Multiple sequence alignment - TraesCS3D01G169600

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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 TraesCS3D01G169600 chr3D 100.000 5285 0 0 1 5285 147816873 147822157 0.000000e+00 9760.0
1 TraesCS3D01G169600 chr3A 98.655 4386 54 5 257 4637 165420834 165416449 0.000000e+00 7768.0
2 TraesCS3D01G169600 chr3A 91.055 559 23 12 4718 5273 165416450 165415916 0.000000e+00 730.0
3 TraesCS3D01G169600 chr3A 88.971 272 15 5 1 258 165421156 165420886 6.600000e-84 322.0
4 TraesCS3D01G169600 chr3A 86.517 89 9 3 4633 4719 507291487 507291574 1.570000e-15 95.3
5 TraesCS3D01G169600 chr3B 98.029 4110 56 14 257 4353 214564360 214560263 0.000000e+00 7118.0
6 TraesCS3D01G169600 chr3B 95.622 571 17 5 4718 5285 214559875 214559310 0.000000e+00 909.0
7 TraesCS3D01G169600 chr3B 97.917 288 6 0 4350 4637 214560161 214559874 2.840000e-137 499.0
8 TraesCS3D01G169600 chr3B 88.889 288 19 5 4 279 214564676 214564390 5.070000e-90 342.0
9 TraesCS3D01G169600 chr3B 88.172 93 10 1 4628 4719 447254400 447254492 5.600000e-20 110.0
10 TraesCS3D01G169600 chr2A 93.852 4099 197 32 560 4634 95991378 95995445 0.000000e+00 6122.0
11 TraesCS3D01G169600 chr2D 93.802 4082 188 36 587 4634 97219730 97223780 0.000000e+00 6076.0
12 TraesCS3D01G169600 chr2D 86.103 331 33 8 257 583 97219322 97219643 1.410000e-90 344.0
13 TraesCS3D01G169600 chr2D 80.303 198 22 7 76 258 97219081 97219276 3.320000e-27 134.0
14 TraesCS3D01G169600 chr2D 88.372 86 7 3 4636 4719 512165924 512165840 3.370000e-17 100.0
15 TraesCS3D01G169600 chr2B 93.353 4122 218 35 540 4634 148237067 148241159 0.000000e+00 6043.0
16 TraesCS3D01G169600 chr1D 86.847 3368 426 14 941 4298 309078511 309081871 0.000000e+00 3749.0
17 TraesCS3D01G169600 chr1D 84.648 469 58 9 257 716 108107354 108106891 6.240000e-124 455.0
18 TraesCS3D01G169600 chr1D 88.506 87 7 3 4636 4721 132857837 132857921 9.360000e-18 102.0
19 TraesCS3D01G169600 chr1B 86.629 3373 434 15 926 4287 418810313 418813679 0.000000e+00 3714.0
20 TraesCS3D01G169600 chr1B 86.061 165 16 6 552 716 158539646 158539803 2.530000e-38 171.0
21 TraesCS3D01G169600 chr1B 88.235 85 9 1 4636 4719 277425367 277425283 3.370000e-17 100.0
22 TraesCS3D01G169600 chr1A 86.637 3360 433 15 947 4298 388838782 388842133 0.000000e+00 3703.0
23 TraesCS3D01G169600 chr1A 84.222 469 60 9 257 716 111129610 111129147 1.350000e-120 444.0
24 TraesCS3D01G169600 chr5D 82.598 3218 518 31 1079 4275 46319141 46322337 0.000000e+00 2802.0
25 TraesCS3D01G169600 chr5D 87.356 87 8 3 4635 4719 188826620 188826535 4.360000e-16 97.1
26 TraesCS3D01G169600 chr4B 82.576 264 33 9 461 716 329805701 329805443 2.480000e-53 220.0
27 TraesCS3D01G169600 chr4A 83.495 206 26 6 4910 5112 598715689 598715489 9.040000e-43 185.0
28 TraesCS3D01G169600 chr4A 86.813 91 5 6 4636 4722 683883575 683883662 1.570000e-15 95.3
29 TraesCS3D01G169600 chr4D 87.640 89 8 3 4636 4722 477107840 477107927 3.370000e-17 100.0
30 TraesCS3D01G169600 chrUn 86.813 91 9 3 4635 4723 42479325 42479236 1.210000e-16 99.0


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 TraesCS3D01G169600 chr3D 147816873 147822157 5284 False 9760.000000 9760 100.000000 1 5285 1 chr3D.!!$F1 5284
1 TraesCS3D01G169600 chr3A 165415916 165421156 5240 True 2940.000000 7768 92.893667 1 5273 3 chr3A.!!$R1 5272
2 TraesCS3D01G169600 chr3B 214559310 214564676 5366 True 2217.000000 7118 95.114250 4 5285 4 chr3B.!!$R1 5281
3 TraesCS3D01G169600 chr2A 95991378 95995445 4067 False 6122.000000 6122 93.852000 560 4634 1 chr2A.!!$F1 4074
4 TraesCS3D01G169600 chr2D 97219081 97223780 4699 False 2184.666667 6076 86.736000 76 4634 3 chr2D.!!$F1 4558
5 TraesCS3D01G169600 chr2B 148237067 148241159 4092 False 6043.000000 6043 93.353000 540 4634 1 chr2B.!!$F1 4094
6 TraesCS3D01G169600 chr1D 309078511 309081871 3360 False 3749.000000 3749 86.847000 941 4298 1 chr1D.!!$F2 3357
7 TraesCS3D01G169600 chr1B 418810313 418813679 3366 False 3714.000000 3714 86.629000 926 4287 1 chr1B.!!$F2 3361
8 TraesCS3D01G169600 chr1A 388838782 388842133 3351 False 3703.000000 3703 86.637000 947 4298 1 chr1A.!!$F1 3351
9 TraesCS3D01G169600 chr5D 46319141 46322337 3196 False 2802.000000 2802 82.598000 1079 4275 1 chr5D.!!$F1 3196

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
229 248 0.033228 CCGGCCTGCAAAATTCACAA 59.967 50.000 0.0 0.0 0.00 3.33 F
231 250 1.526464 CGGCCTGCAAAATTCACAAAC 59.474 47.619 0.0 0.0 0.00 2.93 F
371 454 2.025981 TCAGTTAGCCAGCATTGTCCAT 60.026 45.455 0.0 0.0 0.00 3.41 F
2097 2294 5.394443 GCTTACTGGCAATGATTTGATTGGA 60.394 40.000 0.0 0.0 34.42 3.53 F
3411 3608 6.379133 ACCATGTGTTTGCTAATGAGATCAAT 59.621 34.615 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 1859 1.067199 GCCAGCGAACAAAAGCATCG 61.067 55.000 0.00 0.0 39.47 3.84 R
2097 2294 6.248433 TGAAAGAGGAGACTTTAATGGCAAT 58.752 36.000 0.00 0.0 44.43 3.56 R
2325 2522 3.054802 CAGCTGACTTATCCCCAAACTCT 60.055 47.826 8.42 0.0 0.00 3.24 R
3645 3842 2.997986 CCAGCCAGCTTTTATTGCAAAG 59.002 45.455 1.71 0.0 36.91 2.77 R
4695 5027 0.035176 CCCTCCGTCCCAAAACGTAA 59.965 55.000 0.00 0.0 41.01 3.18 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
19 20 1.922570 GGTTAGTGATGCGATGACGT 58.077 50.000 0.00 0.00 41.98 4.34
89 90 0.908910 TGATTTAGCTTCGGGGCAGA 59.091 50.000 0.00 0.00 34.17 4.26
96 97 1.900351 CTTCGGGGCAGACAGATCA 59.100 57.895 0.00 0.00 0.00 2.92
98 99 0.690192 TTCGGGGCAGACAGATCAAA 59.310 50.000 0.00 0.00 0.00 2.69
192 209 1.194781 TCCTGGGTCTGCAAGTCCTC 61.195 60.000 0.00 0.00 42.16 3.71
229 248 0.033228 CCGGCCTGCAAAATTCACAA 59.967 50.000 0.00 0.00 0.00 3.33
231 250 1.526464 CGGCCTGCAAAATTCACAAAC 59.474 47.619 0.00 0.00 0.00 2.93
245 264 8.606040 AAATTCACAAACAAATAAGGTCATGG 57.394 30.769 0.00 0.00 0.00 3.66
283 360 6.493458 AGGACTTTGCTGAATTTTAGGCTTAA 59.507 34.615 0.00 0.00 0.00 1.85
371 454 2.025981 TCAGTTAGCCAGCATTGTCCAT 60.026 45.455 0.00 0.00 0.00 3.41
425 516 7.860373 TGCACAAAAGCAAACTAATTGTACTAG 59.140 33.333 0.00 0.00 42.46 2.57
479 572 5.412526 TGTTAACTTTCATCCACGTGAAC 57.587 39.130 19.30 9.67 37.80 3.18
558 651 5.921004 TTCAAATGTTAATTGCCTTGCAC 57.079 34.783 0.00 0.00 38.71 4.57
695 871 9.102757 ACATTGTTAGAAGACTATGCAACATAG 57.897 33.333 12.02 12.02 36.60 2.23
783 964 8.570488 TGATGTTTGCTTATGGCTTATTATGAG 58.430 33.333 0.00 0.00 42.39 2.90
2097 2294 5.394443 GCTTACTGGCAATGATTTGATTGGA 60.394 40.000 0.00 0.00 34.42 3.53
3411 3608 6.379133 ACCATGTGTTTGCTAATGAGATCAAT 59.621 34.615 0.00 0.00 0.00 2.57
3645 3842 5.707931 CAAAAGATTCTGAAGAAGGAAGGC 58.292 41.667 0.00 0.00 37.48 4.35
4419 4738 7.836183 ACTGGCTCCTTTTATTCTTCACATTAT 59.164 33.333 0.00 0.00 0.00 1.28
4420 4739 8.593945 TGGCTCCTTTTATTCTTCACATTATT 57.406 30.769 0.00 0.00 0.00 1.40
4635 4967 3.743521 TGCTGAGTTGTAAATCTGTGCT 58.256 40.909 1.99 0.00 0.00 4.40
4636 4968 4.893608 TGCTGAGTTGTAAATCTGTGCTA 58.106 39.130 1.99 0.00 0.00 3.49
4637 4969 4.690748 TGCTGAGTTGTAAATCTGTGCTAC 59.309 41.667 1.99 0.00 0.00 3.58
4638 4970 4.932200 GCTGAGTTGTAAATCTGTGCTACT 59.068 41.667 1.99 0.00 0.00 2.57
4639 4971 5.062809 GCTGAGTTGTAAATCTGTGCTACTC 59.937 44.000 0.00 0.00 35.43 2.59
4640 4972 5.479306 TGAGTTGTAAATCTGTGCTACTCC 58.521 41.667 0.00 0.00 34.50 3.85
4641 4973 4.833390 AGTTGTAAATCTGTGCTACTCCC 58.167 43.478 0.00 0.00 0.00 4.30
4642 4974 4.532521 AGTTGTAAATCTGTGCTACTCCCT 59.467 41.667 0.00 0.00 0.00 4.20
4643 4975 4.737855 TGTAAATCTGTGCTACTCCCTC 57.262 45.455 0.00 0.00 0.00 4.30
4644 4976 4.353777 TGTAAATCTGTGCTACTCCCTCT 58.646 43.478 0.00 0.00 0.00 3.69
4645 4977 3.902881 AAATCTGTGCTACTCCCTCTG 57.097 47.619 0.00 0.00 0.00 3.35
4646 4978 2.541233 ATCTGTGCTACTCCCTCTGT 57.459 50.000 0.00 0.00 0.00 3.41
4647 4979 1.840737 TCTGTGCTACTCCCTCTGTC 58.159 55.000 0.00 0.00 0.00 3.51
4648 4980 0.820871 CTGTGCTACTCCCTCTGTCC 59.179 60.000 0.00 0.00 0.00 4.02
4649 4981 0.614979 TGTGCTACTCCCTCTGTCCC 60.615 60.000 0.00 0.00 0.00 4.46
4650 4982 0.614979 GTGCTACTCCCTCTGTCCCA 60.615 60.000 0.00 0.00 0.00 4.37
4651 4983 0.339859 TGCTACTCCCTCTGTCCCAT 59.660 55.000 0.00 0.00 0.00 4.00
4652 4984 1.573857 TGCTACTCCCTCTGTCCCATA 59.426 52.381 0.00 0.00 0.00 2.74
4653 4985 2.023404 TGCTACTCCCTCTGTCCCATAA 60.023 50.000 0.00 0.00 0.00 1.90
4654 4986 3.243724 GCTACTCCCTCTGTCCCATAAT 58.756 50.000 0.00 0.00 0.00 1.28
4655 4987 4.140782 TGCTACTCCCTCTGTCCCATAATA 60.141 45.833 0.00 0.00 0.00 0.98
4656 4988 5.026790 GCTACTCCCTCTGTCCCATAATAT 58.973 45.833 0.00 0.00 0.00 1.28
4657 4989 6.195700 GCTACTCCCTCTGTCCCATAATATA 58.804 44.000 0.00 0.00 0.00 0.86
4658 4990 6.668283 GCTACTCCCTCTGTCCCATAATATAA 59.332 42.308 0.00 0.00 0.00 0.98
4659 4991 7.147811 GCTACTCCCTCTGTCCCATAATATAAG 60.148 44.444 0.00 0.00 0.00 1.73
4660 4992 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
4661 4993 6.726764 ACTCCCTCTGTCCCATAATATAAGAC 59.273 42.308 0.00 0.00 0.00 3.01
4662 4994 5.715279 TCCCTCTGTCCCATAATATAAGACG 59.285 44.000 0.00 0.00 0.00 4.18
4663 4995 5.480772 CCCTCTGTCCCATAATATAAGACGT 59.519 44.000 0.00 0.00 0.00 4.34
4664 4996 6.014499 CCCTCTGTCCCATAATATAAGACGTT 60.014 42.308 0.00 0.00 0.00 3.99
4665 4997 7.442656 CCTCTGTCCCATAATATAAGACGTTT 58.557 38.462 0.00 0.00 0.00 3.60
4666 4998 7.931948 CCTCTGTCCCATAATATAAGACGTTTT 59.068 37.037 0.00 0.00 0.00 2.43
4667 4999 9.326413 CTCTGTCCCATAATATAAGACGTTTTT 57.674 33.333 0.00 0.00 0.00 1.94
4668 5000 9.104965 TCTGTCCCATAATATAAGACGTTTTTG 57.895 33.333 0.00 0.00 0.00 2.44
4669 5001 7.699566 TGTCCCATAATATAAGACGTTTTTGC 58.300 34.615 0.00 0.00 0.00 3.68
4670 5002 7.337184 TGTCCCATAATATAAGACGTTTTTGCA 59.663 33.333 0.00 0.00 0.00 4.08
4671 5003 8.185505 GTCCCATAATATAAGACGTTTTTGCAA 58.814 33.333 0.00 0.00 0.00 4.08
4672 5004 8.402472 TCCCATAATATAAGACGTTTTTGCAAG 58.598 33.333 0.00 0.00 0.00 4.01
4673 5005 7.167468 CCCATAATATAAGACGTTTTTGCAAGC 59.833 37.037 0.00 0.00 0.00 4.01
4674 5006 7.915397 CCATAATATAAGACGTTTTTGCAAGCT 59.085 33.333 0.00 0.00 0.00 3.74
4675 5007 9.929722 CATAATATAAGACGTTTTTGCAAGCTA 57.070 29.630 0.00 0.00 0.00 3.32
4678 5010 6.986424 ATAAGACGTTTTTGCAAGCTAAAC 57.014 33.333 13.02 13.02 0.00 2.01
4679 5011 4.364415 AGACGTTTTTGCAAGCTAAACA 57.636 36.364 19.80 0.00 32.67 2.83
4680 5012 4.739195 AGACGTTTTTGCAAGCTAAACAA 58.261 34.783 19.80 0.53 32.67 2.83
4681 5013 4.798387 AGACGTTTTTGCAAGCTAAACAAG 59.202 37.500 19.80 10.49 32.67 3.16
4682 5014 4.739195 ACGTTTTTGCAAGCTAAACAAGA 58.261 34.783 19.80 0.00 32.67 3.02
4683 5015 5.348164 ACGTTTTTGCAAGCTAAACAAGAT 58.652 33.333 19.80 4.96 32.67 2.40
4684 5016 5.810074 ACGTTTTTGCAAGCTAAACAAGATT 59.190 32.000 19.80 2.17 32.87 2.40
4694 5026 8.112099 CAAGCTAAACAAGATTGCAATATGTC 57.888 34.615 23.24 14.45 44.05 3.06
4695 5027 7.636150 AGCTAAACAAGATTGCAATATGTCT 57.364 32.000 23.24 16.02 0.00 3.41
4696 5028 8.059798 AGCTAAACAAGATTGCAATATGTCTT 57.940 30.769 23.24 16.07 0.00 3.01
4697 5029 9.177608 AGCTAAACAAGATTGCAATATGTCTTA 57.822 29.630 23.24 20.30 30.29 2.10
4698 5030 9.226345 GCTAAACAAGATTGCAATATGTCTTAC 57.774 33.333 23.24 13.78 30.29 2.34
4699 5031 9.425893 CTAAACAAGATTGCAATATGTCTTACG 57.574 33.333 23.24 11.49 30.29 3.18
4700 5032 6.985188 ACAAGATTGCAATATGTCTTACGT 57.015 33.333 19.44 9.84 30.29 3.57
4701 5033 7.377766 ACAAGATTGCAATATGTCTTACGTT 57.622 32.000 19.44 2.48 30.29 3.99
4702 5034 7.816640 ACAAGATTGCAATATGTCTTACGTTT 58.183 30.769 19.44 0.00 30.29 3.60
4703 5035 8.296713 ACAAGATTGCAATATGTCTTACGTTTT 58.703 29.630 19.44 0.00 30.29 2.43
4704 5036 8.577939 CAAGATTGCAATATGTCTTACGTTTTG 58.422 33.333 12.97 0.00 31.88 2.44
4705 5037 7.250569 AGATTGCAATATGTCTTACGTTTTGG 58.749 34.615 12.97 0.00 30.21 3.28
4706 5038 5.303747 TGCAATATGTCTTACGTTTTGGG 57.696 39.130 0.00 0.00 30.21 4.12
4707 5039 5.004448 TGCAATATGTCTTACGTTTTGGGA 58.996 37.500 0.00 0.00 30.21 4.37
4708 5040 5.106475 TGCAATATGTCTTACGTTTTGGGAC 60.106 40.000 0.00 0.00 30.21 4.46
4710 5042 1.868469 TGTCTTACGTTTTGGGACGG 58.132 50.000 0.00 0.00 46.77 4.79
4711 5043 1.411977 TGTCTTACGTTTTGGGACGGA 59.588 47.619 0.00 0.00 46.77 4.69
4712 5044 2.064014 GTCTTACGTTTTGGGACGGAG 58.936 52.381 0.00 0.54 46.77 4.63
4713 5045 1.001181 TCTTACGTTTTGGGACGGAGG 59.999 52.381 0.00 0.00 46.77 4.30
4714 5046 0.035176 TTACGTTTTGGGACGGAGGG 59.965 55.000 0.00 0.00 46.77 4.30
4715 5047 0.831288 TACGTTTTGGGACGGAGGGA 60.831 55.000 0.00 0.00 46.77 4.20
4716 5048 1.375523 CGTTTTGGGACGGAGGGAG 60.376 63.158 0.00 0.00 39.27 4.30
4748 5083 9.712305 GCTAATGTCATTGTAGTCTATTATGGT 57.288 33.333 8.39 0.00 0.00 3.55
4750 5085 8.908786 AATGTCATTGTAGTCTATTATGGTGG 57.091 34.615 0.00 0.00 0.00 4.61
4908 5246 7.561356 AGATGACAAATATTACCCCTTTCCTTG 59.439 37.037 0.00 0.00 0.00 3.61
4957 5295 5.394738 ACATCCTAATGATCTCGGTTCCTA 58.605 41.667 0.00 0.00 36.67 2.94
5006 5344 4.630097 GGCGTAGTATCGACTGGC 57.370 61.111 0.00 0.00 36.28 4.85
5100 5438 4.515361 ACTGCAGATGATTGAGAAGGAAG 58.485 43.478 23.35 0.00 0.00 3.46
5157 5513 1.202782 AGATGTGGATGCAGAGATGGC 60.203 52.381 0.00 0.00 0.00 4.40
5158 5514 0.549469 ATGTGGATGCAGAGATGGCA 59.451 50.000 0.00 0.00 46.66 4.92
5159 5515 0.328926 TGTGGATGCAGAGATGGCAA 59.671 50.000 0.00 0.00 45.60 4.52
5160 5516 1.022735 GTGGATGCAGAGATGGCAAG 58.977 55.000 0.00 0.00 45.60 4.01
5161 5517 0.622136 TGGATGCAGAGATGGCAAGT 59.378 50.000 0.00 0.00 45.60 3.16
5162 5518 1.022735 GGATGCAGAGATGGCAAGTG 58.977 55.000 0.00 0.00 45.60 3.16
5163 5519 0.381089 GATGCAGAGATGGCAAGTGC 59.619 55.000 0.00 0.00 45.60 4.40
5164 5520 1.073548 TGCAGAGATGGCAAGTGCA 59.926 52.632 11.05 11.05 44.36 4.57
5165 5521 0.958876 TGCAGAGATGGCAAGTGCAG 60.959 55.000 11.05 0.00 44.36 4.41
5166 5522 0.675837 GCAGAGATGGCAAGTGCAGA 60.676 55.000 5.52 0.00 44.36 4.26
5167 5523 1.817357 CAGAGATGGCAAGTGCAGAA 58.183 50.000 5.52 0.00 44.36 3.02
5168 5524 2.366533 CAGAGATGGCAAGTGCAGAAT 58.633 47.619 5.52 0.00 44.36 2.40
5169 5525 3.538591 CAGAGATGGCAAGTGCAGAATA 58.461 45.455 5.52 0.00 44.36 1.75
5170 5526 3.311871 CAGAGATGGCAAGTGCAGAATAC 59.688 47.826 5.52 0.00 44.36 1.89
5171 5527 3.054875 AGAGATGGCAAGTGCAGAATACA 60.055 43.478 5.52 0.00 44.36 2.29
5172 5528 3.689347 AGATGGCAAGTGCAGAATACAA 58.311 40.909 5.52 0.00 44.36 2.41
5173 5529 3.693085 AGATGGCAAGTGCAGAATACAAG 59.307 43.478 5.52 0.00 44.36 3.16
5174 5530 2.161855 TGGCAAGTGCAGAATACAAGG 58.838 47.619 5.52 0.00 44.36 3.61
5219 5575 6.258068 ACAGCAGTGTCTTAGTTTGTTTACTC 59.742 38.462 0.00 0.00 26.76 2.59
5267 5623 5.049612 GCACTTGATCACATACTCCATGATG 60.050 44.000 0.00 0.00 38.10 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.991773 GTGCACTCAACCAGTACGAAATA 59.008 43.478 10.32 0.00 32.21 1.40
108 109 5.570320 AGGCCGCCAGATTATACAAAATAT 58.430 37.500 13.15 0.00 0.00 1.28
109 110 4.980573 AGGCCGCCAGATTATACAAAATA 58.019 39.130 13.15 0.00 0.00 1.40
110 111 3.832527 AGGCCGCCAGATTATACAAAAT 58.167 40.909 13.15 0.00 0.00 1.82
192 209 2.816087 CCGGATTATGAAGCTGGATTGG 59.184 50.000 0.00 0.00 46.30 3.16
229 248 9.872684 AAGATGATATCCATGACCTTATTTGTT 57.127 29.630 0.00 0.00 35.17 2.83
245 264 6.765036 TCAGCAAAGTCCTGAAAGATGATATC 59.235 38.462 0.00 0.00 36.46 1.63
371 454 3.897239 ACATTTCTGTCCTTTGTCACCA 58.103 40.909 0.00 0.00 0.00 4.17
413 496 5.938125 ACAGTTTGTGGGCTAGTACAATTAG 59.062 40.000 9.19 0.00 36.75 1.73
419 502 3.244112 ACAGACAGTTTGTGGGCTAGTAC 60.244 47.826 0.00 0.00 0.00 2.73
425 516 1.360192 GCACAGACAGTTTGTGGGC 59.640 57.895 22.29 8.28 44.66 5.36
521 614 6.409524 ACATTTGAAATCACAGTGGACATT 57.590 33.333 0.00 0.00 0.00 2.71
558 651 1.493861 TGGAGATGGCTGGAGAGAAG 58.506 55.000 0.00 0.00 0.00 2.85
695 871 0.391793 GAGGTCAGGTAAGCTGGTGC 60.392 60.000 0.00 0.00 40.05 5.01
783 964 9.098355 TGTGATGAAGCTAATTATGTAACAGAC 57.902 33.333 0.00 0.00 0.00 3.51
1440 1637 6.036953 CAGCAGCCTTAGATTTCTTACTCTTG 59.963 42.308 0.00 0.00 0.00 3.02
1662 1859 1.067199 GCCAGCGAACAAAAGCATCG 61.067 55.000 0.00 0.00 39.47 3.84
2097 2294 6.248433 TGAAAGAGGAGACTTTAATGGCAAT 58.752 36.000 0.00 0.00 44.43 3.56
2325 2522 3.054802 CAGCTGACTTATCCCCAAACTCT 60.055 47.826 8.42 0.00 0.00 3.24
2496 2693 5.182001 TCCAAGAAGCTTGTTCTTTATCAGC 59.818 40.000 2.10 0.00 36.69 4.26
3411 3608 8.902540 TCTTCTCAGTTTCTTTTACAGCAATA 57.097 30.769 0.00 0.00 0.00 1.90
3645 3842 2.997986 CCAGCCAGCTTTTATTGCAAAG 59.002 45.455 1.71 0.00 36.91 2.77
4051 4257 3.010584 AGCTTCAAATTTAGAGCCTGGGA 59.989 43.478 16.88 0.00 0.00 4.37
4419 4738 5.866633 CAGGCACAAAAACTACAACAGAAAA 59.133 36.000 0.00 0.00 0.00 2.29
4420 4739 5.406649 CAGGCACAAAAACTACAACAGAAA 58.593 37.500 0.00 0.00 0.00 2.52
4645 4977 7.699566 TGCAAAAACGTCTTATATTATGGGAC 58.300 34.615 0.00 0.00 0.00 4.46
4646 4978 7.867305 TGCAAAAACGTCTTATATTATGGGA 57.133 32.000 0.00 0.00 0.00 4.37
4647 4979 7.167468 GCTTGCAAAAACGTCTTATATTATGGG 59.833 37.037 0.00 0.00 0.00 4.00
4648 4980 7.915397 AGCTTGCAAAAACGTCTTATATTATGG 59.085 33.333 0.00 0.00 0.00 2.74
4649 4981 8.841444 AGCTTGCAAAAACGTCTTATATTATG 57.159 30.769 0.00 0.00 0.00 1.90
4652 4984 9.124807 GTTTAGCTTGCAAAAACGTCTTATATT 57.875 29.630 8.93 0.00 0.00 1.28
4653 4985 8.293867 TGTTTAGCTTGCAAAAACGTCTTATAT 58.706 29.630 16.44 0.00 36.19 0.86
4654 4986 7.640852 TGTTTAGCTTGCAAAAACGTCTTATA 58.359 30.769 16.44 0.06 36.19 0.98
4655 4987 6.500041 TGTTTAGCTTGCAAAAACGTCTTAT 58.500 32.000 16.44 0.00 36.19 1.73
4656 4988 5.881447 TGTTTAGCTTGCAAAAACGTCTTA 58.119 33.333 16.44 1.18 36.19 2.10
4657 4989 4.739195 TGTTTAGCTTGCAAAAACGTCTT 58.261 34.783 16.44 0.00 36.19 3.01
4658 4990 4.364415 TGTTTAGCTTGCAAAAACGTCT 57.636 36.364 16.44 4.12 36.19 4.18
4659 4991 4.796312 TCTTGTTTAGCTTGCAAAAACGTC 59.204 37.500 16.44 2.31 36.19 4.34
4660 4992 4.739195 TCTTGTTTAGCTTGCAAAAACGT 58.261 34.783 16.44 0.00 36.19 3.99
4661 4993 5.888412 ATCTTGTTTAGCTTGCAAAAACG 57.112 34.783 16.44 7.07 36.19 3.60
4669 5001 7.972277 AGACATATTGCAATCTTGTTTAGCTTG 59.028 33.333 16.86 0.00 33.98 4.01
4670 5002 8.059798 AGACATATTGCAATCTTGTTTAGCTT 57.940 30.769 16.86 0.00 0.00 3.74
4671 5003 7.636150 AGACATATTGCAATCTTGTTTAGCT 57.364 32.000 16.86 10.90 0.00 3.32
4672 5004 9.226345 GTAAGACATATTGCAATCTTGTTTAGC 57.774 33.333 16.86 8.98 33.53 3.09
4673 5005 9.425893 CGTAAGACATATTGCAATCTTGTTTAG 57.574 33.333 16.86 7.97 43.02 1.85
4674 5006 8.941977 ACGTAAGACATATTGCAATCTTGTTTA 58.058 29.630 16.86 16.19 43.62 2.01
4675 5007 7.816640 ACGTAAGACATATTGCAATCTTGTTT 58.183 30.769 16.86 13.03 43.62 2.83
4676 5008 7.377766 ACGTAAGACATATTGCAATCTTGTT 57.622 32.000 16.86 9.49 43.62 2.83
4677 5009 6.985188 ACGTAAGACATATTGCAATCTTGT 57.015 33.333 21.51 21.51 43.62 3.16
4678 5010 8.577939 CAAAACGTAAGACATATTGCAATCTTG 58.422 33.333 16.86 16.74 43.62 3.02
4679 5011 7.754924 CCAAAACGTAAGACATATTGCAATCTT 59.245 33.333 16.86 15.93 43.62 2.40
4680 5012 7.250569 CCAAAACGTAAGACATATTGCAATCT 58.749 34.615 16.86 4.65 43.62 2.40
4681 5013 6.472163 CCCAAAACGTAAGACATATTGCAATC 59.528 38.462 16.86 1.89 43.62 2.67
4682 5014 6.151985 TCCCAAAACGTAAGACATATTGCAAT 59.848 34.615 17.56 17.56 43.62 3.56
4683 5015 5.473846 TCCCAAAACGTAAGACATATTGCAA 59.526 36.000 0.00 0.00 43.62 4.08
4684 5016 5.004448 TCCCAAAACGTAAGACATATTGCA 58.996 37.500 0.00 0.00 43.62 4.08
4685 5017 5.329493 GTCCCAAAACGTAAGACATATTGC 58.671 41.667 0.00 0.00 43.62 3.56
4686 5018 5.446741 CCGTCCCAAAACGTAAGACATATTG 60.447 44.000 0.00 0.00 41.01 1.90
4687 5019 4.632688 CCGTCCCAAAACGTAAGACATATT 59.367 41.667 0.00 0.00 41.01 1.28
4688 5020 4.081531 TCCGTCCCAAAACGTAAGACATAT 60.082 41.667 0.00 0.00 41.01 1.78
4689 5021 3.257873 TCCGTCCCAAAACGTAAGACATA 59.742 43.478 0.00 0.00 41.01 2.29
4690 5022 2.037511 TCCGTCCCAAAACGTAAGACAT 59.962 45.455 0.00 0.00 41.01 3.06
4691 5023 1.411977 TCCGTCCCAAAACGTAAGACA 59.588 47.619 0.00 0.00 41.01 3.41
4692 5024 2.064014 CTCCGTCCCAAAACGTAAGAC 58.936 52.381 0.00 0.00 41.01 3.01
4693 5025 1.001181 CCTCCGTCCCAAAACGTAAGA 59.999 52.381 0.00 0.00 41.01 2.10
4694 5026 1.435577 CCTCCGTCCCAAAACGTAAG 58.564 55.000 0.00 0.00 41.01 2.34
4695 5027 0.035176 CCCTCCGTCCCAAAACGTAA 59.965 55.000 0.00 0.00 41.01 3.18
4696 5028 0.831288 TCCCTCCGTCCCAAAACGTA 60.831 55.000 0.00 0.00 41.01 3.57
4697 5029 2.108278 CTCCCTCCGTCCCAAAACGT 62.108 60.000 0.00 0.00 41.01 3.99
4698 5030 1.375523 CTCCCTCCGTCCCAAAACG 60.376 63.158 0.00 0.00 42.24 3.60
4699 5031 0.978907 TACTCCCTCCGTCCCAAAAC 59.021 55.000 0.00 0.00 0.00 2.43
4700 5032 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
4701 5033 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
4702 5034 0.115745 AACTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
4703 5035 0.613853 CAACTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
4704 5036 1.957765 GCAACTACTCCCTCCGTCCC 61.958 65.000 0.00 0.00 0.00 4.46
4705 5037 0.971447 AGCAACTACTCCCTCCGTCC 60.971 60.000 0.00 0.00 0.00 4.79
4706 5038 1.760192 TAGCAACTACTCCCTCCGTC 58.240 55.000 0.00 0.00 0.00 4.79
4707 5039 2.226962 TTAGCAACTACTCCCTCCGT 57.773 50.000 0.00 0.00 0.00 4.69
4708 5040 2.431057 ACATTAGCAACTACTCCCTCCG 59.569 50.000 0.00 0.00 0.00 4.63
4709 5041 3.451178 TGACATTAGCAACTACTCCCTCC 59.549 47.826 0.00 0.00 0.00 4.30
4710 5042 4.737855 TGACATTAGCAACTACTCCCTC 57.262 45.455 0.00 0.00 0.00 4.30
4711 5043 5.045578 ACAATGACATTAGCAACTACTCCCT 60.046 40.000 0.00 0.00 0.00 4.20
4712 5044 5.186198 ACAATGACATTAGCAACTACTCCC 58.814 41.667 0.00 0.00 0.00 4.30
4713 5045 7.042335 ACTACAATGACATTAGCAACTACTCC 58.958 38.462 0.00 0.00 0.00 3.85
4714 5046 7.976734 AGACTACAATGACATTAGCAACTACTC 59.023 37.037 0.00 0.00 0.00 2.59
4715 5047 7.841956 AGACTACAATGACATTAGCAACTACT 58.158 34.615 0.00 0.00 0.00 2.57
4716 5048 9.751542 ATAGACTACAATGACATTAGCAACTAC 57.248 33.333 0.00 0.00 0.00 2.73
4749 5084 0.183492 TAAGACATGCATGGCCCTCC 59.817 55.000 29.09 10.51 36.08 4.30
4750 5085 2.157738 GATAAGACATGCATGGCCCTC 58.842 52.381 29.09 18.36 36.08 4.30
4908 5246 8.993121 TCAAAGTCAGACTCATCTCATAAAAAC 58.007 33.333 2.72 0.00 30.42 2.43
4957 5295 3.910627 ACCTGTAGGAGAACAACCAAGAT 59.089 43.478 4.64 0.00 38.94 2.40
5006 5344 4.187694 GCTAGAATCAACAGGAGGAACAG 58.812 47.826 0.00 0.00 0.00 3.16
5100 5438 1.939934 GGCAAAAGCTTGGAAACCAAC 59.060 47.619 0.00 0.00 38.75 3.77
5157 5513 6.992063 AATACTCCTTGTATTCTGCACTTG 57.008 37.500 0.00 0.00 45.74 3.16
5173 5529 7.878127 TGCTGTATATAAAAGCAGGAATACTCC 59.122 37.037 14.46 0.00 41.83 3.85
5174 5530 8.833231 TGCTGTATATAAAAGCAGGAATACTC 57.167 34.615 14.46 0.00 41.83 2.59
5200 5556 6.913873 TGGTGAGTAAACAAACTAAGACAC 57.086 37.500 0.00 0.00 0.00 3.67
5206 5562 7.390996 TCACAACTTTGGTGAGTAAACAAACTA 59.609 33.333 0.00 0.00 40.16 2.24
5219 5575 5.335897 CCAGGAATATGTCACAACTTTGGTG 60.336 44.000 0.00 0.00 37.60 4.17


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

AutoCloner maintained by Alex Coulton.