 0.00 2.59
3419 8901 4.456253 CCACCGACGTCCGACGAG 62.456 72.222 27.03 18.45 46.05 4.18
3445 8927 0.801067 GTCCACACGTATCTGCGACC 60.801 60.000 0.00 0.00 35.59 4.79
3518 9004 1.402259 CCACGCCAACTACAAACACAA 59.598 47.619 0.00 0.00 0.00 3.33
3540 9026 1.514087 CAGGCCACATGCAACATCC 59.486 57.895 5.01 0.00 43.89 3.51
3611 9101 8.560374 GGTCAGCACTCAGATAAATAATAAACC 58.440 37.037 0.00 0.00 0.00 3.27
3612 9102 8.276325 CGGTCAGCACTCAGATAAATAATAAAC 58.724 37.037 0.00 0.00 0.00 2.01
3676 9172 2.809601 CGCCACTACCTCGCACAC 60.810 66.667 0.00 0.00 0.00 3.82
3677 9173 3.277211 GACGCCACTACCTCGCACA 62.277 63.158 0.00 0.00 0.00 4.57
3678 9174 2.506438 GACGCCACTACCTCGCAC 60.506 66.667 0.00 0.00 0.00 5.34
3687 9183 2.590575 CCAAACACGGACGCCACT 60.591 61.111 0.00 0.00 0.00 4.00
3690 9186 4.025401 CAGCCAAACACGGACGCC 62.025 66.667 0.00 0.00 0.00 5.68
3692 9188 2.604174 GGACAGCCAAACACGGACG 61.604 63.158 0.00 0.00 0.00 4.79
3693 9189 2.604174 CGGACAGCCAAACACGGAC 61.604 63.158 0.00 0.00 0.00 4.79
3694 9190 2.280524 CGGACAGCCAAACACGGA 60.281 61.111 0.00 0.00 0.00 4.69
3695 9191 2.590575 ACGGACAGCCAAACACGG 60.591 61.111 0.00 0.00 0.00 4.94
3697 9193 1.381165 AACCACGGACAGCCAAACAC 61.381 55.000 0.00 0.00 0.00 3.32
3698 9194 1.077357 AACCACGGACAGCCAAACA 60.077 52.632 0.00 0.00 0.00 2.83
3699 9195 1.098712 TCAACCACGGACAGCCAAAC 61.099 55.000 0.00 0.00 0.00 2.93
3700 9196 0.179004 ATCAACCACGGACAGCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
3701 9197 0.179004 AATCAACCACGGACAGCCAA 60.179 50.000 0.00 0.00 0.00 4.52
3720 9216 0.109153 TAGCCCGGCTATACTCACGA 59.891 55.000 15.59 0.00 40.44 4.35
3739 9235 3.201290 GAGATGCATCAAAGTGTCGGAT 58.799 45.455 27.81 2.84 0.00 4.18


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

AutoCloner maintained by Alex Coulton.