Multiple sequence alignment - TraesCS5B01G153000

Loading Multiple Alignment...

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 TraesCS5B01G153000 chr5B 100.000 5633 0 0 1 5633 282263824 282269456 0.000000e+00 10403
1 TraesCS5B01G153000 chr5D 92.973 5251 172 62 1 5137 249522512 249527679 0.000000e+00 7470
2 TraesCS5B01G153000 chr5D 85.993 307 33 9 1 297 294616725 294616419 2.530000e-83 320
3 TraesCS5B01G153000 chr5D 80.645 217 18 8 5311 5518 249528066 249528267 4.550000e-31 147
4 TraesCS5B01G153000 chr5A 94.505 3294 105 40 2386 5633 332216881 332220144 0.000000e+00 5011
5 TraesCS5B01G153000 chr5A 94.282 1679 51 17 746 2385 332214972 332216644 0.000000e+00 2527
6 TraesCS5B01G153000 chr5A 88.811 286 19 6 1 274 332214066 332214350 6.990000e-89 339
7 TraesCS5B01G153000 chr5A 89.320 206 18 4 1 202 94307491 94307286 7.240000e-64 255
8 TraesCS5B01G153000 chr5A 87.336 229 8 7 542 755 332214626 332214848 5.640000e-60 243
9 TraesCS5B01G153000 chr4D 83.430 519 69 15 4139 4645 116819741 116819228 3.070000e-127 466
10 TraesCS5B01G153000 chr4D 91.597 238 20 0 1067 1304 116823020 116822783 4.210000e-86 329
11 TraesCS5B01G153000 chr4D 76.585 615 100 26 3332 3932 116820903 116820319 1.190000e-76 298
12 TraesCS5B01G153000 chr4D 97.403 77 2 0 2154 2230 116821745 116821669 1.270000e-26 132
13 TraesCS5B01G153000 chr4D 90.722 97 9 0 1430 1526 116822669 116822573 4.580000e-26 130
14 TraesCS5B01G153000 chr4A 84.382 461 61 10 4182 4635 459630829 459631285 5.180000e-120 442
15 TraesCS5B01G153000 chr4A 91.176 238 21 0 1064 1301 459627685 459627922 1.960000e-84 324
16 TraesCS5B01G153000 chr4A 84.211 323 35 5 1 307 583568269 583568591 3.300000e-77 300
17 TraesCS5B01G153000 chr4A 84.953 319 22 9 3 308 692552158 692551853 3.300000e-77 300
18 TraesCS5B01G153000 chr4A 91.753 97 8 0 1430 1526 459628043 459628139 9.840000e-28 135
19 TraesCS5B01G153000 chr4A 96.104 77 3 0 2154 2230 459628804 459628880 5.920000e-25 126
20 TraesCS5B01G153000 chr4B 84.301 465 57 12 4182 4635 178851220 178850761 1.860000e-119 440
21 TraesCS5B01G153000 chr4B 91.176 238 21 0 1067 1304 178853877 178853640 1.960000e-84 324
22 TraesCS5B01G153000 chr4B 76.509 613 100 28 3332 3932 178851900 178851320 1.530000e-75 294
23 TraesCS5B01G153000 chr4B 80.444 225 36 8 1081 1301 418752298 418752518 1.260000e-36 165
24 TraesCS5B01G153000 chr4B 91.753 97 8 0 1430 1526 178853522 178853426 9.840000e-28 135
25 TraesCS5B01G153000 chr4B 97.403 77 2 0 2154 2230 178852777 178852701 1.270000e-26 132
26 TraesCS5B01G153000 chr3A 88.715 319 19 4 1 306 463123069 463122755 1.920000e-99 374
27 TraesCS5B01G153000 chr3A 84.663 326 29 7 2 313 746561516 746561198 7.090000e-79 305
28 TraesCS5B01G153000 chr3A 82.909 275 36 7 258 523 463122681 463122409 2.620000e-58 237
29 TraesCS5B01G153000 chr2D 85.893 319 27 7 1 302 560983177 560983494 1.960000e-84 324
30 TraesCS5B01G153000 chr2D 83.851 322 32 13 1 306 196461729 196462046 7.140000e-74 289
31 TraesCS5B01G153000 chr2D 79.447 253 45 7 1057 1305 35686256 35686007 7.500000e-39 172
32 TraesCS5B01G153000 chr2B 85.535 318 29 8 1 302 390610514 390610830 3.280000e-82 316
33 TraesCS5B01G153000 chr2B 78.656 253 47 7 1057 1305 58846556 58846307 1.620000e-35 161
34 TraesCS5B01G153000 chr6B 85.185 324 26 7 1 307 687538923 687538605 4.240000e-81 313
35 TraesCS5B01G153000 chr6B 76.736 288 44 10 258 523 13687586 13687300 7.610000e-29 139
36 TraesCS5B01G153000 chr1B 84.568 324 33 4 1 308 340392042 340392364 7.090000e-79 305
37 TraesCS5B01G153000 chr1B 83.978 181 15 7 259 427 599264217 599264039 1.620000e-35 161
38 TraesCS5B01G153000 chr7D 80.967 331 44 12 1 313 517311001 517311330 1.570000e-60 244
39 TraesCS5B01G153000 chr6A 81.494 308 38 15 24 313 603811901 603812207 9.430000e-58 235
40 TraesCS5B01G153000 chr7A 84.444 225 21 8 91 302 719818364 719818587 5.720000e-50 209
41 TraesCS5B01G153000 chr2A 80.263 228 39 6 1081 1305 38915265 38915041 3.490000e-37 167
42 TraesCS5B01G153000 chr3D 90.385 104 6 2 261 361 460925639 460925741 3.540000e-27 134


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 TraesCS5B01G153000 chr5B 282263824 282269456 5632 False 10403.00 10403 100.00000 1 5633 1 chr5B.!!$F1 5632
1 TraesCS5B01G153000 chr5D 249522512 249528267 5755 False 3808.50 7470 86.80900 1 5518 2 chr5D.!!$F1 5517
2 TraesCS5B01G153000 chr5A 332214066 332220144 6078 False 2030.00 5011 91.23350 1 5633 4 chr5A.!!$F1 5632
3 TraesCS5B01G153000 chr4D 116819228 116823020 3792 True 271.00 466 87.94740 1067 4645 5 chr4D.!!$R1 3578
4 TraesCS5B01G153000 chr4A 459627685 459631285 3600 False 256.75 442 90.85375 1064 4635 4 chr4A.!!$F2 3571
5 TraesCS5B01G153000 chr4B 178850761 178853877 3116 True 265.00 440 88.22840 1067 4635 5 chr4B.!!$R1 3568
6 TraesCS5B01G153000 chr3A 463122409 463123069 660 True 305.50 374 85.81200 1 523 2 chr3A.!!$R2 522

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
442 633 0.174617 TGCACGTGGATTAGATGCGA 59.825 50.000 18.88 0.00 39.18 5.10 F
486 689 0.458370 GCATCCACAAATTCGGCCAC 60.458 55.000 2.24 0.00 0.00 5.01 F
681 900 0.464373 ATGGTATGGACGGCAAGCAG 60.464 55.000 0.00 0.00 0.00 4.24 F
883 1245 0.544697 GAGACGAGAGGAGGAGAGGT 59.455 60.000 0.00 0.00 0.00 3.85 F
948 1310 0.694444 TCTCCTCCCCTACCATTGCC 60.694 60.000 0.00 0.00 0.00 4.52 F
2727 3969 1.821136 TGTCACGTGATCAGATCTGCT 59.179 47.619 23.12 8.54 0.00 4.24 F
3130 4404 0.748005 ATCTCAAAATGCCCGGTCCG 60.748 55.000 3.60 3.60 0.00 4.79 F
4180 5869 1.077663 ACCAATGCTCCCCAATGACTT 59.922 47.619 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2140 2865 0.036105 CCTCCTGCACACACATAGCA 60.036 55.000 0.00 0.00 36.72 3.49 R
2348 3107 5.829924 TCTCAAGAAAAATATCTGCCCATCC 59.170 40.000 0.00 0.00 0.00 3.51 R
2407 3626 8.208903 TGCCAAACTCTCTAAACTTTTACTACT 58.791 33.333 0.00 0.00 0.00 2.57 R
2869 4123 7.092716 GCCATAAAAAGGAATATATGCACCAG 58.907 38.462 0.00 0.00 0.00 4.00 R
2945 4211 4.428209 CCACAAACACACACATGCTTTTA 58.572 39.130 0.00 0.00 0.00 1.52 R
4380 6076 0.039256 GCGGTTTCAGCATGCAGAAA 60.039 50.000 28.20 28.20 34.76 2.52 R
4494 6196 0.392863 CGGTGATGAGGTGCATTGGA 60.393 55.000 0.00 0.00 37.34 3.53 R
5519 7507 1.823648 GCTCATCTCCGGATCCTGGTA 60.824 57.143 18.33 10.89 0.00 3.25 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
83 84 1.147824 CATTGAGGAGGCCGCTCAT 59.852 57.895 6.40 0.00 0.00 2.90
100 101 3.694734 CTCATCTGAAGAAGCTCGAGAC 58.305 50.000 18.75 7.74 0.00 3.36
339 486 1.279271 GGTGACCATTCTGTAGGCTGT 59.721 52.381 0.00 0.00 0.00 4.40
366 516 2.047274 CGGCCGTCATGAACTGGT 60.047 61.111 19.50 0.00 0.00 4.00
382 560 1.376683 GGTGTGAACTATGGCCGCA 60.377 57.895 0.00 0.00 0.00 5.69
433 612 2.747396 AAATTTGCATGCACGTGGAT 57.253 40.000 22.58 17.64 0.00 3.41
434 613 2.747396 AATTTGCATGCACGTGGATT 57.253 40.000 22.58 12.44 0.00 3.01
442 633 0.174617 TGCACGTGGATTAGATGCGA 59.825 50.000 18.88 0.00 39.18 5.10
448 639 1.007734 GGATTAGATGCGACCGCGA 60.008 57.895 8.23 0.00 45.51 5.87
449 652 0.596600 GGATTAGATGCGACCGCGAA 60.597 55.000 8.23 2.17 45.51 4.70
479 682 0.461135 GCCCGATGCATCCACAAATT 59.539 50.000 20.87 0.00 40.77 1.82
483 686 1.843992 GATGCATCCACAAATTCGGC 58.156 50.000 16.23 0.00 0.00 5.54
485 688 0.897401 TGCATCCACAAATTCGGCCA 60.897 50.000 2.24 0.00 0.00 5.36
486 689 0.458370 GCATCCACAAATTCGGCCAC 60.458 55.000 2.24 0.00 0.00 5.01
501 704 4.483243 CACCCGCCGCCCTATTGT 62.483 66.667 0.00 0.00 0.00 2.71
507 710 3.043999 GCCGCCCTATTGTCACCCT 62.044 63.158 0.00 0.00 0.00 4.34
517 720 0.542333 TTGTCACCCTCAAACGGACA 59.458 50.000 0.00 0.00 36.76 4.02
522 725 2.882137 TCACCCTCAAACGGACAAAATC 59.118 45.455 0.00 0.00 0.00 2.17
523 726 2.884639 CACCCTCAAACGGACAAAATCT 59.115 45.455 0.00 0.00 0.00 2.40
525 728 4.517453 CACCCTCAAACGGACAAAATCTAA 59.483 41.667 0.00 0.00 0.00 2.10
528 731 5.144359 CCTCAAACGGACAAAATCTAAACG 58.856 41.667 0.00 0.00 0.00 3.60
529 732 5.277634 CCTCAAACGGACAAAATCTAAACGT 60.278 40.000 0.00 0.00 34.25 3.99
530 733 5.740406 TCAAACGGACAAAATCTAAACGTC 58.260 37.500 0.00 0.00 32.18 4.34
535 748 2.406130 ACAAAATCTAAACGTCGCGGA 58.594 42.857 6.13 0.00 0.00 5.54
570 785 6.075315 AGTTGCCCTTAAAACAGATTTAGGT 58.925 36.000 0.00 0.00 35.03 3.08
571 786 5.975693 TGCCCTTAAAACAGATTTAGGTG 57.024 39.130 0.00 0.00 35.03 4.00
680 899 0.747644 CATGGTATGGACGGCAAGCA 60.748 55.000 0.00 0.00 0.00 3.91
681 900 0.464373 ATGGTATGGACGGCAAGCAG 60.464 55.000 0.00 0.00 0.00 4.24
682 901 1.819632 GGTATGGACGGCAAGCAGG 60.820 63.158 0.00 0.00 0.00 4.85
683 902 1.819632 GTATGGACGGCAAGCAGGG 60.820 63.158 0.00 0.00 0.00 4.45
694 913 3.958147 AAGCAGGGTCGCACGATGG 62.958 63.158 0.00 0.00 0.00 3.51
792 1154 1.305381 AGGAGCTCTTGCCCGTAGT 60.305 57.895 14.64 0.00 40.80 2.73
883 1245 0.544697 GAGACGAGAGGAGGAGAGGT 59.455 60.000 0.00 0.00 0.00 3.85
889 1251 2.105821 CGAGAGGAGGAGAGGTGTATCT 59.894 54.545 0.00 0.00 0.00 1.98
940 1302 2.373836 CGAATCTCTCTCTCCTCCCCTA 59.626 54.545 0.00 0.00 0.00 3.53
945 1307 2.178984 CTCTCTCTCCTCCCCTACCATT 59.821 54.545 0.00 0.00 0.00 3.16
946 1308 2.091055 TCTCTCTCCTCCCCTACCATTG 60.091 54.545 0.00 0.00 0.00 2.82
948 1310 0.694444 TCTCCTCCCCTACCATTGCC 60.694 60.000 0.00 0.00 0.00 4.52
991 1357 2.102438 CGCACACGCACAGATCCAT 61.102 57.895 0.00 0.00 38.40 3.41
1333 1700 3.775654 CTTTCTCGCTCCCGGCCT 61.776 66.667 0.00 0.00 37.74 5.19
1674 2099 5.793026 TTGCAATCCTTTGTTTTGTTGAC 57.207 34.783 0.00 0.00 35.17 3.18
1739 2166 3.717707 GAAAGAAGTTGGAAAGGGCAAC 58.282 45.455 0.00 0.00 0.00 4.17
1780 2207 6.569801 GCGAAGTAGCAATTTCCCTTTTACTT 60.570 38.462 0.00 0.00 37.05 2.24
1797 2224 8.995220 CCTTTTACTTACATGTACAAAGCACTA 58.005 33.333 4.68 0.00 0.00 2.74
1889 2316 7.962964 GGAAAAACCCATCTTTCTTTAAAGG 57.037 36.000 15.13 0.04 42.09 3.11
1894 2321 6.214177 ACCCATCTTTCTTTAAAGGAAGGA 57.786 37.500 28.38 19.35 41.17 3.36
1950 2377 5.221501 ACAACGGTTTGTTTACTAGGAGCTA 60.222 40.000 0.00 0.00 43.89 3.32
2140 2865 5.188434 TGAAGCCGATCTGAATCTGATTTT 58.812 37.500 4.11 0.00 26.82 1.82
2306 3064 2.676076 CAATTCCCAAAGGACTTTGCG 58.324 47.619 17.14 10.46 46.25 4.85
2316 3075 2.778299 AGGACTTTGCGCACATAAAGA 58.222 42.857 22.74 0.00 37.35 2.52
2317 3076 3.146066 AGGACTTTGCGCACATAAAGAA 58.854 40.909 22.74 7.34 37.35 2.52
2348 3107 1.925847 GAAACTCAGAGCAGCTCGATG 59.074 52.381 16.99 10.83 35.36 3.84
2405 3624 7.609056 ACCTTGTATTTTATACTGACACTCGT 58.391 34.615 0.00 0.00 0.00 4.18
2406 3625 8.092687 ACCTTGTATTTTATACTGACACTCGTT 58.907 33.333 0.00 0.00 0.00 3.85
2407 3626 9.577110 CCTTGTATTTTATACTGACACTCGTTA 57.423 33.333 0.00 0.00 0.00 3.18
2727 3969 1.821136 TGTCACGTGATCAGATCTGCT 59.179 47.619 23.12 8.54 0.00 4.24
2771 4013 9.961264 TTAGAGAGAGAAAGAAGAGTACACATA 57.039 33.333 0.00 0.00 0.00 2.29
2915 4169 4.142227 GGCATCTTCATCTTGCTTGTCATT 60.142 41.667 0.00 0.00 36.62 2.57
2985 4251 7.337942 TGTTTGTGGCAACCAAAATTCTAATTT 59.662 29.630 5.01 0.00 40.15 1.82
3009 4275 9.995003 TTTGATAGATACTTGCAACCAAAATTT 57.005 25.926 0.00 0.00 0.00 1.82
3010 4276 9.995003 TTGATAGATACTTGCAACCAAAATTTT 57.005 25.926 0.00 0.00 0.00 1.82
3130 4404 0.748005 ATCTCAAAATGCCCGGTCCG 60.748 55.000 3.60 3.60 0.00 4.79
3829 5113 5.403246 ACTAACTCAAGTAGCAATGTCTCG 58.597 41.667 0.00 0.00 0.00 4.04
3832 5121 4.428209 ACTCAAGTAGCAATGTCTCGATG 58.572 43.478 0.00 0.00 0.00 3.84
3834 5123 5.125578 ACTCAAGTAGCAATGTCTCGATGTA 59.874 40.000 0.00 0.00 0.00 2.29
3954 5268 5.811613 GCCTGCTGTATTAATTCATTGCAAA 59.188 36.000 1.71 0.00 0.00 3.68
3975 5289 6.346919 GCAAAGTATATCATGGTCGATGACAC 60.347 42.308 0.00 0.00 44.12 3.67
4009 5425 5.568620 AGGACTACCAGTTTCTGAACATT 57.431 39.130 0.00 0.00 38.26 2.71
4010 5426 6.681729 AGGACTACCAGTTTCTGAACATTA 57.318 37.500 0.00 0.00 38.26 1.90
4011 5427 6.702329 AGGACTACCAGTTTCTGAACATTAG 58.298 40.000 0.00 0.00 38.26 1.73
4012 5428 6.270231 AGGACTACCAGTTTCTGAACATTAGT 59.730 38.462 0.00 0.00 38.26 2.24
4013 5429 6.369065 GGACTACCAGTTTCTGAACATTAGTG 59.631 42.308 0.00 0.00 38.26 2.74
4014 5430 6.827727 ACTACCAGTTTCTGAACATTAGTGT 58.172 36.000 0.00 0.00 41.28 3.55
4059 5476 9.589461 TTTATACCCACTGGAAGAAAACATTAA 57.411 29.630 0.00 0.00 37.43 1.40
4064 5481 4.911610 CACTGGAAGAAAACATTAACTGCG 59.088 41.667 0.00 0.00 37.43 5.18
4124 5566 2.773487 ACGTTTTGCACTGCTATGGTA 58.227 42.857 1.98 0.00 0.00 3.25
4180 5869 1.077663 ACCAATGCTCCCCAATGACTT 59.922 47.619 0.00 0.00 0.00 3.01
4246 5935 3.520696 TCGGGACTATGGATGGATCAAT 58.479 45.455 0.00 0.00 0.00 2.57
4397 6097 4.439305 TGTATTTCTGCATGCTGAAACC 57.561 40.909 38.69 32.34 43.19 3.27
4418 6118 4.401837 ACCGCAACTTTAACCTTGGTTTTA 59.598 37.500 10.52 0.00 0.00 1.52
4419 6119 5.069383 ACCGCAACTTTAACCTTGGTTTTAT 59.931 36.000 10.52 0.00 0.00 1.40
4420 6120 5.404066 CCGCAACTTTAACCTTGGTTTTATG 59.596 40.000 10.52 5.12 0.00 1.90
4494 6196 1.915769 AGAGAAGTCAGGCCCGCTT 60.916 57.895 0.00 0.55 0.00 4.68
4985 6687 2.098117 ACTTTGTGTTTCTCACTGCTGC 59.902 45.455 0.00 0.00 46.27 5.25
5032 6734 6.813293 TTCTCCTGATCTTATCATTGGTGA 57.187 37.500 0.00 0.00 38.85 4.02
5132 6839 4.342352 GCGATAAGGCCAAGTATAATGC 57.658 45.455 5.01 1.62 0.00 3.56
5187 6894 4.320641 GGCATTAACGGCAAGTTTAGTCAA 60.321 41.667 2.16 0.00 43.86 3.18
5188 6895 4.851558 GCATTAACGGCAAGTTTAGTCAAG 59.148 41.667 2.16 0.00 43.86 3.02
5189 6896 5.562113 GCATTAACGGCAAGTTTAGTCAAGT 60.562 40.000 2.16 0.00 43.86 3.16
5201 6908 6.299141 AGTTTAGTCAAGTGGTGATGACAAT 58.701 36.000 8.43 0.00 46.55 2.71
5316 7049 4.376340 AAAGCATAAAGGCCGATTTGAG 57.624 40.909 0.00 0.00 0.00 3.02
5449 7435 5.714806 TGTCAGACCATGTACAATGTAGAGA 59.285 40.000 0.00 0.00 0.00 3.10
5545 7533 2.738510 ATCCGGAGATGAGCGGGGAT 62.739 60.000 11.34 0.00 0.00 3.85
5580 7568 5.554822 TGTAAGCACGACAACTTCTTTTT 57.445 34.783 0.00 0.00 0.00 1.94
5581 7569 5.328691 TGTAAGCACGACAACTTCTTTTTG 58.671 37.500 0.00 0.00 0.00 2.44
5582 7570 3.420839 AGCACGACAACTTCTTTTTGG 57.579 42.857 0.00 0.00 0.00 3.28
5588 7576 3.243367 CGACAACTTCTTTTTGGATGGCA 60.243 43.478 0.00 0.00 0.00 4.92
5603 7591 3.742882 GGATGGCAAAGTTTCAGCTTTTC 59.257 43.478 0.00 0.00 36.64 2.29
5608 7596 5.122082 TGGCAAAGTTTCAGCTTTTCTTTTG 59.878 36.000 0.00 0.00 36.64 2.44
5610 7598 5.351189 GCAAAGTTTCAGCTTTTCTTTTGGA 59.649 36.000 10.16 0.00 36.64 3.53
5614 7602 7.543947 AGTTTCAGCTTTTCTTTTGGATTTG 57.456 32.000 0.00 0.00 0.00 2.32
5619 7607 8.334263 TCAGCTTTTCTTTTGGATTTGTTTTT 57.666 26.923 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 1.911057 TGGTCTCGAGCTTCTTCAGA 58.089 50.000 7.81 0.00 0.00 3.27
212 237 2.579878 CCTAGTTCAGGCCGTCTCA 58.420 57.895 0.00 0.00 37.70 3.27
241 266 0.527817 GAACGGCCATAGTCCACGAG 60.528 60.000 2.24 0.00 0.00 4.18
302 449 2.342279 CCTCCAGTTTCACGCCGA 59.658 61.111 0.00 0.00 0.00 5.54
344 494 2.281831 TTCATGACGGCCGGCAAA 60.282 55.556 41.46 27.16 36.35 3.68
366 516 1.745115 GCTGCGGCCATAGTTCACA 60.745 57.895 6.12 0.00 0.00 3.58
382 560 6.624423 CAACAAAAGATGTAGCTAAATGGCT 58.376 36.000 0.00 0.00 42.99 4.75
411 590 3.982475 TCCACGTGCATGCAAATTTTTA 58.018 36.364 24.58 1.96 0.00 1.52
433 612 0.927537 CAATTCGCGGTCGCATCTAA 59.072 50.000 15.68 4.37 42.06 2.10
434 613 0.874175 CCAATTCGCGGTCGCATCTA 60.874 55.000 15.68 0.00 42.06 1.98
465 668 0.461135 GGCCGAATTTGTGGATGCAT 59.539 50.000 0.00 0.00 0.00 3.96
466 669 0.897401 TGGCCGAATTTGTGGATGCA 60.897 50.000 0.00 0.00 0.00 3.96
485 688 4.171103 GACAATAGGGCGGCGGGT 62.171 66.667 9.78 0.00 0.00 5.28
486 689 4.169696 TGACAATAGGGCGGCGGG 62.170 66.667 9.78 0.00 0.00 6.13
496 699 2.369203 TGTCCGTTTGAGGGTGACAATA 59.631 45.455 0.00 0.00 33.35 1.90
501 704 2.421751 TTTTGTCCGTTTGAGGGTGA 57.578 45.000 0.00 0.00 0.00 4.02
507 710 5.556758 CGACGTTTAGATTTTGTCCGTTTGA 60.557 40.000 0.00 0.00 0.00 2.69
535 748 3.276846 GGCAACTCCAACGCACGT 61.277 61.111 0.00 0.00 34.01 4.49
543 756 3.586470 TCTGTTTTAAGGGCAACTCCA 57.414 42.857 0.00 0.00 36.21 3.86
680 899 4.129737 CGTCCATCGTGCGACCCT 62.130 66.667 0.00 0.00 34.52 4.34
694 913 4.322385 GTTTGGCCGGTGCACGTC 62.322 66.667 11.45 0.00 42.24 4.34
792 1154 1.333177 AATTACCTGCCGGTTTGCAA 58.667 45.000 4.69 0.00 42.13 4.08
883 1245 2.364973 TGGCCGGGCAGAGATACA 60.365 61.111 29.27 0.25 0.00 2.29
975 1341 1.423721 CGGATGGATCTGTGCGTGTG 61.424 60.000 0.00 0.00 0.00 3.82
1333 1700 2.202919 CACGCATCGATCTGGGCA 60.203 61.111 0.00 0.00 32.67 5.36
1660 2085 6.033341 TCGGAGATTTGTCAACAAAACAAAG 58.967 36.000 11.95 5.29 46.45 2.77
1739 2166 1.906757 TCGCAACAGCAAAGTTTGTG 58.093 45.000 16.70 14.74 0.00 3.33
1950 2377 3.466791 AAGACTGTGCAGCACCGCT 62.467 57.895 23.06 13.75 40.77 5.52
2065 2621 7.317722 ACCACTCCATATAAATTACTCCTCC 57.682 40.000 0.00 0.00 0.00 4.30
2066 2622 8.312564 GGTACCACTCCATATAAATTACTCCTC 58.687 40.741 7.15 0.00 0.00 3.71
2140 2865 0.036105 CCTCCTGCACACACATAGCA 60.036 55.000 0.00 0.00 36.72 3.49
2348 3107 5.829924 TCTCAAGAAAAATATCTGCCCATCC 59.170 40.000 0.00 0.00 0.00 3.51
2406 3625 9.702494 GCCAAACTCTCTAAACTTTTACTACTA 57.298 33.333 0.00 0.00 0.00 1.82
2407 3626 8.208903 TGCCAAACTCTCTAAACTTTTACTACT 58.791 33.333 0.00 0.00 0.00 2.57
2727 3969 8.972127 TCTCTCTAAAAAGATCTTAGCTTAGCA 58.028 33.333 8.75 6.01 0.00 3.49
2869 4123 7.092716 GCCATAAAAAGGAATATATGCACCAG 58.907 38.462 0.00 0.00 0.00 4.00
2945 4211 4.428209 CCACAAACACACACATGCTTTTA 58.572 39.130 0.00 0.00 0.00 1.52
2985 4251 9.638239 GAAAATTTTGGTTGCAAGTATCTATCA 57.362 29.630 8.47 0.00 0.00 2.15
3061 4334 5.190677 TGTGCATCTTTGATCTGTGATGAT 58.809 37.500 19.14 4.88 38.72 2.45
3125 4399 4.737353 ACGACAATAAGAAAAACGGACC 57.263 40.909 0.00 0.00 0.00 4.46
3130 4404 5.401376 GGGCAAGAACGACAATAAGAAAAAC 59.599 40.000 0.00 0.00 0.00 2.43
3829 5113 8.081633 TGACATTCACCTGTTTCAAATTACATC 58.918 33.333 0.00 0.00 0.00 3.06
3832 5121 7.867403 ACATGACATTCACCTGTTTCAAATTAC 59.133 33.333 0.00 0.00 0.00 1.89
3834 5123 6.702723 CACATGACATTCACCTGTTTCAAATT 59.297 34.615 0.00 0.00 0.00 1.82
3954 5268 5.565637 GCAGTGTCATCGACCATGATATACT 60.566 44.000 0.00 0.00 43.72 2.12
3975 5289 4.080863 ACTGGTAGTCCTATTTTCCTGCAG 60.081 45.833 6.78 6.78 34.23 4.41
4022 5438 6.519382 TCCAGTGGGTATAAACACTAACAGTG 60.519 42.308 9.92 4.79 45.52 3.66
4059 5476 1.806542 CCAGTGAGTTTATTGCGCAGT 59.193 47.619 11.31 11.23 0.00 4.40
4064 5481 1.804151 TGTCGCCAGTGAGTTTATTGC 59.196 47.619 0.00 0.00 0.00 3.56
4089 5506 4.561213 GCAAAACGTATCCATAAGGCAAAC 59.439 41.667 0.00 0.00 33.74 2.93
4180 5869 1.635487 AGGTAGCTCCATTCCTGCAAA 59.365 47.619 0.00 0.00 39.02 3.68
4246 5935 3.023119 GCCAATGTCATGGTGGATGTTA 58.977 45.455 7.61 0.00 42.75 2.41
4380 6076 0.039256 GCGGTTTCAGCATGCAGAAA 60.039 50.000 28.20 28.20 34.76 2.52
4397 6097 6.210078 TCATAAAACCAAGGTTAAAGTTGCG 58.790 36.000 4.68 0.00 37.35 4.85
4418 6118 2.827921 GCCTTGGTCTGGATTTGTTCAT 59.172 45.455 0.00 0.00 0.00 2.57
4419 6119 2.238521 GCCTTGGTCTGGATTTGTTCA 58.761 47.619 0.00 0.00 0.00 3.18
4420 6120 2.229784 CTGCCTTGGTCTGGATTTGTTC 59.770 50.000 0.00 0.00 0.00 3.18
4494 6196 0.392863 CGGTGATGAGGTGCATTGGA 60.393 55.000 0.00 0.00 37.34 3.53
4821 6523 1.202687 CCGCAATGGGAGAATGCTAGA 60.203 52.381 0.00 0.00 37.92 2.43
4893 6595 5.862924 AATCAATCTGTTACACTGTTCCG 57.137 39.130 0.00 0.00 0.00 4.30
4985 6687 7.840342 AACTTTAGACAGATCTGCATAACTG 57.160 36.000 22.83 16.36 36.29 3.16
5170 6877 2.616842 CCACTTGACTAAACTTGCCGTT 59.383 45.455 0.00 0.00 37.47 4.44
5172 6879 2.032030 CACCACTTGACTAAACTTGCCG 60.032 50.000 0.00 0.00 0.00 5.69
5187 6894 6.959639 ACAACTAAAATTGTCATCACCACT 57.040 33.333 0.00 0.00 38.44 4.00
5188 6895 7.326063 GCTTACAACTAAAATTGTCATCACCAC 59.674 37.037 0.00 0.00 41.89 4.16
5189 6896 7.013750 TGCTTACAACTAAAATTGTCATCACCA 59.986 33.333 0.00 0.00 41.89 4.17
5201 6908 8.443953 AAAAATTGCCATGCTTACAACTAAAA 57.556 26.923 0.00 0.00 0.00 1.52
5228 6935 4.978083 AAGCTGAAACATGCTATCCAAG 57.022 40.909 0.00 0.00 38.75 3.61
5230 6937 5.012239 AGAAAAGCTGAAACATGCTATCCA 58.988 37.500 0.00 0.00 38.75 3.41
5235 6942 4.812626 CCAAAAGAAAAGCTGAAACATGCT 59.187 37.500 0.00 0.00 41.82 3.79
5467 7453 5.433051 ACATCTCCAAGATCCATCCCTAAAA 59.567 40.000 0.00 0.00 31.32 1.52
5519 7507 1.823648 GCTCATCTCCGGATCCTGGTA 60.824 57.143 18.33 10.89 0.00 3.25
5566 7554 3.243367 TGCCATCCAAAAAGAAGTTGTCG 60.243 43.478 0.00 0.00 0.00 4.35
5575 7563 4.024641 GCTGAAACTTTGCCATCCAAAAAG 60.025 41.667 0.00 0.00 42.51 2.27
5580 7568 1.999648 AGCTGAAACTTTGCCATCCA 58.000 45.000 0.00 0.00 0.00 3.41
5581 7569 3.391506 AAAGCTGAAACTTTGCCATCC 57.608 42.857 0.00 0.00 38.43 3.51
5582 7570 4.625028 AGAAAAGCTGAAACTTTGCCATC 58.375 39.130 0.00 0.00 39.76 3.51
5588 7576 8.453320 CAAATCCAAAAGAAAAGCTGAAACTTT 58.547 29.630 0.00 0.00 41.60 2.66


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

AutoCloner maintained by Alex Coulton.