Multiple sequence alignment - TraesCS2A01G037900

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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 TraesCS2A01G037900 chr2A 100.000 3086 0 0 1 3086 15958789 15961874 0.000000e+00 5699.0
1 TraesCS2A01G037900 chr2A 86.643 1123 103 21 999 2093 15756437 15757540 0.000000e+00 1199.0
2 TraesCS2A01G037900 chr2D 92.572 2531 129 21 577 3084 13769797 13772291 0.000000e+00 3578.0
3 TraesCS2A01G037900 chr2D 87.723 1067 92 14 999 2041 13724247 13723196 0.000000e+00 1208.0
4 TraesCS2A01G037900 chr2D 94.828 58 3 0 401 458 13769373 13769430 1.180000e-14 91.6
5 TraesCS2A01G037900 chr2B 91.992 2073 109 14 1022 3086 25069196 25071219 0.000000e+00 2856.0
6 TraesCS2A01G037900 chr2B 85.378 1231 111 29 893 2093 24988736 24987545 0.000000e+00 1212.0
7 TraesCS2A01G037900 chr2B 82.887 672 61 26 353 992 25068550 25069199 3.480000e-154 555.0
8 TraesCS2A01G037900 chr2B 92.213 244 16 3 97 338 25068254 25068496 2.950000e-90 342.0
9 TraesCS2A01G037900 chr2B 92.500 40 3 0 58 97 696662943 696662904 1.200000e-04 58.4
10 TraesCS2A01G037900 chr3B 81.673 1124 148 36 994 2090 700073335 700072243 0.000000e+00 881.0
11 TraesCS2A01G037900 chr3B 81.216 1102 155 31 999 2079 700234826 700235896 0.000000e+00 841.0
12 TraesCS2A01G037900 chr3D 82.044 1086 144 29 1034 2092 529496477 529495416 0.000000e+00 878.0
13 TraesCS2A01G037900 chr3A 82.002 1089 139 35 1034 2092 663441779 663440718 0.000000e+00 872.0
14 TraesCS2A01G037900 chr7D 80.279 1075 172 22 1034 2088 624769141 624770195 0.000000e+00 774.0
15 TraesCS2A01G037900 chr7D 93.182 44 3 0 432 475 42007497 42007540 7.140000e-07 65.8
16 TraesCS2A01G037900 chr5B 79.760 1082 161 32 1034 2086 711858970 711857918 0.000000e+00 732.0
17 TraesCS2A01G037900 chr5D 78.431 969 161 29 1033 1983 557577270 557578208 3.430000e-164 588.0
18 TraesCS2A01G037900 chr7B 76.981 265 40 11 1824 2086 673116 672871 6.940000e-27 132.0
19 TraesCS2A01G037900 chr7B 80.198 101 20 0 403 503 161439337 161439237 3.300000e-10 76.8
20 TraesCS2A01G037900 chr5A 81.319 91 16 1 403 492 305831086 305831176 4.270000e-09 73.1
21 TraesCS2A01G037900 chr7A 83.562 73 12 0 403 475 267128921 267128993 5.520000e-08 69.4
22 TraesCS2A01G037900 chr1D 95.349 43 2 0 57 99 309921721 309921679 5.520000e-08 69.4
23 TraesCS2A01G037900 chr4A 93.182 44 3 0 55 98 716999303 716999346 7.140000e-07 65.8
24 TraesCS2A01G037900 chr1A 91.111 45 4 0 55 99 327527096 327527140 9.240000e-06 62.1
25 TraesCS2A01G037900 chr6A 90.909 44 4 0 432 475 31261895 31261852 3.320000e-05 60.2
26 TraesCS2A01G037900 chr4B 90.698 43 4 0 448 490 27537728 27537770 1.200000e-04 58.4


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 TraesCS2A01G037900 chr2A 15958789 15961874 3085 False 5699.0 5699 100.000000 1 3086 1 chr2A.!!$F2 3085
1 TraesCS2A01G037900 chr2A 15756437 15757540 1103 False 1199.0 1199 86.643000 999 2093 1 chr2A.!!$F1 1094
2 TraesCS2A01G037900 chr2D 13769373 13772291 2918 False 1834.8 3578 93.700000 401 3084 2 chr2D.!!$F1 2683
3 TraesCS2A01G037900 chr2D 13723196 13724247 1051 True 1208.0 1208 87.723000 999 2041 1 chr2D.!!$R1 1042
4 TraesCS2A01G037900 chr2B 25068254 25071219 2965 False 1251.0 2856 89.030667 97 3086 3 chr2B.!!$F1 2989
5 TraesCS2A01G037900 chr2B 24987545 24988736 1191 True 1212.0 1212 85.378000 893 2093 1 chr2B.!!$R1 1200
6 TraesCS2A01G037900 chr3B 700072243 700073335 1092 True 881.0 881 81.673000 994 2090 1 chr3B.!!$R1 1096
7 TraesCS2A01G037900 chr3B 700234826 700235896 1070 False 841.0 841 81.216000 999 2079 1 chr3B.!!$F1 1080
8 TraesCS2A01G037900 chr3D 529495416 529496477 1061 True 878.0 878 82.044000 1034 2092 1 chr3D.!!$R1 1058
9 TraesCS2A01G037900 chr3A 663440718 663441779 1061 True 872.0 872 82.002000 1034 2092 1 chr3A.!!$R1 1058
10 TraesCS2A01G037900 chr7D 624769141 624770195 1054 False 774.0 774 80.279000 1034 2088 1 chr7D.!!$F2 1054
11 TraesCS2A01G037900 chr5B 711857918 711858970 1052 True 732.0 732 79.760000 1034 2086 1 chr5B.!!$R1 1052
12 TraesCS2A01G037900 chr5D 557577270 557578208 938 False 588.0 588 78.431000 1033 1983 1 chr5D.!!$F1 950

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
94 95 0.253347 ATATCATGGGGCGGAGGGAT 60.253 55.0 0.0 0.0 0.0 3.85 F
95 96 0.475632 TATCATGGGGCGGAGGGATT 60.476 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2472 0.179145 CCTTGTAGTACTGCCGGACG 60.179 60.000 5.05 0.0 0.0 4.79 R
2152 2611 3.753815 ACCAAAATTCAAAAGGCATGGG 58.246 40.909 0.00 0.0 0.0 4.00 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
43 44 9.599056 AAAAAGACCCTAAGACTACTAAGTACT 57.401 33.333 0.00 0.00 35.56 2.73
44 45 8.806429 AAAGACCCTAAGACTACTAAGTACTC 57.194 38.462 0.00 0.00 35.56 2.59
45 46 6.899089 AGACCCTAAGACTACTAAGTACTCC 58.101 44.000 0.00 0.00 35.56 3.85
46 47 6.012337 ACCCTAAGACTACTAAGTACTCCC 57.988 45.833 0.00 0.00 35.56 4.30
47 48 5.735624 ACCCTAAGACTACTAAGTACTCCCT 59.264 44.000 0.00 0.00 35.56 4.20
48 49 6.126507 ACCCTAAGACTACTAAGTACTCCCTC 60.127 46.154 0.00 0.00 35.56 4.30
49 50 6.298361 CCTAAGACTACTAAGTACTCCCTCC 58.702 48.000 0.00 0.00 35.56 4.30
50 51 4.420522 AGACTACTAAGTACTCCCTCCG 57.579 50.000 0.00 0.00 35.56 4.63
51 52 3.779738 AGACTACTAAGTACTCCCTCCGT 59.220 47.826 0.00 0.00 35.56 4.69
52 53 4.126437 GACTACTAAGTACTCCCTCCGTC 58.874 52.174 0.00 0.00 35.56 4.79
53 54 2.035530 ACTAAGTACTCCCTCCGTCG 57.964 55.000 0.00 0.00 0.00 5.12
54 55 1.556911 ACTAAGTACTCCCTCCGTCGA 59.443 52.381 0.00 0.00 0.00 4.20
55 56 1.939255 CTAAGTACTCCCTCCGTCGAC 59.061 57.143 5.18 5.18 0.00 4.20
56 57 0.679321 AAGTACTCCCTCCGTCGACC 60.679 60.000 10.58 0.00 0.00 4.79
57 58 1.377725 GTACTCCCTCCGTCGACCA 60.378 63.158 10.58 0.00 0.00 4.02
58 59 1.077930 TACTCCCTCCGTCGACCAG 60.078 63.158 10.58 6.08 0.00 4.00
59 60 1.845627 TACTCCCTCCGTCGACCAGT 61.846 60.000 10.58 5.24 0.00 4.00
60 61 2.675423 TCCCTCCGTCGACCAGTG 60.675 66.667 10.58 2.74 0.00 3.66
61 62 2.989824 CCCTCCGTCGACCAGTGT 60.990 66.667 10.58 0.00 0.00 3.55
62 63 1.676635 CCCTCCGTCGACCAGTGTA 60.677 63.158 10.58 0.00 0.00 2.90
63 64 1.246056 CCCTCCGTCGACCAGTGTAA 61.246 60.000 10.58 0.00 0.00 2.41
64 65 0.599558 CCTCCGTCGACCAGTGTAAA 59.400 55.000 10.58 0.00 0.00 2.01
65 66 1.000060 CCTCCGTCGACCAGTGTAAAA 60.000 52.381 10.58 0.00 0.00 1.52
66 67 2.546373 CCTCCGTCGACCAGTGTAAAAA 60.546 50.000 10.58 0.00 0.00 1.94
86 87 2.770164 ACGCTCTTATATCATGGGGC 57.230 50.000 0.00 0.00 0.00 5.80
87 88 1.066858 ACGCTCTTATATCATGGGGCG 60.067 52.381 9.66 9.66 45.49 6.13
88 89 1.740380 CGCTCTTATATCATGGGGCGG 60.740 57.143 4.00 0.00 38.12 6.13
89 90 1.555075 GCTCTTATATCATGGGGCGGA 59.445 52.381 0.00 0.00 0.00 5.54
90 91 2.419297 GCTCTTATATCATGGGGCGGAG 60.419 54.545 0.00 0.00 0.00 4.63
91 92 2.169352 CTCTTATATCATGGGGCGGAGG 59.831 54.545 0.00 0.00 0.00 4.30
92 93 1.210478 CTTATATCATGGGGCGGAGGG 59.790 57.143 0.00 0.00 0.00 4.30
93 94 0.415830 TATATCATGGGGCGGAGGGA 59.584 55.000 0.00 0.00 0.00 4.20
94 95 0.253347 ATATCATGGGGCGGAGGGAT 60.253 55.000 0.00 0.00 0.00 3.85
95 96 0.475632 TATCATGGGGCGGAGGGATT 60.476 55.000 0.00 0.00 0.00 3.01
96 97 0.475632 ATCATGGGGCGGAGGGATTA 60.476 55.000 0.00 0.00 0.00 1.75
97 98 1.073199 CATGGGGCGGAGGGATTAC 59.927 63.158 0.00 0.00 0.00 1.89
98 99 1.385347 ATGGGGCGGAGGGATTACA 60.385 57.895 0.00 0.00 0.00 2.41
99 100 0.991355 ATGGGGCGGAGGGATTACAA 60.991 55.000 0.00 0.00 0.00 2.41
100 101 1.148498 GGGGCGGAGGGATTACAAG 59.852 63.158 0.00 0.00 0.00 3.16
101 102 1.148498 GGGCGGAGGGATTACAAGG 59.852 63.158 0.00 0.00 0.00 3.61
151 152 1.289066 CCAAACTCGGCTCGACTCA 59.711 57.895 0.00 0.00 0.00 3.41
168 169 2.223294 ACTCATGTAACTCGCGAGCTAC 60.223 50.000 32.52 32.52 32.24 3.58
282 285 6.131544 AGTACACACATTCTTCACAAAACC 57.868 37.500 0.00 0.00 0.00 3.27
283 286 4.027572 ACACACATTCTTCACAAAACCG 57.972 40.909 0.00 0.00 0.00 4.44
284 287 3.181491 ACACACATTCTTCACAAAACCGG 60.181 43.478 0.00 0.00 0.00 5.28
286 289 3.315191 ACACATTCTTCACAAAACCGGAG 59.685 43.478 9.46 0.00 0.00 4.63
287 290 2.293399 ACATTCTTCACAAAACCGGAGC 59.707 45.455 9.46 0.00 0.00 4.70
289 292 2.045561 TCTTCACAAAACCGGAGCAA 57.954 45.000 9.46 0.00 0.00 3.91
290 293 2.582052 TCTTCACAAAACCGGAGCAAT 58.418 42.857 9.46 0.00 0.00 3.56
291 294 2.552315 TCTTCACAAAACCGGAGCAATC 59.448 45.455 9.46 0.00 0.00 2.67
293 296 2.302260 TCACAAAACCGGAGCAATCAA 58.698 42.857 9.46 0.00 0.00 2.57
294 297 2.890311 TCACAAAACCGGAGCAATCAAT 59.110 40.909 9.46 0.00 0.00 2.57
338 341 6.822667 TTGATGCACTCTACAAATGACAAT 57.177 33.333 0.00 0.00 0.00 2.71
340 343 8.510243 TTGATGCACTCTACAAATGACAATAT 57.490 30.769 0.00 0.00 0.00 1.28
341 344 7.922837 TGATGCACTCTACAAATGACAATATG 58.077 34.615 0.00 0.00 0.00 1.78
342 345 6.682423 TGCACTCTACAAATGACAATATGG 57.318 37.500 0.00 0.00 0.00 2.74
343 346 6.413892 TGCACTCTACAAATGACAATATGGA 58.586 36.000 0.00 0.00 0.00 3.41
345 348 7.557358 TGCACTCTACAAATGACAATATGGATT 59.443 33.333 0.00 0.00 0.00 3.01
346 349 8.072567 GCACTCTACAAATGACAATATGGATTC 58.927 37.037 0.00 0.00 0.00 2.52
347 350 8.278408 CACTCTACAAATGACAATATGGATTCG 58.722 37.037 0.00 0.00 0.00 3.34
348 351 7.987458 ACTCTACAAATGACAATATGGATTCGT 59.013 33.333 0.00 0.00 0.00 3.85
349 352 8.731275 TCTACAAATGACAATATGGATTCGTT 57.269 30.769 0.00 0.00 0.00 3.85
350 353 9.825109 TCTACAAATGACAATATGGATTCGTTA 57.175 29.630 0.00 0.00 0.00 3.18
372 414 1.532437 TCGTTAGCTCGAGTCGTTGAA 59.468 47.619 15.13 0.37 34.85 2.69
376 418 0.952280 AGCTCGAGTCGTTGAACTCA 59.048 50.000 15.13 0.00 44.88 3.41
410 452 4.663636 AACAAGCTCGGATTAAAACTCG 57.336 40.909 0.00 0.00 0.00 4.18
499 541 5.533533 TGAGTTTCGAGTTTTCGTTTCAA 57.466 34.783 0.00 0.00 46.72 2.69
505 547 1.672363 GAGTTTTCGTTTCAACCCCGT 59.328 47.619 0.00 0.00 0.00 5.28
513 555 0.759959 TTTCAACCCCGTCTGTGCTA 59.240 50.000 0.00 0.00 0.00 3.49
569 899 5.029650 CAAAAGCATAGCGTTTGTCTACA 57.970 39.130 17.96 0.00 46.80 2.74
570 900 5.448438 CAAAAGCATAGCGTTTGTCTACAA 58.552 37.500 17.96 0.00 46.80 2.41
571 901 5.682943 AAAGCATAGCGTTTGTCTACAAA 57.317 34.783 4.19 4.19 42.90 2.83
572 902 5.682943 AAGCATAGCGTTTGTCTACAAAA 57.317 34.783 9.72 0.00 46.08 2.44
573 903 5.682943 AGCATAGCGTTTGTCTACAAAAA 57.317 34.783 9.72 0.00 46.08 1.94
574 904 5.689819 AGCATAGCGTTTGTCTACAAAAAG 58.310 37.500 9.72 8.44 46.08 2.27
575 905 4.851558 GCATAGCGTTTGTCTACAAAAAGG 59.148 41.667 9.72 4.50 46.08 3.11
637 967 3.650942 AGTCCTTGGTGTTGGTTGAGATA 59.349 43.478 0.00 0.00 0.00 1.98
685 1015 8.742554 AGAATTAGCAAAACCGAATAAAACAG 57.257 30.769 0.00 0.00 0.00 3.16
691 1021 4.577834 AAACCGAATAAAACAGGTGTGG 57.422 40.909 0.00 0.00 37.03 4.17
763 1101 9.743057 CATTGGTAAAAATCTTGTCTTGTAACA 57.257 29.630 0.00 0.00 0.00 2.41
862 1218 1.090052 GGCCAGCAACCACGAGATAC 61.090 60.000 0.00 0.00 0.00 2.24
883 1239 4.012895 CGGCGGCAACACACTGAC 62.013 66.667 10.53 0.00 0.00 3.51
884 1240 2.899838 GGCGGCAACACACTGACA 60.900 61.111 3.07 0.00 0.00 3.58
885 1241 2.327940 GCGGCAACACACTGACAC 59.672 61.111 0.00 0.00 0.00 3.67
886 1242 2.180204 GCGGCAACACACTGACACT 61.180 57.895 0.00 0.00 0.00 3.55
891 1247 1.523711 AACACACTGACACTGGCGG 60.524 57.895 0.00 0.00 0.00 6.13
911 1267 2.412089 GGACACGTTCGATGAAGAAAGG 59.588 50.000 0.00 0.00 34.66 3.11
1196 1568 4.838152 CCTGTCATCCGCCGTGGG 62.838 72.222 0.00 0.00 38.76 4.61
1719 2127 2.031516 CAGCTTCCTCACCGTGCTG 61.032 63.158 0.00 0.00 43.71 4.41
1866 2298 1.444553 CGACAGGTTCAGGAGCGTC 60.445 63.158 0.00 0.00 0.00 5.19
2019 2472 2.675772 ACGACGGTGGAGGAGGTC 60.676 66.667 0.00 0.00 0.00 3.85
2152 2611 4.803426 CTCTGCACCGTCCTCCGC 62.803 72.222 0.00 0.00 34.38 5.54
2162 2621 3.338250 TCCTCCGCCCATGCCTTT 61.338 61.111 0.00 0.00 0.00 3.11
2172 2631 2.488937 GCCCATGCCTTTTGAATTTTGG 59.511 45.455 0.00 0.00 0.00 3.28
2191 2651 1.866601 GGTTGATGCACAAAGCCAAAC 59.133 47.619 0.00 0.00 44.83 2.93
2199 2659 3.115554 GCACAAAGCCAAACAGTAACAG 58.884 45.455 0.00 0.00 37.23 3.16
2273 2738 3.600388 CTTAACTGAGCCTCGTTTCCAT 58.400 45.455 7.13 0.00 0.00 3.41
2306 2771 5.334724 CCAGAAAGAGCAGAGCAAAAGTAAG 60.335 44.000 0.00 0.00 0.00 2.34
2322 2787 7.596248 GCAAAAGTAAGAAGCATGAATTCAGAA 59.404 33.333 14.54 0.00 0.00 3.02
2460 2925 2.565834 TGCAGACTAGTTTACCCTGTCC 59.434 50.000 0.00 0.00 0.00 4.02
2497 2962 6.406400 GGCTGTTGATTACATACTGAGAGAGT 60.406 42.308 0.00 0.00 35.85 3.24
2501 2966 8.035394 TGTTGATTACATACTGAGAGAGTTTCC 58.965 37.037 0.00 0.00 35.96 3.13
2625 3093 5.392919 CGAAAGCCAATGTTGAACCATGATA 60.393 40.000 0.00 0.00 0.00 2.15
2703 3171 0.819259 GTGCTCTGTTTGGGCTGTCA 60.819 55.000 0.00 0.00 0.00 3.58
2733 3201 2.241171 GGGTTCACCTTTTCGGTCG 58.759 57.895 0.00 0.00 44.93 4.79
2764 3232 5.702209 GGCTGAAATTCAACCACATTTTGAT 59.298 36.000 10.31 0.00 32.99 2.57
2772 3240 5.537188 TCAACCACATTTTGATTTACTGCC 58.463 37.500 0.00 0.00 0.00 4.85
2879 3347 0.602638 GCGTGATGAACAGTCCACCA 60.603 55.000 0.00 0.00 0.00 4.17
2903 3371 7.157347 CAGTATAGCATATGTTCCATGTGTCT 58.843 38.462 4.29 4.01 0.00 3.41
2912 3380 2.042686 TCCATGTGTCTATTGCTGCC 57.957 50.000 0.00 0.00 0.00 4.85
2928 3396 0.889186 TGCCGCCTTTCTTTCACCTC 60.889 55.000 0.00 0.00 0.00 3.85
2934 3402 2.355209 GCCTTTCTTTCACCTCTCGGAT 60.355 50.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.599056 AGTACTTAGTAGTCTTAGGGTCTTTTT 57.401 33.333 0.00 0.00 35.78 1.94
18 19 9.241919 GAGTACTTAGTAGTCTTAGGGTCTTTT 57.758 37.037 17.34 0.00 36.05 2.27
19 20 7.833682 GGAGTACTTAGTAGTCTTAGGGTCTTT 59.166 40.741 21.99 0.00 38.23 2.52
20 21 7.345691 GGAGTACTTAGTAGTCTTAGGGTCTT 58.654 42.308 21.99 0.00 38.23 3.01
21 22 6.126507 GGGAGTACTTAGTAGTCTTAGGGTCT 60.127 46.154 21.99 0.30 38.23 3.85
22 23 6.061441 GGGAGTACTTAGTAGTCTTAGGGTC 58.939 48.000 21.99 7.67 38.23 4.46
23 24 5.735624 AGGGAGTACTTAGTAGTCTTAGGGT 59.264 44.000 21.99 3.57 38.23 4.34
24 25 6.264771 AGGGAGTACTTAGTAGTCTTAGGG 57.735 45.833 21.99 0.00 38.23 3.53
25 26 6.298361 GGAGGGAGTACTTAGTAGTCTTAGG 58.702 48.000 21.99 0.00 38.23 2.69
26 27 5.990996 CGGAGGGAGTACTTAGTAGTCTTAG 59.009 48.000 21.99 9.47 38.23 2.18
27 28 5.426833 ACGGAGGGAGTACTTAGTAGTCTTA 59.573 44.000 21.99 0.00 38.23 2.10
28 29 4.227073 ACGGAGGGAGTACTTAGTAGTCTT 59.773 45.833 21.99 13.33 38.23 3.01
29 30 3.779738 ACGGAGGGAGTACTTAGTAGTCT 59.220 47.826 21.99 7.70 38.23 3.24
30 31 4.126437 GACGGAGGGAGTACTTAGTAGTC 58.874 52.174 16.58 16.58 37.64 2.59
31 32 3.431486 CGACGGAGGGAGTACTTAGTAGT 60.431 52.174 0.00 0.00 38.44 2.73
32 33 3.129871 CGACGGAGGGAGTACTTAGTAG 58.870 54.545 0.00 0.00 0.00 2.57
33 34 2.766263 TCGACGGAGGGAGTACTTAGTA 59.234 50.000 0.00 0.00 0.00 1.82
34 35 1.556911 TCGACGGAGGGAGTACTTAGT 59.443 52.381 0.00 0.00 0.00 2.24
35 36 1.939255 GTCGACGGAGGGAGTACTTAG 59.061 57.143 0.00 0.00 0.00 2.18
36 37 1.407437 GGTCGACGGAGGGAGTACTTA 60.407 57.143 9.92 0.00 0.00 2.24
37 38 0.679321 GGTCGACGGAGGGAGTACTT 60.679 60.000 9.92 0.00 0.00 2.24
38 39 1.077858 GGTCGACGGAGGGAGTACT 60.078 63.158 9.92 0.00 0.00 2.73
39 40 1.375098 CTGGTCGACGGAGGGAGTAC 61.375 65.000 9.92 0.00 0.00 2.73
40 41 1.077930 CTGGTCGACGGAGGGAGTA 60.078 63.158 9.92 0.00 0.00 2.59
41 42 2.361357 CTGGTCGACGGAGGGAGT 60.361 66.667 9.92 0.00 0.00 3.85
42 43 2.361357 ACTGGTCGACGGAGGGAG 60.361 66.667 9.92 1.06 0.00 4.30
43 44 2.128290 TACACTGGTCGACGGAGGGA 62.128 60.000 19.31 0.08 0.00 4.20
44 45 1.246056 TTACACTGGTCGACGGAGGG 61.246 60.000 9.92 11.50 0.00 4.30
45 46 0.599558 TTTACACTGGTCGACGGAGG 59.400 55.000 9.92 1.90 0.00 4.30
46 47 2.427232 TTTTACACTGGTCGACGGAG 57.573 50.000 9.92 10.41 0.00 4.63
47 48 2.886862 TTTTTACACTGGTCGACGGA 57.113 45.000 9.92 0.00 0.00 4.69
63 64 4.278419 GCCCCATGATATAAGAGCGTTTTT 59.722 41.667 0.00 0.00 0.00 1.94
64 65 3.821033 GCCCCATGATATAAGAGCGTTTT 59.179 43.478 0.00 0.00 0.00 2.43
65 66 3.412386 GCCCCATGATATAAGAGCGTTT 58.588 45.455 0.00 0.00 0.00 3.60
66 67 2.612972 CGCCCCATGATATAAGAGCGTT 60.613 50.000 0.00 0.00 37.69 4.84
67 68 1.066858 CGCCCCATGATATAAGAGCGT 60.067 52.381 0.00 0.00 37.69 5.07
68 69 1.645034 CGCCCCATGATATAAGAGCG 58.355 55.000 0.00 0.00 36.06 5.03
69 70 1.555075 TCCGCCCCATGATATAAGAGC 59.445 52.381 0.00 0.00 0.00 4.09
70 71 2.169352 CCTCCGCCCCATGATATAAGAG 59.831 54.545 0.00 0.00 0.00 2.85
71 72 2.187958 CCTCCGCCCCATGATATAAGA 58.812 52.381 0.00 0.00 0.00 2.10
72 73 1.210478 CCCTCCGCCCCATGATATAAG 59.790 57.143 0.00 0.00 0.00 1.73
73 74 1.203376 TCCCTCCGCCCCATGATATAA 60.203 52.381 0.00 0.00 0.00 0.98
74 75 0.415830 TCCCTCCGCCCCATGATATA 59.584 55.000 0.00 0.00 0.00 0.86
75 76 0.253347 ATCCCTCCGCCCCATGATAT 60.253 55.000 0.00 0.00 0.00 1.63
76 77 0.475632 AATCCCTCCGCCCCATGATA 60.476 55.000 0.00 0.00 0.00 2.15
77 78 0.475632 TAATCCCTCCGCCCCATGAT 60.476 55.000 0.00 0.00 0.00 2.45
78 79 1.074090 TAATCCCTCCGCCCCATGA 60.074 57.895 0.00 0.00 0.00 3.07
79 80 1.073199 GTAATCCCTCCGCCCCATG 59.927 63.158 0.00 0.00 0.00 3.66
80 81 0.991355 TTGTAATCCCTCCGCCCCAT 60.991 55.000 0.00 0.00 0.00 4.00
81 82 1.616930 TTGTAATCCCTCCGCCCCA 60.617 57.895 0.00 0.00 0.00 4.96
82 83 1.148498 CTTGTAATCCCTCCGCCCC 59.852 63.158 0.00 0.00 0.00 5.80
83 84 1.148498 CCTTGTAATCCCTCCGCCC 59.852 63.158 0.00 0.00 0.00 6.13
84 85 1.070289 CTACCTTGTAATCCCTCCGCC 59.930 57.143 0.00 0.00 0.00 6.13
85 86 1.540580 GCTACCTTGTAATCCCTCCGC 60.541 57.143 0.00 0.00 0.00 5.54
86 87 2.036089 GAGCTACCTTGTAATCCCTCCG 59.964 54.545 0.00 0.00 0.00 4.63
87 88 3.039011 TGAGCTACCTTGTAATCCCTCC 58.961 50.000 0.00 0.00 0.00 4.30
88 89 3.493524 GCTGAGCTACCTTGTAATCCCTC 60.494 52.174 0.00 0.00 0.00 4.30
89 90 2.436173 GCTGAGCTACCTTGTAATCCCT 59.564 50.000 0.00 0.00 0.00 4.20
90 91 2.436173 AGCTGAGCTACCTTGTAATCCC 59.564 50.000 4.49 0.00 36.99 3.85
91 92 3.828875 AGCTGAGCTACCTTGTAATCC 57.171 47.619 4.49 0.00 36.99 3.01
92 93 4.568760 GTCAAGCTGAGCTACCTTGTAATC 59.431 45.833 7.68 0.00 38.25 1.75
93 94 4.223923 AGTCAAGCTGAGCTACCTTGTAAT 59.776 41.667 7.68 0.00 38.25 1.89
94 95 3.578716 AGTCAAGCTGAGCTACCTTGTAA 59.421 43.478 7.68 0.00 38.25 2.41
95 96 3.165875 AGTCAAGCTGAGCTACCTTGTA 58.834 45.455 7.68 0.00 38.25 2.41
96 97 1.974236 AGTCAAGCTGAGCTACCTTGT 59.026 47.619 7.68 0.00 38.25 3.16
97 98 2.615869 GAGTCAAGCTGAGCTACCTTG 58.384 52.381 7.68 1.78 38.25 3.61
98 99 1.203523 CGAGTCAAGCTGAGCTACCTT 59.796 52.381 7.68 0.00 38.25 3.50
99 100 0.814457 CGAGTCAAGCTGAGCTACCT 59.186 55.000 7.68 3.51 38.25 3.08
100 101 0.528470 ACGAGTCAAGCTGAGCTACC 59.472 55.000 7.68 0.00 38.25 3.18
101 102 1.200252 TCACGAGTCAAGCTGAGCTAC 59.800 52.381 7.68 2.74 38.25 3.58
133 134 0.108615 ATGAGTCGAGCCGAGTTTGG 60.109 55.000 6.42 0.00 39.77 3.28
141 142 1.828832 CGAGTTACATGAGTCGAGCC 58.171 55.000 0.00 0.00 43.39 4.70
151 152 1.334243 GAGGTAGCTCGCGAGTTACAT 59.666 52.381 43.10 40.76 43.93 2.29
168 169 4.312443 TGAGTTTAACAAGTTAGGCGAGG 58.688 43.478 0.00 0.00 0.00 4.63
198 199 9.660180 TGTGTACATATACTTTTGCTATTCACA 57.340 29.630 0.00 0.00 32.00 3.58
221 222 9.289303 GTGGATTAGTTGCTTAAATAATGTGTG 57.711 33.333 0.00 0.00 0.00 3.82
260 261 4.967575 CGGTTTTGTGAAGAATGTGTGTAC 59.032 41.667 0.00 0.00 0.00 2.90
264 267 3.283751 TCCGGTTTTGTGAAGAATGTGT 58.716 40.909 0.00 0.00 0.00 3.72
267 270 2.293122 TGCTCCGGTTTTGTGAAGAATG 59.707 45.455 0.00 0.00 0.00 2.67
280 283 5.885912 AGTGTAAATTATTGATTGCTCCGGT 59.114 36.000 0.00 0.00 0.00 5.28
282 285 9.950680 ATTTAGTGTAAATTATTGATTGCTCCG 57.049 29.630 0.00 0.00 34.91 4.63
318 321 7.056006 TCCATATTGTCATTTGTAGAGTGCAT 58.944 34.615 0.00 0.00 0.00 3.96
338 341 5.559608 CGAGCTAACGACTAACGAATCCATA 60.560 44.000 0.00 0.00 45.77 2.74
340 343 3.486375 CGAGCTAACGACTAACGAATCCA 60.486 47.826 0.00 0.00 45.77 3.41
341 344 3.034562 CGAGCTAACGACTAACGAATCC 58.965 50.000 0.00 0.00 45.77 3.01
342 345 3.933031 TCGAGCTAACGACTAACGAATC 58.067 45.455 0.00 0.00 45.77 2.52
343 346 3.373439 ACTCGAGCTAACGACTAACGAAT 59.627 43.478 13.61 0.00 45.77 3.34
345 348 2.341257 ACTCGAGCTAACGACTAACGA 58.659 47.619 13.61 0.00 45.77 3.85
347 350 2.093467 ACGACTCGAGCTAACGACTAAC 59.907 50.000 21.71 0.00 37.37 2.34
348 351 2.341257 ACGACTCGAGCTAACGACTAA 58.659 47.619 21.71 0.00 37.37 2.24
349 352 2.001812 ACGACTCGAGCTAACGACTA 57.998 50.000 21.71 0.00 37.37 2.59
350 353 1.136029 CAACGACTCGAGCTAACGACT 60.136 52.381 21.71 10.27 37.37 4.18
351 354 1.136141 TCAACGACTCGAGCTAACGAC 60.136 52.381 21.71 3.69 37.37 4.34
391 433 2.351726 CCCGAGTTTTAATCCGAGCTTG 59.648 50.000 0.00 0.00 0.00 4.01
397 439 2.282701 TCGACCCGAGTTTTAATCCG 57.717 50.000 0.00 0.00 0.00 4.18
402 444 3.302365 AACGAATCGACCCGAGTTTTA 57.698 42.857 10.55 0.00 39.91 1.52
410 452 2.950433 TGTTGACTAACGAATCGACCC 58.050 47.619 10.55 0.00 39.71 4.46
499 541 0.470766 TTTTGTAGCACAGACGGGGT 59.529 50.000 0.00 0.00 0.00 4.95
552 882 4.851558 CCTTTTTGTAGACAAACGCTATGC 59.148 41.667 7.33 0.00 44.56 3.14
555 885 6.680874 TTTCCTTTTTGTAGACAAACGCTA 57.319 33.333 7.33 0.00 44.56 4.26
637 967 8.162878 TCTCAGTCGACCGAATAATTAGTTAT 57.837 34.615 13.01 0.00 31.89 1.89
647 977 3.130516 TGCTAATTCTCAGTCGACCGAAT 59.869 43.478 13.01 14.59 0.00 3.34
658 988 8.353684 TGTTTTATTCGGTTTTGCTAATTCTCA 58.646 29.630 0.00 0.00 0.00 3.27
789 1129 4.728534 TGTGTGCAGACAAAAACAAGTAC 58.271 39.130 15.24 0.00 32.49 2.73
881 1237 2.279918 AACGTGTCCGCCAGTGTC 60.280 61.111 0.00 0.00 37.70 3.67
882 1238 2.279918 GAACGTGTCCGCCAGTGT 60.280 61.111 0.00 0.00 37.70 3.55
883 1239 3.403057 CGAACGTGTCCGCCAGTG 61.403 66.667 0.00 0.00 37.70 3.66
884 1240 2.927580 ATCGAACGTGTCCGCCAGT 61.928 57.895 0.00 0.00 37.70 4.00
885 1241 2.126071 ATCGAACGTGTCCGCCAG 60.126 61.111 0.00 0.00 37.70 4.85
886 1242 2.423290 TTCATCGAACGTGTCCGCCA 62.423 55.000 0.00 0.00 37.70 5.69
891 1247 2.412089 CCCTTTCTTCATCGAACGTGTC 59.588 50.000 0.00 0.00 0.00 3.67
911 1267 1.668151 GTGAGGTGAAGTCGTGGCC 60.668 63.158 0.00 0.00 0.00 5.36
1386 1758 1.301401 GTTGCTCTGGTACCGCACA 60.301 57.895 11.94 2.83 32.71 4.57
2019 2472 0.179145 CCTTGTAGTACTGCCGGACG 60.179 60.000 5.05 0.00 0.00 4.79
2152 2611 3.753815 ACCAAAATTCAAAAGGCATGGG 58.246 40.909 0.00 0.00 0.00 4.00
2162 2621 5.220815 GCTTTGTGCATCAACCAAAATTCAA 60.221 36.000 0.00 0.00 42.31 2.69
2172 2631 2.540931 CTGTTTGGCTTTGTGCATCAAC 59.459 45.455 0.00 0.00 45.15 3.18
2191 2651 3.466836 TGAAGCACTCAACCTGTTACTG 58.533 45.455 0.00 0.00 0.00 2.74
2199 2659 3.737774 GCTTTTGAATGAAGCACTCAACC 59.262 43.478 4.13 0.00 46.67 3.77
2273 2738 1.153568 CTCTTTCTGGCCGATCGCA 60.154 57.895 10.32 2.05 40.31 5.10
2322 2787 6.909895 GCACAAAGCGTTTGGAAATTTAAAAT 59.090 30.769 12.79 0.00 44.81 1.82
2497 2962 3.308402 CCCCAGCTGATGAACTTAGGAAA 60.308 47.826 17.39 0.00 0.00 3.13
2501 2966 2.338577 CCCCCAGCTGATGAACTTAG 57.661 55.000 17.39 0.00 0.00 2.18
2625 3093 6.994496 TGCCATCGATCTCTTCAAGAATATTT 59.006 34.615 0.00 0.00 37.61 1.40
2703 3171 1.411074 GGTGAACCCTGGTGGAAACTT 60.411 52.381 0.00 0.00 38.00 2.66
2912 3380 1.071605 CGAGAGGTGAAAGAAAGGCG 58.928 55.000 0.00 0.00 0.00 5.52
2928 3396 2.629051 GGTGTTTCCTTGGTATCCGAG 58.371 52.381 0.00 0.00 34.87 4.63
2934 3402 1.301874 CCGCGGTGTTTCCTTGGTA 60.302 57.895 19.50 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.