Multiple sequence alignment - TraesCS4D01G192200

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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 TraesCS4D01G192200 chr4D 100.000 2603 0 0 1 2603 335340812 335343414 0.000000e+00 4807.0
1 TraesCS4D01G192200 chr4D 100.000 2540 0 0 2972 5511 335343783 335346322 0.000000e+00 4691.0
2 TraesCS4D01G192200 chr4A 93.864 1858 76 18 3194 5018 137531178 137529326 0.000000e+00 2765.0
3 TraesCS4D01G192200 chr4A 89.707 1943 142 24 676 2601 137533404 137531503 0.000000e+00 2427.0
4 TraesCS4D01G192200 chr4A 92.768 719 26 9 1 718 137534090 137533397 0.000000e+00 1016.0
5 TraesCS4D01G192200 chr4A 95.982 224 9 0 2972 3195 137531455 137531232 1.130000e-96 364.0
6 TraesCS4D01G192200 chr4A 93.750 192 10 2 5321 5511 137528562 137528372 2.510000e-73 287.0
7 TraesCS4D01G192200 chr4B 93.791 1659 64 12 676 2330 413492307 413493930 0.000000e+00 2457.0
8 TraesCS4D01G192200 chr4B 91.961 1642 69 13 3191 4798 413494694 413496306 0.000000e+00 2242.0
9 TraesCS4D01G192200 chr4B 93.056 720 24 14 1 718 413491619 413492314 0.000000e+00 1029.0
10 TraesCS4D01G192200 chr4B 93.253 415 16 8 5108 5511 413496786 413497199 7.900000e-168 601.0
11 TraesCS4D01G192200 chr4B 95.977 348 14 0 4659 5006 413496439 413496786 2.880000e-157 566.0
12 TraesCS4D01G192200 chr4B 93.636 220 4 3 2972 3191 413494430 413494639 2.480000e-83 320.0
13 TraesCS4D01G192200 chr4B 96.000 175 7 0 2429 2603 413494207 413494381 9.040000e-73 285.0
14 TraesCS4D01G192200 chr4B 95.714 140 6 0 4659 4798 413496303 413496442 5.550000e-55 226.0
15 TraesCS4D01G192200 chr6A 89.766 1456 115 18 3194 4634 81117153 81115717 0.000000e+00 1832.0
16 TraesCS4D01G192200 chr6A 83.123 1031 90 34 807 1831 81121325 81120373 0.000000e+00 863.0
17 TraesCS4D01G192200 chr6A 88.462 468 42 7 1868 2334 81118086 81117630 6.240000e-154 555.0
18 TraesCS4D01G192200 chr6A 88.119 202 20 3 2403 2601 81117621 81117421 2.570000e-58 237.0
19 TraesCS4D01G192200 chr6A 86.099 223 21 4 2974 3195 81117420 81117207 1.190000e-56 231.0
20 TraesCS4D01G192200 chr6A 97.368 38 1 0 5200 5237 280122304 280122341 1.280000e-06 65.8
21 TraesCS4D01G192200 chr6B 85.831 1595 125 49 1045 2601 137459063 137457532 0.000000e+00 1600.0
22 TraesCS4D01G192200 chr6B 91.801 622 38 5 3194 3807 137457242 137456626 0.000000e+00 854.0
23 TraesCS4D01G192200 chr6B 85.185 756 62 21 3885 4634 137456243 137455532 0.000000e+00 730.0
24 TraesCS4D01G192200 chr6B 86.301 73 3 4 3814 3885 137456409 137456343 7.660000e-09 73.1
25 TraesCS4D01G192200 chr6D 91.608 846 50 7 3197 4032 63766692 63765858 0.000000e+00 1149.0
26 TraesCS4D01G192200 chr6D 81.135 1357 125 41 807 2130 63768472 63767214 0.000000e+00 966.0
27 TraesCS4D01G192200 chr6D 88.704 602 50 8 4060 4659 63765858 63765273 0.000000e+00 719.0
28 TraesCS4D01G192200 chr6D 86.697 218 26 2 2981 3195 63766966 63766749 7.130000e-59 239.0
29 TraesCS4D01G192200 chr6D 85.714 77 8 3 5035 5109 63765078 63765003 1.650000e-10 78.7
30 TraesCS4D01G192200 chr2B 93.427 426 26 2 1 425 65314284 65313860 1.010000e-176 630.0
31 TraesCS4D01G192200 chr2D 93.587 421 25 2 6 425 37533924 37533505 1.300000e-175 627.0
32 TraesCS4D01G192200 chr2D 97.368 38 1 0 5200 5237 268204486 268204523 1.280000e-06 65.8
33 TraesCS4D01G192200 chr1D 95.161 310 14 1 4877 5185 247002024 247001715 6.420000e-134 488.0
34 TraesCS4D01G192200 chr2A 92.537 335 23 2 1 334 42398685 42398352 3.860000e-131 479.0


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 TraesCS4D01G192200 chr4D 335340812 335346322 5510 False 4749.000 4807 100.0000 1 5511 2 chr4D.!!$F1 5510
1 TraesCS4D01G192200 chr4A 137528372 137534090 5718 True 1371.800 2765 93.2142 1 5511 5 chr4A.!!$R1 5510
2 TraesCS4D01G192200 chr4B 413491619 413497199 5580 False 965.750 2457 94.1735 1 5511 8 chr4B.!!$F1 5510
3 TraesCS4D01G192200 chr6A 81115717 81121325 5608 True 743.600 1832 87.1138 807 4634 5 chr6A.!!$R1 3827
4 TraesCS4D01G192200 chr6B 137455532 137459063 3531 True 814.275 1600 87.2795 1045 4634 4 chr6B.!!$R1 3589
5 TraesCS4D01G192200 chr6D 63765003 63768472 3469 True 630.340 1149 86.7716 807 5109 5 chr6D.!!$R1 4302

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
813 858 0.045162 ACCGGATCCCCTTCCCTTAA 59.955 55.000 9.46 0.0 31.61 1.85 F
2149 4481 0.176680 TGCGCCTCTCTGAATCCTTC 59.823 55.000 4.18 0.0 0.00 3.46 F
2255 4587 0.592637 TGATGTTGTGCGCTTTCCTG 59.407 50.000 9.73 0.0 0.00 3.86 F
3934 6836 1.077787 GTGGATGGGCCGACATTCA 60.078 57.895 0.00 0.0 40.66 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 4749 1.497286 GGGGAAGGCACATACCCAATA 59.503 52.381 0.00 0.00 43.67 1.90 R
4137 7039 2.111384 CTGACCTGGCACACCTACTAT 58.889 52.381 0.00 0.00 36.63 2.12 R
4339 7244 4.911390 AGCATAAGAACTTGCTAGTGGTT 58.089 39.130 0.36 1.36 46.92 3.67 R
5022 8746 1.072173 AGTCACTGCTGTGGTATGCAA 59.928 47.619 21.80 0.00 43.94 4.08 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
244 245 2.579201 CGGCCGACCTTGATGAGT 59.421 61.111 24.07 0.00 0.00 3.41
256 257 3.453717 CCTTGATGAGTGAGGAGATGGAA 59.546 47.826 0.00 0.00 32.11 3.53
613 622 2.289565 TCCGATGGATCCGATATCTCG 58.710 52.381 7.39 8.22 44.62 4.04
623 632 0.523966 CGATATCTCGGGTCTCCAGC 59.476 60.000 0.34 0.00 41.27 4.85
624 633 1.884497 CGATATCTCGGGTCTCCAGCT 60.884 57.143 0.34 0.00 41.27 4.24
625 634 1.816224 GATATCTCGGGTCTCCAGCTC 59.184 57.143 0.00 0.00 0.00 4.09
626 635 0.847373 TATCTCGGGTCTCCAGCTCT 59.153 55.000 0.00 0.00 0.00 4.09
627 636 0.467290 ATCTCGGGTCTCCAGCTCTC 60.467 60.000 0.00 0.00 0.00 3.20
628 637 2.043852 TCGGGTCTCCAGCTCTCC 60.044 66.667 0.00 0.00 0.00 3.71
629 638 2.363018 CGGGTCTCCAGCTCTCCA 60.363 66.667 0.00 0.00 0.00 3.86
630 639 2.422231 CGGGTCTCCAGCTCTCCAG 61.422 68.421 0.00 0.00 0.00 3.86
631 640 1.305718 GGGTCTCCAGCTCTCCAGT 60.306 63.158 0.00 0.00 0.00 4.00
632 641 1.326951 GGGTCTCCAGCTCTCCAGTC 61.327 65.000 0.00 0.00 0.00 3.51
633 642 1.326951 GGTCTCCAGCTCTCCAGTCC 61.327 65.000 0.00 0.00 0.00 3.85
634 643 0.613292 GTCTCCAGCTCTCCAGTCCA 60.613 60.000 0.00 0.00 0.00 4.02
635 644 0.324183 TCTCCAGCTCTCCAGTCCAG 60.324 60.000 0.00 0.00 0.00 3.86
636 645 0.614415 CTCCAGCTCTCCAGTCCAGT 60.614 60.000 0.00 0.00 0.00 4.00
637 646 0.613292 TCCAGCTCTCCAGTCCAGTC 60.613 60.000 0.00 0.00 0.00 3.51
650 659 3.706373 CAGTCCTCCCCCACACGG 61.706 72.222 0.00 0.00 0.00 4.94
691 700 1.318158 ACCGGGTAGCGTACTCTTGG 61.318 60.000 6.32 0.00 0.00 3.61
696 705 2.483188 GGGTAGCGTACTCTTGGGAATG 60.483 54.545 0.00 0.00 0.00 2.67
702 711 1.138266 GTACTCTTGGGAATGCGCCTA 59.862 52.381 4.18 0.00 0.00 3.93
704 713 0.179000 CTCTTGGGAATGCGCCTACT 59.821 55.000 4.18 0.00 0.00 2.57
709 753 1.173913 GGGAATGCGCCTACTTGTTT 58.826 50.000 4.18 0.00 0.00 2.83
766 810 2.284699 CCGGGGAGTGGGAAGACT 60.285 66.667 0.00 0.00 0.00 3.24
813 858 0.045162 ACCGGATCCCCTTCCCTTAA 59.955 55.000 9.46 0.00 31.61 1.85
850 898 1.454201 GAGGGGAGGAAAAGAAAGCG 58.546 55.000 0.00 0.00 0.00 4.68
915 963 1.756430 GGCTTCTTCTCCAATCCCAC 58.244 55.000 0.00 0.00 0.00 4.61
931 979 0.529378 CCACTCATTGCCTTTCCAGC 59.471 55.000 0.00 0.00 0.00 4.85
1178 1226 2.746803 GCGGTGTCATGGGTAACGC 61.747 63.158 10.45 10.45 38.70 4.84
1179 1227 1.079405 CGGTGTCATGGGTAACGCT 60.079 57.895 0.00 0.00 37.60 5.07
1180 1228 0.672401 CGGTGTCATGGGTAACGCTT 60.672 55.000 0.00 0.00 37.60 4.68
1181 1229 1.084289 GGTGTCATGGGTAACGCTTC 58.916 55.000 0.00 0.00 37.60 3.86
1182 1230 1.338769 GGTGTCATGGGTAACGCTTCT 60.339 52.381 0.00 0.00 37.60 2.85
1183 1231 2.000447 GTGTCATGGGTAACGCTTCTC 59.000 52.381 0.00 0.00 37.60 2.87
1531 1600 7.901377 GCGTACGAACTTAAATATGTTCATGTT 59.099 33.333 21.65 0.00 41.67 2.71
1535 1604 9.959749 ACGAACTTAAATATGTTCATGTTTTGT 57.040 25.926 11.45 8.99 41.67 2.83
1634 1704 5.654603 AACAAAACTTCTTTTCTCCCGTT 57.345 34.783 0.00 0.00 0.00 4.44
1637 1707 4.913335 AAACTTCTTTTCTCCCGTTTCC 57.087 40.909 0.00 0.00 0.00 3.13
1639 1709 3.211865 ACTTCTTTTCTCCCGTTTCCAC 58.788 45.455 0.00 0.00 0.00 4.02
1660 1730 2.286595 CGATCCTTCATGTGAAATGGCG 60.287 50.000 0.00 0.00 33.07 5.69
1807 1882 2.896685 GTTGGGGTCATGAAATCAACCA 59.103 45.455 18.08 9.73 32.15 3.67
1920 4245 1.314730 TGTCTGAAAGGGGTTTTCGC 58.685 50.000 0.00 0.00 46.65 4.70
2149 4481 0.176680 TGCGCCTCTCTGAATCCTTC 59.823 55.000 4.18 0.00 0.00 3.46
2255 4587 0.592637 TGATGTTGTGCGCTTTCCTG 59.407 50.000 9.73 0.00 0.00 3.86
2416 4749 6.099269 TCCGGCTATCAGTTATTCCTTTTAGT 59.901 38.462 0.00 0.00 0.00 2.24
2466 4977 5.463061 GCATGCTTGATTGTACAGTTTTTGT 59.537 36.000 11.37 0.00 43.96 2.83
2472 4983 8.129211 GCTTGATTGTACAGTTTTTGTAGAGTT 58.871 33.333 0.00 0.00 42.75 3.01
3030 5543 7.870954 TGTGAGTACTAGTAACATTTCACTTGG 59.129 37.037 20.91 0.00 35.82 3.61
3147 5661 6.857777 TTGCCCTGTTTAATGATTTGTTTG 57.142 33.333 0.00 0.00 0.00 2.93
3191 5713 8.107729 AGAATCAGTGATATTGATACCATGCAT 58.892 33.333 5.94 0.00 34.30 3.96
3837 6639 6.808008 ACTGTTGATGAGAACCACATTAAG 57.192 37.500 0.00 0.00 0.00 1.85
3933 6835 1.823899 GGTGGATGGGCCGACATTC 60.824 63.158 0.00 0.00 40.66 2.67
3934 6836 1.077787 GTGGATGGGCCGACATTCA 60.078 57.895 0.00 0.00 40.66 2.57
3947 6849 5.451798 GGCCGACATTCATTTTTGGATGTAT 60.452 40.000 0.00 0.00 0.00 2.29
4015 6917 1.692519 AGTTGAAGGGCAGTCGTACTT 59.307 47.619 0.00 0.00 0.00 2.24
4096 6998 8.680903 AGATTTCAGATAGTTTAACCAATGCTG 58.319 33.333 0.00 0.00 0.00 4.41
4234 7137 3.552684 GCTTAGCCAAAGTTGTGATTGCA 60.553 43.478 0.00 0.00 37.53 4.08
4238 7141 5.002464 AGCCAAAGTTGTGATTGCATATC 57.998 39.130 0.00 0.00 0.00 1.63
4275 7180 9.897744 TTTTTGTTACTTCTGATTCAGCTAATG 57.102 29.630 8.89 0.00 0.00 1.90
4276 7181 8.621532 TTTGTTACTTCTGATTCAGCTAATGT 57.378 30.769 8.89 3.75 0.00 2.71
4335 7240 6.588719 TGGATTACAATTAGCAAAGCACTT 57.411 33.333 0.00 0.00 0.00 3.16
4339 7244 8.458843 GGATTACAATTAGCAAAGCACTTTAGA 58.541 33.333 0.00 0.00 0.00 2.10
4388 7293 8.788813 GTTATTCGTTATGCAGTTCAATTTGAG 58.211 33.333 0.00 0.00 0.00 3.02
4634 7545 4.591202 CAATATTCAGTCGTTGGCATGTC 58.409 43.478 0.00 0.00 0.00 3.06
4679 7610 1.676529 TCCATCGCACTGAGTAGCTAC 59.323 52.381 16.43 16.43 0.00 3.58
4745 7948 5.820423 TGGTATACGCATTTTGACTTATGCT 59.180 36.000 0.00 0.00 43.79 3.79
4896 8099 2.048222 TGTGCCGTCACTAGCAGC 60.048 61.111 0.00 0.00 43.49 5.25
4900 8103 3.060020 GCCGTCACTAGCAGCGGTA 62.060 63.158 17.00 0.00 45.30 4.02
4974 8177 4.096231 TCTGTGTCTGTTGTCCATTGTTTG 59.904 41.667 0.00 0.00 0.00 2.93
4989 8192 4.935352 TTGTTTGGAATGGTTTCAGAGG 57.065 40.909 0.00 0.00 33.23 3.69
5008 8211 9.490379 TTCAGAGGACTCTATTTGACTTTTTAC 57.510 33.333 0.82 0.00 37.98 2.01
5009 8212 8.871125 TCAGAGGACTCTATTTGACTTTTTACT 58.129 33.333 0.82 0.00 37.98 2.24
5011 8214 9.495572 AGAGGACTCTATTTGACTTTTTACTTG 57.504 33.333 0.00 0.00 38.35 3.16
5019 8743 9.944663 CTATTTGACTTTTTACTTGTGCTTACA 57.055 29.630 0.00 0.00 0.00 2.41
5022 8746 7.385778 TGACTTTTTACTTGTGCTTACAGTT 57.614 32.000 0.00 0.00 0.00 3.16
5037 8761 1.881973 ACAGTTTGCATACCACAGCAG 59.118 47.619 3.47 0.00 42.39 4.24
5052 8776 2.292267 CAGCAGTGACTTCAAACCTGT 58.708 47.619 0.00 0.00 0.00 4.00
5054 8778 1.604278 GCAGTGACTTCAAACCTGTCC 59.396 52.381 0.00 0.00 0.00 4.02
5068 8819 1.471119 CTGTCCGGTCTTGTAGCCTA 58.529 55.000 0.00 0.00 0.00 3.93
5069 8820 1.405821 CTGTCCGGTCTTGTAGCCTAG 59.594 57.143 0.00 0.00 0.00 3.02
5151 8904 7.067981 GCTCATCTCATTTTCTTGGTAATCCTT 59.932 37.037 0.00 0.00 34.23 3.36
5228 8984 2.217750 TCTTTCCACCACATGTTCACG 58.782 47.619 0.00 0.00 0.00 4.35
5229 8985 1.946768 CTTTCCACCACATGTTCACGT 59.053 47.619 0.00 0.00 0.00 4.49
5241 8997 3.380479 TGTTCACGTTCCAAGGAGTAG 57.620 47.619 0.00 0.00 0.00 2.57
5242 8998 2.067013 GTTCACGTTCCAAGGAGTAGC 58.933 52.381 0.00 0.00 0.00 3.58
5244 9000 1.689813 TCACGTTCCAAGGAGTAGCAA 59.310 47.619 0.00 0.00 0.00 3.91
5283 9048 1.081892 CCAGTTCTCAGTCAATGCGG 58.918 55.000 0.00 0.00 0.00 5.69
5295 9060 0.676466 CAATGCGGTTACAGGCCAGA 60.676 55.000 5.01 0.00 0.00 3.86
5340 9159 4.216042 TGTGTTACAACATCAGCATCAAGG 59.784 41.667 0.00 0.00 41.59 3.61
5344 9163 3.087031 ACAACATCAGCATCAAGGAAGG 58.913 45.455 0.00 0.00 0.00 3.46
5377 9196 2.676342 GCGATGTAAAACTACACCCAGG 59.324 50.000 0.00 0.00 32.16 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
244 245 0.465705 GCATCCGTTCCATCTCCTCA 59.534 55.000 0.00 0.00 0.00 3.86
549 552 2.476619 CACCAAGAGAGTACAACAAGCG 59.523 50.000 0.00 0.00 0.00 4.68
613 622 1.305718 ACTGGAGAGCTGGAGACCC 60.306 63.158 0.00 0.00 0.00 4.46
614 623 1.326951 GGACTGGAGAGCTGGAGACC 61.327 65.000 0.00 0.00 0.00 3.85
615 624 0.613292 TGGACTGGAGAGCTGGAGAC 60.613 60.000 0.00 0.00 0.00 3.36
616 625 0.324183 CTGGACTGGAGAGCTGGAGA 60.324 60.000 0.00 0.00 0.00 3.71
617 626 0.614415 ACTGGACTGGAGAGCTGGAG 60.614 60.000 0.00 0.00 0.00 3.86
618 627 0.613292 GACTGGACTGGAGAGCTGGA 60.613 60.000 0.00 0.00 0.00 3.86
619 628 1.612395 GGACTGGACTGGAGAGCTGG 61.612 65.000 0.00 0.00 0.00 4.85
620 629 0.614415 AGGACTGGACTGGAGAGCTG 60.614 60.000 0.00 0.00 0.00 4.24
621 630 0.324275 GAGGACTGGACTGGAGAGCT 60.324 60.000 0.00 0.00 0.00 4.09
622 631 1.326951 GGAGGACTGGACTGGAGAGC 61.327 65.000 0.00 0.00 0.00 4.09
623 632 0.686112 GGGAGGACTGGACTGGAGAG 60.686 65.000 0.00 0.00 0.00 3.20
624 633 1.388531 GGGAGGACTGGACTGGAGA 59.611 63.158 0.00 0.00 0.00 3.71
625 634 1.687493 GGGGAGGACTGGACTGGAG 60.687 68.421 0.00 0.00 0.00 3.86
626 635 2.450243 GGGGAGGACTGGACTGGA 59.550 66.667 0.00 0.00 0.00 3.86
627 636 2.689034 GGGGGAGGACTGGACTGG 60.689 72.222 0.00 0.00 0.00 4.00
628 637 2.122729 TGGGGGAGGACTGGACTG 59.877 66.667 0.00 0.00 0.00 3.51
629 638 2.122954 GTGGGGGAGGACTGGACT 59.877 66.667 0.00 0.00 0.00 3.85
630 639 2.203938 TGTGGGGGAGGACTGGAC 60.204 66.667 0.00 0.00 0.00 4.02
631 640 2.203938 GTGTGGGGGAGGACTGGA 60.204 66.667 0.00 0.00 0.00 3.86
632 641 3.706373 CGTGTGGGGGAGGACTGG 61.706 72.222 0.00 0.00 0.00 4.00
633 642 3.706373 CCGTGTGGGGGAGGACTG 61.706 72.222 0.00 0.00 0.00 3.51
656 665 2.110352 GGTTCCAATACCCGTGCGG 61.110 63.158 3.25 3.25 37.81 5.69
658 667 2.110352 CCGGTTCCAATACCCGTGC 61.110 63.158 0.00 0.00 40.10 5.34
659 668 1.450669 CCCGGTTCCAATACCCGTG 60.451 63.158 0.00 0.00 40.10 4.94
660 669 0.617249 TACCCGGTTCCAATACCCGT 60.617 55.000 0.00 0.00 40.10 5.28
661 670 0.105408 CTACCCGGTTCCAATACCCG 59.895 60.000 0.00 0.00 41.37 5.28
662 671 0.179037 GCTACCCGGTTCCAATACCC 60.179 60.000 0.00 0.00 34.56 3.69
691 700 1.135402 CCAAACAAGTAGGCGCATTCC 60.135 52.381 10.83 0.00 0.00 3.01
696 705 1.084289 CTACCCAAACAAGTAGGCGC 58.916 55.000 0.00 0.00 33.73 6.53
702 711 1.074248 CCCCGCTACCCAAACAAGT 59.926 57.895 0.00 0.00 0.00 3.16
704 713 1.377229 CTCCCCGCTACCCAAACAA 59.623 57.895 0.00 0.00 0.00 2.83
709 753 4.392166 TCTGCTCCCCGCTACCCA 62.392 66.667 0.00 0.00 40.11 4.51
766 810 3.535629 CTGGTGCGTGCCTCTTCCA 62.536 63.158 0.00 0.00 0.00 3.53
813 858 1.966451 CCAAGAAAAGAGGCGGCGT 60.966 57.895 9.37 0.00 0.00 5.68
850 898 2.093394 GCTACTTGTCCTCCTTCCCTTC 60.093 54.545 0.00 0.00 0.00 3.46
915 963 1.332997 GATCGCTGGAAAGGCAATGAG 59.667 52.381 0.00 0.00 0.00 2.90
1178 1226 2.808919 TGGAGGTGGTGAGTAGAGAAG 58.191 52.381 0.00 0.00 0.00 2.85
1179 1227 2.897969 GTTGGAGGTGGTGAGTAGAGAA 59.102 50.000 0.00 0.00 0.00 2.87
1180 1228 2.110188 AGTTGGAGGTGGTGAGTAGAGA 59.890 50.000 0.00 0.00 0.00 3.10
1181 1229 2.494073 GAGTTGGAGGTGGTGAGTAGAG 59.506 54.545 0.00 0.00 0.00 2.43
1182 1230 2.158370 TGAGTTGGAGGTGGTGAGTAGA 60.158 50.000 0.00 0.00 0.00 2.59
1183 1231 2.248248 TGAGTTGGAGGTGGTGAGTAG 58.752 52.381 0.00 0.00 0.00 2.57
1531 1600 4.696402 ACAAGTGAGTACAACGGAAACAAA 59.304 37.500 0.00 0.00 0.00 2.83
1535 1604 5.518848 TCTACAAGTGAGTACAACGGAAA 57.481 39.130 0.00 0.00 0.00 3.13
1539 1608 5.279384 ACAGTTCTACAAGTGAGTACAACG 58.721 41.667 0.00 0.00 36.55 4.10
1634 1704 3.694043 TTCACATGAAGGATCGTGGAA 57.306 42.857 0.00 1.87 45.20 3.53
1637 1707 3.488047 GCCATTTCACATGAAGGATCGTG 60.488 47.826 0.00 0.00 46.15 4.35
1639 1709 2.286595 CGCCATTTCACATGAAGGATCG 60.287 50.000 0.00 0.81 35.21 3.69
1833 1908 9.768662 TTAAAGTCTTTGAAAGGTAATACTCGT 57.231 29.630 8.14 0.00 0.00 4.18
1920 4245 3.427233 GCAGCAACCTTTCTAATGCTCTG 60.427 47.826 0.00 0.00 45.49 3.35
2027 4353 5.008316 GTCAGACCAACCTTCAATAAACGTT 59.992 40.000 0.00 0.00 0.00 3.99
2131 4463 2.984871 GAAGGATTCAGAGAGGCGC 58.015 57.895 0.00 0.00 46.62 6.53
2149 4481 1.804601 TCTTGCAGCACTGACATGAG 58.195 50.000 0.00 0.00 0.00 2.90
2255 4587 6.434340 AGGTCAGATTGGTTGAAAATAAGGAC 59.566 38.462 0.00 0.00 0.00 3.85
2295 4628 2.749621 CAAACATCCAAGGCAGAGGTAC 59.250 50.000 0.00 0.00 0.00 3.34
2341 4674 6.743575 AAAACTACTCCATTACATGACTGC 57.256 37.500 0.00 0.00 0.00 4.40
2416 4749 1.497286 GGGGAAGGCACATACCCAATA 59.503 52.381 0.00 0.00 43.67 1.90
3002 5515 7.948357 AGTGAAATGTTACTAGTACTCACACA 58.052 34.615 19.78 14.64 35.50 3.72
3030 5543 6.918022 GCTGTTGGAAAACTACATATATTGCC 59.082 38.462 0.00 0.00 34.41 4.52
3147 5661 8.207545 ACTGATTCTATCCTCTAAACCATCAAC 58.792 37.037 0.00 0.00 0.00 3.18
3191 5713 5.592282 TGATTGTTGGCTGTTGTCTTAAGAA 59.408 36.000 6.78 0.00 0.00 2.52
3621 6208 3.769739 TGTCACACTGCATCTACCTTT 57.230 42.857 0.00 0.00 0.00 3.11
3811 6402 3.213506 TGTGGTTCTCATCAACAGTTGG 58.786 45.455 13.52 0.00 0.00 3.77
3837 6639 8.579682 GAGCATAAATTGATCCATGGTAAAAC 57.420 34.615 12.58 0.90 34.60 2.43
3947 6849 6.989155 TTAGAGTGAGGTTACTTCCTTTCA 57.011 37.500 0.00 0.00 38.02 2.69
4015 6917 3.132824 CCTGGCACACTGACTACATGATA 59.867 47.826 0.00 0.00 0.00 2.15
4096 6998 7.865706 AATTCCCAAATACAGACAGACATAC 57.134 36.000 0.00 0.00 0.00 2.39
4137 7039 2.111384 CTGACCTGGCACACCTACTAT 58.889 52.381 0.00 0.00 36.63 2.12
4335 7240 6.594159 GCATAAGAACTTGCTAGTGGTTCTAA 59.406 38.462 19.43 0.00 45.73 2.10
4339 7244 4.911390 AGCATAAGAACTTGCTAGTGGTT 58.089 39.130 0.36 1.36 46.92 3.67
4368 7273 7.538334 TGAAATCTCAAATTGAACTGCATAACG 59.462 33.333 0.00 0.00 0.00 3.18
4396 7304 8.040727 GCAAGAAAAATACCAATTCCATTAGGT 58.959 33.333 0.00 0.00 38.14 3.08
4634 7545 3.119316 GGTCACACCATCTCTGAGTACAG 60.119 52.174 4.32 0.00 40.68 2.74
4679 7610 3.686726 GGCTACAGACTGGAGAAACAATG 59.313 47.826 19.49 0.00 26.39 2.82
4745 7948 4.520874 AGAAATGCAGCTAGCTACGAGATA 59.479 41.667 18.86 0.00 45.94 1.98
4974 8177 3.990959 AGAGTCCTCTGAAACCATTCC 57.009 47.619 0.00 0.00 38.75 3.01
4989 8192 8.560374 AGCACAAGTAAAAAGTCAAATAGAGTC 58.440 33.333 0.00 0.00 0.00 3.36
5008 8211 4.023279 TGGTATGCAAACTGTAAGCACAAG 60.023 41.667 8.90 0.00 41.60 3.16
5009 8212 3.885901 TGGTATGCAAACTGTAAGCACAA 59.114 39.130 8.90 0.00 41.60 3.33
5011 8214 3.252215 TGTGGTATGCAAACTGTAAGCAC 59.748 43.478 8.90 0.00 41.60 4.40
5017 8741 1.881973 CTGCTGTGGTATGCAAACTGT 59.118 47.619 0.00 0.00 38.81 3.55
5019 8743 1.881973 CACTGCTGTGGTATGCAAACT 59.118 47.619 15.43 0.00 40.33 2.66
5022 8746 1.072173 AGTCACTGCTGTGGTATGCAA 59.928 47.619 21.80 0.00 43.94 4.08
5037 8761 1.226746 CCGGACAGGTTTGAAGTCAC 58.773 55.000 0.00 0.00 34.04 3.67
5052 8776 2.422519 CCTACTAGGCTACAAGACCGGA 60.423 54.545 9.46 0.00 0.00 5.14
5068 8819 7.792032 TGCTATTATTACTTTGTCAGCCTACT 58.208 34.615 0.00 0.00 0.00 2.57
5069 8820 8.608844 ATGCTATTATTACTTTGTCAGCCTAC 57.391 34.615 0.00 0.00 0.00 3.18
5104 8857 3.102204 CCTACTAAACCGGAAAGGAGGA 58.898 50.000 21.98 3.76 43.15 3.71
5105 8858 2.419713 GCCTACTAAACCGGAAAGGAGG 60.420 54.545 22.10 22.10 43.32 4.30
5195 8951 6.831353 TGTGGTGGAAAGAAGTGAAATAAGAA 59.169 34.615 0.00 0.00 0.00 2.52
5228 8984 9.262358 CTTATTATAGTTGCTACTCCTTGGAAC 57.738 37.037 3.45 0.00 35.78 3.62
5229 8985 7.931948 GCTTATTATAGTTGCTACTCCTTGGAA 59.068 37.037 3.45 0.00 35.78 3.53
5241 8997 4.924462 GTCCTCCTCGCTTATTATAGTTGC 59.076 45.833 0.00 0.00 0.00 4.17
5242 8998 5.010719 TGGTCCTCCTCGCTTATTATAGTTG 59.989 44.000 0.00 0.00 34.23 3.16
5244 9000 4.737578 TGGTCCTCCTCGCTTATTATAGT 58.262 43.478 0.00 0.00 34.23 2.12
5283 9048 4.575885 TGATAAGTGTTCTGGCCTGTAAC 58.424 43.478 3.32 10.66 0.00 2.50
5295 9060 5.068987 ACATGTTTGCACCTTGATAAGTGTT 59.931 36.000 0.00 0.00 0.00 3.32
5377 9196 9.331282 AGTAGATAGATTTGGCACTTGTTATTC 57.669 33.333 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.