Multiple sequence alignment - TraesCS2D01G021100

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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 TraesCS2D01G021100 chr2D 100.000 4454 0 0 1 4454 9855632 9860085 0.000000e+00 8226
1 TraesCS2D01G021100 chr2D 77.143 910 189 15 2552 3453 76752455 76751557 1.110000e-140 510
2 TraesCS2D01G021100 chr2A 92.690 3940 245 26 2 3922 9940330 9936415 0.000000e+00 5640
3 TraesCS2D01G021100 chr2A 83.956 455 46 14 271 712 9124090 9124530 1.150000e-110 411
4 TraesCS2D01G021100 chr2A 89.272 261 20 7 1 257 9123849 9124105 2.000000e-83 320
5 TraesCS2D01G021100 chr2B 94.346 3148 164 12 901 4043 13201680 13204818 0.000000e+00 4815
6 TraesCS2D01G021100 chr2B 92.331 2986 203 14 857 3836 13337872 13340837 0.000000e+00 4222
7 TraesCS2D01G021100 chr2B 93.326 2682 165 7 1166 3836 13388843 13391521 0.000000e+00 3949
8 TraesCS2D01G021100 chr2B 90.046 3034 215 40 40 3041 13357138 13360116 0.000000e+00 3849
9 TraesCS2D01G021100 chr2B 92.627 1275 93 1 2648 3922 13144730 13146003 0.000000e+00 1832
10 TraesCS2D01G021100 chr2B 83.824 1156 105 38 40 1168 13378454 13379554 0.000000e+00 1024
11 TraesCS2D01G021100 chr2B 84.036 877 64 33 2 858 13326961 13327781 0.000000e+00 774
12 TraesCS2D01G021100 chr2B 76.541 925 194 18 2539 3453 117992690 117991779 6.700000e-133 484
13 TraesCS2D01G021100 chr2B 92.834 307 17 4 4149 4454 13145996 13146298 1.470000e-119 440
14 TraesCS2D01G021100 chr2B 82.189 466 51 21 444 897 13197606 13198051 5.440000e-99 372
15 TraesCS2D01G021100 chr2B 97.159 176 4 1 4272 4446 13204997 13205172 3.370000e-76 296
16 TraesCS2D01G021100 chrUn 94.588 425 23 0 2464 2888 476519407 476519831 0.000000e+00 658
17 TraesCS2D01G021100 chrUn 93.182 396 27 0 1245 1640 479131598 479131993 2.310000e-162 582
18 TraesCS2D01G021100 chr3D 76.279 919 205 12 2516 3430 32586007 32586916 1.120000e-130 477


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 TraesCS2D01G021100 chr2D 9855632 9860085 4453 False 8226.000000 8226 100.000000 1 4454 1 chr2D.!!$F1 4453
1 TraesCS2D01G021100 chr2D 76751557 76752455 898 True 510.000000 510 77.143000 2552 3453 1 chr2D.!!$R1 901
2 TraesCS2D01G021100 chr2A 9936415 9940330 3915 True 5640.000000 5640 92.690000 2 3922 1 chr2A.!!$R1 3920
3 TraesCS2D01G021100 chr2A 9123849 9124530 681 False 365.500000 411 86.614000 1 712 2 chr2A.!!$F1 711
4 TraesCS2D01G021100 chr2B 13337872 13340837 2965 False 4222.000000 4222 92.331000 857 3836 1 chr2B.!!$F2 2979
5 TraesCS2D01G021100 chr2B 13388843 13391521 2678 False 3949.000000 3949 93.326000 1166 3836 1 chr2B.!!$F5 2670
6 TraesCS2D01G021100 chr2B 13357138 13360116 2978 False 3849.000000 3849 90.046000 40 3041 1 chr2B.!!$F3 3001
7 TraesCS2D01G021100 chr2B 13197606 13205172 7566 False 1827.666667 4815 91.231333 444 4446 3 chr2B.!!$F7 4002
8 TraesCS2D01G021100 chr2B 13144730 13146298 1568 False 1136.000000 1832 92.730500 2648 4454 2 chr2B.!!$F6 1806
9 TraesCS2D01G021100 chr2B 13378454 13379554 1100 False 1024.000000 1024 83.824000 40 1168 1 chr2B.!!$F4 1128
10 TraesCS2D01G021100 chr2B 13326961 13327781 820 False 774.000000 774 84.036000 2 858 1 chr2B.!!$F1 856
11 TraesCS2D01G021100 chr2B 117991779 117992690 911 True 484.000000 484 76.541000 2539 3453 1 chr2B.!!$R1 914
12 TraesCS2D01G021100 chr3D 32586007 32586916 909 False 477.000000 477 76.279000 2516 3430 1 chr3D.!!$F1 914

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
540 601 0.482446 TGGAGAAAACCCACCAGCAT 59.518 50.0 0.0 0.0 0.00 3.79 F
1623 5355 0.043334 ATCCAGCTCCCGGCCTATAT 59.957 55.0 0.0 0.0 43.05 0.86 F
2250 5988 0.460311 GCACTGCGTACTCCTATGGT 59.540 55.0 0.0 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 6083 0.252479 CACCTCTCCAGCAGCAAGAT 59.748 55.000 0.00 0.0 0.00 2.40 R
2472 6211 1.843851 GGGGGATGAGAACACCACATA 59.156 52.381 0.00 0.0 0.00 2.29 R
4076 7834 0.035317 TGAGCAGTGCTACACCAAGG 59.965 55.000 19.77 0.0 39.88 3.61 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
54 55 4.380867 GCTTAGCTGCCAAATGCTTTTCTA 60.381 41.667 0.00 0.00 42.00 2.10
71 72 4.689612 TTCTATGTTGCTCCCTGGATAC 57.310 45.455 0.00 0.00 0.00 2.24
145 148 8.134895 GGAGTGTTCAGTTGAATCACAATTTTA 58.865 33.333 19.72 0.00 40.76 1.52
194 201 2.030274 GGGGTGTGTGAAAAGTGTATGC 60.030 50.000 0.00 0.00 0.00 3.14
212 220 9.042008 AGTGTATGCTTATTTTTGTCCTATACG 57.958 33.333 0.00 0.00 0.00 3.06
257 300 4.251268 GTTGCGGTATTAACCTCTCACTT 58.749 43.478 0.00 0.00 44.35 3.16
258 301 4.546829 TGCGGTATTAACCTCTCACTTT 57.453 40.909 0.00 0.00 44.35 2.66
259 302 4.501071 TGCGGTATTAACCTCTCACTTTC 58.499 43.478 0.00 0.00 44.35 2.62
260 303 4.222145 TGCGGTATTAACCTCTCACTTTCT 59.778 41.667 0.00 0.00 44.35 2.52
261 304 4.804665 GCGGTATTAACCTCTCACTTTCTC 59.195 45.833 0.00 0.00 44.35 2.87
262 305 5.035443 CGGTATTAACCTCTCACTTTCTCG 58.965 45.833 0.00 0.00 44.35 4.04
263 306 4.804665 GGTATTAACCTCTCACTTTCTCGC 59.195 45.833 0.00 0.00 43.08 5.03
264 307 4.537135 ATTAACCTCTCACTTTCTCGCA 57.463 40.909 0.00 0.00 0.00 5.10
265 308 2.910688 AACCTCTCACTTTCTCGCAA 57.089 45.000 0.00 0.00 0.00 4.85
266 309 2.910688 ACCTCTCACTTTCTCGCAAA 57.089 45.000 0.00 0.00 0.00 3.68
267 310 3.194005 ACCTCTCACTTTCTCGCAAAA 57.806 42.857 0.00 0.00 0.00 2.44
268 311 3.541632 ACCTCTCACTTTCTCGCAAAAA 58.458 40.909 0.00 0.00 0.00 1.94
403 454 0.667792 GCCTCAACTGACCGTCACTC 60.668 60.000 0.00 0.00 0.00 3.51
471 527 4.143137 GGCGCATTTGTTTCCACTTAATTG 60.143 41.667 10.83 0.00 0.00 2.32
486 542 0.951558 AATTGGTTGCCGTGTGTCTC 59.048 50.000 0.00 0.00 0.00 3.36
540 601 0.482446 TGGAGAAAACCCACCAGCAT 59.518 50.000 0.00 0.00 0.00 3.79
542 603 1.547675 GGAGAAAACCCACCAGCATGA 60.548 52.381 0.00 0.00 39.69 3.07
564 625 9.143631 CATGATACAAAAAGCTTCCTAAAAAGG 57.856 33.333 0.00 0.00 0.00 3.11
689 788 6.867519 TTAACCTCTCACCATTATCTGTGA 57.132 37.500 0.00 0.00 39.08 3.58
792 894 1.469079 CCAAAATTTCCGGTCGCATCC 60.469 52.381 0.00 0.00 0.00 3.51
876 979 3.095738 CGTCCGTCAAAACTTGTTGAAC 58.904 45.455 0.00 0.00 39.18 3.18
1013 4743 3.683365 ACCCACCATGCTTCATTTTTC 57.317 42.857 0.00 0.00 0.00 2.29
1018 4748 4.632688 CCACCATGCTTCATTTTTCCATTC 59.367 41.667 0.00 0.00 0.00 2.67
1030 4760 6.429692 TCATTTTTCCATTCTCTTCGTGCTTA 59.570 34.615 0.00 0.00 0.00 3.09
1038 4768 5.592104 TTCTCTTCGTGCTTACCATATCA 57.408 39.130 0.00 0.00 0.00 2.15
1055 4787 3.692406 AGTTCCTCCGGTGGCGTC 61.692 66.667 18.03 9.97 0.00 5.19
1074 4806 0.815734 CCTCTTCTGCAGCAAATGGG 59.184 55.000 9.47 2.46 0.00 4.00
1110 4842 4.400961 GGCCAAGAGCTCAGCGGT 62.401 66.667 17.77 0.00 43.05 5.68
1207 4939 1.000993 AACACCACCTTGCCCAACA 59.999 52.632 0.00 0.00 0.00 3.33
1254 4986 2.638480 TCCCAAAGTTCACTCCTGTG 57.362 50.000 0.00 0.00 45.07 3.66
1263 4995 1.059098 TCACTCCTGTGTGGATTGCT 58.941 50.000 0.08 0.00 45.16 3.91
1287 5019 4.892433 ACAGAGAGAAACCAATCACTGAG 58.108 43.478 6.63 0.00 0.00 3.35
1311 5043 2.887152 CAAGTTTAGACTGCCCAAGCTT 59.113 45.455 0.00 0.00 40.80 3.74
1466 5198 5.872617 CAGACGATGGTAACCTTGTCATAAA 59.127 40.000 6.25 0.00 45.28 1.40
1482 5214 0.388907 TAAAAGACGCCTCGAACCCG 60.389 55.000 0.00 0.00 37.07 5.28
1491 5223 1.378882 CCTCGAACCCGTCCATCGTA 61.379 60.000 0.00 0.00 37.79 3.43
1603 5335 8.376942 GTCTTGTTTCGAAGAAGAATCTGATAC 58.623 37.037 18.26 2.87 45.90 2.24
1614 5346 3.582208 AGAATCTGATACATCCAGCTCCC 59.418 47.826 0.00 0.00 0.00 4.30
1623 5355 0.043334 ATCCAGCTCCCGGCCTATAT 59.957 55.000 0.00 0.00 43.05 0.86
1633 5365 1.278985 CCGGCCTATATTGCATGGAGA 59.721 52.381 0.00 0.00 0.00 3.71
1640 5372 5.130145 GCCTATATTGCATGGAGATAGACCT 59.870 44.000 15.54 0.00 0.00 3.85
1668 5400 7.504238 ACTGGTGATCCACAATACTTTGTTAAA 59.496 33.333 0.00 0.00 43.57 1.52
1688 5420 7.816995 TGTTAAACTTTGTAATTCATCCATGGC 59.183 33.333 6.96 0.00 0.00 4.40
1713 5451 3.330192 TCCACGGGGGAATGGATG 58.670 61.111 2.42 0.00 44.80 3.51
1770 5508 3.821033 GCAGTAACTTTCTCCACACCAAT 59.179 43.478 0.00 0.00 0.00 3.16
1785 5523 4.853196 CACACCAATTTCATCGACAATGAC 59.147 41.667 0.00 0.00 44.14 3.06
1807 5545 5.068636 ACGAAGAGGAGTACTTCACTTACA 58.931 41.667 13.21 0.00 42.39 2.41
1833 5571 2.614057 GACGGATCCAACAATGATCACC 59.386 50.000 13.41 0.00 40.32 4.02
1884 5622 3.243975 CCAAGCAACTTCTTTGGCTTGAT 60.244 43.478 22.51 0.00 44.10 2.57
1977 5715 2.183478 TCACGGTCTGCAATGACAAT 57.817 45.000 8.22 0.00 38.61 2.71
2112 5850 5.385509 ACAGCAACAAAAGTAACACAACT 57.614 34.783 0.00 0.00 0.00 3.16
2116 5854 5.047660 AGCAACAAAAGTAACACAACTGGAA 60.048 36.000 0.00 0.00 0.00 3.53
2168 5906 8.534333 AGTGTTAGATTACCATATTATGCACG 57.466 34.615 0.00 0.00 0.00 5.34
2172 5910 9.084164 GTTAGATTACCATATTATGCACGTAGG 57.916 37.037 0.00 0.00 0.00 3.18
2250 5988 0.460311 GCACTGCGTACTCCTATGGT 59.540 55.000 0.00 0.00 0.00 3.55
2345 6083 2.642807 ACGGGGAGATTCTTTTCCTTCA 59.357 45.455 0.00 0.00 33.85 3.02
2369 6107 1.860484 GCTGCTGGAGAGGTGCAAAC 61.860 60.000 0.00 0.00 36.22 2.93
2414 6152 7.229506 AGGAAATAAAAGAATGATCATCGGTCC 59.770 37.037 9.06 6.18 0.00 4.46
2472 6211 4.750941 TGATGATTTGGAAGGGGAAAAGT 58.249 39.130 0.00 0.00 0.00 2.66
2679 6418 2.222027 CGCCAAGGAGAGAAACAGTTT 58.778 47.619 0.00 0.00 0.00 2.66
2874 6613 0.798009 GAATTGCCATCGGTGTTGCG 60.798 55.000 0.00 0.00 0.00 4.85
3181 6920 5.769662 TCACCTCAAGAATGTACAAGCAATT 59.230 36.000 0.00 0.00 0.00 2.32
3472 7211 9.888878 CAACTTGAATATAATCCATGTAAGCAG 57.111 33.333 0.00 0.00 0.00 4.24
3553 7292 9.778993 CAAACTTTTCCATAGTGATTGATACTG 57.221 33.333 0.00 0.00 0.00 2.74
3555 7294 7.112122 ACTTTTCCATAGTGATTGATACTGCA 58.888 34.615 0.00 0.00 0.00 4.41
3559 7298 8.523915 TTCCATAGTGATTGATACTGCAAAAT 57.476 30.769 0.00 0.00 0.00 1.82
3572 7311 8.453320 TGATACTGCAAAATACATGTCTTGAAG 58.547 33.333 16.41 16.41 31.69 3.02
3609 7352 2.737679 CGTACAAACTAGTAGGGCAGCC 60.738 54.545 1.26 1.26 0.00 4.85
3610 7353 1.358152 ACAAACTAGTAGGGCAGCCA 58.642 50.000 15.19 0.00 0.00 4.75
3623 7366 2.094675 GGCAGCCAAATGTATCTGTGT 58.905 47.619 6.55 0.00 0.00 3.72
3624 7367 3.278574 GGCAGCCAAATGTATCTGTGTA 58.721 45.455 6.55 0.00 0.00 2.90
3625 7368 3.313526 GGCAGCCAAATGTATCTGTGTAG 59.686 47.826 6.55 0.00 0.00 2.74
3648 7393 3.066291 AGGTTTGTCATGTATCGCCAA 57.934 42.857 0.00 0.00 0.00 4.52
3659 7404 5.238432 TCATGTATCGCCAATTGTATCAACC 59.762 40.000 4.43 0.00 0.00 3.77
3750 7496 2.178912 TTTCCATGACGGGTGTTCTC 57.821 50.000 0.00 0.00 34.36 2.87
3888 7635 2.234908 GCCGCTCTATCCAAGTATCCAT 59.765 50.000 0.00 0.00 0.00 3.41
3925 7672 1.376466 CACCAAGGACCCTCAGTGG 59.624 63.158 9.39 7.00 35.39 4.00
3942 7689 3.504906 CAGTGGCAGACATCAGAAAATGT 59.495 43.478 0.00 0.00 42.49 2.71
3976 7723 7.979537 ACTAAAGGAAACAAATTCACAGAAACC 59.020 33.333 0.00 0.00 39.98 3.27
3987 7734 6.976934 ATTCACAGAAACCTTATTTGTGGT 57.023 33.333 3.44 0.00 39.56 4.16
4029 7776 4.357279 GGAGCCTTGGCAGCTGGT 62.357 66.667 17.12 0.00 41.75 4.00
4030 7777 3.060615 GAGCCTTGGCAGCTGGTG 61.061 66.667 17.12 1.76 41.75 4.17
4033 7780 2.113774 CCTTGGCAGCTGGTGACA 59.886 61.111 17.12 12.07 45.30 3.58
4036 7783 4.624364 TGGCAGCTGGTGACACCG 62.624 66.667 19.67 14.77 40.35 4.94
4043 7790 4.293648 TGGTGACACCGTCTGCCG 62.294 66.667 19.67 0.00 42.58 5.69
4052 7799 2.048597 CGTCTGCCGGCTGTGTTA 60.049 61.111 29.70 8.29 0.00 2.41
4053 7800 2.380410 CGTCTGCCGGCTGTGTTAC 61.380 63.158 29.70 19.08 0.00 2.50
4055 7802 0.673644 GTCTGCCGGCTGTGTTACAT 60.674 55.000 29.70 0.00 0.00 2.29
4060 7818 1.808411 CCGGCTGTGTTACATTGTCT 58.192 50.000 0.00 0.00 0.00 3.41
4063 7821 2.344441 CGGCTGTGTTACATTGTCTACG 59.656 50.000 0.00 0.00 0.00 3.51
4076 7834 0.456628 GTCTACGCTCTGAAGGGGTC 59.543 60.000 0.00 0.00 39.68 4.46
4078 7836 0.684805 CTACGCTCTGAAGGGGTCCT 60.685 60.000 0.00 0.00 39.68 3.85
4080 7838 1.078848 CGCTCTGAAGGGGTCCTTG 60.079 63.158 3.67 0.00 44.82 3.61
4081 7839 1.301293 GCTCTGAAGGGGTCCTTGG 59.699 63.158 3.67 0.00 44.82 3.61
4082 7840 1.492993 GCTCTGAAGGGGTCCTTGGT 61.493 60.000 3.67 0.00 44.82 3.67
4083 7841 0.326264 CTCTGAAGGGGTCCTTGGTG 59.674 60.000 3.67 0.00 44.82 4.17
4084 7842 0.401395 TCTGAAGGGGTCCTTGGTGT 60.401 55.000 3.67 0.00 44.82 4.16
4085 7843 1.132657 TCTGAAGGGGTCCTTGGTGTA 60.133 52.381 3.67 0.00 44.82 2.90
4086 7844 1.279271 CTGAAGGGGTCCTTGGTGTAG 59.721 57.143 3.67 0.00 44.82 2.74
4087 7845 0.035343 GAAGGGGTCCTTGGTGTAGC 60.035 60.000 3.67 0.00 44.82 3.58
4088 7846 0.770557 AAGGGGTCCTTGGTGTAGCA 60.771 55.000 0.00 0.00 42.96 3.49
4089 7847 1.002502 GGGGTCCTTGGTGTAGCAC 60.003 63.158 0.00 0.00 0.00 4.40
4090 7848 1.489560 GGGGTCCTTGGTGTAGCACT 61.490 60.000 0.00 0.00 34.40 4.40
4091 7849 0.321653 GGGTCCTTGGTGTAGCACTG 60.322 60.000 0.00 0.00 34.40 3.66
4092 7850 0.955919 GGTCCTTGGTGTAGCACTGC 60.956 60.000 0.00 0.00 34.40 4.40
4093 7851 0.035458 GTCCTTGGTGTAGCACTGCT 59.965 55.000 8.95 8.95 43.41 4.24
4094 7852 0.321671 TCCTTGGTGTAGCACTGCTC 59.678 55.000 6.86 0.26 40.44 4.26
4095 7853 0.035317 CCTTGGTGTAGCACTGCTCA 59.965 55.000 6.86 3.03 40.44 4.26
4096 7854 1.151668 CTTGGTGTAGCACTGCTCAC 58.848 55.000 6.86 14.39 40.44 3.51
4097 7855 0.250295 TTGGTGTAGCACTGCTCACC 60.250 55.000 28.34 28.34 46.58 4.02
4098 7856 1.738099 GGTGTAGCACTGCTCACCG 60.738 63.158 24.61 0.00 42.22 4.94
4099 7857 1.738099 GTGTAGCACTGCTCACCGG 60.738 63.158 6.86 0.00 40.44 5.28
4100 7858 1.906333 TGTAGCACTGCTCACCGGA 60.906 57.895 9.46 0.00 40.44 5.14
4101 7859 1.446272 GTAGCACTGCTCACCGGAC 60.446 63.158 9.46 0.00 40.44 4.79
4102 7860 2.646175 TAGCACTGCTCACCGGACC 61.646 63.158 9.46 0.00 40.44 4.46
4128 7886 1.207329 ACGGAGGTGATAAACAGGCTC 59.793 52.381 0.00 0.00 0.00 4.70
4153 7911 5.970317 TCTTCGGTTCTGTAATAGACACA 57.030 39.130 0.00 0.00 34.43 3.72
4155 7913 5.475909 TCTTCGGTTCTGTAATAGACACACT 59.524 40.000 0.00 0.00 34.43 3.55
4186 7945 6.148150 GTGTTTTGAAATGAATGGTGCATCAT 59.852 34.615 6.64 6.64 0.00 2.45
4200 7959 5.589855 TGGTGCATCATTGTTATACTTCCTG 59.410 40.000 0.00 0.00 0.00 3.86
4225 7984 6.803807 GTGGAAACATTGTAAAGCTGAATCTC 59.196 38.462 0.00 0.00 46.14 2.75
4243 8002 7.116736 TGAATCTCTGGTCTATATGCCGTATA 58.883 38.462 0.00 0.00 0.00 1.47
4270 8029 3.127589 AGGCGTTGTAAATTTTGTTGGC 58.872 40.909 0.00 0.00 0.00 4.52
4426 8185 3.091545 TCCTCAAAGCATGTTCAATCCC 58.908 45.455 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.308570 TGTTGTATCCAGGGAGCAACAT 59.691 45.455 24.65 0.94 0.00 2.71
71 72 8.649841 CAATGTTTTAGATTTGCCACTATGTTG 58.350 33.333 0.00 0.00 0.00 3.33
105 106 8.492415 ACTGAACACTCCAGCCTAAATATATA 57.508 34.615 0.00 0.00 35.14 0.86
171 176 1.358759 CACTTTTCACACACCCCGC 59.641 57.895 0.00 0.00 0.00 6.13
172 177 1.956297 TACACTTTTCACACACCCCG 58.044 50.000 0.00 0.00 0.00 5.73
220 228 8.896320 AATACCGCAACAAATATAGTACATCA 57.104 30.769 0.00 0.00 0.00 3.07
240 253 4.804665 GCGAGAAAGTGAGAGGTTAATACC 59.195 45.833 0.00 0.00 45.39 2.73
265 308 9.990868 ATAATGGGTGAGAGGTTAATACTTTTT 57.009 29.630 0.00 0.00 0.00 1.94
266 309 9.990868 AATAATGGGTGAGAGGTTAATACTTTT 57.009 29.630 0.00 0.00 0.00 2.27
267 310 9.990868 AAATAATGGGTGAGAGGTTAATACTTT 57.009 29.630 0.00 0.00 0.00 2.66
268 311 9.408648 CAAATAATGGGTGAGAGGTTAATACTT 57.591 33.333 0.00 0.00 0.00 2.24
269 312 8.557450 ACAAATAATGGGTGAGAGGTTAATACT 58.443 33.333 0.00 0.00 0.00 2.12
270 313 8.747538 ACAAATAATGGGTGAGAGGTTAATAC 57.252 34.615 0.00 0.00 0.00 1.89
272 315 9.185680 GTAACAAATAATGGGTGAGAGGTTAAT 57.814 33.333 0.00 0.00 0.00 1.40
273 316 8.164733 TGTAACAAATAATGGGTGAGAGGTTAA 58.835 33.333 0.00 0.00 0.00 2.01
274 317 7.691213 TGTAACAAATAATGGGTGAGAGGTTA 58.309 34.615 0.00 0.00 0.00 2.85
275 318 6.548321 TGTAACAAATAATGGGTGAGAGGTT 58.452 36.000 0.00 0.00 0.00 3.50
276 319 6.134535 TGTAACAAATAATGGGTGAGAGGT 57.865 37.500 0.00 0.00 0.00 3.85
277 320 5.066505 GCTGTAACAAATAATGGGTGAGAGG 59.933 44.000 0.00 0.00 0.00 3.69
278 321 5.647658 TGCTGTAACAAATAATGGGTGAGAG 59.352 40.000 0.00 0.00 0.00 3.20
279 322 5.565509 TGCTGTAACAAATAATGGGTGAGA 58.434 37.500 0.00 0.00 0.00 3.27
280 323 5.895636 TGCTGTAACAAATAATGGGTGAG 57.104 39.130 0.00 0.00 0.00 3.51
281 324 6.040955 TGTTTGCTGTAACAAATAATGGGTGA 59.959 34.615 0.00 0.00 41.31 4.02
282 325 6.219473 TGTTTGCTGTAACAAATAATGGGTG 58.781 36.000 0.00 0.00 41.31 4.61
283 326 6.412362 TGTTTGCTGTAACAAATAATGGGT 57.588 33.333 0.00 0.00 41.31 4.51
328 372 3.685139 AGGAAACAGTGATCGTGATGT 57.315 42.857 0.00 0.00 0.00 3.06
471 527 1.961277 CCTGAGACACACGGCAACC 60.961 63.158 0.00 0.00 0.00 3.77
540 601 8.245195 ACCTTTTTAGGAAGCTTTTTGTATCA 57.755 30.769 0.00 0.00 0.00 2.15
542 603 7.931407 CCAACCTTTTTAGGAAGCTTTTTGTAT 59.069 33.333 0.00 0.00 0.00 2.29
564 625 8.133627 CACAATATTCCAGAATCAAGATCCAAC 58.866 37.037 0.00 0.00 32.50 3.77
718 817 3.486841 GCATGTTGTGTGCACACTAAAAG 59.513 43.478 40.79 29.59 46.55 2.27
792 894 6.234177 AGTACAGAAAGGGAATTCTCAACTG 58.766 40.000 18.25 18.25 37.56 3.16
990 4718 2.307496 AATGAAGCATGGTGGGTTGA 57.693 45.000 0.00 0.00 0.00 3.18
1013 4743 2.972625 TGGTAAGCACGAAGAGAATGG 58.027 47.619 0.00 0.00 0.00 3.16
1018 4748 4.938080 ACTGATATGGTAAGCACGAAGAG 58.062 43.478 0.00 0.00 0.00 2.85
1055 4787 0.815734 CCCATTTGCTGCAGAAGAGG 59.184 55.000 20.43 10.03 0.00 3.69
1074 4806 1.654317 CTTCTGTCAGGATGCTGCTC 58.346 55.000 9.76 5.88 34.76 4.26
1110 4842 0.401356 TTGAGATGAGCCTGTTGCCA 59.599 50.000 0.00 0.00 42.71 4.92
1207 4939 7.924358 TGTTGAACCATATACCTACATACCT 57.076 36.000 0.00 0.00 0.00 3.08
1254 4986 4.393371 GGTTTCTCTCTGTTAGCAATCCAC 59.607 45.833 0.00 0.00 0.00 4.02
1263 4995 6.419484 TCAGTGATTGGTTTCTCTCTGTTA 57.581 37.500 0.00 0.00 35.52 2.41
1287 5019 0.251165 TGGGCAGTCTAAACTTGGGC 60.251 55.000 0.00 0.00 31.71 5.36
1311 5043 4.662179 AGATTGCCATCCCTTGAGATTCTA 59.338 41.667 0.00 0.00 0.00 2.10
1372 5104 4.235079 TGGCTGCTATTATTTGACTGGT 57.765 40.909 0.00 0.00 0.00 4.00
1466 5198 3.278592 GACGGGTTCGAGGCGTCTT 62.279 63.158 4.69 0.00 40.11 3.01
1491 5223 1.005097 TGATCAAAGCTCTGCCACCAT 59.995 47.619 0.00 0.00 0.00 3.55
1603 5335 0.904865 TATAGGCCGGGAGCTGGATG 60.905 60.000 2.18 0.00 43.05 3.51
1614 5346 2.768253 TCTCCATGCAATATAGGCCG 57.232 50.000 0.00 0.00 0.00 6.13
1623 5355 3.133542 CAGTGAGGTCTATCTCCATGCAA 59.866 47.826 0.00 0.00 33.04 4.08
1668 5400 4.016444 ACGCCATGGATGAATTACAAAGT 58.984 39.130 18.40 0.00 0.00 2.66
1688 5420 1.252904 TTCCCCCGTGGAGAAGTACG 61.253 60.000 0.00 0.00 46.24 3.67
1713 5451 2.560981 CACCAAATTGAAGTACCACCCC 59.439 50.000 0.00 0.00 0.00 4.95
1770 5508 3.926527 CCTCTTCGTCATTGTCGATGAAA 59.073 43.478 17.53 0.00 45.96 2.69
1785 5523 5.392286 GTGTAAGTGAAGTACTCCTCTTCG 58.608 45.833 0.00 0.00 42.68 3.79
1807 5545 1.559065 ATTGTTGGATCCGTCGGGGT 61.559 55.000 12.29 0.00 37.00 4.95
1833 5571 2.094286 AGAGACGTCAAGGAAGCAGATG 60.094 50.000 19.50 0.00 0.00 2.90
1884 5622 2.825532 GGTTTCCCAATCTTGCAAGCTA 59.174 45.455 21.99 5.89 0.00 3.32
1977 5715 4.027572 GCAGTTACACAAAGAAAGTGCA 57.972 40.909 8.75 0.00 44.95 4.57
1984 5722 4.218200 CCCATTCATGCAGTTACACAAAGA 59.782 41.667 0.00 0.00 0.00 2.52
1986 5724 3.894427 ACCCATTCATGCAGTTACACAAA 59.106 39.130 0.00 0.00 0.00 2.83
2168 5906 5.355350 CCACTCTCAATTGTTTCCATCCTAC 59.645 44.000 5.13 0.00 0.00 3.18
2172 5910 4.761739 TGTCCACTCTCAATTGTTTCCATC 59.238 41.667 5.13 0.00 0.00 3.51
2250 5988 3.133003 GCCAGATAGAACAGCCACTCTTA 59.867 47.826 0.00 0.00 0.00 2.10
2328 6066 5.651576 AGCAAGATGAAGGAAAAGAATCTCC 59.348 40.000 0.00 0.00 0.00 3.71
2345 6083 0.252479 CACCTCTCCAGCAGCAAGAT 59.748 55.000 0.00 0.00 0.00 2.40
2369 6107 5.799827 TCCTTTTATGTTGTTTCCCCAAG 57.200 39.130 0.00 0.00 0.00 3.61
2472 6211 1.843851 GGGGGATGAGAACACCACATA 59.156 52.381 0.00 0.00 0.00 2.29
2874 6613 4.943705 TCATGCAAGTAGGACAATCCTTTC 59.056 41.667 1.99 0.00 46.91 2.62
3181 6920 8.245491 CACAGGAAAATAAACATCATGATCACA 58.755 33.333 4.86 0.00 0.00 3.58
3405 7144 1.973138 CTTGAAGCAATCTTGGCACG 58.027 50.000 0.00 0.00 31.48 5.34
3470 7209 4.038402 ACCCTGCTGAAATTTGAACTTCTG 59.962 41.667 0.00 0.00 0.00 3.02
3472 7211 4.590850 ACCCTGCTGAAATTTGAACTTC 57.409 40.909 0.00 0.00 0.00 3.01
3529 7268 7.611467 TGCAGTATCAATCACTATGGAAAAGTT 59.389 33.333 0.00 0.00 0.00 2.66
3553 7292 9.118236 GACTAAACTTCAAGACATGTATTTTGC 57.882 33.333 2.21 0.00 0.00 3.68
3600 7343 2.509548 ACAGATACATTTGGCTGCCCTA 59.490 45.455 17.53 4.04 31.74 3.53
3609 7352 7.334421 ACAAACCTAGCTACACAGATACATTTG 59.666 37.037 0.00 0.00 33.07 2.32
3610 7353 7.394816 ACAAACCTAGCTACACAGATACATTT 58.605 34.615 0.00 0.00 0.00 2.32
3623 7366 4.500887 GGCGATACATGACAAACCTAGCTA 60.501 45.833 0.00 0.00 0.00 3.32
3624 7367 3.458189 GCGATACATGACAAACCTAGCT 58.542 45.455 0.00 0.00 0.00 3.32
3625 7368 2.544267 GGCGATACATGACAAACCTAGC 59.456 50.000 0.00 0.00 0.00 3.42
3648 7393 7.725251 ACAAACATTTGACAGGTTGATACAAT 58.275 30.769 11.24 0.00 40.55 2.71
3659 7404 5.261209 TGGGAGAAACAAACATTTGACAG 57.739 39.130 11.24 0.00 40.55 3.51
3888 7635 1.233919 GGCCGTTAAACACCGGTTTA 58.766 50.000 2.97 0.00 45.12 2.01
3987 7734 3.362706 CAGTAGCCTAGACAGGTAACCA 58.637 50.000 0.00 0.00 44.68 3.67
4002 7749 3.787001 AAGGCTCCGGGCAGTAGC 61.787 66.667 15.49 10.06 44.01 3.58
4017 7764 2.263741 GGTGTCACCAGCTGCCAAG 61.264 63.158 17.59 0.00 38.42 3.61
4026 7773 4.293648 CGGCAGACGGTGTCACCA 62.294 66.667 21.91 0.00 38.47 4.17
4036 7783 0.673644 ATGTAACACAGCCGGCAGAC 60.674 55.000 31.54 15.27 0.00 3.51
4043 7790 2.093783 GCGTAGACAATGTAACACAGCC 59.906 50.000 0.00 0.00 0.00 4.85
4044 7791 2.993899 AGCGTAGACAATGTAACACAGC 59.006 45.455 0.00 0.00 0.00 4.40
4045 7792 4.324669 CAGAGCGTAGACAATGTAACACAG 59.675 45.833 0.00 0.00 0.00 3.66
4046 7793 4.022676 TCAGAGCGTAGACAATGTAACACA 60.023 41.667 0.00 0.00 0.00 3.72
4047 7794 4.482386 TCAGAGCGTAGACAATGTAACAC 58.518 43.478 0.00 0.00 0.00 3.32
4048 7795 4.776795 TCAGAGCGTAGACAATGTAACA 57.223 40.909 0.00 0.00 0.00 2.41
4049 7796 4.563184 CCTTCAGAGCGTAGACAATGTAAC 59.437 45.833 0.00 0.00 0.00 2.50
4050 7797 4.381612 CCCTTCAGAGCGTAGACAATGTAA 60.382 45.833 0.00 0.00 0.00 2.41
4051 7798 3.130516 CCCTTCAGAGCGTAGACAATGTA 59.869 47.826 0.00 0.00 0.00 2.29
4052 7799 2.093973 CCCTTCAGAGCGTAGACAATGT 60.094 50.000 0.00 0.00 0.00 2.71
4053 7800 2.544685 CCCTTCAGAGCGTAGACAATG 58.455 52.381 0.00 0.00 0.00 2.82
4055 7802 0.895530 CCCCTTCAGAGCGTAGACAA 59.104 55.000 0.00 0.00 0.00 3.18
4060 7818 0.252103 AAGGACCCCTTCAGAGCGTA 60.252 55.000 0.00 0.00 40.17 4.42
4063 7821 1.301293 CCAAGGACCCCTTCAGAGC 59.699 63.158 0.00 0.00 42.67 4.09
4076 7834 0.035317 TGAGCAGTGCTACACCAAGG 59.965 55.000 19.77 0.00 39.88 3.61
4078 7836 0.250295 GGTGAGCAGTGCTACACCAA 60.250 55.000 36.24 15.04 46.15 3.67
4079 7837 1.371183 GGTGAGCAGTGCTACACCA 59.629 57.895 36.24 23.47 46.15 4.17
4080 7838 1.738099 CGGTGAGCAGTGCTACACC 60.738 63.158 34.02 34.02 44.88 4.16
4081 7839 1.738099 CCGGTGAGCAGTGCTACAC 60.738 63.158 26.42 26.42 39.88 2.90
4082 7840 1.906333 TCCGGTGAGCAGTGCTACA 60.906 57.895 19.77 14.84 39.88 2.74
4083 7841 1.446272 GTCCGGTGAGCAGTGCTAC 60.446 63.158 19.77 15.66 39.88 3.58
4084 7842 2.646175 GGTCCGGTGAGCAGTGCTA 61.646 63.158 19.77 3.80 39.88 3.49
4085 7843 4.008933 GGTCCGGTGAGCAGTGCT 62.009 66.667 19.86 19.86 43.88 4.40
4087 7845 4.742201 CCGGTCCGGTGAGCAGTG 62.742 72.222 23.02 0.00 42.73 3.66
4092 7850 3.834799 GTAGCCCGGTCCGGTGAG 61.835 72.222 28.39 14.72 46.80 3.51
4102 7860 0.748450 TTTATCACCTCCGTAGCCCG 59.252 55.000 0.00 0.00 0.00 6.13
4103 7861 1.483415 TGTTTATCACCTCCGTAGCCC 59.517 52.381 0.00 0.00 0.00 5.19
4104 7862 2.483188 CCTGTTTATCACCTCCGTAGCC 60.483 54.545 0.00 0.00 0.00 3.93
4105 7863 2.822764 CCTGTTTATCACCTCCGTAGC 58.177 52.381 0.00 0.00 0.00 3.58
4106 7864 2.431057 AGCCTGTTTATCACCTCCGTAG 59.569 50.000 0.00 0.00 0.00 3.51
4107 7865 2.429610 GAGCCTGTTTATCACCTCCGTA 59.570 50.000 0.00 0.00 0.00 4.02
4108 7866 1.207329 GAGCCTGTTTATCACCTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
4109 7867 1.482593 AGAGCCTGTTTATCACCTCCG 59.517 52.381 0.00 0.00 0.00 4.63
4110 7868 3.636153 AAGAGCCTGTTTATCACCTCC 57.364 47.619 0.00 0.00 0.00 4.30
4128 7886 6.866770 TGTGTCTATTACAGAACCGAAGAAAG 59.133 38.462 0.00 0.00 39.29 2.62
4153 7911 6.702723 CCATTCATTTCAAAACACATGTGAGT 59.297 34.615 31.94 16.13 0.00 3.41
4155 7913 6.479331 CACCATTCATTTCAAAACACATGTGA 59.521 34.615 31.94 8.27 0.00 3.58
4169 7927 8.698210 AGTATAACAATGATGCACCATTCATTT 58.302 29.630 2.32 0.28 34.77 2.32
4186 7945 7.504238 ACAATGTTTCCACAGGAAGTATAACAA 59.496 33.333 4.83 0.00 43.06 2.83
4200 7959 6.681777 AGATTCAGCTTTACAATGTTTCCAC 58.318 36.000 0.00 0.00 0.00 4.02
4225 7984 4.640647 TCTGCTATACGGCATATAGACCAG 59.359 45.833 11.55 9.59 43.98 4.00
4243 8002 4.202111 ACAAAATTTACAACGCCTTCTGCT 60.202 37.500 0.00 0.00 38.05 4.24
4347 8106 3.304257 CGGAATAAATCATGGTGCAGAGC 60.304 47.826 0.00 0.00 0.00 4.09
4426 8185 3.316308 AGTTTTGTTTAGCTGTGCTCCAG 59.684 43.478 0.00 0.20 44.53 3.86


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

AutoCloner maintained by Alex Coulton.