Multiple sequence alignment - TraesCS2B01G589800

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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 TraesCS2B01G589800 chr2B 100.000 5800 0 0 1 5800 776218037 776223836 0.000000e+00 10711
1 TraesCS2B01G589800 chr2B 99.434 884 3 1 4919 5800 53421412 53422295 0.000000e+00 1604
2 TraesCS2B01G589800 chr2B 86.232 414 48 4 202 610 776218323 776218732 1.920000e-119 440
3 TraesCS2B01G589800 chr2B 95.455 154 6 1 4059 4211 778332893 778333046 1.610000e-60 244
4 TraesCS2B01G589800 chr2D 93.721 4794 152 58 202 4925 632983279 632978565 0.000000e+00 7047
5 TraesCS2B01G589800 chr2D 92.109 697 50 3 1 696 632983648 632982956 0.000000e+00 977
6 TraesCS2B01G589800 chr2D 88.163 490 49 3 217 701 632983350 632982865 5.040000e-160 575
7 TraesCS2B01G589800 chr2D 87.089 395 45 4 217 610 632983174 632982785 5.330000e-120 442
8 TraesCS2B01G589800 chr2D 86.466 399 46 3 302 696 632983436 632983042 1.150000e-116 431
9 TraesCS2B01G589800 chr2D 85.976 328 36 3 373 696 632983449 632983128 5.570000e-90 342
10 TraesCS2B01G589800 chr2D 87.727 220 25 2 216 434 632983003 632982785 7.460000e-64 255
11 TraesCS2B01G589800 chr2A 92.162 2322 131 22 196 2493 759460921 759463215 0.000000e+00 3232
12 TraesCS2B01G589800 chr2A 91.158 1131 40 22 3221 4300 759463879 759465000 0.000000e+00 1480
13 TraesCS2B01G589800 chr2A 89.670 697 63 5 1 696 759460558 759461246 0.000000e+00 880
14 TraesCS2B01G589800 chr2A 90.839 644 27 16 4295 4925 759465034 759465658 0.000000e+00 833
15 TraesCS2B01G589800 chr2A 89.113 496 49 2 202 696 759460841 759461332 3.840000e-171 612
16 TraesCS2B01G589800 chr2A 85.528 615 30 23 2599 3176 759463207 759463799 6.470000e-164 588
17 TraesCS2B01G589800 chr3B 99.772 878 2 0 4923 5800 702857657 702856780 0.000000e+00 1611
18 TraesCS2B01G589800 chr6A 99.772 877 2 0 4924 5800 616131294 616132170 0.000000e+00 1609
19 TraesCS2B01G589800 chr5B 99.435 885 3 2 4917 5800 641128788 641127905 0.000000e+00 1605
20 TraesCS2B01G589800 chr5B 99.658 877 2 1 4924 5800 158571214 158570339 0.000000e+00 1602
21 TraesCS2B01G589800 chr7A 99.658 876 3 0 4925 5800 39015367 39016242 0.000000e+00 1602
22 TraesCS2B01G589800 chr3A 99.321 884 6 0 4917 5800 9952649 9953532 0.000000e+00 1600
23 TraesCS2B01G589800 chr1B 99.322 885 4 2 4916 5800 302243307 302242425 0.000000e+00 1600
24 TraesCS2B01G589800 chr4B 99.316 877 5 1 4924 5800 368430369 368429494 0.000000e+00 1585


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 TraesCS2B01G589800 chr2B 776218037 776223836 5799 False 10711.000000 10711 100.000000 1 5800 1 chr2B.!!$F2 5799
1 TraesCS2B01G589800 chr2B 53421412 53422295 883 False 1604.000000 1604 99.434000 4919 5800 1 chr2B.!!$F1 881
2 TraesCS2B01G589800 chr2D 632978565 632983648 5083 True 1438.428571 7047 88.750143 1 4925 7 chr2D.!!$R1 4924
3 TraesCS2B01G589800 chr2A 759460558 759465658 5100 False 1270.833333 3232 89.745000 1 4925 6 chr2A.!!$F1 4924
4 TraesCS2B01G589800 chr3B 702856780 702857657 877 True 1611.000000 1611 99.772000 4923 5800 1 chr3B.!!$R1 877
5 TraesCS2B01G589800 chr6A 616131294 616132170 876 False 1609.000000 1609 99.772000 4924 5800 1 chr6A.!!$F1 876
6 TraesCS2B01G589800 chr5B 641127905 641128788 883 True 1605.000000 1605 99.435000 4917 5800 1 chr5B.!!$R2 883
7 TraesCS2B01G589800 chr5B 158570339 158571214 875 True 1602.000000 1602 99.658000 4924 5800 1 chr5B.!!$R1 876
8 TraesCS2B01G589800 chr7A 39015367 39016242 875 False 1602.000000 1602 99.658000 4925 5800 1 chr7A.!!$F1 875
9 TraesCS2B01G589800 chr3A 9952649 9953532 883 False 1600.000000 1600 99.321000 4917 5800 1 chr3A.!!$F1 883
10 TraesCS2B01G589800 chr1B 302242425 302243307 882 True 1600.000000 1600 99.322000 4916 5800 1 chr1B.!!$R1 884
11 TraesCS2B01G589800 chr4B 368429494 368430369 875 True 1585.000000 1585 99.316000 4924 5800 1 chr4B.!!$R1 876

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
343 346 0.039437 ATCCGATAATCTTCGCGCGT 60.039 50.000 30.98 12.90 37.80 6.01 F
1480 1656 0.046242 TCTGTCCCTTCCCATCCCAT 59.954 55.000 0.00 0.00 0.00 4.00 F
2069 2258 0.678395 ATGGCTACCATCAGAGCTCG 59.322 55.000 8.37 3.55 40.74 5.03 F
3434 3753 1.955778 CATCCAAAGCTGAACCACACA 59.044 47.619 0.00 0.00 0.00 3.72 F
4559 4967 0.319728 GTCTTCAGCTCAGCACCAGA 59.680 55.000 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2138 2327 0.179037 GCTGCTGTATGCCATGAGGA 60.179 55.000 0.00 0.00 42.00 3.71 R
3090 3336 4.051922 GCATAGTGAAGTGAATAGGACGG 58.948 47.826 0.00 0.00 0.00 4.79 R
3615 3934 0.813184 GTGGCACCTAGCTACGTACA 59.187 55.000 6.29 0.00 45.00 2.90 R
4732 5145 0.753262 GCTAGCTGCTAAGGCCTACA 59.247 55.000 5.16 3.96 38.95 2.74 R
5663 6083 1.342555 CAACATGCGCAACCATTCTG 58.657 50.000 17.11 9.07 0.00 3.02 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
36 37 7.390996 CCCATCAAATTGAATTGAATCAAACCA 59.609 33.333 0.00 0.00 42.22 3.67
45 46 8.830201 TGAATTGAATCAAACCAAATCGAATT 57.170 26.923 0.00 0.00 0.00 2.17
112 113 2.704725 ACAAAAATCGCGCAATCACT 57.295 40.000 8.75 0.00 0.00 3.41
128 129 5.336213 GCAATCACTCCATCATCAAAACTGT 60.336 40.000 0.00 0.00 0.00 3.55
146 147 4.476752 GGCGGTACAATGGCGGGA 62.477 66.667 0.00 0.00 0.00 5.14
182 184 3.260100 CCAGAGCCAACACCCCCT 61.260 66.667 0.00 0.00 0.00 4.79
213 215 1.406447 GCGCGCAATACCTAGTACTC 58.594 55.000 29.10 0.00 0.00 2.59
214 216 1.929482 GCGCGCAATACCTAGTACTCC 60.929 57.143 29.10 0.00 0.00 3.85
225 227 5.893897 ACCTAGTACTCCGTAACTCTTTG 57.106 43.478 0.00 0.00 0.00 2.77
343 346 0.039437 ATCCGATAATCTTCGCGCGT 60.039 50.000 30.98 12.90 37.80 6.01
426 429 4.120589 AGAAAGATCCGATAAACTTCGCC 58.879 43.478 0.00 0.00 37.80 5.54
452 455 1.073199 CCTTCCTTCAACGGTGGCT 59.927 57.895 0.00 0.00 0.00 4.75
567 742 1.869132 GATACCCGGCAATTCGTAACC 59.131 52.381 0.00 0.00 0.00 2.85
575 750 3.685756 CGGCAATTCGTAACCCTTTAGAA 59.314 43.478 0.00 0.00 0.00 2.10
649 824 1.064060 GCACGATACCTGGCAATTCAC 59.936 52.381 0.00 0.00 0.00 3.18
763 938 5.550290 CCATTTTGGTAGGTTTGAAATGCT 58.450 37.500 0.00 0.00 36.74 3.79
797 972 5.645056 AAACCCCTCAACATTTCCATTTT 57.355 34.783 0.00 0.00 0.00 1.82
817 992 1.229177 ACACCCCCATTTCCCTTGC 60.229 57.895 0.00 0.00 0.00 4.01
839 1015 0.533491 CCATGTTCCCATTGTGGCTG 59.467 55.000 0.00 0.00 35.79 4.85
920 1096 1.603455 CCCCGCCTCTTCAAAAGCA 60.603 57.895 0.00 0.00 0.00 3.91
921 1097 1.581447 CCCGCCTCTTCAAAAGCAC 59.419 57.895 0.00 0.00 0.00 4.40
922 1098 1.207593 CCGCCTCTTCAAAAGCACG 59.792 57.895 0.00 0.00 0.00 5.34
1277 1453 3.785859 GTCCCGCTGATCCAGGCA 61.786 66.667 0.00 0.00 31.21 4.75
1480 1656 0.046242 TCTGTCCCTTCCCATCCCAT 59.954 55.000 0.00 0.00 0.00 4.00
1605 1781 2.155155 CACGTCGTTCTAGGTTTTCTGC 59.845 50.000 0.00 0.00 0.00 4.26
1765 1941 8.761575 AATCACGCATTTCATCTTGTTAATTT 57.238 26.923 0.00 0.00 0.00 1.82
1996 2182 2.873472 GGACCATGTACAACGTCAACAA 59.127 45.455 20.90 0.00 0.00 2.83
2069 2258 0.678395 ATGGCTACCATCAGAGCTCG 59.322 55.000 8.37 3.55 40.74 5.03
2138 2327 3.118738 CGAGGAGCCCTTACAGTGTTTAT 60.119 47.826 0.00 0.00 31.76 1.40
2352 2558 6.867816 TCGGGTTCAATTTCTTTGATTGATTG 59.132 34.615 0.91 0.00 43.73 2.67
2470 2680 7.335127 AGGGCTTTATGATGGTATAGATTGT 57.665 36.000 0.00 0.00 0.00 2.71
2504 2714 9.372369 ACAAATTTTCTAAAACGATTTGTCCAA 57.628 25.926 10.42 0.00 35.43 3.53
2587 2797 8.830201 TTACTTTGCATAGACAAAATTGCATT 57.170 26.923 11.39 0.00 43.91 3.56
2662 2872 6.500910 CATTCATGCTACTATTGCACATTGT 58.499 36.000 0.00 0.00 43.59 2.71
2889 3107 5.186409 ACAGCTAGGAAACATGCAAATCATT 59.814 36.000 0.00 0.00 31.79 2.57
2898 3116 8.330302 GGAAACATGCAAATCATTTATGCTTAC 58.670 33.333 0.00 0.00 40.66 2.34
2927 3145 6.540189 AGTTTAATTACCATGAGCTAGCACAG 59.460 38.462 19.62 9.98 0.00 3.66
3134 3380 4.090930 GCATGCTGTTCTTAATTTGCTGTG 59.909 41.667 11.37 0.00 0.00 3.66
3402 3721 7.816995 TGTATTAAAATGATGAAGGTGCCAAAC 59.183 33.333 0.00 0.00 0.00 2.93
3433 3752 1.956477 ACATCCAAAGCTGAACCACAC 59.044 47.619 0.00 0.00 0.00 3.82
3434 3753 1.955778 CATCCAAAGCTGAACCACACA 59.044 47.619 0.00 0.00 0.00 3.72
3435 3754 2.363306 TCCAAAGCTGAACCACACAT 57.637 45.000 0.00 0.00 0.00 3.21
3436 3755 3.500448 TCCAAAGCTGAACCACACATA 57.500 42.857 0.00 0.00 0.00 2.29
3615 3934 5.652452 GGAAGAATTGTACTGCCAAAGGTAT 59.348 40.000 0.00 0.00 33.46 2.73
3633 3952 1.771565 ATGTACGTAGCTAGGTGCCA 58.228 50.000 25.46 21.02 44.23 4.92
3634 3953 0.813184 TGTACGTAGCTAGGTGCCAC 59.187 55.000 25.46 17.23 44.23 5.01
3652 3984 8.088981 AGGTGCCACTATTACTCTAATTAATCG 58.911 37.037 0.00 0.00 0.00 3.34
3722 4066 5.184892 ACTGAATTTTGTAGAGGGATGCT 57.815 39.130 0.00 0.00 0.00 3.79
3831 4175 6.287589 AGTTCAGGTAATCACTAGTTCAGG 57.712 41.667 0.00 0.00 0.00 3.86
3910 4261 7.577303 TGGAGAGTTAATATCTGCCTCATTTT 58.423 34.615 8.88 0.00 34.50 1.82
4013 4370 6.455646 GCAGAATGTATGTCTTGGAAAGTACG 60.456 42.308 0.00 0.00 41.80 3.67
4173 4533 4.701651 CACCTTCATCATCTACAAAAGCCA 59.298 41.667 0.00 0.00 0.00 4.75
4229 4589 6.398655 TCTACTCTACCCCACTTTCTCTTA 57.601 41.667 0.00 0.00 0.00 2.10
4256 4616 8.010697 TCCTCAGTAATAAATAGTCCATCCAGA 58.989 37.037 0.00 0.00 0.00 3.86
4300 4664 3.666274 GCCAGCTCTCTCGATACTACTA 58.334 50.000 0.00 0.00 0.00 1.82
4346 4750 1.998315 CTCATTCTGCAAGTCACTCGG 59.002 52.381 0.00 0.00 33.76 4.63
4469 4873 0.322456 TTGTCCGGAATGCAAGGAGG 60.322 55.000 5.23 0.00 34.29 4.30
4470 4874 2.115291 GTCCGGAATGCAAGGAGGC 61.115 63.158 5.23 0.00 34.29 4.70
4524 4928 0.323178 AGGAACCTGCATGCCAAGAG 60.323 55.000 16.68 5.42 0.00 2.85
4538 4942 5.946942 TGCCAAGAGAAGAAGATAGATGT 57.053 39.130 0.00 0.00 0.00 3.06
4556 4964 1.011451 GTCGTCTTCAGCTCAGCACC 61.011 60.000 0.00 0.00 0.00 5.01
4557 4965 1.005748 CGTCTTCAGCTCAGCACCA 60.006 57.895 0.00 0.00 0.00 4.17
4558 4966 1.013005 CGTCTTCAGCTCAGCACCAG 61.013 60.000 0.00 0.00 0.00 4.00
4559 4967 0.319728 GTCTTCAGCTCAGCACCAGA 59.680 55.000 0.00 0.00 0.00 3.86
4560 4968 1.051008 TCTTCAGCTCAGCACCAGAA 58.949 50.000 0.00 0.00 0.00 3.02
4561 4969 1.417517 TCTTCAGCTCAGCACCAGAAA 59.582 47.619 0.00 0.00 0.00 2.52
4562 4970 1.805345 CTTCAGCTCAGCACCAGAAAG 59.195 52.381 0.00 0.00 0.00 2.62
4563 4971 0.604780 TCAGCTCAGCACCAGAAAGC 60.605 55.000 0.00 0.00 0.00 3.51
4564 4972 0.887836 CAGCTCAGCACCAGAAAGCA 60.888 55.000 0.00 0.00 35.42 3.91
4565 4973 0.888285 AGCTCAGCACCAGAAAGCAC 60.888 55.000 0.00 0.00 35.42 4.40
4659 5072 0.735471 CCAGAAGCATCGTCGAGAGA 59.265 55.000 0.00 0.00 38.16 3.10
4660 5073 1.268488 CCAGAAGCATCGTCGAGAGAG 60.268 57.143 0.00 0.00 43.49 3.20
4661 5074 0.380378 AGAAGCATCGTCGAGAGAGC 59.620 55.000 0.00 2.48 43.49 4.09
4662 5075 0.380378 GAAGCATCGTCGAGAGAGCT 59.620 55.000 0.00 4.85 43.24 4.09
4795 5212 5.046663 GCCCCATCCAAGAAAAACATCTTTA 60.047 40.000 0.00 0.00 37.56 1.85
4796 5213 6.519891 GCCCCATCCAAGAAAAACATCTTTAA 60.520 38.462 0.00 0.00 37.56 1.52
4797 5214 7.623630 CCCCATCCAAGAAAAACATCTTTAAT 58.376 34.615 0.00 0.00 37.56 1.40
4798 5215 8.102676 CCCCATCCAAGAAAAACATCTTTAATT 58.897 33.333 0.00 0.00 37.56 1.40
4799 5216 9.506018 CCCATCCAAGAAAAACATCTTTAATTT 57.494 29.630 0.00 0.00 37.56 1.82
4803 5220 8.417884 TCCAAGAAAAACATCTTTAATTTCCGT 58.582 29.630 0.00 0.00 37.56 4.69
5663 6083 1.538512 TGAACTGCAAGAAGAGCATGC 59.461 47.619 10.51 10.51 41.82 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 7.427030 TGCGCGATTTTTGTAGTTATATGTTTC 59.573 33.333 12.10 0.00 0.00 2.78
104 105 5.100259 CAGTTTTGATGATGGAGTGATTGC 58.900 41.667 0.00 0.00 0.00 3.56
112 113 1.811965 CGCCACAGTTTTGATGATGGA 59.188 47.619 0.00 0.00 0.00 3.41
128 129 4.787286 CCCGCCATTGTACCGCCA 62.787 66.667 0.00 0.00 0.00 5.69
146 147 2.456840 CTGGTCCCTCCCCCTCTT 59.543 66.667 0.00 0.00 34.77 2.85
166 167 0.909610 TAGAGGGGGTGTTGGCTCTG 60.910 60.000 0.00 0.00 0.00 3.35
181 183 0.032130 TGCGCGCCTAAGGAATAGAG 59.968 55.000 30.77 0.00 33.04 2.43
182 184 0.462375 TTGCGCGCCTAAGGAATAGA 59.538 50.000 30.77 0.96 33.04 1.98
213 215 7.817962 TCTTTCTCTAAATCCAAAGAGTTACGG 59.182 37.037 0.00 0.00 40.17 4.02
214 216 8.758633 TCTTTCTCTAAATCCAAAGAGTTACG 57.241 34.615 0.00 0.00 40.17 3.18
225 227 9.936759 AAGATTATCGGATCTTTCTCTAAATCC 57.063 33.333 0.00 0.00 42.24 3.01
343 346 0.179040 ACCGTTGAAGGAAGGCGAAA 60.179 50.000 0.00 0.00 34.73 3.46
452 455 8.102800 ACGAATTGTCAGGTATATATCGTACA 57.897 34.615 0.00 1.15 38.99 2.90
485 574 7.863375 AGTTTATCGGATCGTTCTCTAAATCTG 59.137 37.037 0.00 0.00 0.00 2.90
544 719 0.808453 ACGAATTGCCGGGTATCGTG 60.808 55.000 12.03 0.00 44.20 4.35
575 750 7.371936 CGAAGATTATCGGACCTTTCTCTAAT 58.628 38.462 0.00 0.00 39.12 1.73
759 934 2.821969 GGGTTTTGTGAGATGTGAGCAT 59.178 45.455 0.00 0.00 38.18 3.79
763 938 2.441375 TGAGGGGTTTTGTGAGATGTGA 59.559 45.455 0.00 0.00 0.00 3.58
797 972 0.114168 CAAGGGAAATGGGGGTGTGA 59.886 55.000 0.00 0.00 0.00 3.58
1261 1437 3.785859 GTGCCTGGATCAGCGGGA 61.786 66.667 0.00 0.00 0.00 5.14
1442 1618 2.163815 AGATCACGGAGAAAACGATCGT 59.836 45.455 16.60 16.60 38.00 3.73
1480 1656 2.276732 CTGGAACTGGAAGAAAGCCA 57.723 50.000 0.00 0.00 37.43 4.75
1832 2012 4.888326 AAACAGCATTAATCAAGGCCAA 57.112 36.364 5.01 0.00 42.39 4.52
1867 2047 1.880027 AGTTGTGCGTCCCTGAAAATC 59.120 47.619 0.00 0.00 0.00 2.17
2001 2187 2.355837 GCAGGCGACAGACACGAA 60.356 61.111 0.00 0.00 0.00 3.85
2034 2220 1.007964 CATTGTTGTTGCCGCGGAA 60.008 52.632 33.48 19.06 0.00 4.30
2069 2258 4.416738 GTGGGGGAGCACAGCCTC 62.417 72.222 0.00 0.00 0.00 4.70
2099 2288 2.822255 GGCGGCGGCATGAAGTTA 60.822 61.111 29.41 0.00 42.47 2.24
2119 2308 3.200165 AGGATAAACACTGTAAGGGCTCC 59.800 47.826 0.00 0.00 45.89 4.70
2138 2327 0.179037 GCTGCTGTATGCCATGAGGA 60.179 55.000 0.00 0.00 42.00 3.71
2338 2544 6.211184 ACCCTTGCATACAATCAATCAAAGAA 59.789 34.615 0.00 0.00 34.61 2.52
2352 2558 8.671384 TTCAACTATACATAACCCTTGCATAC 57.329 34.615 0.00 0.00 0.00 2.39
2401 2607 8.025243 GCACAATGCTAAACTAAACAGTACTA 57.975 34.615 0.00 0.00 40.96 1.82
2402 2608 6.899114 GCACAATGCTAAACTAAACAGTACT 58.101 36.000 0.00 0.00 40.96 2.73
2470 2680 8.467402 TCGTTTTAGAAAATTTGTTTGCTTCA 57.533 26.923 0.00 0.00 0.00 3.02
2504 2714 7.092712 TGACTCAGATTATTTGGAATGAGGACT 60.093 37.037 5.15 0.00 38.74 3.85
2612 2822 9.950680 GCAATTTAGCTAGTCTGCAAAATATAA 57.049 29.630 14.63 0.00 34.99 0.98
2613 2823 9.119418 TGCAATTTAGCTAGTCTGCAAAATATA 57.881 29.630 18.11 0.34 36.89 0.86
2614 2824 7.999679 TGCAATTTAGCTAGTCTGCAAAATAT 58.000 30.769 18.11 0.00 36.89 1.28
2662 2872 5.743872 CACGAGATCGATGTACAGAATGAAA 59.256 40.000 0.54 0.00 43.02 2.69
2898 3116 9.056005 TGCTAGCTCATGGTAATTAAACTTATG 57.944 33.333 17.23 0.00 0.00 1.90
2927 3145 5.919141 GGAAATTAATCTCACATGCATCAGC 59.081 40.000 0.00 0.00 42.57 4.26
2928 3146 7.034685 TGGAAATTAATCTCACATGCATCAG 57.965 36.000 0.00 0.00 0.00 2.90
2929 3147 6.040054 CCTGGAAATTAATCTCACATGCATCA 59.960 38.462 0.00 0.00 0.00 3.07
2930 3148 6.263842 TCCTGGAAATTAATCTCACATGCATC 59.736 38.462 0.00 0.00 0.00 3.91
2931 3149 6.040166 GTCCTGGAAATTAATCTCACATGCAT 59.960 38.462 0.00 0.00 0.00 3.96
2932 3150 5.357878 GTCCTGGAAATTAATCTCACATGCA 59.642 40.000 0.00 0.00 0.00 3.96
2933 3151 5.221126 GGTCCTGGAAATTAATCTCACATGC 60.221 44.000 0.00 0.00 0.00 4.06
2934 3152 5.300286 GGGTCCTGGAAATTAATCTCACATG 59.700 44.000 0.00 0.00 0.00 3.21
2935 3153 5.449553 GGGTCCTGGAAATTAATCTCACAT 58.550 41.667 0.00 0.00 0.00 3.21
3090 3336 4.051922 GCATAGTGAAGTGAATAGGACGG 58.948 47.826 0.00 0.00 0.00 4.79
3091 3337 4.682787 TGCATAGTGAAGTGAATAGGACG 58.317 43.478 0.00 0.00 0.00 4.79
3375 3689 7.099266 TGGCACCTTCATCATTTTAATACAG 57.901 36.000 0.00 0.00 0.00 2.74
3402 3721 5.759273 TCAGCTTTGGATGTTTGAAAATTGG 59.241 36.000 0.00 0.00 0.00 3.16
3433 3752 7.551617 TGCAGCAACCTGATGATCTTATATATG 59.448 37.037 0.00 0.00 41.77 1.78
3434 3753 7.627311 TGCAGCAACCTGATGATCTTATATAT 58.373 34.615 0.00 0.00 41.77 0.86
3435 3754 7.008021 TGCAGCAACCTGATGATCTTATATA 57.992 36.000 0.00 0.00 41.77 0.86
3436 3755 5.872963 TGCAGCAACCTGATGATCTTATAT 58.127 37.500 0.00 0.00 41.77 0.86
3615 3934 0.813184 GTGGCACCTAGCTACGTACA 59.187 55.000 6.29 0.00 45.00 2.90
3652 3984 8.812329 CAGCTAACAGATAGTAACTTTCATGTC 58.188 37.037 0.00 0.00 33.87 3.06
3711 4055 2.320781 GTTAGCCTCAGCATCCCTCTA 58.679 52.381 0.00 0.00 43.56 2.43
3722 4066 3.088923 AGCTGGAAGGTTAGCCTCA 57.911 52.632 0.00 0.00 46.63 3.86
3854 4199 6.034591 CGAGACTATGATTTACGGAGTTGTT 58.965 40.000 0.00 0.00 37.78 2.83
4013 4370 5.533528 AGTCAGTGTTAAAACCAACATACCC 59.466 40.000 0.00 0.00 40.36 3.69
4173 4533 1.802365 GTACAAATTTGCCGGACTCGT 59.198 47.619 18.12 0.00 33.95 4.18
4229 4589 8.742125 TGGATGGACTATTTATTACTGAGGAT 57.258 34.615 0.00 0.00 0.00 3.24
4256 4616 4.396166 CGAGTTTAGTTTGCAGATGGGAAT 59.604 41.667 0.00 0.00 0.00 3.01
4380 4784 9.293404 TCTGATCAAGAGATGACAAAAAGAATT 57.707 29.630 0.00 0.00 41.93 2.17
4381 4785 8.859236 TCTGATCAAGAGATGACAAAAAGAAT 57.141 30.769 0.00 0.00 41.93 2.40
4382 4786 8.859236 ATCTGATCAAGAGATGACAAAAAGAA 57.141 30.769 0.00 0.00 41.93 2.52
4383 4787 8.727910 CAATCTGATCAAGAGATGACAAAAAGA 58.272 33.333 0.00 0.00 41.93 2.52
4469 4873 1.305219 TTGTTGTAGATGCGGCCTGC 61.305 55.000 11.92 11.92 46.70 4.85
4470 4874 1.135689 GTTTGTTGTAGATGCGGCCTG 60.136 52.381 0.00 0.00 0.00 4.85
4516 4920 5.451103 CGACATCTATCTTCTTCTCTTGGCA 60.451 44.000 0.00 0.00 0.00 4.92
4524 4928 5.685511 GCTGAAGACGACATCTATCTTCTTC 59.314 44.000 17.11 12.59 46.54 2.87
4538 4942 1.290324 GGTGCTGAGCTGAAGACGA 59.710 57.895 5.83 0.00 0.00 4.20
4556 4964 4.713824 ATCATTGTGATGGTGCTTTCTG 57.286 40.909 0.00 0.00 35.43 3.02
4659 5072 7.450634 TGATAATTTAGGGTGATACGACTAGCT 59.549 37.037 0.00 0.00 0.00 3.32
4660 5073 7.600065 TGATAATTTAGGGTGATACGACTAGC 58.400 38.462 0.00 0.00 0.00 3.42
4661 5074 9.790389 GATGATAATTTAGGGTGATACGACTAG 57.210 37.037 0.00 0.00 0.00 2.57
4662 5075 8.456471 CGATGATAATTTAGGGTGATACGACTA 58.544 37.037 0.00 0.00 0.00 2.59
4732 5145 0.753262 GCTAGCTGCTAAGGCCTACA 59.247 55.000 5.16 3.96 38.95 2.74
4733 5146 3.597550 GCTAGCTGCTAAGGCCTAC 57.402 57.895 5.16 0.00 38.95 3.18
5663 6083 1.342555 CAACATGCGCAACCATTCTG 58.657 50.000 17.11 9.07 0.00 3.02


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

AutoCloner maintained by Alex Coulton.