Multiple sequence alignment - TraesCS2B01G358900

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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 TraesCS2B01G358900 chr2B 100.000 5087 0 0 1 5087 512302545 512307631 0.000000e+00 9395.0
1 TraesCS2B01G358900 chr2B 92.283 2475 112 35 982 3413 505009504 505007066 0.000000e+00 3439.0
2 TraesCS2B01G358900 chr2B 98.454 841 11 2 1 840 680579095 680579934 0.000000e+00 1480.0
3 TraesCS2B01G358900 chr2B 97.635 761 14 2 3410 4167 505006878 505006119 0.000000e+00 1303.0
4 TraesCS2B01G358900 chr2B 92.603 365 23 3 4231 4592 505006114 505005751 5.840000e-144 521.0
5 TraesCS2B01G358900 chr2B 86.082 388 39 8 1895 2272 166210752 166210370 2.210000e-108 403.0
6 TraesCS2B01G358900 chr2B 85.196 358 34 10 4732 5087 505005601 505005261 2.910000e-92 350.0
7 TraesCS2B01G358900 chr2B 91.406 128 9 2 4591 4716 505005713 505005586 1.880000e-39 174.0
8 TraesCS2B01G358900 chr2B 88.158 76 5 4 4166 4239 538631092 538631019 2.520000e-13 87.9
9 TraesCS2B01G358900 chr2A 92.704 2467 103 32 989 3413 559606453 559608884 0.000000e+00 3487.0
10 TraesCS2B01G358900 chr2A 96.966 758 21 1 3410 4167 559609071 559609826 0.000000e+00 1271.0
11 TraesCS2B01G358900 chr2A 91.886 875 37 13 4231 5086 559609831 559610690 0.000000e+00 1192.0
12 TraesCS2B01G358900 chr2A 97.500 40 1 0 899 938 559606355 559606394 9.140000e-08 69.4
13 TraesCS2B01G358900 chr2D 94.021 1957 87 16 1480 3413 427972436 427970487 0.000000e+00 2939.0
14 TraesCS2B01G358900 chr2D 96.970 759 21 2 3410 4167 427970299 427969542 0.000000e+00 1273.0
15 TraesCS2B01G358900 chr2D 94.109 645 8 4 840 1482 427974519 427973903 0.000000e+00 953.0
16 TraesCS2B01G358900 chr2D 91.713 362 26 3 4231 4592 427969537 427969180 2.730000e-137 499.0
17 TraesCS2B01G358900 chr2D 89.589 365 28 3 4732 5087 427969007 427968644 6.000000e-124 455.0
18 TraesCS2B01G358900 chr2D 85.825 388 39 9 1895 2272 628284495 628284876 1.030000e-106 398.0
19 TraesCS2B01G358900 chr2D 91.406 128 8 2 4591 4715 427969120 427968993 6.770000e-39 172.0
20 TraesCS2B01G358900 chr2D 91.071 56 5 0 3042 3097 93090267 93090212 5.460000e-10 76.8
21 TraesCS2B01G358900 chr7A 99.049 841 7 1 1 840 24594812 24593972 0.000000e+00 1507.0
22 TraesCS2B01G358900 chr7A 98.335 841 11 2 1 840 256007584 256006746 0.000000e+00 1472.0
23 TraesCS2B01G358900 chr7A 79.208 303 63 0 3767 4069 41449777 41450079 1.430000e-50 211.0
24 TraesCS2B01G358900 chr7A 95.833 48 2 0 2917 2964 271734848 271734895 1.520000e-10 78.7
25 TraesCS2B01G358900 chr3B 98.930 841 6 3 1 840 814366727 814365889 0.000000e+00 1500.0
26 TraesCS2B01G358900 chr3B 87.037 54 3 3 2377 2426 167723997 167723944 1.980000e-04 58.4
27 TraesCS2B01G358900 chr5B 98.692 841 9 2 1 840 580489722 580488883 0.000000e+00 1491.0
28 TraesCS2B01G358900 chr5B 98.335 841 11 3 1 840 415793240 415792402 0.000000e+00 1472.0
29 TraesCS2B01G358900 chr5B 91.304 69 6 0 4166 4234 283027575 283027507 1.510000e-15 95.3
30 TraesCS2B01G358900 chr5B 92.537 67 4 1 2911 2976 347698841 347698775 1.510000e-15 95.3
31 TraesCS2B01G358900 chr5B 91.667 48 4 0 3047 3094 62145099 62145146 3.290000e-07 67.6
32 TraesCS2B01G358900 chr5B 90.196 51 5 0 3047 3097 62175020 62174970 3.290000e-07 67.6
33 TraesCS2B01G358900 chr4B 98.692 841 10 1 1 840 115079307 115078467 0.000000e+00 1491.0
34 TraesCS2B01G358900 chr4B 91.176 68 6 0 4166 4233 171114570 171114637 5.420000e-15 93.5
35 TraesCS2B01G358900 chr4B 92.308 39 3 0 3287 3325 387105074 387105036 7.120000e-04 56.5
36 TraesCS2B01G358900 chr6B 98.573 841 10 2 1 840 715712229 715713068 0.000000e+00 1485.0
37 TraesCS2B01G358900 chr6B 84.091 88 10 4 4166 4250 574464749 574464835 1.170000e-11 82.4
38 TraesCS2B01G358900 chr1B 98.573 841 10 2 1 840 543481439 543482278 0.000000e+00 1485.0
39 TraesCS2B01G358900 chr1B 92.537 67 5 0 4166 4232 15438597 15438531 4.190000e-16 97.1
40 TraesCS2B01G358900 chr1B 82.353 68 12 0 3257 3324 56831660 56831593 5.500000e-05 60.2
41 TraesCS2B01G358900 chr1D 86.082 388 38 9 1895 2272 394177727 394178108 2.210000e-108 403.0
42 TraesCS2B01G358900 chr1D 82.090 67 11 1 3261 3326 4280036 4280102 7.120000e-04 56.5
43 TraesCS2B01G358900 chrUn 85.825 388 39 9 1895 2272 405771740 405771359 1.030000e-106 398.0
44 TraesCS2B01G358900 chr1A 85.825 388 39 9 1895 2272 554466211 554465830 1.030000e-106 398.0
45 TraesCS2B01G358900 chr1A 95.455 44 2 0 3287 3330 344027489 344027532 2.540000e-08 71.3
46 TraesCS2B01G358900 chr5A 85.309 388 40 10 1895 2272 684324426 684324806 7.990000e-103 385.0
47 TraesCS2B01G358900 chr5A 89.474 57 6 0 3036 3092 395055964 395056020 7.060000e-09 73.1
48 TraesCS2B01G358900 chr3A 87.347 245 25 3 2725 2964 456444391 456444634 5.020000e-70 276.0
49 TraesCS2B01G358900 chr3A 85.437 103 11 3 4880 4978 683361810 683361912 2.510000e-18 104.0
50 TraesCS2B01G358900 chr3A 91.429 70 6 0 4166 4235 707615409 707615478 4.190000e-16 97.1
51 TraesCS2B01G358900 chr7D 79.167 312 60 4 3767 4074 41800439 41800749 1.430000e-50 211.0
52 TraesCS2B01G358900 chr4A 93.671 79 4 1 2896 2973 13760386 13760308 3.220000e-22 117.0
53 TraesCS2B01G358900 chr7B 92.537 67 5 0 4166 4232 697033571 697033505 4.190000e-16 97.1
54 TraesCS2B01G358900 chr7B 90.000 70 5 2 4168 4235 43510275 43510206 7.020000e-14 89.8
55 TraesCS2B01G358900 chr7B 93.182 44 2 1 3288 3331 58836361 58836319 4.250000e-06 63.9
56 TraesCS2B01G358900 chr7B 89.796 49 5 0 3035 3083 330539571 330539619 4.250000e-06 63.9
57 TraesCS2B01G358900 chr3D 88.312 77 8 1 2901 2976 554073862 554073786 1.950000e-14 91.6
58 TraesCS2B01G358900 chr6A 88.732 71 8 0 4167 4237 5278100 5278030 2.520000e-13 87.9
59 TraesCS2B01G358900 chr5D 89.041 73 4 1 2896 2964 302885898 302885826 2.520000e-13 87.9
60 TraesCS2B01G358900 chr4D 91.489 47 4 0 3282 3328 434487890 434487936 1.180000e-06 65.8


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 TraesCS2B01G358900 chr2B 512302545 512307631 5086 False 9395.00 9395 100.0000 1 5087 1 chr2B.!!$F1 5086
1 TraesCS2B01G358900 chr2B 680579095 680579934 839 False 1480.00 1480 98.4540 1 840 1 chr2B.!!$F2 839
2 TraesCS2B01G358900 chr2B 505005261 505009504 4243 True 1157.40 3439 91.8246 982 5087 5 chr2B.!!$R3 4105
3 TraesCS2B01G358900 chr2A 559606355 559610690 4335 False 1504.85 3487 94.7640 899 5086 4 chr2A.!!$F1 4187
4 TraesCS2B01G358900 chr2D 427968644 427974519 5875 True 1048.50 2939 92.9680 840 5087 6 chr2D.!!$R2 4247
5 TraesCS2B01G358900 chr7A 24593972 24594812 840 True 1507.00 1507 99.0490 1 840 1 chr7A.!!$R1 839
6 TraesCS2B01G358900 chr7A 256006746 256007584 838 True 1472.00 1472 98.3350 1 840 1 chr7A.!!$R2 839
7 TraesCS2B01G358900 chr3B 814365889 814366727 838 True 1500.00 1500 98.9300 1 840 1 chr3B.!!$R2 839
8 TraesCS2B01G358900 chr5B 580488883 580489722 839 True 1491.00 1491 98.6920 1 840 1 chr5B.!!$R5 839
9 TraesCS2B01G358900 chr5B 415792402 415793240 838 True 1472.00 1472 98.3350 1 840 1 chr5B.!!$R4 839
10 TraesCS2B01G358900 chr4B 115078467 115079307 840 True 1491.00 1491 98.6920 1 840 1 chr4B.!!$R1 839
11 TraesCS2B01G358900 chr6B 715712229 715713068 839 False 1485.00 1485 98.5730 1 840 1 chr6B.!!$F2 839
12 TraesCS2B01G358900 chr1B 543481439 543482278 839 False 1485.00 1485 98.5730 1 840 1 chr1B.!!$F1 839

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
967 1003 1.301244 CTATCCAATCGCTGCCGCT 60.301 57.895 0.0 0.0 0.00 5.52 F
1998 3548 1.133025 CGTTGGATGAACTGCATTCCC 59.867 52.381 0.0 0.0 37.34 3.97 F
2755 4343 1.136446 CGAACGACTAAAAGTTGGCCG 60.136 52.381 0.0 0.0 33.85 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 3805 0.037975 CCTGTTCATTGCAGGTTGGC 60.038 55.0 3.37 0.0 46.22 4.52 R
3049 4642 0.456628 GTTCTGGGGTAGCGACTCTC 59.543 60.0 0.00 0.0 0.00 3.20 R
4470 6260 0.041312 CAGCGTGCACAAACCTGTAC 60.041 55.0 18.64 0.0 33.22 2.90 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
303 305 1.412710 GAATCCTATCCCGTGCTGTGA 59.587 52.381 0.00 0.00 0.00 3.58
764 766 8.094548 CCTGATTGATCCGGTATTACAGATTTA 58.905 37.037 0.00 0.00 0.00 1.40
897 902 8.867097 AGGTTTGGGCATATATATATACTACCG 58.133 37.037 4.54 0.00 0.00 4.02
961 997 2.883828 CGCCCCCTATCCAATCGCT 61.884 63.158 0.00 0.00 0.00 4.93
962 998 1.302832 GCCCCCTATCCAATCGCTG 60.303 63.158 0.00 0.00 0.00 5.18
963 999 1.302832 CCCCCTATCCAATCGCTGC 60.303 63.158 0.00 0.00 0.00 5.25
964 1000 1.302832 CCCCTATCCAATCGCTGCC 60.303 63.158 0.00 0.00 0.00 4.85
965 1001 1.669115 CCCTATCCAATCGCTGCCG 60.669 63.158 0.00 0.00 0.00 5.69
966 1002 2.320587 CCTATCCAATCGCTGCCGC 61.321 63.158 0.00 0.00 0.00 6.53
967 1003 1.301244 CTATCCAATCGCTGCCGCT 60.301 57.895 0.00 0.00 0.00 5.52
968 1004 1.563435 CTATCCAATCGCTGCCGCTG 61.563 60.000 0.00 0.00 0.00 5.18
969 1005 2.026945 TATCCAATCGCTGCCGCTGA 62.027 55.000 0.73 0.00 0.00 4.26
970 1006 2.874648 ATCCAATCGCTGCCGCTGAA 62.875 55.000 0.73 0.00 0.00 3.02
971 1007 2.099062 CAATCGCTGCCGCTGAAC 59.901 61.111 0.73 0.00 0.00 3.18
972 1008 3.490759 AATCGCTGCCGCTGAACG 61.491 61.111 0.73 0.00 43.15 3.95
1150 1222 3.251004 GGAAGCATGATTGATTACGGTCC 59.749 47.826 0.00 0.00 29.99 4.46
1336 1414 1.157585 GGAACGGGAGAAGAAACTGC 58.842 55.000 0.00 0.00 0.00 4.40
1502 3049 3.574396 GGTCTGAGATCGGTGGATATGAA 59.426 47.826 0.00 0.00 31.51 2.57
1548 3095 3.941483 ACCGAGTCTCAAAATTGGCTATG 59.059 43.478 0.00 0.00 0.00 2.23
1849 3399 7.881232 TGTTTCGTGGGATTAGAACTTTAAGAT 59.119 33.333 0.00 0.00 0.00 2.40
1998 3548 1.133025 CGTTGGATGAACTGCATTCCC 59.867 52.381 0.00 0.00 37.34 3.97
2018 3568 7.732222 TTCCCAATATTGCTACCAAGAAAAT 57.268 32.000 10.11 0.00 33.80 1.82
2059 3611 2.568956 TCCATATGAGTAGCCAGCCATC 59.431 50.000 3.65 0.00 0.00 3.51
2071 3623 1.682854 CCAGCCATCCGCATTGTAAAT 59.317 47.619 0.00 0.00 41.38 1.40
2073 3625 3.304659 CCAGCCATCCGCATTGTAAATAC 60.305 47.826 0.00 0.00 41.38 1.89
2123 3675 3.009584 GGGCCTCCTAAAAGGATCTATGG 59.990 52.174 0.84 0.00 44.81 2.74
2138 3690 7.102346 AGGATCTATGGATTCATCGATTTGTC 58.898 38.462 2.67 0.00 36.37 3.18
2180 3741 3.358111 TTATTCCTTGTCGGCATTCCA 57.642 42.857 0.00 0.00 0.00 3.53
2185 3746 1.402968 CCTTGTCGGCATTCCATGAAG 59.597 52.381 0.00 0.00 0.00 3.02
2244 3805 7.838771 AAGCTAAACCCGTACTAACAAATAG 57.161 36.000 0.00 0.00 37.66 1.73
2281 3842 7.235079 TGAACAGGGAAGGTATTACATTCAAA 58.765 34.615 19.47 0.00 40.33 2.69
2311 3872 6.348540 CCGTTAGAATCCCTTTGTTTCTTCTG 60.349 42.308 0.00 0.00 35.25 3.02
2392 3953 5.402398 GTGTGGAATTTTCTCTATGTTGGC 58.598 41.667 0.00 0.00 0.00 4.52
2513 4090 6.013379 TCCATTTGTTCCTTTATGTTAGGCA 58.987 36.000 0.00 0.00 32.59 4.75
2629 4210 4.155826 CCTCACGATAAAATCAAGCCAACA 59.844 41.667 0.00 0.00 0.00 3.33
2755 4343 1.136446 CGAACGACTAAAAGTTGGCCG 60.136 52.381 0.00 0.00 33.85 6.13
2790 4378 2.237393 TTCCCATTTGCTTGCACAAC 57.763 45.000 0.00 0.00 0.00 3.32
2821 4409 1.343069 ACCTAGATCGCCCCAGAATC 58.657 55.000 0.00 0.00 0.00 2.52
3214 4807 7.520937 GCTTGTGTTTCCGGTCTTTTAATCTTA 60.521 37.037 0.00 0.00 0.00 2.10
3215 4808 7.804843 TGTGTTTCCGGTCTTTTAATCTTAA 57.195 32.000 0.00 0.00 0.00 1.85
3264 4857 2.054799 AGCCCCAATCGCTCCTTAATA 58.945 47.619 0.00 0.00 0.00 0.98
3271 4864 5.180117 CCCAATCGCTCCTTAATAATGTCTG 59.820 44.000 0.00 0.00 0.00 3.51
3276 4869 4.260784 CGCTCCTTAATAATGTCTGTTGGC 60.261 45.833 0.00 0.00 0.00 4.52
3281 4874 6.096705 TCCTTAATAATGTCTGTTGGCCATTG 59.903 38.462 6.09 0.00 31.63 2.82
3285 4878 2.647683 TGTCTGTTGGCCATTGTGTA 57.352 45.000 6.09 0.00 0.00 2.90
3353 4946 4.543692 GCATGCCATTCTATTCATGTGTC 58.456 43.478 6.36 0.00 38.72 3.67
3423 5208 9.597170 CCTTAGTTCTGTAACCTATCTTTAACC 57.403 37.037 0.00 0.00 36.15 2.85
3624 5409 1.933021 ACGTCTTCTATGTGGACCCA 58.067 50.000 0.00 0.00 0.00 4.51
3638 5423 4.348461 TGTGGACCCATACTTCTGTAACAA 59.652 41.667 0.00 0.00 31.80 2.83
3729 5514 1.876156 GCTATACAGGCCAGATTGTGC 59.124 52.381 5.01 0.00 0.00 4.57
4020 5808 6.426646 GGTGATCTTACCTTCTACCATGAT 57.573 41.667 0.00 0.00 37.74 2.45
4175 5963 9.288576 TGGATCAGCTGGATTTATATAAAAGTG 57.711 33.333 15.13 6.76 36.00 3.16
4176 5964 8.734386 GGATCAGCTGGATTTATATAAAAGTGG 58.266 37.037 15.13 5.05 36.00 4.00
4177 5965 9.289782 GATCAGCTGGATTTATATAAAAGTGGT 57.710 33.333 15.13 6.04 36.00 4.16
4178 5966 9.646522 ATCAGCTGGATTTATATAAAAGTGGTT 57.353 29.630 15.13 0.00 29.81 3.67
4179 5967 9.474313 TCAGCTGGATTTATATAAAAGTGGTTT 57.526 29.630 15.13 0.00 0.00 3.27
4180 5968 9.736023 CAGCTGGATTTATATAAAAGTGGTTTC 57.264 33.333 11.80 3.60 0.00 2.78
4181 5969 9.474313 AGCTGGATTTATATAAAAGTGGTTTCA 57.526 29.630 11.80 0.00 0.00 2.69
4205 5993 9.982291 TCATAACTATTTTAGTGATTTGAACGC 57.018 29.630 0.00 0.00 39.39 4.84
4206 5994 9.988350 CATAACTATTTTAGTGATTTGAACGCT 57.012 29.630 0.00 0.00 39.39 5.07
4208 5996 7.907214 ACTATTTTAGTGATTTGAACGCTCT 57.093 32.000 0.00 0.00 37.69 4.09
4209 5997 8.324163 ACTATTTTAGTGATTTGAACGCTCTT 57.676 30.769 0.00 0.00 37.69 2.85
4210 5998 9.431887 ACTATTTTAGTGATTTGAACGCTCTTA 57.568 29.630 0.00 0.00 37.69 2.10
4218 6006 9.601217 AGTGATTTGAACGCTCTTATATTAGTT 57.399 29.630 0.00 0.00 0.00 2.24
4223 6011 7.919313 TGAACGCTCTTATATTAGTTTACGG 57.081 36.000 0.00 0.00 0.00 4.02
4224 6012 7.706159 TGAACGCTCTTATATTAGTTTACGGA 58.294 34.615 0.00 0.00 0.00 4.69
4225 6013 7.859377 TGAACGCTCTTATATTAGTTTACGGAG 59.141 37.037 0.00 0.00 0.00 4.63
4226 6014 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
4227 6015 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
4228 6016 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
4229 6017 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
4250 6038 5.480073 GGAGTATATCTCTCTGAATGGCTGT 59.520 44.000 7.47 0.00 42.40 4.40
4382 6170 2.041244 GTCAACGCGTGGAAATTGTTC 58.959 47.619 19.89 0.00 0.00 3.18
4390 6178 4.219033 GCGTGGAAATTGTTCTACAGTTG 58.781 43.478 4.23 0.00 43.50 3.16
4395 6183 5.530915 TGGAAATTGTTCTACAGTTGTGAGG 59.469 40.000 0.00 0.00 33.92 3.86
4521 6311 3.181465 CGGCAGATAGGACCATGTACTTT 60.181 47.826 0.00 0.00 0.00 2.66
4522 6312 4.381411 GGCAGATAGGACCATGTACTTTC 58.619 47.826 0.00 0.00 0.00 2.62
4523 6313 4.141711 GGCAGATAGGACCATGTACTTTCA 60.142 45.833 0.00 0.00 28.94 2.69
4622 6487 8.584157 TCATGCCAAATTCTTTTTGTACATAGT 58.416 29.630 0.00 0.00 0.00 2.12
4687 6555 5.248640 TGTCTTTTCCAATTTGTTTTGCCA 58.751 33.333 0.00 0.00 0.00 4.92
4720 6589 7.881775 AGTGAACATATTATTTCTTCCACCC 57.118 36.000 0.00 0.00 0.00 4.61
4928 6806 6.839124 ATTCTTACATTTGCCATCTGTTCA 57.161 33.333 0.00 0.00 0.00 3.18
4958 6836 1.004679 CCCCAACTTTGCCATGTGC 60.005 57.895 0.00 0.00 41.77 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
192 194 1.039068 CAGCACACCCACCAATTCAA 58.961 50.000 0.00 0.00 0.00 2.69
303 305 0.394762 ATGCAACTCACATCGGGCAT 60.395 50.000 0.00 0.00 37.17 4.40
764 766 1.603634 ACCGGATTAATCACCCCCTT 58.396 50.000 17.07 0.00 0.00 3.95
897 902 1.934220 TAGATCGATCCGATGGCGCC 61.934 60.000 22.73 22.73 47.00 6.53
964 1000 1.712081 CATGCTTCTCCGTTCAGCG 59.288 57.895 0.00 0.00 36.24 5.18
965 1001 1.427020 GCATGCTTCTCCGTTCAGC 59.573 57.895 11.37 0.00 0.00 4.26
966 1002 1.699656 CGGCATGCTTCTCCGTTCAG 61.700 60.000 18.92 0.00 38.47 3.02
967 1003 1.741401 CGGCATGCTTCTCCGTTCA 60.741 57.895 18.92 0.00 38.47 3.18
968 1004 3.093278 CGGCATGCTTCTCCGTTC 58.907 61.111 18.92 0.00 38.47 3.95
969 1005 3.127533 GCGGCATGCTTCTCCGTT 61.128 61.111 18.92 0.00 44.58 4.44
1181 1253 4.800023 TCAGGAGAGGATCGGTTATTGTA 58.200 43.478 0.00 0.00 42.67 2.41
1183 1255 4.672587 TTCAGGAGAGGATCGGTTATTG 57.327 45.455 0.00 0.00 42.67 1.90
1184 1256 4.469945 TGTTTCAGGAGAGGATCGGTTATT 59.530 41.667 0.00 0.00 42.67 1.40
1185 1257 4.030913 TGTTTCAGGAGAGGATCGGTTAT 58.969 43.478 0.00 0.00 42.67 1.89
1290 1362 0.115152 CTTGCCCTTTCCCTTTCCCT 59.885 55.000 0.00 0.00 0.00 4.20
1291 1363 0.904865 CCTTGCCCTTTCCCTTTCCC 60.905 60.000 0.00 0.00 0.00 3.97
1292 1364 0.904865 CCCTTGCCCTTTCCCTTTCC 60.905 60.000 0.00 0.00 0.00 3.13
1293 1365 0.904865 CCCCTTGCCCTTTCCCTTTC 60.905 60.000 0.00 0.00 0.00 2.62
1294 1366 1.158466 CCCCTTGCCCTTTCCCTTT 59.842 57.895 0.00 0.00 0.00 3.11
1295 1367 1.376249 TTCCCCTTGCCCTTTCCCTT 61.376 55.000 0.00 0.00 0.00 3.95
1502 3049 7.288158 GGTGGAATATCCTTTCTGTAGTACTCT 59.712 40.741 0.00 0.00 37.46 3.24
1548 3095 4.854291 CGATAGATTAATGCTGTCTCCGTC 59.146 45.833 0.00 0.00 39.76 4.79
1789 3336 9.899226 GATCTAAATCCTACAAAAACCATATGC 57.101 33.333 0.00 0.00 0.00 3.14
2043 3595 1.750930 CGGATGGCTGGCTACTCAT 59.249 57.895 2.00 0.00 0.00 2.90
2044 3596 3.094062 GCGGATGGCTGGCTACTCA 62.094 63.158 2.00 0.00 39.11 3.41
2059 3611 5.305585 ACCTATCCTGTATTTACAATGCGG 58.694 41.667 0.00 0.00 35.50 5.69
2071 3623 3.889538 CCACAGATCGAACCTATCCTGTA 59.110 47.826 0.00 0.00 0.00 2.74
2073 3625 2.695666 ACCACAGATCGAACCTATCCTG 59.304 50.000 0.00 0.00 0.00 3.86
2123 3675 9.773328 TGTTTCTTTATGACAAATCGATGAATC 57.227 29.630 0.00 0.00 0.00 2.52
2138 3690 6.538189 AAACGGCCATTTTGTTTCTTTATG 57.462 33.333 2.24 0.00 30.41 1.90
2180 3741 1.274167 TCGGCCAAACGAGTACTTCAT 59.726 47.619 2.24 0.00 38.06 2.57
2185 3746 1.066136 GTCTTCGGCCAAACGAGTAC 58.934 55.000 2.24 0.00 44.47 2.73
2244 3805 0.037975 CCTGTTCATTGCAGGTTGGC 60.038 55.000 3.37 0.00 46.22 4.52
2281 3842 3.329814 ACAAAGGGATTCTAACGGAAGGT 59.670 43.478 0.00 0.00 37.36 3.50
2311 3872 1.202132 TGCAAGAGTGTTTGACAACGC 60.202 47.619 0.00 0.00 42.83 4.84
2426 3990 8.442384 CGAAAACCATATGGAAATTTTTGAAGG 58.558 33.333 28.77 8.99 38.94 3.46
2658 4244 7.174772 ACAAACCAAAATGAAAATATTGGGAGC 59.825 33.333 8.14 0.00 45.22 4.70
2917 4505 4.785453 GCAACCAGGGGAGGAGCG 62.785 72.222 0.00 0.00 0.00 5.03
3031 4624 4.020396 ACTCTCGACTAGTCCTGACTGTAA 60.020 45.833 17.23 0.00 42.52 2.41
3049 4642 0.456628 GTTCTGGGGTAGCGACTCTC 59.543 60.000 0.00 0.00 0.00 3.20
3079 4672 4.412796 TGGGTCATGCAATGTTTTTGAA 57.587 36.364 0.00 0.00 46.80 2.69
3179 4772 2.238521 GGAAACACAAGCTGGAATCCA 58.761 47.619 0.48 0.48 0.00 3.41
3214 4807 3.054361 ACCTTGCTAATCCCTTCGATGTT 60.054 43.478 0.00 0.00 0.00 2.71
3215 4808 2.505819 ACCTTGCTAATCCCTTCGATGT 59.494 45.455 0.00 0.00 0.00 3.06
3264 4857 2.318908 ACACAATGGCCAACAGACATT 58.681 42.857 10.96 0.00 35.36 2.71
3314 4907 5.249163 TGGCATGCCATCTTATACTCACTAT 59.751 40.000 35.59 0.00 41.89 2.12
3316 4909 3.392285 TGGCATGCCATCTTATACTCACT 59.608 43.478 35.59 0.00 41.89 3.41
3423 5208 8.674263 AAGATATACTGCCTTCATTTCAAGAG 57.326 34.615 0.00 0.00 0.00 2.85
3464 5249 8.410030 TGGAATAAAATGATTCAAAAGATGCG 57.590 30.769 0.00 0.00 37.53 4.73
3729 5514 3.615937 CAGATGTGAGATCAAGGTTGACG 59.384 47.826 0.00 0.00 40.49 4.35
4020 5808 4.334552 TGCAGATTGCCTTTTCATACTGA 58.665 39.130 0.00 0.00 44.23 3.41
4179 5967 9.982291 GCGTTCAAATCACTAAAATAGTTATGA 57.018 29.630 0.00 0.00 36.76 2.15
4180 5968 9.988350 AGCGTTCAAATCACTAAAATAGTTATG 57.012 29.630 0.00 0.00 36.76 1.90
4182 5970 9.431887 AGAGCGTTCAAATCACTAAAATAGTTA 57.568 29.630 1.01 0.00 36.76 2.24
4183 5971 8.324163 AGAGCGTTCAAATCACTAAAATAGTT 57.676 30.769 1.01 0.00 36.76 2.24
4184 5972 7.907214 AGAGCGTTCAAATCACTAAAATAGT 57.093 32.000 1.01 0.00 40.28 2.12
4192 5980 9.601217 AACTAATATAAGAGCGTTCAAATCACT 57.399 29.630 1.01 0.00 0.00 3.41
4197 5985 8.810427 CCGTAAACTAATATAAGAGCGTTCAAA 58.190 33.333 1.01 0.00 0.00 2.69
4198 5986 8.190122 TCCGTAAACTAATATAAGAGCGTTCAA 58.810 33.333 1.01 0.00 0.00 2.69
4199 5987 7.706159 TCCGTAAACTAATATAAGAGCGTTCA 58.294 34.615 1.01 0.00 0.00 3.18
4200 5988 7.325579 CCTCCGTAAACTAATATAAGAGCGTTC 59.674 40.741 0.00 0.00 0.00 3.95
4201 5989 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
4202 5990 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
4203 5991 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
4204 5992 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
4205 5993 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4211 5999 9.678260 GAGATATACTCCCTCCGTAAACTAATA 57.322 37.037 0.00 0.00 39.53 0.98
4212 6000 8.392479 AGAGATATACTCCCTCCGTAAACTAAT 58.608 37.037 0.00 0.00 45.96 1.73
4213 6001 7.753630 AGAGATATACTCCCTCCGTAAACTAA 58.246 38.462 0.00 0.00 45.96 2.24
4214 6002 7.237263 AGAGAGATATACTCCCTCCGTAAACTA 59.763 40.741 5.97 0.00 45.96 2.24
4215 6003 6.044637 AGAGAGATATACTCCCTCCGTAAACT 59.955 42.308 5.97 0.00 45.96 2.66
4216 6004 6.149807 CAGAGAGATATACTCCCTCCGTAAAC 59.850 46.154 5.97 0.00 45.96 2.01
4217 6005 6.044054 TCAGAGAGATATACTCCCTCCGTAAA 59.956 42.308 5.97 0.00 45.96 2.01
4218 6006 5.546887 TCAGAGAGATATACTCCCTCCGTAA 59.453 44.000 5.97 0.00 45.96 3.18
4219 6007 5.092259 TCAGAGAGATATACTCCCTCCGTA 58.908 45.833 5.97 0.00 45.96 4.02
4220 6008 3.911260 TCAGAGAGATATACTCCCTCCGT 59.089 47.826 5.97 0.00 45.96 4.69
4221 6009 4.561500 TCAGAGAGATATACTCCCTCCG 57.438 50.000 5.97 0.00 45.96 4.63
4222 6010 5.656416 CCATTCAGAGAGATATACTCCCTCC 59.344 48.000 5.97 0.00 45.96 4.30
4223 6011 5.127031 GCCATTCAGAGAGATATACTCCCTC 59.873 48.000 5.97 0.00 45.96 4.30
4224 6012 5.022787 GCCATTCAGAGAGATATACTCCCT 58.977 45.833 5.97 0.00 45.96 4.20
4225 6013 5.022787 AGCCATTCAGAGAGATATACTCCC 58.977 45.833 5.97 0.00 45.96 4.30
4226 6014 5.480073 ACAGCCATTCAGAGAGATATACTCC 59.520 44.000 5.97 0.00 45.96 3.85
4227 6015 6.350110 GGACAGCCATTCAGAGAGATATACTC 60.350 46.154 0.00 0.00 45.22 2.59
4228 6016 5.480073 GGACAGCCATTCAGAGAGATATACT 59.520 44.000 0.00 0.00 0.00 2.12
4229 6017 5.621104 CGGACAGCCATTCAGAGAGATATAC 60.621 48.000 0.00 0.00 0.00 1.47
4382 6170 1.419374 GACACGCCTCACAACTGTAG 58.581 55.000 0.00 0.00 0.00 2.74
4390 6178 0.170561 ATAGACACGACACGCCTCAC 59.829 55.000 0.00 0.00 0.00 3.51
4395 6183 1.153823 AGCCATAGACACGACACGC 60.154 57.895 0.00 0.00 0.00 5.34
4448 6237 1.340017 CCCCAGGCTTCAAATCTTCGA 60.340 52.381 0.00 0.00 0.00 3.71
4470 6260 0.041312 CAGCGTGCACAAACCTGTAC 60.041 55.000 18.64 0.00 33.22 2.90
4521 6311 0.981183 AGTGTAAAGGCATCCGGTGA 59.019 50.000 0.00 0.00 0.00 4.02
4522 6312 2.684001 TAGTGTAAAGGCATCCGGTG 57.316 50.000 0.00 0.00 0.00 4.94
4523 6313 2.158813 CCATAGTGTAAAGGCATCCGGT 60.159 50.000 0.00 0.00 0.00 5.28
4622 6487 7.388437 AGGTCATGGTAGATTTTTAACGTACA 58.612 34.615 0.00 0.00 0.00 2.90
4638 6505 7.849322 AAACCTGTTTTATAAAGGTCATGGT 57.151 32.000 7.62 9.75 43.62 3.55
4872 6742 8.553459 AGACACATGGTAAATTTAGTTCTCTG 57.447 34.615 0.00 0.00 0.00 3.35
4928 6806 5.187772 GGCAAAGTTGGGGATTATTTCTTCT 59.812 40.000 0.00 0.00 0.00 2.85
4958 6836 4.937015 CAGCTTTTGGGAATTTGTAATGGG 59.063 41.667 0.00 0.00 0.00 4.00
5022 6901 2.042686 TCAGGAATTCTTCATGGGCG 57.957 50.000 5.23 0.00 41.48 6.13


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

AutoCloner maintained by Alex Coulton.